Miracle-dz/UniFAR-FTUs huggingface dataset:
Aspects of neutrino oscillation in alternative gravity theories

Neutrino spin and flavour oscillation in curved spacetime have been studied for the most general static spherically symmetric configuration. Having exploited the spherical symmetry we have confined ourselves to the equatorial plane in order to determine the spin and flavour oscillation frequency in this general set-up. Using the symmetry properties we have derived spin oscillation frequency for neutrino moving along a geodesic or in a circular orbit. Starting from the expression of neutrino spin oscillation frequency we have shown that even in this general context, in high energy limit the spin oscillation frequency for neutrino moving along circular orbit vanishes. We have verified previous results along this line by transforming to Schwarzschild coordinates under appropriate limit. This finally lends itself to the probability of neutrino helicity flip which turns out to be non-zero. While for neutrino flavour oscillation we have derived general results for oscillation phase, which subsequently have been applied to three different gravity theories. One, of them appears as low-energy approximation to string theory, where we have an additional field, namely, dilaton field coupled to Maxwell field tensor. This yields a realization of Reissner-Nordström solution in string theory at low-energy. Next one corresponds to generalization of Schwarzschild solution by introduction of quadratic curvature terms of all possible form to the Einstein-Hilbert action. Finally, we have also discussed regular black hole solutions. In all these cases the flavour oscillation probabilities can be determined for solar neutrinos and thus can be used to put bounds on the parameters of these gravity theories. While for spin oscillation probability, we have considered two cases, Gauss-Bonnet term added to the Einstein-Hilbert action and the f(R) gravity theory. In both these cases we could impose bounds on the parameters which are consistent with previous considerations. In a nutshell, in this work we have presented both spin and flavour oscillation frequency of neutrino in most general static spherically symmetric spacetime, encompassing a vast class of solutions, which when applied to three such instances in alternative theories for flavour oscillation and two alternative theories for spin oscillation put bounds on the parameters of these theories. Implications are also discussed.
A novel missense variant in endothelin‐2 (EDN2) causes a growth and respiratory lethal syndrome in bovine

Abstract The high level of fragmentation of the Spanish Lidia cattle breed, divided into lineages called ‘castas’ and into herds within lineages based on reproductive isolation, increases the risk of homozygosity and the outbreak of recessive genetic defects. Since 2004, an increasing number of calves have been identified in a Lidia herd with signs of severe growth retardation, respiratory alterations and juvenile lethality, which constitutes a novel inherited syndrome in cattle and was subsequently termed growth and respiratory lethal syndrome. We performed a genome‐wide association study on a cohort of 13 affected calves and 24 putative non‐carrier parents, mapping the disease to a wide 6 cM region on bovine chromosome 3 (p < 10−7). Whole genome re‐sequencing of three affected calves and three putative non‐carrier parents identified a novel missense variant (c.149G>A|p.Cys50Tyr) in exon 2 of the endothelin 2 (EDN2) gene. Bioinformatic analyses of p.Cys50Tyr effects predicted them to be damaging for both the structure and the function of the edn2 protein, and to create a new site of splicing that may also affect the pattern of pre‐mRNA splicing and exon definition. Sanger sequencing of this variant on the rest of the sample set confirmed the segregation pattern obtained with whole genome re‐sequencing. The identification of the causative variant and the development of a diagnostic genetic test enable the efficient design of matings to keep the effective population size as high as possible, as well as providing insights into the first EDN2‐associated hereditary disease in cattle or other species.
Molecular characterisation, temporal expression and involvement of ANGPTL4 in fat deposition in Muscovy ducks

ABSTRACT 1. Angiopoietin-like protein 4 (ANGPTL4) plays a key role in promoting fat metabolism and reducing blood lipid. This study characterised the ANGPTL4 gene in Muscovy ducks (Cairina moschata) and investigated its potential functions in fat metabolism in Muscovy ducks. 2. The Muscovy duck ANGPTL4 cDNA was successfully cloned for the first time, showing a length of 2591 bp. After phylogenetic analysis by RT-qPCR analysis, it was found that the ANGPTL4 gene of Anas platyrhynchos shared the highest sequence similarity with that of Muscovy ducks. 3. The ANGPTL4 gene was commonly expressed in 23 different tissues with the highest expression in the abdominal fat in Muscovy ducks. A significant association was observed between abdominal fat percentage (AFP) and the mRNA expression of the ANGPTL4 gene. Moreover, Muscovy ducks showed a peak of ANGPTL4 expression in the liver and abdominal fat at 1–2 weeks old. 4. These findings suggest that the ANGPTL4 gene is related to fat deposition and regulation in Muscovy ducks.
Mediterranean diet and physical activity in Down syndrome pediatric subjects: the DONUT STUDY

