Miracle-dz/UniFAR-FTUs huggingface dataset:
Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency

Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.
Disulfide Crosslinked Hydrogels Made From the Hydra Stinging Cell Protein, Minicollagen-1

Minicollagens from cnidarian nematocysts are attractive potential building blocks for the creation of strong, lightweight and tough polymeric materials with the potential for dynamic and reconfigurable crosslinking to modulate functionality. In this study, the Hydra magnipapillata minicollagen-1 isoform was recombinantly expressed in bacteria, and a high throughput purification protocol was developed to generate milligram levels of pure protein without column chromatography. The resulting minicollagen-1 preparation demonstrated spectral properties similar to those observed with collagen and polyproline sequences as well as the ability to self-assemble into oriented fibers and bundles. Photo-crosslinking with Ru(II)(bpy)32+ was used to create robust hydrogels that were analyzed by mechanical testing. Interestingly, the minicollagen-1 hydrogels could be dissolved with reducing agents, indicating that ruthenium-mediated photo-crosslinking was able to induce disulfide metathesis to create the hydrogels. Together, this work is an important first step in creating minicollagen-based materials whose properties can be manipulated through static and reconfigurable post-translational modifications.
Unbalance Between Sarcoplasmic Reticulum Ca2 + Uptake and Release: A First Step Toward Ca2 + Triggered Arrhythmias and Cardiac Damage

The present review focusses on the regulation and interplay of cardiac SR Ca2+ handling proteins involved in SR Ca2+ uptake and release, i.e., SERCa2/PLN and RyR2. Both RyR2 and SERCA2a/PLN are highly regulated by post-translational modifications and/or different partners’ proteins. These control mechanisms guarantee a precise equilibrium between SR Ca2+ reuptake and release. The review then discusses how disruption of this balance alters SR Ca2+ handling and may constitute a first step toward cardiac damage and malignant arrhythmias. In the last part of the review, this concept is exemplified in different cardiac diseases, like prediabetic and diabetic cardiomyopathy, digitalis intoxication and ischemia-reperfusion injury.
Is the Landing Error Scoring System Reliable and Valid? A Systematic Review

Context: The Landing Error Scoring System (LESS) is a clinical tool often used in research and practice to identify athletes presenting high injury-risk biomechanical patterns during a jump-landing task. Objective: To systematically review the literature addressing the psychometric properties of the LESS. Data Sources: Three electronic databases (PubMed, Web of Science, and Scopus) were searched on March 28, 2018, using the term “Landing Error Scoring System. ” Study Selection: All studies using the LESS as main outcome measure and addressing its reliability, validity against motion capture system, and predictive validity were included. Original English-language studies published in peer-reviewed journals were reviewed. Studies using modified versions of the LESS were excluded. Study Design: Systematic literature review. Level of Evidence: Level 4. Data Extraction: Study design, population, LESS testing procedures, LESS scores, statistical analysis, and main results were extracted from studies using a standardized template. Results: Ten studies met inclusion criteria and were appraised using Newcastle-Ottawa Quality Assessment Scale adapted for cross-sectional studies. The overall LESS score demonstrated good-to-excellent intrarater (intraclass correlation coefficient [ICC], 0.82-0.99), interrater (ICC, 0.83-0.92), and intersession reliability (ICC, 0.81). The validity of the overall LESS score against 3-dimensional jump-landing biomechanics was good when individuals were divided into 4 quartiles based on LESS scores. The validity of individual LESS items versus 3-dimensional motion capture data was moderate-to-excellent for most of the items addressing key risk factors for anterior cruciate ligament (ACL) injury. The predictive value of the LESS for ACL and other noncontact lower-extremity injuries remains uncertain based on the current scientific evidence. Conclusion: The LESS is a reliable screening tool. However, further work is needed to improve the LESS validity against motion capture system and confirm its predictive validity for ACL and other noncontact lower-extremity injuries.
Ruminant Fecal Contamination of Drinking Water Introduced Post-Collection in Rural Kenyan Households

