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Shotgun sequencing and generation of metagenome-assembled genomes

In our previous study, 78 Holstein Friesian dairy cows were sampled for rumen content, metagenomic shotgun sequencing was carried out, and raw Illumina sequencing reads were assembled into contigs using megahit assembler using default settings [7]. We used a pooled assembly of the original 78 samples to increase the quality of the metagenome-assembled genomes (MAGs) with the syntax: megahit [14] -t 60 -m 0.5 1 [Illumina R1 files] 2 [Illumina R2 files]. Next, the assembled contigs were indexed using BBMap [15]: bbmap.sh threads=60 ref=[contigs filename]. Thereafter, reads from each sample were mapped to the assembled contigs using BBTools bbwrap.sh script. In order to determine the depth (coverage) of each contig within each sample, the gi_summarize_bam_contig_depths tool was applied with the parameters: gi_summarize_bam_contig_depths --outputDepth depth.txt --pairedContigs paired.txt *.bam --outputDepth depth.txt --pairedContigs paired.txt.

Using the depth information, metabat2 [16] was executed to bind genes together into reconstructed genomes, with parameters: metabat2 -t40 -a depth.txt.

To evaluate genomic bin quality, we used the CheckM [17] tool, with parameters: checkm lineage_wf [in directory] [out directory] -x faa --genes -t10.

We generated 93 unique high-quality MAGs, and further increased our MAG database by including phyla that were not represented in our set of MAGs. In order to do so, we used the published compendium of 4,941 rumen metagenome-assembled genomes [18] and dereplicated those MAGs using dRep [19]. We then selected MAGs from phylum Spirochaetes, Actinomycetota, Proteobacteria, Firmicutes, Elusimicrobia, Bacillota, Fibrobacteres and Fusobacteria, which had the highest mean coverage in our samples as calculated using BBMap and gi_summarize_bam_contig_depths as described above [15]. This strategy minimized the false discovery rate (FDR), that would have been obtained if larger and unspecific databases would have been employed [20] and allowed the addition of 14 MAGs to our database.

In order to create the proteomic search library, genes were identified along the 107 MAGs using the Prodigal tool [21], with parameters: prodigal meta and translated in silico into proteins, using the same tool. Replicates sequences were removed. Protein sequences from the hosting animal (Bos taurus) and common contaminant protein sequences (64,701 in total) were added to the proteomic search library in order to avoid erroneous target protein identification originating from the host or common contaminants. Finally, in order to subsequently assess the percentage of false-positive identifications within the proteomic search [22], the proteomic search library sequences were reversed in order and served as a decoy database.

The bacterial fraction from rumen fluid of the 12 selected animals selected from extreme feed efficiency phenotypes, were obtained at the same time as the samples analyzed for metagenomics and stored at 20C until extraction. To extract total proteins, a modified protocol from Deusch and Seifert was used [23]. Briefly, cell pellets were resuspended in 100l in 50 mM Tris-HCl (pH 7.5; 0.1 mg/ml chloramphenicol; 1 mM phenylmethylsulfonyl fluoride (PMSF)) and incubated for 10min at 60C and 1200rpm in a thermo-mixer after addition of 150l 20mM Tris-HCl (pH 7.5; 2% sodium dodecyl sulfate (SDS)). After the addition of 500l DNAse buffer (20mM Tris-HCl pH 7.5; 0.1mg/ml MgCl2, 1mM PMSF, 1g/ml DNAse I), the cells were lysed by ultra-sonication (amplitude 5160%; cycle 0.5; 4 2min) on ice, incubated in the thermo-mixer (10min at 37C and 1,200rpm) and centrifuged at 10,000 g for 10min at 4C. The supernatant was collected and centrifuged again. The proteins in the supernatant were precipitated by adding 20% pre-cooled trichloroacetic acid (TCA; 20% v/v). After centrifugation (12,000 g; 30min; 4C), the protein pellets were washed twice in pre-cooled (20C) acetone (2 10min; 12,000 g; 4C) and dried by vacuum centrifugation. The protein pellet was resuspended in 2 SDS sample buffer (4% SDS (w/v); 20% glycerin (w/v); 100mM Tris-HCl pH 6.8; a pinch of bromophenol blue, 3.6% 2mercaptoethanol (v/v)) by 5min sonication bath and vortexing. Samples were incubated for 5min at 95C and separated by 1D SDS-PAGE (Criterion TG 4-20% Precast Midi Gel, BIO-RAD Laboratories, Inc., USA).

As previously described, after fixation and staining, each gel line was cut into 10 pieces, destained, desiccated, and rehydrated in trypsin [24]. The in-gel digest was performed by incubation overnight at 37C. Peptides were eluted with Aq. dest. by sonication for 15min The sample volume was reduced in a vacuum centrifuge.

