Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the bacterial community across the gastrointestinal tract of goats: Composition and potential function

The composition and function of the microbial community in the gastrointestinal tract (GIT) have increasingly captured the attention of nutritionists because these traits affect the nutrient utilization efficiency and health of host animals. Little information has been reported on these aspects of the goat GIT. This study used 12 female goats (weighing 20.70 ± 1.60 kg and 10 months of age) to examine the composition and function of the microbiota in the rumen, abomasum, jejunum, cecum, and colon. Total genomic DNA was extracted from chyme samples from different sections of the GIT, and the hypervariable region of the 16S rRNA gene was amplified by PCR using bacterial universal primers. The amplicons were sequenced on an Illumina MiSeq platform, and the biological information was analyzed using QIIME software. A total of 857 genera that belonged to 39 phyla were observed across the goat GIT, with Bacteroidetes and Firmicutes dominating. Our results revealed significant differences in the composition, diversity, and species abundance of the bacterial communities in the different sections of the GIT. However, the compositions of the bacterial communities in adjacent GIT segments showed similarities in addition to differences. The study indicated that there were significant differences in microbial function among the GIT regions. In particular, the relative abundances of genes involved in energy metabolism, amino acid metabolism, nucleotide metabolism, and glycan metabolism were overrepresented in samples from the forestomach, and genes related to energy metabolism, amino acid metabolism, and glycan metabolism were mainly enriched in samples from the small intestine. Additionally, the relative abundances of bacteria at the phylum and genus levels were significantly correlated with these metabolic functions. In general, there were significant differences in composition and potential function among the bacterial communities in the goat GIT.
Bisphenol S Adsorption Behavior on Ferralsol and Biochar Modified Soil with Dissolved Organic Matter

Bisphenol S (BPs) has been found in a variety of common consumer products surrounding human living, despite the fact that it could damage the human digestive system and genital system. In China, straw-returning to the field is a common soil improvement technology used to increase the concentration of dissolved organic matter (DOM), which plays an important role in the natural environment as a microreactor of contaminants. Additionally, the biochar obtained by the straw is an effective soil conditioner. DOM is a key influencing factor when biochar is employed as the conditioner of BPs contaminated soil. However, the BPs adsorption behavior on the Ferralsol affected by DOM and biochar is also unclear. Hence, DOM was prepared and the effect of DOM on the BPs adsorption behavior on soil and biochar modified soil was investigated. DOM was characterized by Elemental analysis, Fourier transforming infrared spectra (FT-IR), and three-dimensional excitation-emission matrix spectra (3D-EEM). The results of the adsorption experiments indicated that both biochar and DOM could improve the BPs adsorption capacity in Ferralsol, while DOM suppressed the BPs adsorption capacity of biochar modified soil, indicating that DOM and BPs could not be applied at the same time for BPs adsorption.
Acute Hemodynamic Changes after Single Administration of Udenafil in Pulmonary Arterial Hypertension: a Phase IIa Study

Background and Objectives Udenafil, a new phosphodiesterase-5 inhibitor (PDE5i), has been used to treat erectile dysfunction. Given the proven benefit of PDE5i in pulmonary arterial hypertension (PAH), we evaluated serial hemodynamic changes after single udenafil administration to determine the appropriate therapeutic dose. Methods Eighteen patients were randomly allocated into one of 3 groups: placebo, udenafil 50 mg (U50), and udenafil 100 mg (U100). Diagnosis for inclusion was idiopathic PAH or PAH associated with connective tissue disease. Patients with any contraindication to PDE5i, and/or PDE5i treatment in the past 1 month were excluded. Continuous hemodynamic monitoring was performed by placing a Swan-Ganz catheter. Information on cardiac index (CI), mean pulmonary arterial pressure (mPAP), mean systemic arterial pressure (mSAP), pulmonary arterial wedge pressure (PAWP), and pulmonary vascular resistance index (PVRI) was obtained for 4 hours after drug administration. Results The mPAP significantly decreased in both the U50 and U100 (−11 mmHg and −8 mmHg from baseline, respectively, p<0.1). The mSAP also decreased in both U50 and U100; however, the decrease was greater in the U100 (Δ=−8.5 mmHg and Δ=−14.0 mmHg). CI increased in the U50, but decreased in the U100. Although PVRI decreased in both, statistical significance was only achieved in the U50 compared to placebo. PAWP was stable during monitoring. U50 had at least 4 hour-effect after administration. Only 2 patients with U100 experienced mild adverse events. Conclusions This is the first demonstration of the acute hemodynamic changes induced by udenafil. U50 is considered an optimal dose for treating PAH with more than 4-hour treatment effect. Trial Registration ClinicalTrials.gov Identifier: NCT01553721.
Dietary Chitin Particles Called Mimetic Fungi Ameliorate Colitis in Toll-Like Receptor 2/CD14- and Sex-Dependent Manners