In sub-Saharan Africa, many families travel to collect water and store it in their homes for daily use, presenting an opportunity for the introduction of fecal contamination. One stored and one source water sample were each collected from 45 households in rural Kenya. All 90 samples were analyzed for fecal indicator bacteria (E. coli and enterococci) and species-specific contamination using molecular microbial source tracking assays. Human (HF183), avian (GFD), and ruminant (BacR) contamination were detected in 52, two, and four samples, respectively. Stored water samples had elevated enterococci concentrations (p < 0.01, Wilcoxon matched pairs test) and more frequent BacR detection (89% versus 27%, p < 0.01, McNemar’s exact test) relative to source water samples. fsQCA (fuzzy set qualitative comparative analysis) was conducted on the subset of households with no source water BacR contamination to highlight combinations of factors associated with the introduction of BacR contamination to stored water supplies. Three combinations were identified: (i) ruminants in the compound, safe water extraction methods, and long storage time, (ii) ruminants, unsafe water extraction methods, and no soap at the household handwashing station, and (iii) long storage time and no soap. This suggests that multiple pathways contribute to the transmission of ruminant fecal contamination in this context, which would have been missed if data were analyzed using standard regression techniques.
Multifunctional Hydroxyapatite Coated with Arthemisia absinthium Composites

There is significant research showing that essential oils extracted from the plants have antibacterial effects. The purpose of this study was to develop a biocomposite based on hydroxyapatite coated with Artemisia absinthium essential oil and to highlight its antibacterial activity. Therefore, present studies are aimed at developing new materials combining hydroxyapatite with Artemisia absinthium essential oil, in order to avoid postoperative infections. The purpose of this work is to highlight the antimicrobial properties of the Artemisia absinthium essential oil-hydroxyapatite composites obtained by a simple method and at low costs. The structural properties and antimicrobial efficiency of the Artemisia absinthium essential oil-hydroxyapatite composite have been studied. The samples based on Artemisia absinthium essential oil analyzed in this study showed that wormwood essential oil presented the highest efficacy against the fungal strain of C. parapsilosis. It has been shown that wormwood essential oil has a strong antimicrobial effect against the microbial strains tested in this study. Furthermore, the antimicrobial properties of the biocomposites based on hydroxyapatite and essential oil are due to the presence of the essential oil in the samples.
PM2.5-Related Health Economic Benefits Evaluation Based on Air Improvement Action Plan in Wuhan City, Middle China

On the basis of PM2.5 data of the national air quality monitoring sites, local population data, and baseline all-cause mortality rate, PM2.5-related health economic benefits of the Air Improvement Action Plan implemented in Wuhan in 2013–2017 were investigated using health-impact and valuation functions. Annual avoided premature deaths driven by the average concentration of PM2.5 decrease were evaluated, and the economic benefits were computed by using the value of statistical life (VSL) method. Results showed that the number of avoided premature deaths in Wuhan are 21,384 (95% confidence interval (CI): 15,004 to 27,255) during 2013–2017, due to the implementation of the Air Improvement Action Plan. According to the VSL method, the obtained economic benefits of Huangpi, Wuchang, Hongshan, Xinzhou, Jiang’an, Hanyang, Jiangxia, Qiaokou, Jianghan, Qingshan, Caidian, Dongxihu, and Hannan District were 8.55, 8.19, 8.04, 7.39, 5.78, 4.84, 4.37, 4.04, 3.90, 3.30, 2.87, 2.42, and 0.66 billion RMB (1 RMB = 0.1417 USD On 14 October 2019), respectively. These economic benefits added up to 64.35 billion RMB (95% CI: 45.15 to 82.02 billion RMB), accounting for 4.80% (95% CI: 3.37% to 6.12%) of the total GDP of Wuhan in 2017. Therefore, in the process of formulating a regional air quality improvement scheme, apart from establishing hierarchical emission-reduction standards and policies, policy makers should give integrated consideration to the relationship between regional economic development, environmental protection and residents’ health benefits. Furthermore, for improving air quality, air quality compensation mechanisms can be established on the basis of the status quo and trends of air quality, population distribution, and economic development factors.
Three New Species and Two New Records of Parasesarma De Man, 1895 (Crustacea: Brachyura: Sesarmidae) from Taiwan and the Philippines from Morphological and Molecular Evidence.

Three new coastal crabs, Parasesarma aurifrons n. sp. , P. sanguimanus n. sp. and P. gemmatum n. sp. (Sesarmidae), are described from Taiwan and the Philippines. Parasesarma aurifrons is morphologically similar to P. ungulatum (H. Milne Edwards, 1853), P. liho Koller, Liu & Schubart, 2010, and P. obliquefrons (Rathbun, 1924); P. sanguimanus most closely resembles P. cricotus (Rahayu & Davie, 2002); and P. gemmatum is related to P. lenzii (De Man, 1895), but they can be distinguished by a suite of characters, including the structures of the chelipeds, gonopods and vulvae. The three new species are also supported by genetic data from the mitochondrial cytochrome oxidase subunit I (COI). Two species, P. lenzii and P. dumacense (Rathbun, 1914), are also recorded from Taiwan for the first time. The poorly known P. obliquefrons (Rathbun, 1924) from Samoa is figured for the first time as part of the comparisons and its taxonomically important gonopod structures are illustrated.
In pancreatic islets from type 2 diabetes patients, the dampened circadian oscillators lead to reduced insulin and glucagon exocytosis

