Miracle-dz/UniFAR-FTUs huggingface dataset:
High‐accuracy protein structure prediction in CASP14

The application of state‐of‐the‐art deep‐learning approaches to the protein modeling problem has expanded the “high‐accuracy” category in CASP14 to encompass all targets. Building on the metrics used for high‐accuracy assessment in previous CASPs, we evaluated the performance of all groups that submitted models for at least 10 targets across all difficulty classes, and judged the usefulness of those produced by AlphaFold2 (AF2) as molecular replacement search models with AMPLE. Driven by the qualitative diversity of the targets submitted to CASP, we also introduce DipDiff as a new measure for the improvement in backbone geometry provided by a model versus available templates. Although a large leap in high‐accuracy is seen due to AF2, the second‐best method in CASP14 out‐performed the best in CASP13, illustrating the role of community‐based benchmarking in the development and evolution of the protein structure prediction field.
Genome survey and microsatellite motif identification of Pogonophryne albipinna

Abstract The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.
The I COPPE Scale Short Form for measuring multidimensional well‐being: Construct validity and reliability from US, Argentinian, and Italian large samples

Abstract The aim of this study is to present a short form of the I COPPE scale of multidimensional well‐being. We conducted two studies, which include four samples collected across three countries, namely United States, Argentina, and Italy. In the pilot study we tested during the data analysis phase whether it was feasible to reduce the full I COPPE scale by omitting the items dealing with past well‐being. Prompted by the positive results of the pilot study, we launched a final validation study with a sample of 2682 Italian people who completed the I COPPE scale short form, which is designed without items referring to past well‐being. Results from a series of confirmatory factor analyses show that the I COPPE scale short form presents acceptable levels of construct validity and reliability. Moreover, the 7‐factor correlated‐trait model proved to be the best fit for the data. We discuss advantaged of using the I COPPE scale short form along with limitations and future recommendations.
RETRACTED ARTICLE: Hsa_circ_0008360 sponges miR-186-5p to target CCND2 to modulate high glucose-induced vascular endothelial dysfunction

Statement of Retraction We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: Qian-Qian Zhu, Xi-Bin Pu, Tian-Chi Chen, Chen-Yang Qiu, Zi-Heng Wu, Lu Tian, Yang-Yan He, Xiao-Hui Wang, Tao Shang, Xun Wang, Yi-Lang Xiang, Dong-Lin Li, and Hong-Kun Zhang. Hsa_circ_0008360 sponges miR-186-5p to target CCND2 to modulate high glucose-induced vascular endothelial dysfunction. Cell Cycle. 2021;20(14):1389-1401. doi: 10.1080/15384101.2021. 1918877 Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors have been unable to address all the concerns raised. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The corresponding author listed in this publication has been informed. The authors do not agree with the retraction. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
Stopgap coagulation technology for arsenic removal from rural household drinking water

This study is intended to develop a stopgap coagulation protocol for immediate health protection of residents exposed to high arsenic from drinking water. The results of a simulated manual jar-test showed that ferric sulfate can maintain a satisfactory arsenic removal efficiency (>95%), and be relatively independent of water conditions. Combining with effective sand filtration, 20, 30, 60 mg/L of ferric sulfate were suitable for removing < 0.5, 0.5 - 1.0, 1.0 - 2.0 mg/L of As(V), respectively. With decanting (after settling for 8 ∼ 10h), however, ferric sulfate of 60 or 70 mg/L was needed to remove <0.5 or 0.5-1.0 mg/L of As(V), respectively. The removal rates of As(ill) could achieve similar levels to that of As(V) once the water samples were pre-oxidized. The javelle water was selected as site applicable oxidant for As(III), although ozone sparging, hydrogen dioxide solution and bleaching powder also showed good performances. It was noted that the stopgap coagulation protocol was readily and acceptable to be applied by the local residents. The makeshift strategy will immediately protect the health of local residents before some kinds of long term and effective ways could be applied. Experiences obtained in this study provide valuable information for other places encountering the arsenic problem in rural drinking water.
Effect of intestinal dialysis using polyethylene glycol on fluid balance and thirst in maintenance hemodialysis patients: A comparative study