Abstract Introduction Children with Down syndrome (DS) are characterised by peculiar dietary choices and approach to physical activity. The aim of this study is to quantify their adherence to the Mediterranean diet, their level of physical activity and lipid profile. Methods Cross-sectional study, involving 61 children affected by DS. Parents of the patients were requested to complete two questionnaires, Mediterranean Diet Quality Index in children and adolescents (KIDMED) and Godin Leisure-Time Physical Activity Questionnaire (Godin). In addition, children underwent a venous sampling to check their lipid profile. Results High scores on KIDMED and Godin were found and were associated with a reduced likelihood of being overweight or obese (0.001< p < 0.077; 0.001< p < 0.248). The level of physical activity and the probability of finding pathological HDL values in plasma were inversely related (0.001< p < 0.263). Conclusions The DONUT study proves that KIDMED and Godin questionnaires can identify children affected by DS that can lead to develop inadequate anthropometric variables and low levels of HDL cholesterol. Moreover, the results of this study show that, despite potential difficulties in the pursuit of a correct diet and an adequate approach to physical activity, children with DS could achieve results that are substantially like those of non-DS children.
Dipeptidyl peptidase 9 triggers BRCA2 degradation and promotes DNA damage repair

N‐terminal sequences are important sites for post‐translational modifications that alter protein localization, activity, and stability. Dipeptidyl peptidase 9 (DPP9) is a serine aminopeptidase with the rare ability to cleave off N‐terminal dipeptides with imino acid proline in the second position. Here, we identify the tumor‐suppressor BRCA2 as a DPP9 substrate and show this interaction to be induced by DNA damage. We present crystallographic structures documenting intracrystalline enzymatic activity of DPP9, with the N‐terminal Met1‐Pro2 of a BRCA21‐40 peptide captured in its active site. Intriguingly, DPP9‐depleted cells are hypersensitive to genotoxic agents and are impaired in the repair of DNA double‐strand breaks by homologous recombination. Mechanistically, DPP9 targets BRCA2 for degradation and promotes the formation of RAD51 foci, the downstream function of BRCA2. N‐terminal truncation mutants of BRCA2 that mimic a DPP9 product phenocopy reduced BRCA2 stability and rescue RAD51 foci formation in DPP9‐deficient cells. Taken together, we present DPP9 as a regulator of BRCA2 stability and propose that by fine‐tuning the cellular concentrations of BRCA2, DPP9 alters the BRCA2 interactome, providing a possible explanation for DPP9's role in cancer.
Entanglement dynamics in three-qubit X states

I explore the entanglement dynamics of a three-qubit system in an initial X state undergoing decoherence including the possible exhibition of entanglement sudden death. To quantify entanglement I utilize negativity measures and make use of appropriate entanglement witnesses. The negativity results are then extended to X states with an arbitraty number of qubits. I also demonstrate nonstandard behavior of the tripartite negativity entanglement metric: its sudden appearance after some amount of decoherence, followed quickly by its disappearance. Finally, I solve for a lower bound on the three-qubit X-state concurrence, demonstrate when this bound goes to 0, and outline simplifcations for the calculation of higher-order X-state concurrences.
Transcriptome analysis of female western flower thrips, Frankliniella occidentalis, exhibiting neo-panoistic ovarian development