Significance Here we report that intact islets and islet cells from type 2 diabetes (T2D) donors exhibit attenuated molecular oscillators bearing lower circadian amplitude and compromised synchronization capacity in vitro. Furthermore, we reveal that secretion profiles of insulin, proinsulin, and glucagon were circadian rhythmic under physiological conditions. The temporal coordination of the islet hormone secretion was perturbed in human T2D islets, concomitant with the islet molecular clock alterations. Strikingly, clock-deficient human islet cells exhibited disrupted insulin and glucagon granule docking and exocytosis. Treating the T2D islets with the clock modulator Nobiletin boosted circadian amplitude and insulin secretion. Our study uncovers a link between human molecular clockwork and T2D, thus considering clock modulators as putative pharmacological intervention to combat this disorder. Circadian clocks operative in pancreatic islets participate in the regulation of insulin secretion in humans and, if compromised, in the development of type 2 diabetes (T2D) in rodents. Here we demonstrate that human islet α- and β-cells that bear attenuated clocks exhibit strongly disrupted insulin and glucagon granule docking and exocytosis. To examine whether compromised clocks play a role in the pathogenesis of T2D in humans, we quantified parameters of molecular clocks operative in human T2D islets at population, single islet, and single islet cell levels. Strikingly, our experiments reveal that islets from T2D patients contain clocks with diminished circadian amplitudes and reduced in vitro synchronization capacity compared to their nondiabetic counterparts. Moreover, our data suggest that islet clocks orchestrate temporal profiles of insulin and glucagon secretion in a physiological context. This regulation was disrupted in T2D subjects, implying a role for the islet cell-autonomous clocks in T2D progression. Finally, Nobiletin, an agonist of the core-clock proteins RORα/γ, boosted both circadian amplitude of T2D islet clocks and insulin secretion by these islets. Our study emphasizes a link between the circadian clockwork and T2D and proposes that clock modulators hold promise as putative therapeutic agents for this frequent disorder.
Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2.

INTRODUCTION HIV-1 and HIV-2 differ in their antiretroviral (ARV) susceptibilities and drug resistance mutations (DRMs). METHODS We analyzed published HIV-2 pol sequences to identify HIV-2 treatment-selected mutations (TSMs). Mutation prevalences were determined by HIV-2 group and ARV status. Nonpolymorphic mutations were those in <1% of ARV-naïve persons. TSMs were those associated with ARV therapy after multiple comparisons adjustment. RESULTS We analyzed protease (PR) sequences from 483 PR inhibitor (PI)-naïve and 232 PI-treated persons; RT sequences from 333 nucleoside RT inhibitor (NRTI)-naïve and 252 NRTI-treated persons; and integrase (IN) sequences from 236 IN inhibitor (INSTI)-naïve and 60 INSTI-treated persons. In PR, 12 nonpolymorphic TSMs occurred in ≥11 persons: V33I, K45R, V47A, I50V, I54M, T56V, V62A, A73G, I82F, I84V, F85L, L90M. In RT, 9 nonpolymorphic TSMs occurred in ≥10 persons: K40R, A62V, K70R, Y115F, Q151M, M184VI, S215Y. In IN, 11 nonpolymorphic TSMs occurred in ≥4 persons: Q91R, E92AQ, T97A, G140S, Y143G, Q148R, A153G, N155H, H156R, R231 5-amino acid insertions. Nine of 32 nonpolymorphic TSMs were previously unreported. CONCLUSIONS This meta-analysis confirmed the ARV association of previously reported HIV-2 DRMs and identified novel TSMs. Genotypic and phenotypic studies of HIV-2 TSMs will improve approaches to predicting HIV-2 ARV susceptibility and treating HIV-2-infected persons.
Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region

Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region.
Cooperation between MYC and β-catenin in liver tumorigenesis requires Yap/Taz

