Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Housing Systems on Physiological and Immunological Parameters in Laying Hens

ABSTRACT The aim of this study was to assess the effects of housing systems on physiological and immunological responses as stress indicators in laying hens. A total of 500 White Leghorn aged 16 weeks were allotted into ten conventional cages (10 birds/cage and 810 cm 2 /bird) and four floor pens (100 birds/pen and 2,800 cm 2 /bird) for 24 weeks. The hens housed in conventional cages with higher stocking density resulted in a significantly (P<0.05) lower BW compared with those housed in floor pens with lower stocking density without affecting the relative weights of immune organs between housing conditions. In plasma biochemical values, cholesterol and corticosterone were significantly (P<0.05) lower in the hens housed in floor pens compared with those housed in conventional cages. In pro-inflammatory cytokines, hepatic interleukin (IL)-10 and interferon-gamma (IFN-γ) levels were significantly (P<0.05) higher in the hens housed in conventional cages compared with those kept in floor pens. Splenic and thymic IFN-γ expression was significantly (P<0.05) up-regulated in the hens kept in conventional cages compared with those kept in floor pens without affecting IL-1, IL-10, lipopolysaccharide- induced tumor necrosis factor-α factor (LITAF) and inducible nitric oxide synthase (iNOS). In the bursa of Fabricius, IL-10 and iNOS expression of the hens housed in conventional cages were significantly (P<0.05) higher compared with those of the hens housed in floor pens. In conclusion, layers housed in conventional cages enhanced plasma cholesterol, corticosterone and some pro-inflammatory cytokines in the immune organs compared with those in floor pens. (
Segmenting Teeth from Volumetric CT Data with a Hierarchical CNN-based Approach

This paper addresses the automatic segmentation of teeth in volumetric Computed Tomography (CT) scans of the human skull. Our approach is based on a convolutional neural network employing 3D volumetric convolutions. To tackle data scale issues, we apply a hierarchical coarse-to ﬁne approach combining two CNNs, one for low-resolution detection and one for high-resolution reﬁnement. In quantitative experiments on 40 CT scans with manually acquired ground truth, we demonstrate that our approach displays remarkable robustness across different patients and device vendors. Furthermore, our hierarchical extension outperforms a single-scale segmentation, and network size can be reduced compared to previous architectures without loss of accuracy.
Classification of acute myeloid leukemia

The World Health Organization (WHO) Classification of Tumors of Hematopoietic and Lymphoid Tissues was revised in 2017 on the basis of recent high-throughput sequencing and gene expression data on hematologic malignancies. This review explores the current WHO classification of acute myeloid leukemia (AML) and related precursor neoplasms, highlighting the changes made in the current edition and focusing on the diagnosis of AML.
Peptidyl Acyloxymethyl Ketones as Activity‐Based Probes for the Main Protease of SARS‐CoV‐2 **

The global pandemic caused by SARS‐CoV‐2 calls for the fast development of antiviral drugs against this particular coronavirus. Chemical tools to facilitate inhibitor discovery as well as detection of target engagement by hit or lead compounds from high‐throughput screens are therefore in urgent need. We here report novel, selective activity‐based probes that enable detection of the SARS‐CoV‐2 main protease. The probes are based on acyloxymethyl ketone reactive electrophiles combined with a peptide sequence including unnatural amino acids that targets the nonprimed site of the main protease substrate binding cleft. They are the first activity‐based probes for the main protease of coronaviruses and display target labeling within a human proteome without background. We expect that these reagents will be useful in the drug‐development pipeline, not only for the current SARS‐CoV‐2, but also for other coronaviruses.
Sequence Diversity of SLG and SRK in Brassica oleracea L.