Before MS analysis, the tryptic peptide mixture was loaded on an Easy-nLC II or Easy-nLC 1000 (Thermo Fisher Scientific, USA) system equipped with an in-house built 20cm column (inner diameter 100m; outer diameter 360m) filled with ReproSil-Pur 120 C18-AQ reversed-phase material (3m particles, Dr. Maisch GmbH, Germany). Peptides were eluted with a nonlinear 156min gradient from 1 to 99% solvent B (95% acetonitrile (v/v); 0.1% acetic acid (v/v)) in solvent A (0.1% acetic acid (v/v)) with a flow rate of 300ml/min and injected online into an LTQ Orbitrap Velos or Orbitrap Velos Pro (Thermo Fisher Scientific, USA). Overview scan at a resolution of 30,000 in the Orbitrap in a range of 300-2,000m/z was followed by 20 MS/MS fragment scans of the 20 most abundant precursor ions. Ions without detected charge state as well as singly charged ions were excluded from MS/MS analysis. Original raw spectra files were converted into the common mzXML format, in order to further process it in downstream analysis. The spectra file from each proteomic run of a given sample was searched against the protein search library, using the Comet [25] search engine with default settings.

The TPP pipeline (Trans Proteomic Pipeline) [26] was used to further process the Comet [25, 27] search results and produce a protein abundance table for each sample. In detail, PeptideProphet [28] was applied to validate peptide assignments, with filtering criteria set to probability of 0.001, accurate mass binning, non-parametric errors model (decoy model) and decoy hits reporting. In addition, iProphet [28, 29] was applied to refine peptide identifications coming from PeptideProphet. Finally, ProteinProphet [28,29,30] was applied to statistically validate peptide identifications at the protein level. This was carried out using the command: xinteract -N[my_sample_nick].pep.xml -THREADS=40 -p0.001 -l6 -PPM -OAPd -dREVERSE_ -ip [file1].pep.xml [file2].pep.xml.. [fileN].pep.xml>xinteract.out 2>xinteract.err. Then, TPP GUI was used in order to produce a protein table from the resulting ProtXML files (extension ipro.prot.xml).

Subsequently, proteins that had an identification probability < 0.9 were also removed as well as proteins supported with less than 2 unique peptides (see Supplementary Table1).

A reference database containing all 107 MAGs contigs was created (bbmap.sh command, default settings). Then, the paired-end short reads from each sample (FASTQ files) were mapped into the reference database (bbwrap.sh, default settings), producing alignment (SAM) files, which were converted into BAM format. Subsequently, a contig depth (coverage) table was produced using the command jgi_summarize_bam_contig_depths --outputDepth depth.txt --pairedContigs paired.txt *.bam. As each of the MAGs span on more than one contig, MAG depth in each sample was calculated as contig length weighted by the average depth. Finally, to account for unequal sequencing depth, each MAG depth was normalized to the number of short sequencing reads within the given sample.

In order to compare metagenomic and proteomic structures, we first calculated the mean coding gene abundance and mean production levels of each of the 1629 detected core proteins over all 12 cows. Both mean gene abundance and mean production level were translated into ranks using the R rank function. The produced proteins were ranked in descending order and the coding genes in the gene abundance vector were reordered accordingly. The two reordered ranked vectors then plotted using the R pheatmap function, and colored using the same color scale.

As our goal was to analyze plasticity in microbial protein production in varying environments, e.g., as a function of host state, only MAGs that were identified in all of the 12 proteomic samples were kept for further analysis. Consequently, only proteins that were identified in at least half of the proteomic samples (e.g., in at least six samples) were selected. This last step aimed to reduce spurious correlation results. These filtering steps retained 79 MAGs coding for a total of 1,629 measurable proteins.

In order to calculate the accuracy in predicting host feed efficiency state based on the different data layers available (16S rRNA (Supplementary Table2), metagenomics, metaproteomics), the principal component analysis (PCA) axes for all the samples based on the microbial protein production profiles were calculated. Then, twelve cycles of model building and prediction were made. Each time, the two first PCs of each of five cows along with their phenotype (efficiency state) were used to build a Support Vector Machine (SVM) [R caret package] prediction model and one sample was left out. The model was then used to perform subsequent prediction of the left-out animal phenotype (feed efficiency) by feeding the model with that animals first two PCs. This leave-one-out methodology was then repeated over all the samples. Finally, the prediction accuracy was determined as the percent of the cases where the correct label was assigned to the left-out sample. For the proteomics data, this procedure was applied on both the raw protein counts, and the protein production normalized based on MAG abundance, which enabled us to compare the prediction accuracies of the microbial protein production to that of the raw protein counts.

In order to split the proteomics dataset into microbial proteins that tend to be produced differently as a function of the host feed efficiency states, each microbial protein profile was correlated to the samples host feed efficiency measure (as calculated by RFI) using the Spearman correlation (R function cor), disregarding the p value. Proteins that had a positive correlation to RFI were grouped as inefficiency associated proteins. In contrast, proteins that presented a negative correlation to RFI were grouped as efficiency associated proteins. To test for equal sizes of these two protein groups, a binomial test was performed (R function binom.test) to examine the probability to get a low number of feed efficient proteins from the overall proteins under examination, when the expected probability was set to 0.5.