The western flower thrips, Frankliniella occidentalis, is one of the most devastating insect pests with explosive reproductive potential. However, its reproductive physiological processes are not well understood. This study reports the ovarian development and associated transcriptomes of F. occidentalis. Each ovary consisted of four ovarioles, each of which contained a maximum of nine follicles in the vitellarium. The germarium consisted of several dividing cells forming a germ cell cluster, presumably consisting of oocytes and nurse cells. The nurse cells were restricted to the germarium while the subsequent follicles did not possess nurse cells or a nutritive cord, supporting the neo-panoistic ovariole usually found in thysanopteran insects. Oocyte development was completed 72 h after adult emergence (AAE). Transcriptome analysis was performed at mid (36 h AAE) and late (60 h AAE) ovarian developmental stages using RNA sequencing (RNASeq) technology. More than 120 million reads per replication were matched to ≈ 15,000 F. occidentalis genes. Almost 500 genes were differentially expressed at each of the mid and late ovarian developmental stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these differentially expressed genes (DEGs) were associated with metabolic pathways along with protein and nucleic acid biosynthesis. In both ovarian developmental stages, vitellogenin, mucin, and chorion genes were highly (> 8-fold) expressed. Endocrine signals associated with ovarian development were further investigated from the DEGs. Insulin and juvenile hormone signals were upregulated only at 36 h AAE, whereas the ecdysteroid signal was highly maintained at 60 h AAE. This study reports the transcriptome associated with the ovarian development of F. occidentalis, which possesses a neo-panoistic ovariole.
Transcriptional Regulation by the Velvet Protein VE-1 during Asexual Development in the Fungus Neurospora crassa

Most fungi disperse in nature and infect new hosts by producing vegetative spores or conidia during asexual development. This is a process that is regulated by environmental signals like light and the availability of nutrients. ABSTRACT Asexual reproduction in fungi facilitates the dispersal and colonization of new substrates and, in pathogenic fungi, allows infection of plants and animals. The velvet complex is a fungus-specific protein complex that participates in the regulation of gene expression in response to environmental signals like light, as well as developmental processes, pathogenesis, and secondary metabolism. The velvet complex in the fungus Neurospora crassa is composed of three proteins, VE-1, VE-2, and LAE-1. Mutations in ve-1 or ve-2, but not in lae-1, led to shorter heights of aerial tissue, a mixture of aerial hyphae and developing macroconidia, and increased microconidiation when they were combined with mutations in the transcription factor gene fl. VE-2 and LAE-1 were detected during vegetative growth and conidiation, unlike VE-1, which was mostly observed in samples obtained from submerged vegetative hyphae. We propose that VE-1 is the limiting component of the velvet complex during conidiation and has a major role in the transcriptional regulation of conidiation. Characterization of the role of VE-1 during mycelial growth and asexual development (conidiation) by transcriptome sequencing (RNA-seq) experiments allowed the identification of a set of genes regulated by VE-1 that participate in the regulation of conidiation, most notably the transcription factor genes vib-1 and fl. We propose that VE-1 and VE-2 regulate the development of aerial tissue and the balance between macro- and microconidiation in coordination with FL and VIB-1. IMPORTANCE Most fungi disperse in nature and infect new hosts by producing vegetative spores or conidia during asexual development. This is a process that is regulated by environmental signals like light and the availability of nutrients. A protein complex, the velvet complex, participates in the integration of environmental signals to regulate conidiation. We have found that a key component of this complex in the fungus Neurospora crassa, VE-1, has a major role in the regulation of transcription during conidiation. VE-1 regulates a large number of genes, including the genes for the transcription factors FL and VIB-1. Our results will help to understand how environmental signals are integrated in the fungal cell to regulate development.
Prophylactic onlay mesh at emergency laparotomy: promising early outcomes with long‐acting synthetic resorbable mesh

Careful surgical strategy is paramount in balancing the prevention of fascial dehiscence, incisional hernia (IH) and fear of additional mesh‐related wound complications post‐laparotomy. This study aims to review early outcomes of patients undergoing an emergency laparotomy with prophylactic TIGR® mesh, used to reduce early fascial dehiscence and potential subsequent IH.
Landscapes of Enteric Virome Signatures in Early-Weaned Piglets