Abstract DNA sequences of SLG and SRK , believed to function in self-pollen recognition of self-incompatibility, were analysed and compared between many S haplotypes of Brassica oleracea . Some different S haplotypes have highly similar SLGs (more than 97.5% amino acid sequence identity), while their SRKs are less similar (less than 88% identity). Different lines having the same recognition specificity often show a high degree of sequence variation in SLG (88.5% identity in the S 2 haplotype), but their SRKs are very similar to each other (97.3% identity). S haplotypes, in which SLG protein is undetectable by Western blot analysis, have stop codons in the middle of the coding region of SLG , or lack an SLG gene in the genome, suggesting that these haplotypes do not synthesize the functional SLG protein. The SRK alleles in these haplotypes are normal. The function of SLG and SRK in self-incompatibility and the evolution of these alleles are discussed.
Bioethics Emergencies Can Be Used to Perform a Real-World Test of Utilitarian Policies

6736(09)60137-9. Persad, G. , and J. Du Toit. 2020. The case for valuing nonhealth and indirect benefits. In Global Health PrioritySetting: Beyond Cost-Effectiveness, Ole F. Norheim, Ezekiel J. Emanuel, and Joseph Millum, eds. Oxford: Oxford University Press. Powell, T. , and E. Chuang. 2020. COVID in NYC: what we could do better. American Journal of Bioethics 20(7): 62–66. Richardson, H. S. 2008. Discerning subordination and inviolability: A comment on Kamm’s Intricate ethics. Utilitas 20(1): 81–91. doi:10.1017/S0953820807002920. Savulescu, J., J. Cameron, and D. Wilkinson. 2020. Equality or utility? Ethics and law of rationing ventilators. British Journal of Anaesthesia. doi:10.1016/j.bja. 2020.04. 011. Schoch-Spana, M. , E. K. Brunson, H. Gwon, A. Regenberg, E. S. Toner, and E. L. Daugherty-Biddison. 2020. Influence of community and culture in the ethical allocation of scarce medical resources in a pandemic situation: Deliberative democracy study. Journal of Participatory Medicine 12(1): e18272. doi:10.2196/18272. Sharp, D. , and J. Millum. 2018. Prioritarianism for global health investments: Identifying the worst off. Journal of Applied Philosophy 35(1): 112–132. doi:10.1111/japp.12142. White, D. B, et al. 2020. Model hospital policy for fair allocation of scarce medications to treat COVID-19. https:// ccm.pitt. edu/sites/default/files/2020-05-28b%20Model% 20hospital%20policy%20for%20allocating%20scarce% 20COVID%20meds.pdf White, D. B. , and B. Lo. 2020. A framework for rationing ventilators and critical care beds during the COVID-19 pandemic. JAMA 323(18): 1773. doi:10.1001/jama.2020. 5046.
Trimethylamine N-oxide: heart of the microbiota–CVD nexus?

Abstract We critically review potential involvement of trimethylamine N-oxide (TMAO) as a link between diet, the gut microbiota and CVD. Generated primarily from dietary choline and carnitine by gut bacteria and hepatic flavin-containing mono-oxygenase (FMO) activity, TMAO could promote cardiometabolic disease when chronically elevated. However, control of circulating TMAO is poorly understood, and diet, age, body mass, sex hormones, renal clearance, FMO3 expression and genetic background may explain as little as 25 % of TMAO variance. The basis of elevations with obesity, diabetes, atherosclerosis or CHD is similarly ill-defined, although gut microbiota profiles/remodelling appear critical. Elevated TMAO could promote CVD via inflammation, oxidative stress, scavenger receptor up-regulation, reverse cholesterol transport (RCT) inhibition, and cardiovascular dysfunction. However, concentrations influencing inflammation, scavenger receptors and RCT (≥100 µm) are only achieved in advanced heart failure or chronic kidney disease (CKD), and greatly exceed pathogenicity of <1–5 µm levels implied in some TMAO–CVD associations. There is also evidence that CVD risk is insensitive to TMAO variance beyond these levels in omnivores and vegetarians, and that major TMAO sources are cardioprotective. Assessing available evidence suggests that modest elevations in TMAO (≤10 µm) are a non-pathogenic consequence of diverse risk factors (ageing, obesity, dyslipidaemia, insulin resistance/diabetes, renal dysfunction), indirectly reflecting CVD risk without participating mechanistically. Nonetheless, TMAO may surpass a pathogenic threshold as a consequence of CVD/CKD, secondarily promoting disease progression. TMAO might thus reflect early CVD risk while providing a prognostic biomarker or secondary target in established disease, although mechanistic contributions to CVD await confirmation.
Therapeutic Strategies for Duchenne Muscular Dystrophy: An Update