Protein functions were assigned based on the KEGG (Kegg Encyclopedia of Genes and Genomes) [31] database. The entire KEGG genes database was compiled into a Diamond [32] search library. Then, the selected microbial proteins were searched against the database using the Diamond search tool. Significant hits (evalue < 5e-5) were further analyzed to identify the corresponding KO (KEGG Ortholog number). Annotations of glycoside hydrolases were performed using dbcan2 [33].

The checkerboard distribution in protein production profiles was estimated separately within the feed efficient and inefficient animal groups. To enable the comparison between the two groups checkerboardness level, we chose a standardized C-score estimate (Standardized Effect Size C-score - S.E.S C-Score), based on the comparison of the observed C-score to a null-model distribution derived from simulations. The S.E.S C-score was estimated using the oecosimu function from R vegan package with 100,000 simulated null-model communities.

The functional redundancy within a given group of proteins was measured as the mean number of times a given KO occurred within a given group, while neglecting proteins that have not been assigned a KO level functional annotation.

In order to test whether a given group of proteins exhibits more or less functional redundancy than would have been expected, a null distribution for functional redundancy was created, based on the number of proteins in the given group. A random group of proteins was drawn from the entire set, keeping the same sample size as in the tested group, and the process was repeated 100 times. Then, the functional redundancy for each random protein group was calculated. Thereafter, the null distribution was used to obtain a p value to measure the likelihood of obtaining such a value under the null.

Examining the functional divergence between the two groups of proteins, e.g. the feed efficiency and inefficiency associated proteins, was done by first counting the amount of shared functional annotations, in terms of KOs between the two groups. Thereafter, a null distribution for the expected count of KOs was built by randomly splitting in an iterative manner the proteins into groups of the same sizes and calculating the number of shared KOs. A p value for the actual count of shared proteins was obtained by ranking the actual count over the null distribution.

ANN Ratio analysis was carried out independently for each protein function (KO), containing more than 14 proteins with at least 5 proteins within each feed efficiency group. Initially, all proteins assigned to a given KO were split into two sets, in accordance to their feed efficiency affiliation group. Thereafter, proteins within each set were independently projected into two-dimensional space by PCA applied directly to Sequence Matrix [34]. Average nearest neighbor ratio within each set was then calculated within the minimum enclosing rectangle defined by principal component axes PC1 and PC2, as defined by Clark and Evans [35].

Microorganism feed efficiency score was calculated for each MAG individually by first ranking each protein being produced by the given microbe along the 12 animals, based on the normalized protein production levels. Thereafter, a representative production value for the microbe in each animal was calculated as the average of the ranked (normalized) protein production levels in that animal (using R rank function). This ranking allowed us to alleviate the potential skewing effect of highly expressed proteins. The microorganisms Feed Efficiency Score was calculated as the difference between its mean representative production value within feed efficient animals to that within feed inefficient animals. Values close to zero will reflect similar distribution between the two animal groups, positive values will indicate higher expression among efficient animals, and negative values will indicate higher expression among inefficient animals. To calculate significance, the actual feed efficiency score was compared to values in a distribution derived from a permutation based null model. Each of the permuted Feed Efficiency Scores (10,000 for each microbe) was obtained by independently shuffling each of the proteins produced by the MAG between the animals, prior to calculating the actual microorganism feed efficiency score. By positioning the absolute score value over its distribution under permuted assumptions (absolute values), we obtained a significance p value.

In order to assess the link between phylogenetic similarity between the MAGs and their association with feed efficiency, phylogenetic tree estimating evolutionary relationships between the MAGs was constructed using the PhyloPhlAn pipeline [36]. The phylogenetic signal for Microorganism Feed Efficiency Score was estimated by providing the phylogSignal function from R phylosignal [37] package with MAGs phylogenetic tree and respective values. Pagels Lambda statistics was chosen for the analysis, owing to its robustness [38].

All bar plots, scatter plots and other point plots were generated with R package ggplot2. Heatmaps were produced by either ggplot2 [39] or pheatmap [https://cran.r-project.org/web/packages/pheatmap/index.html] R packages. KEGG map was produced using the online KEGG Mapper tool [40]. Phylocorrelogram was produced with phyloCorrelogram function from R package phylosignal [37].

MAGs that contain a minimal number of proteins (50 functions) were selected for differential protein production analysis, in order to have sufficient data to perform statistical tests. For each MAG, the relative production was used in order to calculate the Jaccard pairwise dissimilarity for core protein production between feed efficient and inefficient cows using the R vegan package. Analysis of similarity between efficiency and inefficiency associated proteins for each MAG (ANOSIM) values and p values were then calculated using the same package.

Using all GH annotated proteins, a feature table that sums the count of each GH family within each sample was produced. Thereafter a leave-one-out cross-validation (LOOCV) [R caret package] was performed, each time building a Random Forest (RF) prediction model from the GH family counts and efficiency state of 11 samples, leaving one sample outside. Each one of the RF models, in its turn, was applied on the left-out animal to predict its efficiency state. Model accuracy and AUC curve were calculated based on the LOOCV performance.

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Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits | The ISME Journal - Nature.com

Nothing recently dropped the advertised peak brightness of the phone (1) after it was discovered that the handset's screen is only capable of hitting 700 nits as it stands, but the company maintains that the original claim is correct.