This study systematically reveals the biological diversity, structure, and composition of intestinal DNA and RNA virus profiles in early-weaned piglets. Furthermore, characteristics of differences in gut viromes between early-weaned healthy piglets and piglets with diarrhea were also elucidated. ABSTRACT Diarrhea caused by early-weaning-induced stress can increase mortality rates and reduce growth performance of piglets, seriously harming the livestock industry. To date, studies on the gut microbiome of early-weaned piglets have focused almost exclusively on bacteria, while studies on their gut virome are extremely lacking. Here, we used metagenomic and metatranscriptomic sequencing combined with bioinformatic analysis techniques to preliminarily characterize the intestinal virome of early-weaned piglets at different biological classification levels. The alpha diversity of enteroviruses was generally elevated in early-weaned piglets with diarrhea, compared to healthy piglets, whereas the two groups of piglets showed no significant difference in beta diversity. In addition, the species compositions of the gut virome were similar between healthy piglets and piglets with diarrhea, while their respective dominant species were somewhat different. We also identified 58 differential DNA viruses and 16 differential RNA viruses between the two groups of piglets at all biological taxonomic levels. Of these, 1 (family Dhakavirus) and 6 (phylum Artverviricota, class Revtraviricetes, order Ortervirales, family Retroviridae, genus Gammaretrovirus, and species Kirsten murine sarcoma virus) specific viruses disappeared from the intestines of healthy piglets and piglets with diarrhea, respectively. Moreover, we found that some DNA and RNA viruses formed strong correlations among themselves or between them. IMPORTANCE This study systematically reveals the biological diversity, structure, and composition of intestinal DNA and RNA virus profiles in early-weaned piglets. Furthermore, characteristics of differences in gut viromes between early-weaned healthy piglets and piglets with diarrhea were also elucidated. Importantly, some potential biomarkers for early-weaned piglets with diarrhea were identified. These findings fill a gap for the early-weaned piglet gut virome and lay the foundation for the development of strategies to target enteroviruses for the prevention and treatment of early-weaning-induced piglet diarrhea.
CroR Regulates Expression of pbp4(5) to Promote Cephalosporin Resistance in Enterococcus faecalis

Investigation into molecular mechanisms used by enterococci to subvert cephalosporin antibiotics is imperative for preventing and treating life-threatening infections. In this study, we used genetic means to investigate the functional output of the CroS/R TCS required for enterococcal resistance to cephalosporins. ABSTRACT Enterococcus faecalis is an opportunistic pathogen and a major cause of severe nosocomial infections. Treatment options against enterococcal infections are declining due to the resistance of enterococci to numerous antibiotics. A key risk factor for developing enterococcal infections is treatment with cephalosporin antibiotics, to which enterococci are intrinsically resistant. For susceptible organisms, cephalosporins inhibit bacterial growth by acylating the active site of penicillin-binding proteins (PBPs), key enzymes that catalyze peptidoglycan cross-linking. Two specific PBPs of enterococci, Pbp4(5) and PbpA(2b), exhibit low reactivity toward cephalosporins, allowing these PBPs to cross-link peptidoglycan in the presence of cephalosporins to drive resistance in enterococci, but the mechanisms by which these PBPs are regulated are poorly understood. The CroS/R two-component signal transduction system (TCS) is also required for cephalosporin resistance. Activation of CroS/R by cephalosporins leads to CroR-dependent changes in gene expression. However, the specific genes regulated by CroS/R that are responsible for cephalosporin resistance remain largely unknown. In this study, we characterized CroR-dependent transcriptome remodeling by RNA-seq, identifying pbp4(5) as a CroR regulon member in multiple, diverse lineages of E. faecalis. Through genetic analysis of the pbp4(5) and croR promoters, we uncovered a CroR-dependent regulatory motif. Mutations in this motif to disrupt CroR-dependent upregulation of pbp4(5) in the presence of cell wall stress resulted in a reduction of resistance to cephalosporins in E. faecalis, demonstrating that enhanced production of Pbp4(5) and likely other proteins involved in peptidoglycan biogenesis by the CroS/R system drives enterococcal cephalosporin resistance. IMPORTANCE Investigation into molecular mechanisms used by enterococci to subvert cephalosporin antibiotics is imperative for preventing and treating life-threatening infections. In this study, we used genetic means to investigate the functional output of the CroS/R TCS required for enterococcal resistance to cephalosporins. We found that enhanced production of the penicillin-binding protein Pbp4(5) upon exposure to cell wall stress was mediated by CroS/R and was critical for intrinsic cephalosporin resistance of E. faecalis.
Validity and reproducibility of a FFQ for assessing dietary intake among residents of northeast China: northeast cohort study of China