Neuromuscular disorders encompass a heterogeneous group of conditions that impair the function of muscles, motor neurons, peripheral nerves, and neuromuscular junctions. Being the most common and most severe type of muscular dystrophy, Duchenne muscular dystrophy (DMD), is caused by mutations in the X-linked dystrophin gene. Loss of dystrophin protein leads to recurrent myofiber damage, chronic inflammation, progressive fibrosis, and dysfunction of muscle stem cells. Over the last few years, there has been considerable development of diagnosis and therapeutics for DMD, but current treatments do not cure the disease. Here, we review the current status of DMD pathogenesis and therapy, focusing on mutational spectrum, diagnosis tools, clinical trials, and therapeutic approaches including dystrophin restoration, gene therapy, and myogenic cell transplantation. Furthermore, we present the clinical potential of advanced strategies combining gene editing, cell-based therapy with tissue engineering for the treatment of muscular dystrophy.
SnS nanosheets for harmonic pulses generation in near infrared region

Two-dimensional materials have attracted increasing attention because of their excellent mechanical, thermodynamic, magnetic, electrical and optical properties. Here, a new two-dimensional material of tin sulfide (SnS) is experimentally prepared. It is layered like black phosphorus and owns distinct optoelectronic properties, but eliminates the disadvantage of instability. The nonlinear saturable absorption characteristics of the SnS nanosheets is investigated at 1563.3 nm by the double-balanced detection method. The obtained modulation depth and saturation intensity are 5.4% and 66.3 MW/cm2, respectively. A passively harmonic mode-locked erbium-doped fiber laser based on the SnS saturable absorber (SA) has been demonstrated. The results show that mode-locking with fundamental frequency of 5.47 MHz is realized at pump power of 28.38 mW. With the increase of pump power, the laser can operate from fundamental frequency to high-order harmonic mode-locking. The maximum repetition rate of 412.73 MHz has been obtained, which is equivalent to the 76th harmonic mode-locking. This work reveals that SnS nanosheets is a novel and efficient SA with high damage threshold, which will find potential applications in optical communication, photoelectric detection, laser medicine, etc.
We Never Built Small Modular Reactors (SMRs), but What Do We Know About Modularization in Construction?

The key characteristics of small modular reactors (SMRs), as their name emphasized, are their size and modularity. Since SMRs are a family of novel reactor designs, there is a gap of empirical knowledge about the cost/benefit analysis of modularization. Conversely, in other sectors (e.g. Oil & Gas) the empirical experience on modularization is much greater. This paper provides a structured knowledge transfer from the general literature (i.e. other major infrastructure) and the Oil & Gas sector to the nuclear power plant construction world. Indeed, in the project management literature, a number of references discuss the costs and benefits determined by the transition from the stick-built construction to modularization, and the main benefits presented in the literature are the reduction of the construction cost and the schedule compression. Additional costs might arise from an increased management hurdle and higher transportation expenses. The paper firstly provides a structured literature review of the benefits and costs of modularization divided into qualitative and quantitative references. In the second part, the paper presents the results of series of interviews with Oil & Gas project managers about the value of modularization in this sector.
A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature

A new regulatory model can describe acclimation of phytoplankton growth rate (µ), chlorophyll a:carbon ratio and nitrogen: carbon ratio to irradiance, temperature and nutrient availability. The model uses three indices of phytoplankton biomass‐phytoplankton carbon (C), phytoplankton nitrogen (N), and chlorophyll a (Chl). The model links the light‐saturated rate of photosynthesis to N:C, requires that Chl a synthesis be coupled to nitrogen assimilation, and includes several regulatory features. These include feedback inhibition of the nitrogen assimilation rate by increases in the N:C ratio, as well as regulation of Chl a synthesis by the balance between light absorption and photosynthetic carbon fixation. The model treats respiration as the sum of the maintenance metabolic requirement and the cost of biosynthesis. In addition, the model can account for accumulation and mobilization of energy reserves (i.e. variability of N:C) and photoacclimation (i.e. variability of Chl:N and Chl:C) in response to variations in irradiance and nutrient availability. The assumptions of the model are shown to be in agreement with experimental observations and the model output compares favorably with data for cultures in balanced and unbalanced growth.
Semiparametric estimation of the cure fraction in population‐based cancer survival analysis