The controversy stemmed from Nothing's advertising of 1,200 nits of peak brightness for the phone (1). However, a test performed by German tech site ComputerBase revealed that the Nothing phone (1) could not achieve a brightness higher than 700 nits despite efforts to create scenarios that would cause it to achieve its advertised rating.

Nothing clarifies that this is due to software limitations.

"The hardware is capable of reaching up to 1,200 nits peak brightness, but this is currently capped by the software to 700 nits," a company spokesperson told Android Central. "This decision was made to ensure a balanced user experience regarding heat and battery consumption."

To provide more context, Nothing explained that normal conditions permit a minimum brightness of 500 nits, though this relies on the environment and content being viewed on a device. In addition, a phone can achieve up to 700 nits of peak brightness when "in auto brightness mode under strong light environment," according to the company.

On the other hand, the 700-1,200 nits range is considered a "special mode" that can only be reached through software optimizations.

However, Nothing says this feature is currently unavailable on the phone (1). The company did not say whether it intends to release a software update to fill this gap in the future.

Regardless, the phone (1) is a strong competitor to the best budget Android phones on the market. The handset recently picked up a few improvements, including better third-party charger compatibility, always-on display enhancements, and a few UI tweaks.

Our own Harish Jonnalagadda touted the handset's battery life, clean interface, cameras, wireless charging capability, and unique design with LEDs on the back.

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Nothing sheds light on the phone (1) screen brightness controversy - Android Central

Heliogen, Inc. (NYSE:HLGN) shareholders should be happy to see the share price up 30% in the last month. But that isn't much consolation for the painful drop we've seen in the last year. Indeed, the share price is down a whopping 74% in the last year. It's not uncommon to see a bounce after a drop like that. The real question is whether the company can turn around its fortunes.

Since Heliogen has shed US$65m from its value in the past 7 days, let's see if the longer term decline has been driven by the business' economics.

See our latest analysis for Heliogen

Heliogen wasn't profitable in the last twelve months, it is unlikely we'll see a strong correlation between its share price and its earnings per share (EPS). Arguably revenue is our next best option. When a company doesn't make profits, we'd generally expect to see good revenue growth. That's because fast revenue growth can be easily extrapolated to forecast profits, often of considerable size.

Heliogen grew its revenue by 810% over the last year. That's a strong result which is better than most other loss making companies. So the hefty 74% share price crash makes us think the company has somehow offended market participants. Something weird is definitely impacting the stock price; we'd venture the company has destroyed value somehow. What is clear is that the market is not judging the company on its revenue growth right now. Of course, investors do over-react when they are stressed out, so the sell-off could be unjustifiably severe.

You can see below how earnings and revenue have changed over time (discover the exact values by clicking on the image).

Balance sheet strength is crucial. It might be well worthwhile taking a look at our free report on how its financial position has changed over time.

We doubt Heliogen shareholders are happy with the loss of 74% over twelve months. That falls short of the market, which lost 7.6%. There's no doubt that's a disappointment, but the stock may well have fared better in a stronger market. With the stock down 25% over the last three months, the market doesn't seem to believe that the company has solved all its problems. Given the relatively short history of this stock, we'd remain pretty wary until we see some strong business performance. I find it very interesting to look at share price over the long term as a proxy for business performance. But to truly gain insight, we need to consider other information, too. For instance, we've identified 3 warning signs for Heliogen (2 are potentially serious) that you should be aware of.

If you would prefer to check out another company -- one with potentially superior financials -- then do not miss this free list of companies that have proven they can grow earnings.

Please note, the market returns quoted in this article reflect the market weighted average returns of stocks that currently trade on US exchanges.

Have feedback on this article? Concerned about the content? Get in touch with us directly. Alternatively, email editorial-team (at) simplywallst.com.

This article by Simply Wall St is general in nature. We provide commentary based on historical data and analyst forecasts only using an unbiased methodology and our articles are not intended to be financial advice. It does not constitute a recommendation to buy or sell any stock, and does not take account of your objectives, or your financial situation. We aim to bring you long-term focused analysis driven by fundamental data. Note that our analysis may not factor in the latest price-sensitive company announcements or qualitative material. Simply Wall St has no position in any stocks mentioned.

Simply Wall St does a detailed discounted cash flow calculation every 6 hours for every stock on the market, so if you want to find the intrinsic value of any company just search here. Its FREE.

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Investors one-year losses grow to 74% as the stock sheds US$65m this past week - Simply Wall St

The Hope and Remembrance memorial was created in 2020 to remember those who have lost their lives to the disease of addiction.

Camden County will host its sixth annual Remembrance and Hope Memorial Vigil in memory of those who lost their lives to a drug overdose on Aug. 31, International Overdose Awareness Day.

Back when we began our opioid addiction task force (in 2014), one of our objectives was to educate the public about the problem of addiction disorders and also to try and remove the stigma that was associated with the disorder, said County Commissioner Louis Cappelli.

We thought by recognizing those who had tragically lost their lives to addiction disorders, we could remove the stigma and educate the public at the same time.