Abstract The study was to evaluate the reproducibility and validity of the FFQ for residents of northeast China. A total of 131 participants completed two FFQ (FFQ1 and FFQ2) within a 3-month period, 125 participants completed 8-d weighed diet records (WDR) and 112 participants completed blood biomarker testing. Reproducibility was measured by comparing nutrient and food intake between FFQ1 and FFQ2. The validity of the FFQ was assessed by WDR and the triad method. The Spearman correlation coefficients (SCC) and intraclass correlation coefficients (ICC) for reproducibility ranged from 0·41 to 0·69 (median = 0·53) and from 0·18 to 0·68 (median = 0·53) for energy and nutrients and from 0·37 to 0·73 (median = 0·59) and from 0·33 to 0·86 (median = 0·60) for food groups, respectively. The classifications of same or adjacent quartiles ranged from 73·64 to 93·80 % for both FFQ. The crude SCC between the FFQ and WDR ranged from 0·27 to 0·55 (median = 0·46) for the energy and nutrients and from 0·26 to 0·70 (median = 0·52) for food groups, and classifications of the same or adjacent quartiles ranged from 65·32 to 86·29 %. The triad method indicated that validation coefficients for the FFQ were above 0·3 for most nutrients, which indicated a moderate or high level of validity. The FFQ that was developed for residents of northeast China for the Northeast Cohort Study of China is reliable and valid for assessing the intake of most foods and nutrients.
“Do we even have a voice?” Health providers’ perspective on the patient accommodation strategies in Bangladesh

Objective In a resource-constrained setting like Bangladesh, effective patient-provider communication is critical to the delivery of maternal healthcare services. Using communication accommodation theory, this study tried to understand how providers perceive, engage, and accommodate patients’ needs in maternity wards. Methods This qualitative exploratory study used a semi-structured interview guide to conduct in-depth face-to-face interviews of ten healthcare providers in two government-funded public health facilities in Bangladesh. The interview data were analyzed using MAXQDA 2020 software. Results The thematic analyses revealed that nurses and midwives faced conceivable neglect from patients and their attendees due to possible service and facility constraints, indicating their low status and control within the service operation. Despite efforts to address patients’ emotional and psychological concerns, providers appear to avoid (divergence strategy) confronting patients and their irate visitors. Unimodal convergence emerged when providers accepted patients’ arguments about the systematic inadequacy of service facilities. Providers have employed interpretability tactics to communicate medical opinions and applied nonverbal cues where necessary. Conclusion A lack of open communication between healthcare providers and patients necessitated various forms of accommodation. Integrated strategies addressing service restrictions and initiatives fostering patient understanding and cooperation may improve patient-provider communication.
Vascular topology and blood flow are acutely impacted by experimental febrile status epilepticus

Febrile status epilepticus (FSE) is an important risk factor for temporal lobe epilepsy and early identification of those at high risk for epilepsy is vital. In a rat model of FSE, we identified an acute (2 hrs) novel MRI signal where reduced T2 relaxation values in the basolateral amygdala (BLA) predicted epilepsy in adulthood; this T2 signal remains incompletely understood and we hypothesized that it may be influenced by vascular topology. Experimental FSE induced in rat pups reduced blood vessel density of the cortical vasculature in a lateralized manner at 2 hrs post FSE. Middle cerebral artery (MCA) exhibited abnormal topology in FSE pups but not in controls. In the BLA, significant vessel junction reductions and decreased vessel diameter were observed, together with a strong trend for reduced vessel length. Perfusion weighted MRI (PWI) was acutely increased cerebral blood flow (CBF) in cortex, amygdala and hippocampus of FSE pups that correlated to decreased T2 relaxation values compared to controls. This is consistent with increased levels of deoxyhemoglobin associated with increased metabolic demand. In summary, FSE acutely modifies vascular topological and CBF in cortex and BLA that may underlie acute MRI signal changes that predict progression to future epilepsy.