With rapid development in medical research, the treatment of diseases including cancer has progressed dramatically and those survivors may die from causes other than the one under study, especially among elderly patients. Motivated by the Surveillance, Epidemiology, and End Results (SEER) female breast cancer study, background mortality is incorporated into the mixture cure proportional hazards (MCPH) model to improve the cure fraction estimation in population‐based cancer studies. Here, that patients are “cured” is defined as when the mortality rate of the individuals in diseased group returns to the same level as that expected in the general population, where the population level mortality is presented by the mortality table of the United States. The semiparametric estimation method based on the EM algorithm for the MCPH model with background mortality (MCPH+BM) is further developed and validated via comprehensive simulation studies. Real data analysis shows that the proposed semiparametric MCPH+BM model may provide more accurate estimation in population‐level cancer study.
The Spinal Nerves of the Dogfish (Scyliorhinus)

The locomotory musculature of dogfish is innervated by the segmental spinal nerves. The sensory and motor innervation of the abdominal musculature was studied in a preparation consisting of a strip of the abdominal body wall innervated by the ventral rami of the spinal nerves. Each ventral ramus consists of two separate nerve bundles which were found to be peripheral extensions of the dorsal and ventral spinal roots. Recordings from the sensory bundles showed that there are few sensory endings in the musculature and body wall of the dogfish. It was possible to differentiate between ephemeral responses produced by cutaneous free-nerve endings and prolonged discharges which were generated by more specialized sensory endings. In some details these endings were found to be unlike either muscle spindles or tendon organs. Further, skinning experiments suggested that these mechanoreceptors lay in the skin or the very outer layers of the myotome. Histological searching, together with physiological isolation of units, suggested that these receptors were the corpuscular endings distributed sparsely amongst subcutaneous tissue. These endings are apparently the same as those described by Wunderer (1908) in the fins of elasmobranchs.
No Effect of Diet-Induced Mild Hyperhomocysteinemia on Vascular Methylating Capacity, Atherosclerosis Progression, and Specific Histone Methylation

Hyperhomocysteinemia (HHcy) is a risk factor for atherosclerosis through mechanisms which are still incompletely defined. One possible mechanism involves the hypomethylation of the nuclear histone proteins to favor the progression of atherosclerosis. In previous cell studies, hypomethylating stress decreased a specific epigenetic tag (the trimethylation of lysine 27 on histone H3, H3K27me3) to promote endothelial dysfunction and activation, i.e., an atherogenic phenotype. Here, we conducted a pilot study to investigate the impact of mild HHcy on vascular methylating index, atherosclerosis progression and H3K27me3 aortic content in apolipoprotein E-deficient (ApoE −/−) mice. In two different sets of experiments, male mice were fed high-fat, low in methyl donors (HFLM), or control (HF) diets for 16 (Study A) or 12 (Study B) weeks. At multiple time points, plasma was collected for (1) quantification of total homocysteine (tHcy) by high-performance liquid chromatography; or (2) the methylation index of S-adenosylmethionine to S-adenosylhomocysteine (SAM:SAH ratio) by liquid chromatography tandem-mass spectrometry; or (3) a panel of inflammatory cytokines previously implicated in atherosclerosis by a multiplex assay. At the end point, aortas were collected and used to assess (1) the methylating index (SAM:SAH ratio); (2) the volume of aortic atherosclerotic plaque assessed by high field magnetic resonance imaging; and (3) the vascular content of H3K27me3 by immunohistochemistry. The results showed that, in both studies, HFLM-fed mice, but not those mice fed control diets, accumulated mildly elevated tHcy plasmatic concentrations. However, the pattern of changes in the inflammatory cytokines did not support a major difference in systemic inflammation between these groups. Accordingly, in both studies, no significant differences were detected for the aortic methylating index, plaque burden, and H3K27me3 vascular content between HF and HFLM-fed mice. Surprisingly however, a decreased plasma SAM: SAH was also observed, suggesting that the plasma compartment does not always reflect the vascular concentrations of these two metabolites, at least in this model. Mild HHcy in vivo was not be sufficient to induce vascular hypomethylating stress or the progression of atherosclerosis, suggesting that only higher accumulations of plasma tHcy will exhibit vascular toxicity and promote specific epigenetic dysregulation.
The ubiquitin-like modifier FAT10 – much more than a proteasome-targeting signal