Chitin is a natural N-acetylglucosamine polymer and a major structural component of fungal cell walls. Dietary chitin is mucoadhesive; anti-inflammatory effects of chitin microparticles (CMPs; 1- to 10-μm diameters) have been demonstrated in models of inflammatory bowel disease (IBD). ABSTRACT Chitin is a natural N-acetylglucosamine polymer and a major structural component of fungal cell walls. Dietary chitin is mucoadhesive; anti-inflammatory effects of chitin microparticles (CMPs; 1- to 10-μm diameters) have been demonstrated in models of inflammatory bowel disease (IBD). The goals of this study were to assess (i) whether CMPs among various chitin preparations are the most effective against colitis in male and female mice and (ii) whether host chitin-binding Toll-like receptor 2 (TLR2) and CD14 are required for the anti-inflammatory effect of chitin. We found that colitis in male mice was ameliorated by CMPs and large chitin beads (LCBs; 40 to 70 μm) but not by chitosan (deacetylated chitin) microparticles, oligosaccharide chitin, or glucosamine. In fact, LCBs were more effective than CMPs. In female colitis, on the other hand, CMPs and LCBs were equally and highly effective. Neither sex of TLR2-deficient mice showed anti-inflammatory effects when treated with LCBs. No anti-inflammatory effect of LCBs was seen in either CD14-deficient males or females. Furthermore, an in vitro study indicated that when LCBs and CMPs were digested with stomach acidic mammalian chitinase (AMC), their size-dependent macrophage activations were modified, at least in part, suggesting reduced particle sizes of dietary chitin in the stomach. Interestingly, stomach AMC activity was greater in males than females. Our results indicated that dietary LCBs were the most effective preparation for treating colitis in both sexes; these anti-inflammatory effects of LCBs were dependent on host TLR2 and CD14.
Exploring the legacy and impact of historical IJRB articles and contributions to ICRP publications and Radiation Research articles through graphical reference mapping

Abstract The International Journal of Radiation Biology (IJRB) celebrates its 60th birthday this year. Ahead of this very special issue, we wanted to produce strong representations of the journal’s publication history in order to celebrate the current status of the journal and to look forward to its future. This was accomplished using ‘reference maps’. Reference data were used from 1959 onward from the highest-cited paper in IJRB, for each respective year, to create a figure displaying when those articles were cited in IJRB since their publication. This was done to show the relative impact of historical IJRB papers to future research. Common themes of research were also examined by decade. Additionally, to show the historical impact of the journal outside of its immediate area of research and its practical applications, information on IJRB articles cited by the International Commission on Radiological Protection (ICRP) was collected. It was in 1959 when IJRB published the first issue, and when ICRP also issued Publication 1. Among all Publications (1–139), 43 publications have thus far cited 320 IJRB papers and each of which have been cited 1–7 times. Most notably, Publications 90, 99, 118, and 131 cited more than 40 IJRB papers. Further research was done into references for IJRB’s contemporary journal: Radiation Research. The most highly cited IJRB articles for each year together since its inception were cited 16,760 times since they were published and cited 1385 times in Radiation Research. Together, these three datasets and their representations show the diversity of historical IJRB publications, the impact of historical IJRB articles in both future research in the journal and outside of it, and articles which new prospective authors contributing to IJRB might find useful in their own research.
Tracking the affective state of unseen persons

