Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

In December 2019, several patients were hospitalized and diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection, which subsequently led to a global pandemic. To date, there are no studies evaluating the relationship between the respiratory phageome and the SARS‐CoV‐2 infection. The current study investigated the phageome profiles in the nasopharyngeal swabs collected from 55 patients during the three different waves of coronavirus disease 2019 (COVID‐19) in the Campania Region (Southern Italy). Data obtained from the taxonomic profiling show that phage families belonging to the order Caudovirales have a high abundance in the patient samples. Moreover, the severity of the COVID‐19 infection seems to be correlated with the phage abundance.
The relationship between hard and soft tissue structures of the eye in extant lizards

The sizes of the eye structures, such as the lens diameter and the axial length, are important factors for the visual performance and are considered to be related to the mode of life. Although the size of these soft structures cannot be directly observed in fossil taxa, such information may be obtained from measuring size and morphology of the bony scleral ossicle ring, which is present in the eyes of extant saurospids, excluding crocodiles and snakes, and is variously preserved in fossil taxa. However, there have been only a few studies investigating the relationships between the size, the scleral ossicle ring, and soft structures of the eye. We investigated such relationships among the eye structures in extant Squamata, to establish the basis for inferring the size of the soft structures in the eye in fossil squamates. Three‐dimensional morphological data on the eye and head region of 59 lizard species covering most major clades were collected using micro‐computed tomography scanners. Strong correlations were found between the internal and external diameters of the scleral ossicle ring and soft structures. The tight correlations found here will allow reliable estimations of the sizes of soft structures and inferences on the visual performance and mode of life in fossil squamates, based on the diameters of their preserved scleral ossicle rings. Furthermore, the comparison of the allometric relationships between structures in squamates eyes with those in avian eyes suggest the possibility that the similarities of these structures closely reflect the mechanism of accommodation.
Feasibility of family-directed home-based bimanual intensive therapy combined with modified constraint induced movement therapy (h-BITmCI) in very low and low bimanual functional level: A brief report

ABSTRACT Objective To examine the feasibility of a home-based hybrid Bimanual-Intensive-Therapy combined with modified Constraint-Induced-Movement-Therapy (h-BITmCI) in children with spastic unilateral cerebral palsy (SUCP) with low and very low bimanual functional level. Methods A single-group of 10 children aged 5–8 years old, performed the hybrid home Bimanual-Intensive-Therapy (BIT, 80 hours) combined with modified Constraint-Induced-Movement-Therapy (mCIMT, 20 hours): h-BITmCI. Thus, Bimanual Functional Performance (BFP), Quality of Life (QoL) and expectations from families were measured through the Assisting Hand Assessment, (AHA), Pediatric Quality of Life Inventory, for Cerebral Palsy, (PedsQLTM v. 3.0, CP) and a specific questionnaire for families for baseline period (week 0), during the treatment phase (week 4 and week 8) and after the intervention (week 10). Repeated measures ANOVA analysis (with post hoc test correction) was used for the BFP and QoL, with a confidence interval (CI) of 95% and with p value <. 008 considered statistically significant. Results Ten children completed the study with an average of 77-hours-BIT and 17-hours-mCIMT. None of the participants dropped out of the study during the follow-up process, and the parents’ expectations were fulfilled, indicating high caregiver compliance. During the first 80 hours of BIT, a mean increase of 3.7 AHA units was obtained for the BFP (p = 1.00) and 1.64 points in the QoL (p = 1.00). Clinically relevant changes were observed in the last two weeks (20 hours mCIMT) with a mean increase of 10.6 AHA units in BFP and 6.29 points in QoL (p < .001). Conclusions h-BITmCI protocol is feasible to be performed at home with the family’s involvement, obtaining the greatest improvements after 100 hours of both therapies. Thus, mCIMT would be a relevant condition to increase the affected upper limb functionality, rather than the dosage used to obtain clinically relevant changes.
Branched sexuality and sexual health among Black cisgender sexual minority men in Baltimore, Maryland: an exploratory study