Cappelli noted that factors driving the number of overdoses include abuse of addictive prescription drugs.

When the manufacturers of these pills went to doctors, they said that the pills are not addictive, so our medical community has come to largely depend on opioids for pain treatment, Cappelli explained. Unfortunately, the pills are addictive. The manufacturers knew about it, and therefore we must educate the public on the dangers of taking these prescribed drugs.

A slideshow during the vigil will identify those who lost their lives to overdose and feature speakers who will address the impact of overdose on loved ones. New pavers will also be added to the memorial site.

The CDC estimates that more than 100,000 people in the U.S. have died from a drug overdose between April 2020 and April 2021, an increase of 56,000 compared with the year before. According to nj.gov, New Jersey saw 3,124 suspected drug overdoses in 2021, 335 of them in Camden County.

The vigils keynote speaker will be Mantua resident Tanya Niederman, whose 19-year-old son Justin died earlier this year from fentanyl poisoning.

Im hoping we can find ways to make this (reality) more real so that people can kind of understand, Niederman said, noting that her son was a recreational user of cocaine. I feel like each opportunity I get to tell a story and what happened to him, and our family is an opportunity to save a life.

The reality is that nothing I do or say is going to bring him back, but we can try to keep it from happening to someone else.

Camden County offers many resources on mental health and addiction, including a fentanyl awareness campaign and an addiction task force that recommends policies and initiatives. Cappelli said a policy to make narcan more widely available in schools and buses is in the works.

The Remembrance and Hope Memorial Vigil will take place at 7:30 p.m. at Timber Creek Park in Blackwood. Those interested in having their loved one featured in the slide show should submit their name and picture at https://bit.ly/3dA89L8. People who have submitted pictures in the past will have to resubmit for this year.

Those struggling with addiction can call the county help hotline at (877) 266-8882. To learn more about addiction resources, visit https://www.camdencounty.com/service/mental-health-and-addiction/addiction-resources/

More here:
County vigil to shed light on addictive prescription drugs - The Sun Newspapers

STATEN ISLAND, N.Y. Staten Island is the borough of parks.

Its also the borough of wildlife, particularly squirrels as many borough residents can attest to, the furry animals are in no short supply on our streets and backyards.

So its very possible youve encountered one of the critters lying on the ground with its arms and legs spread out in different directions during the steamy summer weve experienced.

Dont worry, the New York City Parks Department says.

Its actually a healthy activity the creatures are performing called splooting, designed to keep them cool on hot days.

If you see a squirrel lying down like this, dont worry; its just fine, said a Parks Department tweet this week, which included a photo of a sprawled out squirrel. On hot days, squirrels keep cool by splooting (stretching out) on cool surfaces to reduce body heat. It is sometimes referred to as heat dumping.

They arent the only animals that do it, either.

A PennLive.com article from 2020 explained:

Squirrels and chipmunks have always splooted, as have rabbits and foxes and raccoons and many, many other creatures. Birds have their own versions of the sploot. Squirrels also regularly sploot on tree branches.

See the original post here:
Splooting squirrels on Staten Island? NYC Parks sheds light on this bizarre behavior. - SILive.com

A worker sorts ordered goods into an automated shelving system during operations on Cyber Monday at Amazon's fulfillment center in Robbinsville, New Jersey, November 29, 2021.

Mike Segar | Reuters

Layoffs and hiring slowdowns have been the top talking points from tech leaders on earnings calls over the past few weeks.

Then there was last week's job report.

More than a half million jobs were added in July, well beyond the expectation of 258,000. Wage growth was up 0.5% for the month (5.2% year-over-year), and the unemployment rate is now 3.5%, tied for the lowest since 1969.

In such a tight labor market, when companies are still struggling to find the talent they need, why are tech companies like Amazon, Oracle, and Microsoft shedding workers?

For starters, economists point out that what's happening in one sector isn't representative of the entire economy. Just as the early days of the pandemic lockdown impacted industries differently (airlines and hotels were slammed, while e-commerce and streaming platforms boomed) so too will this next phase of the economic cycle.

Throughout the pandemic, tech companies added workers at a rapid clip. Now, with worries of a looming recession and sky high inflation dampening consumer spending, many of these same companies are looking to cut costs and shore up capital. Amazon almost doubled in size over the past few years as it needed to staff up its warehouses to meet customer demand. Now it's cutting workers, announcing last month that it reduced its headcount by 99,000 people to 1.52 million.

Shopify began adding workers in 2020 in response to the tremendous growth in the number of stores and restaurants that went digital during the Covid-19 lockdown. In July, the company announced it's laying off about 1,000 people, or 10% of its global workforce. CEO Tobi Lutke, in a memo to employees, acknowledged that he miscalculated how long the pandemic-fueled e-commerce boom would last.

Changing demographics are also at play in the current labor picture. George Washington University management professor Christopher Kayes points out that constricted immigration policies have led to fewer workers, as have the significant number of people retiring, and retiring earlier since the pandemic. Working mothers still on the sidelines because of struggles with childcare are also a factor. It all adds up to fewer workers available for the increased number of jobs that have been created as the economy grew.