Background & Aims Activation of MYC and CTNNB1 (encoding β-catenin) can co-occur in liver cancer, but how these oncogenes cooperate in tumorigenesis remains unclear. Approach & Results We generated a mouse model allowing conditional activation of MYC and WNT/β-catenin signaling (through either β-catenin activation or Apc loss) upon expression of CRE recombinase in the liver, and monitored their effects on hepatocyte proliferation, apoptosis, gene expression profiles and tumorigenesis. Conditional activation of WNT/β-catenin signaling strongly accelerated MYC-driven carcinogenesis in the mouse liver. Both pathways also cooperated in promoting cellular transformation in vitro, demonstrating their cell-autonomous action. Short-term induction of MYC and β-catenin in hepatocytes followed by RNA-seq profiling allowed the identification of a “Myc/β-catenin signature”, composed of a discrete set of Myc-activated genes whose expression increased in presence of active β-catenin. Notably this signature enriched for targets of Yap and Taz, two transcriptional co-activators known to be activated by WNT/β-catenin signaling, and to cooperate with MYC in mitogenic activation and liver transformation. Consistent with these regulatory connections, Yap/Taz accumulated upon Myc/β-catenin activation and were required not only for the ensuing proliferative response, but also for tumor cell growth and survival. Finally, the Myc/β-catenin signature was enriched in a subset of human hepatocellular carcinomas characterized by comparatively poor prognosis. Conclusions Yap and Taz mediate the cooperative action of Myc and β-catenin in liver tumorigenesis. This warrants efforts toward therapeutic targeting of Yap/Taz in aggressive liver tumors marked by elevated Myc/β-catenin activity.
Lactational changes of fatty acids and fat-soluble antioxidants in human milk from healthy Chinese mothers

Abstract Human milk fat is specially tailored to supply the developing infant with adequate and balanced nutrients. The present study aimed to quantify the composition of fatty acids, tocopherols and carotenoids in human milk, with special emphasis on the lactational changes. Colostrum, transitional and mature milk samples were collected longitudinally from the same forty-two healthy, well-nourished Chinese mothers. Fatty acids were quantified by GC with carotenoids (carotenes and xanthophylls) and tocopherols (α-, γ-tocopherol) determined by HPLC. Total fatty acid (TFA) content increased from 15·09 g/l in colostrum to 32·57 g/l in mature milk with the percentages of DHA and arachidonic acid (ARA) decreased. The ratio of n-6:n-3 PUFA and ARA:DHA remained constant during lactation at about 11:1 and 1·3:1, respectively. Both α-tocopherol and γ-tocopherol decreased over lactation with the ratio of α-:γ-tocopherol declined significantly from 7·21:1 to 4·21:1 (P < 0·001). Carotenoids all dropped from colostrum to mature milk as the less polar carotenes dropped by 88·67 %, while xanthophylls only dropped by 35·92 %. Lutein was predominated in both transitional and mature milk carotenoids (51·64–52·49 %), while colostrum carotenoids were mainly composed of lycopene (32·83 %) and β-carotene (30·78 %). The concentrations of tocopherols and xanthophylls but not carotenes were positively associated with TFA content in milk. These results suggested that colostrum and mature milk contained divergent lipid profiles and selective transfer mechanisms related to polarity might be involved. The present outcomes provide new insights for future breast-feeding studies, which also add in scientific evidences for the design of both initial and follow-on infant formulas.
Multi-Theory Model and Predictors of Likelihood of Accepting the Series of HPV Vaccination: A Cross-Sectional Study among Ghanaian Adolescents

HPV vaccines are efficacious in preventing HPV related cancers. However, the vaccination uptake in Ghana is very low. Studies that utilize theoretical frameworks to identify contributory factors to HPV vaccination uptake in Ghana are understudied. We used multi-theory model (MTM) constructs to predict initiation and completion of HPV vaccination series in Ghanaian adolescents. Adolescents (n = 285) between the ages of 12 and 17 years old were recruited from four selected schools in Ghana to participate in the cross-sectional study. Linear regressions were used to analyze the data. Most participants were female (91.2%) and senior high school students (60.0%). Many of the participants had neither heard about HPV (92.3%) nor HPV vaccinations (95.4%). Significant predictors of adolescents’ likelihood of getting the first dose of HPV vaccination were perceived beliefs and change in a physical environment (p < 0.001), with each variable accounting for 6.1%and 8.8% of the variance respectively. Significant predictors of adolescents’ likelihood of completing HPV vaccination recommended series were perceived beliefs, practice for change, and emotional transformation (p < 0.001), with each variable accounting for 7.8%, 8.1%, and 1.1% of the variance respectively. Findings underscore important opportunities for developing educational interventions for adolescents in Ghana to increase the HPV vaccination uptake.