Abstract Branched sexuality – in form of combinations of sexual identity, behaviour and attraction (e.g. heterosexual identity, sex with men, attraction to women) that differ from coincident combinations (e.g. gay/homosexual/same-gender-loving identity, sex with men, attraction to men) – has been observed among Black sexual minority men and may correlate with sexual health. Using baseline survey data from Black sexual minority men (N = 323) enrolled in a sexual health intervention trial, we examined sexual identity, behaviour and attraction to determine the prevalence of branched sexuality and used modified Poisson regression with robust variance estimation to test associations with sexual health. Black sexual minority men reporting branched sexuality (n = 50, 15.5%) were marginally more likely to endorse negative condom-use attitudes compared to those reporting coincident sexuality (n = 273, 84.5%; adjusted prevalence ratio [aPR] = 1.48, 95% confidence interval [CI] = 0.94, 2.32) and significantly more likely to endorse negative condom-use attitudes compared to those reporting gay/homosexual/same-gender-loving-coincident sexuality (aPR = 1.85, 95% CI = 01.07, 3.22). Those reporting branched sexuality were significantly less likely to report past-year testing for sexually transmitted infections compared to those reporting coincident (PR = 0.52, 95% CI = 0.28, 0.94) or gay/homosexual/same-gender-loving-coincident sexuality (PR = 0.46, 95% CI = 0.25, 0.84) in bivariate analyses only. Increased understanding of Black sexual minority men’s sexuality and improved sexuality data collection efforts are needed.
Estimating interactions and subgroup‐specific treatment effects in meta‐analysis without aggregation bias: A within‐trial framework

Estimation of within‐trial interactions in meta‐analysis is crucial for reliable assessment of how treatment effects vary across participant subgroups. However, current methods have various limitations. Patients, clinicians and policy‐makers need reliable estimates of treatment effects within specific covariate subgroups, on relative and absolute scales, in order to target treatments appropriately—which estimation of an interaction effect does not in itself provide. Also, the focus has been on covariates with only two subgroups, and may exclude relevant data if only a single subgroup is reported. Therefore, in this article we further develop the “within‐trial” framework by providing practical methods to (1) estimate within‐trial interactions across two or more subgroups; (2) estimate subgroup‐specific (“floating”) treatment effects that are compatible with the within‐trial interactions and make maximum use of available data; and (3) clearly present this data using novel implementation of forest plots. We described the steps involved and apply the methods to two examples taken from previously published meta‐analyses, and demonstrate a straightforward implementation in Stata based upon existing code for multivariate meta‐analysis. We discuss how the within‐trial framework and plots can be utilised with aggregate (or “published”) source data, as well as with individual participant data, to effectively demonstrate how treatment effects differ across participant subgroups.
Nanotopography modulates cytoskeletal organization and dynamics during T cell activation

Exposure to MHC-antigen complexes on the surface of antigen-presenting cells (APCs) activates T cells, inducing the formation of the immune synapse (IS). Antigen detection at the APC surface is thus a critical step in the adaptive immune response. The physical properties of antigen-presenting surfaces encountered by T cells in vivo are believed to modulate T cell activation and proliferation. Although stiffness and ligand mobility influence IS formation, the effect of the complex topography of the APC surface on this process is not well understood. Here we investigate how nanotopography modulates cytoskeletal dynamics and signaling during the early stages of T cell activation using high-resolution fluorescence microscopy on nanofabricated surfaces with parallel nanoridges of different spacings. We find that although nanoridges reduce the maximum spread area as compared with cells on flat surfaces, the ridges enhance the accumulation of actin and the signaling kinase ZAP-70 at the IS. Actin polymerization is more dynamic in the presence of ridges, which influence the directionality of both actin flows and microtubule (MT) growth. Our results demonstrate that the topography of the activating surface exerts both global effects on T cell morphology and local changes in actin and MT dynamics, collectively influencing T cell signaling.
Plant–microbial responses to reduced precipitation depend on tree species in a temperate forest

Given that global change is predicted to increase the frequency and severity of drought in temperate forests, it is critical to understand the degree to which plant belowground responses cascade through the soil system to drive ecosystem responses to water stress. While most research has focused on plant and microbial responses independently of each other, a gap in our understanding lies in the integrated response of plant‐microbial interactions to water stress. We investigated the extent to which divergent belowground responses to reduced precipitation between sugar maple trees (Acer saccharum) versus oak trees (Oak spp.) may influence microbial activity via throughfall exclusion in the field. Evidence that oak trees send carbon belowground to prime microbial activity more than maples under ambient conditions and in response to water stress suggests there is the potential for corresponding impacts of reduced precipitation on microbial activity. As such, we tested the hypothesis that differences in belowground C allocation between oaks and maples would stimulate microbial activity in the oak treatment soils and reduce microbial activity in in the sugar maple treatment soils compared to their respective controls. We found that the treatment led to declines in N mineralization, soil respiration, and oxidative enzyme activity in the sugar maple treatment plot. These declines may be due to sugar maple trees reducing root C transfers to the soil. By contrast, the reduced precipitation treatment enhanced soil respiration, as well as rates of N mineralization and peroxidase activity in the oak rhizosphere. This enhanced activity suggests that oak roots provided optimal rhizosphere conditions during water stress to prime microbial activity to support net primary production. With future changes in precipitation predicted for forests in the Eastern US, we show that the strength of plant‐microbial interactions drives the degree to which reduced precipitation impacts soil C and nutrient cycling.
Investigating the protective effects of estrogen on beta cell health and the progression of hyperglycemia-induced atherosclerosis.