"When you combine the growth in jobs with a smaller labor pool and workers who are just more selective about the jobs they're taking, you're going to have this mismatch," Kayes says.

Dannie Combs, chief information security officer at Donnelley Financial Solutions, says he's never seen an environment like this. He works primarily in Austin, Texas "and there's not a recession here that I can see. There are thousands of jobs available." At the same time, he recognizes that inflation is an undeniable factor for the company, and that he's had to be "creative in our compensation packages and our offers in terms of location and flexibility."

Sanjay Macwan, chief information officer and chief information security officer at Vonage, says the digital transformation that has exploded over the past few years has naturally required and attracted huge numbers of skilled tech workers so there's room to reduce headcount.

At the same time, industries like retail, airlines, and hospitality that ramped down quickly and drastically during the pandemic are now struggling to add those workers back onto their payrolls. "There's a lot of friction in those industries," he adds. "Workers can get harassed and abused by customers, so they leave and go elsewhere and that makes the hiring even more difficult."

Even amid layoffs and labor tumult, both Combs and Macwan are bullish on tech long-term. Says Combs: "In segments like technology, I still believe there are endless opportunities."

Read more from the original source:
Tech companies shed workers even as the talent shortage rages on - CNBC

Authorities search New Jersey residence of Hadi Matar

Fairview police closed Morningside Avenue in the borough on Friday, Aug. 12, 2022 as authorities search the home of Hadi Matar, who was arrested following an attack on Salman Rushdie in Chautauqua, N.Y.

Anne-Marie Caruso, NorthJersey.com

Silvana Fardos, mother of the accused attacker of author Salman Rushdie, darted out of her two-story tan brick home in Fairview on Tuesday afternoon and ducked into a maroon sedan, a hat and medical mask covering her face. Reporters who had camped out on the quiet street shouted questions, but Fardos replied that she had nothing left to say" and drove away.

Four days before, a man authorities say is her son, Hadi Matar, stunned the world when he rushed onto a stage in western New York and stabbed the renowned author repeatedly in the neck, stomach and right eye. Rushdie, 75, remains hospitalized with serious injuries.

Matar, 24, who lives with his mother in Fairview, hadnt been born when the former Supreme Leader of Iran, Ayatollah Khomeini, called for Rushdies death over passages in his novel, The Satanic Verses, that some Muslims viewed as blasphemous. But on Friday, authorities said he charged the stage in a frenzy, stabbing Rushdie around 10 times until attendees were able to pull him away.

What we know:Iran denies involvement, justifies attack on Rushdie

Since the brazen and bloody attack, a picture has started to emerge of a young man who in recent years had seemed isolated and depressed to those around him, including his mother. He also had grown fixated on religion and admired Khomeini and Irans Revolutionary Guard, posting images of Iranian figures on his social media.

In a weekend interview with the Daily Mail, Fardos said she was shell-shocked by the news of her sons arrest, which she learned about when her daughter, 14, called her saying the FBI was at their home. Still, his withdrawn behavior prior to the attack had seemed to trouble her.

New Jersey:Suspect in Salman Rushdie attack from Bergen County

Fardos told the tabloid that Matar had been moody and introverted and isolated himself in the basement of their home on Morningside Street. He sleeps during the day and wakes and eats during the night," she said. "He lives in the basement. He cooks his own food.

Matar was born and raised in California and moved to New Jersey in recent years, law enforcement authorities said. His parents divorced in 2004, and his father returned to his native Lebanon. Matar changed after traveling to Lebanon for a month in 2018 to visit his father, Fardos told the Daily Mail.

She hoped the trip would motivate him to finish school and get a job but instead he seemed more withdrawn and more religious upon his return and didnt say anything to me or his sisters for months. He criticized her for not giving him a strict Muslim upbringing, she told the paper.

Fardos shed more light on that trip in an interview with a Lebanese television station late Tuesday. In Lebanon, Matar's father refused to see him, Fardos told Al-Jadeed TV in Arabic, alleging that her son was treated poorly by his father.

She said her son grew up enjoying festivities for Christmas and Halloween and read both the Bible and the Quran, although he identified as Muslim. She said she "raised an angel" and that he was a good boy, but that he had changed after a trip to see his father and returned deeply depressed.

At the State of Fitness Boxing Club in North Bergen, where Matar was a member, staff and gym users described him as quiet and a loner.

Several of our members and coaches made efforts to get to know him and pull him into the fellowship of our tight-knit club, as we do with all our members, owner Desmond Boyle said in a statement posted online. It was, however, obvious that he wanted to keep to himself in a quiet and sad manner.

Health news:NJ adds monkeypox vaccine sites for people at high risk of the disease

Police officials have not explained the suspect's motives. They are looking into his social media accounts, which showed images of Khomeini and appeared sympathetic to Iran's Islamic Revolutionary Guard Corps that Khomeini founded, according to reports.

Khomeini issued a fatwa, or religious edict,calling on Muslims to kill Rushdie for blasphemy, in 1989.