Significance Emotion recognition is widely assumed to be determined by face and body features, and measures of emotion perception typically use unnatural, static, or decontextualized face stimuli. Using our method called affective tracking, we show that observers can infer, recognize, and track over time the affect of an invisible person based solely on visual spatial context. We further show that visual context provides a substantial and unique contribution to the perception of human affect, beyond the information available from face and body. This method reveals that emotion recognition is, at its heart, a context-based process. Emotion recognition is an essential human ability critical for social functioning. It is widely assumed that identifying facial expression is the key to this, and models of emotion recognition have mainly focused on facial and bodily features in static, unnatural conditions. We developed a method called affective tracking to reveal and quantify the enormous contribution of visual context to affect (valence and arousal) perception. When characters’ faces and bodies were masked in silent videos, viewers inferred the affect of the invisible characters successfully and in high agreement based solely on visual context. We further show that the context is not only sufficient but also necessary to accurately perceive human affect over time, as it provides a substantial and unique contribution beyond the information available from face and body. Our method (which we have made publicly available) reveals that emotion recognition is, at its heart, an issue of context as much as it is about faces.
Microstructural and Thermo-Physical Characterization of a Water Hyacinth Petiole for Thermal Insulation Particle Board Manufacture

Water Hyacinth (Eichhornia crassipes) is a dangerous and invasive aquatic species, of which global concern has sharply risen due to its rapid growth. Despite ample research on its possible applications in the construction field, there are no clear references on the optimal use of the plant in finding the most efficient-use building material. In this paper, a microstructural and chemical characterization of the Water Hyacinth petiole was performed, in order to find the most efficient use as a construction material. Subsequently, two types of binder-less insulation panels were developed, with two types of particle size (pulp and staple). A physical, mechanical, and thermal characterization of the boards was performed. These results demonstrated that it is possible to manufacture self-supporting Water Hyacinth petiole panels without an artificial polymer matrix for thermal insulation. The boards showed good thermal conductivity values, ranging from 0.047–0.065 W/mK. In addition, clear differences were found in the properties of the boards, depending on the type of Water Hyacinth petiole particle size, due to the differences in the microstructure.
Organization and function of tension-dependent complexes at adherens junctions

ABSTRACT Adherens junctions provide attachments between neighboring epithelial cells and a physical link to the cytoskeleton, which enables them to sense and transmit forces and to initiate biomechanical signaling. Examination of the Ajuba LIM protein Jub in Drosophila embryos revealed that it is recruited to adherens junctions in tissues experiencing high levels of myosin activity, and that the pattern of Jub recruitment varies depending upon how tension is organized. In cells with high junctional myosin, Jub is recruited to puncta near intercellular vertices, which are distinct from Ena-containing puncta, but can overlap Vinc-containing puncta. We identify roles for Jub in modulating tension and cellular organization, which are shared with the cytohesin Step, and the cytohesin adapter Sstn, and show that Jub and Sstn together recruit Step to adherens junctions under tension. Our observations establish Jub as a reporter of tension experienced at adherens junctions, and identify distinct types of tension-dependent and tension-independent junctional complexes. They also identify a role for Jub in mediating a feedback loop that modulates the distribution of tension and cellular organization in epithelia. Summary: This study characterizes the localization of Jub during development in Drosophila, and identifies a novel role for Jub in controlling myosin distribution and epithelial organization through regulation of cytohesin localization.
Clinical validation of the ThyroSeq v3 genomic classifier in thyroid nodules with indeterminate FNA cytology

Molecular testing of thyroid fine‐needle aspiration specimens has been developed with the primary goals of resolving the uncertainty of indeterminate cytology and avoiding the diagnostic surgeries generally recommended for these patients. A recent prospective, double‐blinded, multicenter study reported the results of the clinical validation of the ThyroSeq v3 genomic classifier in thyroid nodules with indeterminate fine‐needle aspiration cytology.
No evidence of carbapenemase-producing Enterobacteriaceae in stool samples of 1,544 asylum seekers arriving in Rhineland-Palatinate, Germany, April 2016 to March, 2017