Sex differences in the prevalence and development of diabetes and associated cardiometabolic complications are well established. The objective of this study was to analyze the effects of estrogen on the maintenance of beta cell health/function and atherosclerosis progression, using a mouse model of hyperglycemia-induced atherosclerosis, the ApoE-/-:Ins2+/Akita mouse. ApoE-/-:Ins2+/Akita mice exhibit sexual dimorphism in the control of blood glucose levels. Male ApoE-/-:Ins2+/Akita mice are chronically hyperglycemic due to a significant reduction in pancreatic beta cell mass. Female mice are only transiently hyperglycemic, maintain beta cell mass, and blood glucose levels normalize at 35±1 days of age. To determine the effects of estrogen on pancreatic beta cell health and function, ovariectomies and estrogen supplementation experiments were performed, and pancreatic health and atherosclerosis were assessed at various time points. Ovariectomized ApoE-/-:Ins2+/Akita mice developed chronic hyperglycemia with significantly reduced beta cell mass. To determine whether the observed effects on ovariectomized ApoE-/-:Ins2+/Akita mice were due to lack of estrogens, slow-releasing estradiol pellets were inserted subcutaneously. Ovariectomized ApoE-/-:Ins2+/Akita mice treated with exogenous estradiol showed normalized blood glucose levels, and maintained beta cell mass. Exogenous estradiol significantly reduced atherosclerosis in both ovariectomized female and male ApoE-/-:Ins2+/Akita mice relative to controls. Together, these findings suggest that estradiol confers significant protection to pancreatic beta cell health and can directly and indirectly slow the progression of atherosclerosis.
Basolateral Sorting of the Sodium/Iodide Symporter Is Mediated by Adaptor Protein 1 Clathrin Adaptor Complexes

Background: The sodium/iodide symporter (NIS) is a transmembrane protein located on the basolateral membrane of thyrocytes. Despite its physiological and clinical relevance, little is known about the mechanisms that mediate NIS subcellular sorting. In the present study, we examined NIS basolateral trafficking in vitro using non-thyroid and thyroid epithelial cells. Methods: Immunofluorescence and Western blotting were performed to analyze NIS subcellular location and function in cells grown in monolayers under unpolarized and/or polarized conditions. Strategic NIS residues were mutated, and binding of NIS to clathrin adaptor complexes was determined by immunoprecipitation. Results: We show that NIS reaches the plasma membrane (PM) through a thyrotropin-dependent mechanism 24 hours after treatment with the hormone. We demonstrate that NIS basolateral trafficking is a clathrin-mediated mechanism, in which the clathrin adaptor complexes AP-1 (A and B) sort NIS from the trans-Golgi network (TGN) and recycling endosomes (REs). Specifically, we show that the AP-1B μ1 subunit controls NIS basolateral sorting through common REs. In its absence, NIS is apically missorted but remains functional. Additionally, direct NIS basolateral transport from the TGN to the basolateral membrane is mediated by AP-1A through clathrin-coated vesicles that also carry the transferrin receptor. Loss of the μ1 subunit of AP-1A is functionally compensated by AP-1B. Furthermore, loss of both subunits diminishes NIS trafficking to the PM. Finally, we demonstrate that AP-1A binds to the L121 and LL562/563 residues on NIS, whereas AP-1B binds to L583. Conclusions: Our findings highlight the novel involvement of the clathrin-coated machinery in basolateral NIS trafficking. Given that AP-1A expression is reduced in tumors, and its expression correlates with that of NIS, these findings will help uncover new targets in thyroid cancer treatment.
Effects of Aronia melanocarpa on Cardiometabolic Diseases: A Systematic Review of Quasi-Design Studies and Randomized Controlled Trials