Irans government has long since distanced itself from Khomeinis decree, but anti-Rushdie sentiment lingered. In 2012, a semi-official Iranian religious foundation raised the bounty for Rushdie from $2.8 million to $3.3 million, USA TODAY reported.

On Saturday, Matar pleaded not guilty in Chautauqua County Court to attempted murder and assault charges in connection with the attack at The Chautauqua Institute, a nonprofit education and retreat center. He is being held without bail in the Chautauqua County Jail.

Suspect in Rushdie attack pleads not guilty

The man accused of a stabbing attack on "Satanic Verses" author Salman Rushdie has entered a not-guilty plea to charges of attempted murder and assault. (Aug.13) (AP video: Carolyn Thompson)

AP

In her interview on Lebanese television, Fardos was asked if she wanted to see her son. She said she did not. I always talked to him about the future," she said. "Now there is no future.

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Mother of NJ man charged in Salman Rushdie attack sheds light on life - NorthJersey.com

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Sheryl Crow opened up about what it was like filming her documentary, "Sheryl," and having to relive her darkest moments.

The documentary chronicles Crows rise to fame, starting from when she was a young girl, the challenges she faced early on in her career and all the highs and lows she has experienced both in her personal life and in her career.

During an appearance on "The Today Show," Crow revealed what experiences were the most difficult for her to revisit while filming the documentary.

"There was a lot of stuff I had never talked about in there," Crow said. "There have been some deaths along the way that have really affected me, certainly John OBrians death from Leaving Las Vegas. My battle with the real low lows and having to go get help, its all in there. Actually, to be honest, it was really liberating finally just talking about it."

Sheryl Crow says her documentary features a lot of experiences she had never spoken about publicly, and called the process of filming liberating. (Getty Images)

SHERYL CROW FELT IT WAS NECESSARY TO TELL HER BEHIND-THE-SCENES STORY IN NEW DOCUMENTARY

Despite feeling liberated in finally telling her story, Crow admitted to feeling terrified during the process, and even more so now that the documentary is out there and people are coming up to her saying they watched it. She noted, "It was king of terrifying laying it all out" and knowing people know "all the good stuff and all of the heavy stuff."

Crow explained many of her popular songs give off the impression that her music is always upbeat and happy, leading them to think her life has always been the same. She believes, however, that the songs about her struggles tell the real story of her life and are the ones audiences can relate to, leaving them feeling something after hearing them.

"People think you have All I Wanna Do and Everyday is a Winding Road and youre upbeat and youre happy all the time, and Soak Up the Sun, but ultimately, its your deep cuts that tell the story," Crow explained.

Crow believes that while her upbeat songs are more popular, it is her slower songs which tell a darker story that resonate more with fans and better tell the story of her life. (Photo by Jim Spellman/Getty Images)

Crow's documentary includes her battle with breast cancer, her relationship with Lance Armstrong during his scandal, as well as her other high-profile relationships, her struggles with depression and her time on tour with Michael Jackson.

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While there is some focus on the tougher moments in her life, the documentary also includes some happier moments in her life, and even features her sons. Crow has two sons, Wyatt Steven Crow, 15, and Levi James Crow, 12, who she adopted in 2007 and 2010, respectively.

Crow explained she is usually very strict with her children and their exposure to the public, explaining she doesnt allow them to have a presence on social media, but that they are in the documentary and even inspired her to write her new song "Forever," which is featured at the end of the film.

Crow usually keeps her sons out of the public eye, but the both appeared in her documentary, and even inspired Crow to write a song played at the end of the film. (Photo by Taylor Hill/Getty Images)

"They are living through a pandemic, they are worried about their planet, theyre worried about going to school and not being safe with guns and all, and I didnt have that stress," Crow explained. "The song really is to remind us all that every moment is a gift and we have to stay in that moment. Dont be distracted by a phone in between you and your loved ones and make the most of every moment. I wrote it for them."

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The documentary, "Sheryl," is available to stream on Showtime.

Lori Bashian is an entertainment production assistant for Fox News Digital.

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Sheryl Crow's eponymous documentary sheds light on battle with the real low lows: 'It was really liberating' - Fox News

Tiger Woods remained loyal to the PGA Tour by declining the LIV Golfs offer. Moreover, the star has been acting as a leader to make sure the existing PGA Tour golfers get the proper guidance. Around the 2nd round of the FedEx Playoffs, 22 PGA Tour players including Tiger Woods held a meeting to discuss and set 2 appeals to the Tour commissioner, Jay Monohan.

The meeting was held to discuss the further actions that can be taken by the PGA Tour against the LIV Golf stars. The 15-time Major Champion will not be a part of the BMW Championship in Delaware. However, he made sure to attend the meeting, flying all the way from his Florida home.

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Moreover, Tiger took the initiative to set the mindset of the young PGA Tour stars. He later received appreciation for his leadership in the meeting from his fellow PGA Tour golfers.

In the meeting, two appeals were set by the golfers to give to the PGA Tour commissioner, Jay Monahan. Firstly, to play against each other more often. And the second was to not compete against the LIV Golf stars in any PGA Tour events apart from the Majors.