Introduction: Since 2015, increased migration from Asia and Africa to Europe has raised public health concerns about potential importation of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE), specifically those producing carbapenemases (C-PE), into European hospitals. Aims: To inform infection control practices about ESBL-PE prevalence in asylum seekers and to investigate whether C-PE prevalence exceeds that in the German population. Methods: Cross-sectional study from April 2016–March 2017. Routinely collected stool samples from asylum seekers were tested for antibiotic resistant Enterobacteriaceae. Country/region of origin and demographic characteristics were explored as risk factors for faecal colonisation. Results: Of 1,544 individuals, 294 tested positive for ESBL-PE colonisation (19.0%; 95% confidence intervals (CI): 17.0–21.0). Asylum seekers originating from Afghanistan/Pakistan/Iran had a prevalence of 29.3% (95% CI: 25.6–33.2), from Syria 20.4% (95% CI: 16.1–25.2) and from Eritrea/Somalia 11.9% (95% CI: 8.7–15.7). CTX-M-15 (79%) and CTX-M-27 (10%) were the most common ESBL determinants. Highest ESBL-PE prevalences were observed in boys under 10 years and women aged 20–39 years (interaction: p = 0.03). No individuals tested positive for C-PE. Faecal C-PE colonisation prevalence in asylum seekers was not statistically significantly different from prevalence reported in German communities. Conclusion: In absence of other risk factors, being a newly arrived asylum seeker from a region with increased faecal ESBL-PE colonisation prevalence is not an indicator for C-PE colonisation and thus not a reason for pre-emptive screening and isolation upon hospital admission.
Molecular Crowding Tunes Material States of Ribonucleoprotein Condensates

Ribonucleoprotein (RNP) granules are membraneless liquid condensates that dynamically form, dissolve, and mature into a gel-like state in response to changing cellular environment. RNP condensation is largely governed by the promiscuous attractive inter-chain interactions, mediated by low-complexity domains (LCDs). Using an archetypal disordered RNP, Fused in Sarcoma (FUS), here we study how molecular crowding impacts the RNP liquid condensation. We observe that the liquid-liquid coexistence boundary of FUS is lowered by polymer crowders, consistent with the excluded volume model. With increasing bulk crowder concentration, RNP partition increases and the diffusion rate decreases in the condensed phase. Furthermore, we show that RNP condensates undergo substantial hardening wherein protein-dense droplets transition from viscous fluid to a viscoelastic gel-like state in a crowder concentration-dependent manner. Utilizing two distinct LCDs that broadly represent the most commonly occurring sequence motifs driving RNP phase transition, we reveal that the impact of crowding is largely independent of LCD charge/sequence patterns. These results are consistent with a thermodynamic model of crowder-mediated depletion interaction where inter-RNP attraction is enhanced by molecular crowding. The depletion force is likely to play key roles in tuning the physical properties of RNP condensates within a crowded intracellular space.
Bacterial Standards for Retail Meats.

Unsuccessful efforts of the Oregon retail meat industry to comply with the subsequently revoked Oregon bacterial standards for raw meats are reviewed. The satisfactory role of bacterial standards in regulation of pasteurized milk in contrast to their unsatisfactory role in retail raw meats is discussed. It is concluded that bacterial counts on raw meat cannot serve as indicators of: (a) health hazards, (b) insanitary conditions. (c) product spoilage, or (d) an aesthetic value of the food. Bacterial standards on raw meats, as applied in Oregon for 4 years, are considered as unjustifiable because they: (a) could not accomplish what they purported to do, i.e., reduce public health hazards, (b) were not technically feasible, i.e., were unattainable under the conditions of current good manufacturing practice in the industry, and (c) were not administratively feasible.
Vulvovaginal Lichen Planus: A Disease in Need of Consensus-Based Clinicopathologic Diagnostic Criteria.