OBJECTIVES Aronia melanocarpa (Aronia) is a shrub with small berries, chokeberries. Chokeberries are claimed to possess health benefits due to a high content of polyphenols. Aronia is known to be extremely antioxidant; however, evidence for its health benefits is not established. This review gives an overview of the impact of Aronia on cardiometabolic risk factors and diseases. METHODS Seventeen studies on cardiometabolic risk factors and diseases were identified through a systematic search on PubMed, Embase, and Cochrane. Inclusion criteria were studies with Aronia as intervention, performed in individuals with cardiometabolic disease or risk factors, e.g., type 2 diabetes (T2D), cardiovascular disease, hypertension, dyslipidaemia, impaired glucose tolerance, overweight, central obesity and smoking. Four of these studies were applicable for a quantitative analysis. RESULTS Aronia did not influence body weight, circulating triglycerides, total cholesterol, high-density lipoprotein (HDL) cholesterol, or blood pressure. The quantitative analysis revealed a mean reduction in blood glucose of 0.44 mmol/l (P=0.0001) in the treatment group compared with the control group suggesting that Aronia treatment may have a beneficial impact on blood glucose. In addition, treatment durations of 6 weeks to 3 months tended to decrease low-density lipoprotein (LDL) cholesterol, while shorter treatment durations had no effect on LDL cholesterol. The quantitative analysis did not provide data on long-term effects of Aronia on lipids. CONCLUSIONS More long-term high-quality randomized controlled studies are needed to clarify if dietary supplementation with Aronia has beneficial effects on cardiometabolic diseases.
Normal Table of Xenopus development: a new graphical resource

ABSTRACT Normal tables of development are essential for studies of embryogenesis, serving as an important resource for model organisms, including the frog Xenopus laevis. Xenopus has long been used to study developmental and cell biology, and is an increasingly important model for human birth defects and disease, genomics, proteomics and toxicology. Scientists utilize Nieuwkoop and Faber's classic ‘Normal Table of Xenopus laevis (Daudin)’ and accompanying illustrations to enable experimental reproducibility and reuse the illustrations in new publications and teaching. However, it is no longer possible to obtain permission for these copyrighted illustrations. We present 133 new, high-quality illustrations of X. laevis development from fertilization to metamorphosis, with additional views that were not available in the original collection. All the images are available on Xenbase, the Xenopus knowledgebase (http://www.xenbase.org/entry/zahn.do), for download and reuse under an attributable, non-commercial creative commons license. Additionally, we have compiled a ‘Landmarks Table’ of key morphological features and marker gene expression that can be used to distinguish stages quickly and reliably (https://www.xenbase.org/entry/landmarks-table.do). This new open-access resource will facilitate Xenopus research and teaching in the decades to come.
Downregulation of hsa‐miR‐548d‐3p and overexpression of HOXA9 in diffuse large B‐cell lymphoma patients and the risk of R‐CHOP chemotherapy resistance and disease progression

Routine categorization of DLBCL patients into GCB and non‐GCB groups by Hans' criteria could not accurately predict chemotherapy resistance and disease progression in patients treated with standard R‐CHOP therapy. There is a need to identify better biomarker predictors to enhance assisted selection of chemotherapy regimens for DLBCL patients.
Avian Cytokine and TLR Gene Classes The Differential Evolutionary Dynamics of

The potential for investigating immune gene diversity has been greatly enhanced by recent advances in sequencing power. In this study, variation at two categories of avian immune genes with differing functional roles, pathogen detection and mediation of immune mechanisms, was examined using high-throughput sequencing. TLRs identify and alert the immune system by detecting molecular motifs that are conserved among pathogenic microorganisms, whereas cytokines act as mediators of resulting inﬂammation and immunity. Nine genes from each class were resequenced in a panel of domestic chickens and wild jungle fowl (JF). Tests on population-wide genetic variation between the gene classes indicated that allele frequency spectra at each group were distinctive. TLRs showed evidence pointing toward directional selection, whereas cytokines had signals more suggestive of frequency-dependent selection. This difference persisted between the distributions considering only coding sites, suggesting functional relevance. The unique patterns of variation at each gene class may be constrained by their different functional roles in the immune response. TLRs identify a relatively limited number of exogeneous pathogenic-related patterns and would be required to adapt quickly in response to evolving novel microbes encountered in new environmental niches. In contrast, cytokines interact with many molecules in mediating the power of immune mechanisms, and accordingly respond to the selective stimuli of many infectious diseases. Analyses also indicated that a general pattern of high variability has been enhanced by widespread genetic exchange between chicken and red JF, and possibly between chicken and gray JF at TLR1LA and TLR2A. The Journal of Immunology , 2010, 184: 6993–7000. domain locations of nonsynonymous mutations were ascer-tained from Uniprot (www.uniprot.org). If there were no annotated chicken gene protein domains, these were determined by aligning the chicken genes with their human orthologs using T-Coffee (63). The sizes of the TLR protein extracellular, cytoplasmic and transmembrane domains were estimated using TMpred (www.ch.embnet.org/software/TMPRED_form. html) (64). determine the relationship between chicken and each JF species, median-joining phylogenetic haplotype networks constructed for each gene using Network version 4.2. 0.1 (www.ﬂuxus-technology.com) (65), F ST (66) permutations