Woods, who has been part of the PGA Tour for nearly 25 years, was reportedly very much vocal in the meeting. He allegedly declined an offer of $700 million from Saudi funded Tour. So it is quite apparent that the 46-year-old does share a great bond with his Tour.

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Tiger has managed to win 82 PGA Tour wins including his 15 Major titles. This single-handedly depicts his talent, dedication, and contribution to the Tour as well as the sport of golf. One of the PGA Tour pros from the meeting reportedly said, Look at all these build-outs, Tiger Woods built this. And he wants to make sure the place he built continues to be the strongest place in the PGA Tour.

Later on, Woods good friend and fellow PGA star Rory McIlroy too had some wise words for the Hall of Famer. McIlroy added, He is the hero that weve all looked up to. His voice carries further than anyone elses in the game of golf.

The 46-year-old is widely respected among the upcoming stars of the PGA Tour. Moreover, Woods considers most of the golfers as his friends rather than his juniors. This display of leadership and unity is what makes the legacy of Tiger Woods much greater than it already is.

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What are your thoughts on Tiger Woods legacy? Let us know in the comments section below!

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Tiger Woods Built This: PGA Tour Pro Sheds Light on the Idea Behind the PGA Tours Exclusive Meeting - EssentiallySports

Andy Douglas| Press-Citizen opinion writer

Why do we always think we have more time?

More time to address climate change, more time to stop the coral reefs from bleaching?

Fred Meyer, Backyard Abundance director, thinks its because were in a perpetual state of denial. And yet deep down we know our actions are destabilizing the ecosystem to the point where it cannot recover.

You may know Backyard Abundance as a local organization helping people turn their yards into food landscapes. Founded in 2006, the group continues to evolve, especially when it comes to addressing the urgency of climate change.

Meyer and I sat on his back porch last month, overlooking his own abundant yard, musing about the Iowa prairie, a large ecosystem destroyed in the span of 80 years. Before founding Backyard Abundance, Meyer had gone through Master Gardener training, but wanted to do more.

My fascination was with growing food, specifically in ways that helps increase the resiliency of the land, he said.

He soon learned about permaculture, a concept coined in the 70s as a response to the industrialized way growing food was despoiling the planet.

Meyer decided to travel to California for a two-week certification course.

We learned techniques to actually increase the resiliency of land while growing food, he said.

Putting these techniques into practice in his own yard, he felt the joy of working in harmony with nature, especially every time a bee visited the beebalm, or robins communed with the anise hyssop.

I had this idea that people could enhance the environment by making small changes to the landscape. So I thought I should start a group to work on this local level, Meyer said.

He began meeting with people from environmental organizations, and met many folks who had done the work of enhancing their own yards, people who would go on to serve on Backyard Abundances board. As a first project, they created a yard tour to demonstrate what was possible. The first presentation: Meyers own backyard, on a sweltering July day.

One of the first mistakes I made was to have a yard tour in Iowa at noon in July, he laughed.

But 100 people showed up, as well as reporters from two radio stations, and several TV stations and newspapers, demonstrating the level of interest in this approach.

Backyard Abundance established itself as a nonprofit in 2009, and began offering classes. In 2011, it started to offer landscape design services. One of the first projects was the childrens discovery garden on the north side of the Iowa City Rec Center.

Next came the Wetherby Park edible forest. It was a fertile period, as the nonprofit developed a garden in McPherson Park, and an edible classroom also near the Rec Center.

Many people benefitted from this work. Im one of them, as BA consultants 15 years ago helped me start a vegetable garden, which is still going strong.

But Meyer was thinking ahead. Permaculture had taught him to look at the landscape and try to understand its gifts. And his concern about climate change was intensifying.

This carried him down a path of learning wilderness skills, going into resilient landscapes and learning how to thrive on the land.

Basically, observing a healthy ecosystem, he said, and trying to understand what was really going on.

He and I agree that the prevailing human story is too often one of domination, the idea that nature is this messy thing we need to control.

To evolve out of this, to create life-enhancing landscapes, we need a completely different way of thinking, one of cooperating with nature.

Backyard Abundance has recently been organizing wild harvesting workshops.

The first class was named meet our edible friends. Everything we do is about experience and immersion and helping people to learn and connect, Meyer said.

The nonprofitreworked its mission statement, with a focus on "wellness."Meyer sees the mental health crisis as related to our disconnection from the natural world.

Were offering classes around therapy in nature. After all, were a part of nature, he said.

Lately, he has been teaching edible forest gardening classes at the university and saidhis students have a level of awareness that he didn't have at their age. Theyve been handed a future, he said, that is laughable.

The Union of Concerned Scientists did a study and found that Iowa will eventually have the climate of Oklahoma, he noted. Well have the same amount of rainfall but with big deluges and big droughts. Were going to need to learn how to collect rainwater.

Why do we always think we have more time?

Andy Douglas is the author of"Redemption Songs: A Year in the Life of a Community Prison Choir" and"The Curve of the World: Into the Spiritual Heart of Yoga."

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Opinion: Nonprofit shows we can take the time to help the climate - Iowa City Press-Citizen