C omment on Reply to “Is Vulvovaginal Lichen Planus Associated With Squamous Cell Carcinoma” We appreciate Basile et al's interest in our article and summarize their 4main points: (a) the existing literature establishes an association between vulvovaginal lichen planus (LP) and squamous cell carcinoma (SCC), (b) a “well-described association of LP and oral cancers” supports the same relationship in genital disease, (c) the lack of cases with vaginal tumor origin undermines our results, and (d) our methodology is inadequate to investigate an LP-SCC association. We disagree that the literature provides convincing cases of human papillomavirus (HPV)-independent SCC arising from LP. The singular obstacle to high-quality research in vulvovaginal LP is the lack of consensusbased clinicopathologic criteria that distinguish it from other disorders. One explanation for widely varying descriptions of symptoms, signs, and outcomes of women in cohorts of LP is that participants do not all have the disease of interest or have an additional comorbid disease. We argue that the long-standing debate regarding oral LP's malignant potential has not been settled by Aghbari's metaanalysis. The authors report a pooled proportion of risk of 0.9% among publications using the 2003 modified World Health Organization diagnostic criteria. However, tumor site was not identified as arising out of LP, studies did not uniformly manage confounders such as smoking and alcoholism, and data were unavailable on HPV and immunosuppression.
Brief (<4 hr) sleep episodes are insufficient for restoring performance in first-year resident physicians working overnight extended-duration work shifts.

STUDY OBJECTIVES The Accreditation Council for Graduate Medical Education (ACGME) recently reinstated extended-duration (24-28 hr) work shifts (EDWS) for postgraduate year 1 (PGY-1) resident physicians. This study examined the relationship between overnight sleep duration during EDWS and subsequent "post-call" performance in PGY-1 resident physicians. METHODS Thirty-four PGY-1 resident physicians (23 males; 24-32 years) were studied between 2002 and 2004 during 3-week Q3 "on-call" rotation schedules in the Medical and Cardiac Intensive Care Units at Brigham and Women's Hospital in Boston. Daily sleep logs (validated by ambulatory polysomnography) were collected and the 10 min psychomotor vigilance task (PVT) was administered every ~6 hr during each EDWS. Generalized estimating equations were used to examine the relationship between overnight sleep duration and PVT performance "post-call" (0500-1900 hr). Postcall performance during EDWS was compared with sessions matched for time-of-day and weeks-into-schedule in the same resident physician during an intervention schedule that eliminated EDWS. RESULTS Resident physicians obtained an average of 1.6 ± 1.5 hr cumulative sleep overnight during EDWS (<4 hr on 92% of nights). PVT attentional failures were significantly reduced only after >4 hr sleep (p = 0.027 versus no sleep). Despite this apparent improvement, the odds of incurring >1 attentional failure were 2.72 times higher during postcall following >4 hr sleep compared with matched sessions during non-EDWS. CONCLUSIONS Even with >4 hr sleep overnight (8% of EDWS), performance remained significantly impaired. These findings suggest that even "strategic napping," a recommendation recently removed from ACGME guidelines, is insufficient to mitigate severe performance impairment introduced by extending duty beyond 16 hr.
Temporal trends in relative survival following percutaneous coronary intervention

Objective Percutaneous coronary intervention (PCI) has seen substantial shifts in patient selection in recent years that have increased baseline patient mortality risk. It is unclear to what extent observed changes in mortality are attributable to background mortality risk or the indication and selection for PCI itself. PCI-attributable mortality can be estimated using relative survival, which adjusts observed mortality by that seen in a matched control population. We report relative survival ratios and compare these across different time periods. Methods National Health Service PCI activity in England and Wales from 2007 to 2014 is considered using data from the British Cardiovascular Intervention Society PCI Registry. Background mortality is as reported in Office for National Statistics life tables. Relative survival ratios up to 1 year are estimated, matching on patient age, sex and procedure date. Estimates are stratified by indication for PCI, sex and procedure date. Results 549 305 procedures were studied after exclusions for missing age, sex, indication and mortality status. Comparing from 2007 to 2008 to 2013–2014, differences in crude survival at 1 year were consistently lower in later years across all strata. For relative survival, these differences remained but were smaller, suggesting poorer survival in later years is partly due to demographic characteristics. Relative survival was higher in older patients. Conclusions Changes in patient demographics account for some but not all of the crude survival changes seen during the study period. Relative survival is an under-used methodology in interventional settings like PCI and should be considered wherever survival is compared between populations with different demographic characteristics, such as between countries or time periods.