High inter‐dialytic weight gains (IDWG) and Hyperkalemia have been associated with adverse outcomes like poor quality of life and high mortality. Thirst remains an unsolved problem in hemodialysis (HD) patients. The aim of this study was to evaluate the effect of polyethylene glycol (PEG) based intestinal dialysis on IDWG, thirst and biochemical parameters. A prospective interventional evidenced based paired comparative single center study was conducted. Thirty‐five anuric patients on weekly thrice HD were studied for four consecutive dialysis weeks. Before the mid‐week dialysis day of week 3, Patients received 2 L PEG solution. The primary end points were change in mean relative IDWG and change in mean subjective thirst feeling as measured on visual analog scale (VAS) with secondary endpoints being change in small molecule clearance. There was significant reduction in IDWG after the therapy from 3 ± 0.81 L to 2.35 ± 0.72 (P = 0.002). The therapy also reduced the % IDWG BW from 5.1 ± 1.7% to 4.15 ± 1.6% (P = 0.017). No change in thirst was seen, that is, 6.16 ± 0.66, 6.14 ± 0.64, and 6.16 ± 0.65 (P = 0.986). A multivariate linear regression did not reveal any effect of age, gender, and co‐morbidities on the reduction of IDWG and thirst. The therapy achieved a significant urea, creatinine, and potassium reduction of 8.23%, 8.13%, and 8.33% respectively with an increase in sodium levels by 0.86%. This modality reduced the IDWG, was found to be a potent treatment modality for hyperkalemia but did not affect thirst sensation even after consumption of 2 L solution.
Dexamethasone induces pancreatic β-cell apoptosis through upregulation of TRAIL death receptor.

Long-term medication with dexamethasone (a synthetic glucocorticoid (GC) drug) results in hyperglycemia, or steroid-induced diabetes. Although recent studies revealed dexamethasone directly induces pancreatic β-cell apoptosis, its molecular mechanisms remain unclear. In our initial analysis of mRNA transcripts, we discovered the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) pathway may be involved in dexamethasone-induced pancreatic β-cell apoptosis. In the present study, a mechanism of dexamethasone-induced pancreatic β-cell apoptosis through the TRAIL pathway was investigated in cultured cells and isolated mouse islets. INS-1 cells were cultured with and without dexamethasone in the presence or absence of a glucocorticoid receptor (GR) inhibitor, RU486. We found that dexamethasone induced pancreatic β-cell apoptosis in association with the upregulation of TRAIL mRNA and protein expression. Moreover, dexamethasone upregulated the TRAIL death receptor (DR5) protein but suppressed the decoy receptor (DcR1) protein. Similar findings were observed in mouse isolated islets: dexamethasone increased TRAIL and DR5 compared to that of control mice. Furthermore, dexamethasone stimulated pro-apoptotic signaling including superoxide production, caspase-8, -9, and -3 activities, NF-B, and Bax, but repressed the anti-apoptotic protein, Bcl-2. All these effects were inhibited by the GR-inhibitor, RU486. Furthermore, knock down DR5 decreased dexamethasone-induced caspase 3 activity. Caspase-8 and caspase-9 inhibitors protected pancreatic β-cells from dexamethasone-induced apoptosis. Taken together, dexamethasone induced pancreatic β-cell apoptosis by binding to the GR and inducing DR5 and TRAIL pathway.
The effect of honey on lipid profiles: a systematic review and meta-analysis of controlled clinical trials

Abstract Honey is known not only as a natural food but also as complementary medicine. According to the controversial evidence about the effects of honey on blood lipids, this meta-analysis was performed to investigate the potential effects of honey on lipid profiles. Relevant studies were identified by searching PubMed, Web of Science, Scopus, Embase and Cochrane databases. All human controlled clinical trials (either with a parallel or a crossover design) published in English that reported changes in serum lipid markers (total cholesterol (TC), TAG, LDL-cholesterol, HDL-cholesterol and LDL-cholesterol:HDL-cholesterol ratio) following honey consumption were considered. Standardised mean differences and their respective 95 % CI were calculated to assess the changes in lipid profiles following honey consumption by random effects model. Statistical heterogeneity, sensitivity analysis, publication bias and quality of the included studies were assessed, as well. The meta-analysis of twenty-three trials showed that honey had no significant effects on TC, TAG, LDL-cholesterol, HDL-cholesterol and LDL-cholesterol:HDL-cholesterol ratio. Significant heterogeneity was seen among the studies for all the studied factors (I 2 index > 50 %). Subgroup analysis based on the lipid profile status, types of honey and intervention duration revealed no significant effect on TC, TAG, LDL-cholesterol and HDL-cholesterol. Quality of the evidences varied from very low to moderate according to various parameters. In conclusion, honey consumption did not affect serum lipid profiles (TC, TAG, LDL-cholesterol, HDL-cholesterol and LDL-cholesterol:HDL-cholesterol ratio).
Interleukin polymorphisms and protein levels associated with lung cancer susceptibility and phenotypes