ABSTRACT Human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10) also called ubiquitin D (UBD) is a member of the ubiquitin-like modifier (ULM) family. The FAT10 gene is localized in the MHC class I locus and FAT10 protein expression is mainly restricted to cells and organs of the immune system. In all other cell types and tissues, FAT10 expression is highly inducible by the pro-inflammatory cytokines interferon (IFN)-γ and tumor necrosis factor (TNF). Besides ubiquitin, FAT10 is the only ULM which directly targets its substrates for degradation by the 26S proteasome. This poses the question as to why two ULMs sharing the proteasome-targeting function have evolved and how they differ from each other. This Review summarizes the current knowledge of the special structure of FAT10 and highlights its differences from ubiquitin. We discuss how these differences might result in differential outcomes concerning proteasomal degradation mechanisms and non-covalent target interactions. Moreover, recent insights about the structural and functional impact of FAT10 interacting with specific non-covalent interaction partners are reviewed. Summary: The determination of the structure of FAT10 has advanced our understanding of this unique ubiquitin-like modifier. Here, the latest insights about the function of non-covalent binding and conjugation to recently identified substrates are reviewed.
Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations

Gluten protein crosslinking is a predetermined process where specific intra- and intermolecular disulfide bonds differ depending on the protein and cysteine motif. In this article, all-atom Monte Carlo simulations were used to understand the formation of disulfide bonds in gliadins and low molecular weight glutenin subunits (LMW-GS). The two intrinsically disordered proteins appeared to contain mostly turns and loops and showed “self-avoiding walk” behavior in water. Cysteine residues involved in intramolecular disulfide bonds were located next to hydrophobic peptide sections in the primary sequence. Hydrophobicity of neighboring peptide sections, synthesis chronology, and amino acid chain flexibility were identified as important factors in securing the specificity of intramolecular disulfide bonds formed directly after synthesis. The two LMW-GS cysteine residues that form intermolecular disulfide bonds were positioned next to peptide sections of lower hydrophobicity, and these cysteine residues are more exposed to the cytosolic conditions, which influence the crosslinking behavior. In addition, coarse-grained Monte Carlo simulations revealed that the protein folding is independent of ionic strength. The potential molecular behavior associated with disulfide bonds, as reported here, increases the biological understanding of seed storage protein function and provides opportunities to tailor their functional properties for different applications.
Weighing up the benefits and challenges of hosting physiotherapy student placements in private practice; a qualitative exploration

ABSTRACT Introduction New graduate physiotherapists are entering private practice in increasing numbers despite limited opportunity to experience this setting during training. Exploring the perceived benefits and challenges of physiotherapy private practices in hosting students is important to help understand what motivates private practices to engage in clinical education and inform how practices can be best supported in student placement provision. Objective The aim of this study was to explore the benefits and challenges of hosting physiotherapy students from the perspective of private practice providers. Methods A qualitative study with an inductive thematic analytical approach was used. Semi-structured interviews of 10 physiotherapy private practice placement providers responsible for student placement provision were undertaken. Results Five themes emerged: 1) value to client care; 2) value to staff; 3) value to future planning; 4) contribution to students and the profession; and 5) stress associated with resources. Discussion and Conclusion Private practice placement providers perceive a range of benefits to their practice, staff and clients, including rich opportunities for future recruitment when hosting physiotherapy students. These benefits are carefully weighed up against the required resources of time, physical space and opportunities for students to participate in client care. This study has identified implications for education providers in supporting physiotherapy student placements within private practice and may enhance placement capacity within this sector.