ABSTRACT Background We conducted a comprehensive analysis to explore whether multiple interleukin (IL), IL-1β, IL-4, IL-6, IL-8 and IL-10, polymorphisms and IL proteins (IL-6, IL-10) relate to lung cancer (LC) susceptibility or clinical characteristics. Methods We performed the standard meta-analysis procedures according to PRISMA. The odds ratio (OR) and mean difference (MD) were used for analysis. Results We investigated 11 variants from 43 articles, and found that IL-1β rs16944 (p = 0.04) and IL-10 rs1800872 (p = 0.003) decreased while IL-10 rs1800896 (p = 0.007) increased LC risks. We also found that IL-1β rs1143627 decreased NSCLC risks (p = 0.03). The heterozygotes and homozygotes contributed differently. In addition, another 15 articles were involved to explore the relationship between IL proteins and LC. We found that LC patients accounted for higher serum IL-6 of 16.60 pg/mL (p < 0.00001) and higher serum IL-10 of 3.47 pg/mL (p = 0.02) than that of controls. Furthermore, IIIA-Ⅳ LC patients tended to have higher proportion of positive IL-6 staining in lung tumor tissue in contrast with IA-IIB patients by TNM stage (p = 0.0002). Conclusions Four variants from IL-1β and IL-10, and serum IL-6 and IL-10 levels are associated with LC risks.
What's your gut telling you? How researchers are investigating the link between myocarditis and intestinal microbiota.

1 His investigative work in cardio immunology and discoveries surrounding the links between myocarditis and bacteria found in the gut have led to his group being selected for a prestigious European Research Council (ERC) Advanced Grant. He talks to CardioPulse about what the award means for his team, his ongoing work, and why you cannot always trust your gut.
Antibiotic prophylaxis for prevention of spontaneous bacterial peritonitis in liver cirrhosis: systematic review.

Background and aim Spontaneous bacterial peritonitis is a potentially life-threatening infection in patients with liver cirrhosis and ascites. Its prevention is vital to improve prognosis of cirrhotic patients. The main objective of this systematic review was to evaluate what is the most efficacious and safest antibiotic prophylactic strategy. Methods Studies were located by searching PubMed and Cochrane Central Register of Controlled Trials in The Cochrane Library until February 2019. Randomized controlled trials evaluating primary or secondary spontaneous bacterial peritonitis prophylaxis in cirrhotic patients with ascites were included. The selection of studies was performed in two stages: screening of titles and abstracts, and assessment of the full papers identified as relevant, considering the inclusion criteria. Data were extracted in a standardized way and synthesized qualitatively. Results Fourteen studies were included. This systematic review demonstrated that daily norfloxacin is effective as a prophylactic antibiotic for the prevention of spontaneous bacterial peritonitis in patients with cirrhosis. Once weekly ciprofloxacin was not inferior to once daily norfloxacin, with good tolerance and no induced resistance. Trimethoprim-sulfamethoxazole and norfloxacin have similar efficacy for primary and secondary prophylaxis of spontaneous bacterial peritonitis, however, trimethoprim-sulfamethoxazole was associated with an increased risk of developing an adverse event. Rifaximin was more effective than norfloxacin in the secondary prophylaxis of spontaneous bacterial peritonitis, with a significant decrease in adverse events and mortality rate. Conclusions Continuous long-term selective intestinal decontamination with norfloxacin is the most widely used prophylactic strategy in spontaneous bacterial peritonitis, yet other equally effective and safe options are available.
Examination of race and gender differences in predictors of neuropsychological decline and development of Alzheimer’s disease

Abstract Objective Black adults are diagnosed with Alzheimer’s disease (AD) at higher rates than White adults. Biopsychosocial risk factors that differentially affect individuals by race, including health, education, and APOE e4, may explain these findings. Some research suggests that the risk for AD associated with the APOE e4 allele may differ by race. Gender differences in AD have also been identified but remain understudied. We examined race, APOE status, vascular risk factors, education, and the interaction of APOE e4 status and race as predictors of cognitive decline and the development of Alzheimer’s disease between genders in a large longitudinal sample of older adults. Methods: Participants (N = 4336) were selected from the National Alzheimer’s Coordinating Center’s Uniform Data Set who completed measures of verbal fluency, naming, and immediate/delayed story memory across 5 years. Analyses were stratified by gender. Follow up interactions examined statistical significance of differences. Results: APOE e4 by race interactions were largely non-significant and dropped from most models. When controlling for health, education, referral source, and Uniform Data Set form (when applicable), few racial differences in cognitive performance over time emerged. Black participants obtained lower scores than White participants on a majority of baseline measures. Race findings did not differ by gender. Hypertension was more strongly predictive of decline in delayed memory among women. Conclusions: Analyses did not support that APOE e4 differentially affects Black individuals. Hypertension may be a more relevant risk factor among women. Results raise questions regarding the accuracy of baseline scores in predicting decline for Black individuals.
Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long‐term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.
Genetics of quantitative traits with dominance under stabilizing and directional selection in partially selfing species

Recurrent self‐fertilization is thought to lead to reduced adaptive potential by decreasing the genetic diversity of populations, thus leading selfing lineages down an evolutionary “blind alley. ” Although well supported theoretically, empirical support for reduced adaptability in selfing species is limited. One limitation of classical theoretical models is that they assume pure additivity of the fitness‐related traits that are under stabilizing selection, despite ample evidence that quantitative traits are subject to dominance. Here, we relax this assumption and explore the effect of dominance on a fitness‐related trait under stabilizing selection for populations that differ in selfing rates. By decomposing the genetic variance into additional components specific to inbred populations, we show that dominance components can explain a substantial part of the genetic variance of inbred populations. We also show that ignoring these components leads to an upward bias in the predicted response to selection. Finally, we show that when considering the effect of dominance, the short‐term evolutionary potential of populations remains comparable across the entire gradient in outcrossing rates, and genetic associations can even make selfing populations more evolvable on the longer term, reconciling theoretical, and empirical results.
Clinical usefulness of noninvasive fibrosis indices for predicting hepatocellular carcinoma in treatment‐naïve patients with chronic hepatitis B following entecavir therapy

This study aimed to evaluate the clinical usefulness of the aminotransferase to platelet ratio index (APRI), fibrosis‐4 (FIB‐4), and modified FIB‐4 (mFIB‐4) indices in predicting hepatocellular carcinoma (HCC) in patients receiving entecavir (ETV) treatment.
Child Welfare System Involvement Among Children With Medical Complexity

Children with medical complexity may be at elevated risk of experiencing child maltreatment and child welfare system involvement, though empirical data are limited. This study examined the extent of child welfare system involvement among children with medical complexity and investigated associated health and social factors. A retrospective chart review of children with medical complexity (N = 208) followed at a pediatric hospital-based complex care program in Canada was conducted. Descriptive statistics and odds ratios using logistic regression were computed. Results showed that nearly one-quarter (23.6%) had documented contact with the child welfare system, most commonly for neglect; of those, more than one-third (38.8%) were placed in care. Caregiver reported history of mental health problems (aOR = 3.19, 95%CI = 1.55–6.56), chronic medical conditions (aOR = 2.86, 95%CI = 1.09–7.47), and interpersonal violence or trauma (aOR = 17.58, 95%CI = 5.43–56.98) were associated with increased likelihood of child welfare system involvement, while caregiver married/common-law relationship status (aOR = 0.35, 95%CI = 0.16–0.74) and higher number of medical technology supports (aOR = 0.75, 95%CI = 0.57–0.99) were associated with decreased likelihood. Implications for intervention and prevention of maltreatment in children with high healthcare needs are discussed.
Evidence of the impact of a national anti-tobacco prevention campaign across demographic subgroups.

Mass media campaigns are an effective population-level intervention for preventing tobacco use. However, little evidence exists for whether these campaigns similarly influence demographic subgroups. This study examined the effects of the truth® campaign to reduce tobacco use among demographic subgroups. We used data from a national, continuous, cross-sectional tracking survey of 15-24-year-olds (n = 32 331). We used a measure of weekly aggregated campaign exposure to assess whether cigarette smoking intentions and current cigarette use varied by race/ethnicity, financial situation and population density subgroups, controlling for factors known to be associated with tobacco use. Examining estimates across subgroup categories in light of the overall model estimates revealed that the effects of week-level campaign exposure on cigarette smoking intentions and current cigarette use were similar across subgroups. Wald tests of equality across estimates in each subgroup suggested that the estimates did not differ from one another in any given instance. The truth campaign does not differ significantly in its capacity to prompt declines in tobacco use across a broad spectrum of US youth and young adults. Mass media tobacco prevention campaigns can be an effective and critical component of a comprehensive tobacco control program, particularly with respect to reducing tobacco-related disparities among demographic subgroups.