Miracle-dz/UniFAR-FTUs huggingface dataset:
How Often, Where, and by Which Specialty Do Long-Term Care Home Residents Receive Specialist Physician Care? A Retrospective Cohort Study

This retrospective cohort study describes the rates, location, and determinants of specialist physician visits among 257,216 long-term care (LTC) residents across 648 LTC homes in Ontario, Canada, between 2007 and 2016. Visit rates in the last year of life were calculated for a sub-cohort of residents who died in LTC between 2013 and 2016. Visits were measured per resident-year using physician billings. Over 10 years, the rate of visits to specialists outside the LTC home was consistently higher than within LTC (2.99 vs. 1.55 visits/resident-year). Residents were less likely to receive specialist care if they were older, had dementia, or lived in urban LTC homes. From 12 months before death to the last week of life, rates of specialist visits increased by 246% and 56% inside and outside of LTC, respectively. Improving access to physician specialist care in LTC homes may reduce burdensome transitions and improve resident quality of life.
Comparison of Methods Used to Correct Self-Reported Protein Intake for Systematic Variation in Reported Energy Intake Using Quantitative Biomarkers of Dietary Intake.

BACKGROUND Multiple methods of correcting nutrient intake for misreported energy intake have been proposed but have not been extensively compared. The availability of the Women's Health Initiative (WHI) data set, which includes several objective recovery biomarkers, offers an opportunity to compare these corrections with respect to protein intake. OBJECTIVE We compared 5 energy-correction methods for self-reported dietary protein against urinary nitrogen-derived protein intake. METHODS As part of the WHI Nutritional Biomarkers Study (NBS) 544 participants (50- to 80-y-old women) completed a FFQ and biomarker assessments using doubly labeled water (DLW) for total energy expenditure (TEE) and 24-h urinary nitrogen. Correction methods evaluated were as follows: 1) DLW-TEE; 2) the Institute of Medicine's (IOM's) estimated energy requirement (EER) TEE prediction equation based on sex, height, weight, and age; 3) published NBS total energy TEE prediction (WHI-NBS-TEE) using age, BMI, race, and income; 4) reported protein versus reported energy linear regression-based residual method; and 5) a Goldberg cutoff to exclude subjects reporting energy intakes <1.35 times their basal metabolic rate. Efficacy was evaluated using correlations obtained by regressing corrected protein against biomarker protein (6.25 × urinary nitrogen/0.81). RESULTS Unadjusted self-reported protein intake from the FFQ (mean = 66.7 g) correlated weakly (r = 0.31) with biomarker protein (mean = 74.9 g). DLW-TEE-corrected self-reported protein intake (mean = 90.7 g) had the strongest correlation with biomarker protein (r = 0.47). Other energy corrections yielded lower, but still significant correlations: EER, r = 0.44 (mean = 92.1 g); WHI-NBS-TEE, r = 0.37 (mean = 90.4 g); Goldberg cutoff, r = 0.36 (mean = 88.4 g); and residual method, r = 0.35 (mean = 66.7 g). CONCLUSIONS Our data indicate that proportional correction of reported protein intake using a measure of energy requirement from DLW-TEE or IOM-EER performed modestly better than other methods in this cohort. These energy adjustments, however, yielded corrected protein exceeding the biomarker protein, indicating that energy adjustment alone does not eliminate all self-reported protein reporting bias.
Biochemical and Molecular Characterization of PvNTD2, a Nucleotidase Highly Expressed in Nodules from Phaseolus vulgaris

Nucleotides are molecules of great importance in plant physiology. In addition to being elementary units of the genetic material, nucleotides are involved in bio-energetic processes, play a role as cofactors, and are also components of secondary metabolites and the hormone cytokinin. The common bean (Phaseolus vulgaris) is a legume that transports the nitrogen fixed in nodules as ureides, compounds synthetized from purine nucleotides. The first step in this pathway is the removal of the 5’-phosphate group by a phosphatase. In this study, a gene that codes for a putative nucleotidase (PvNTD2) has been identified in P. vulgaris. The predicted peptide contains the conserved domains for haloacid dehalogenase-like hydrolase superfamily. The protein has been overexpressed in Escherichia coli, and the purified protein showed molybdate-resistant phosphatase activity with nucleoside monophosphates as substrates, confirming that the identified gene codes for a nucleotidase. The optimum pH for the activity was 7–7.5. The recombinant enzyme did not show special affinity for any particular nucleotide, although the behaviour with AMP was different from that with the other nucleotides. The activity was inhibited by adenosine, and a regulatory role for this nucleoside was proposed. The expression pattern of PvNTD2 shows that it is ubiquitously expressed in all the tissues analysed, with higher expression in nodules of adult plants. The expression was maintained during leaf ontogeny, and it was induced during seedling development. Unlike PvNTD1, another NTD previously described in common bean, the high expression of PvNTD2 was maintained during nodule development, and its possible role in this organ is discussed.
Transmission Fourier Transform Infrared Spectroscopic Imaging, Mapping, and Synchrotron Scanning Microscopy with Zinc Sulfide Hemispheres on Living Mammalian Cells at Sub-Cellular Resolution

Fourier transform infrared (FT-IR) spectroscopic imaging and microscopy of single living cells are established label-free technique for the study of cell biology. The constant driver to improve the spatial resolution of the technique is due to the diffraction limit given by infrared (IR) wavelength making subcellular study challenging. Recently, we have reported, with the use of a prototype zinc sulfide (ZnS) transmission cell made of two hemispheres, that the spatial resolution is improved by the factor of the refractive index of ZnS, achieving a λ/2.7 spatial resolution using the synchrotron–IR microscopy with a 36× objective with numerical aperture of 0.5. To refine and to demonstrate that the ZnS hemisphere transmission device can be translated to standard bench-top FT-IR imaging systems, we have, in this work, modified the device to achieve a more precise path length, which has improved the spectral quality of the living cells, and showed for the first time that the device can be applied to study live cells with three different bench-top FT-IR imaging systems. We applied focal plane array (FPA) imaging, linear array, and a synchrotron radiation single-point scanning method and demonstrated that in all cases, subcellular details of individual living cells can be obtained. Results have shown that imaging with the FPA detector can measure the largest area in a given time, while measurements from the scanning methods produced a smoother image. Synchrotron radiation single-point mapping produced the best quality image and has the flexibility to introduce over sampling to produce images of cells with great details, but it is time consuming in scanning mode. In summary, this work has demonstrated that the ZnS hemispheres can be applied in all three spectroscopic approaches to improve the spatial resolution without any modification to the existing microscopes.
Urinary Tumor Necrosis Factor–Like Weak Inducer of Apoptosis as a Biomarker for Diagnosis and Evaluating Activity in Lupus Nephritis

Supplemental digital content is available in the text. Objective Urinary tumor necrosis factor–like weak inducer of apoptosis (uTWEAK) has been identified as a candidate biomarker for lupus nephritis (LN). However, its diagnostic value remains unclear. This meta-analysis was conducted to comprehensively evaluate the value of uTWEAK for diagnosis and evaluating activity in LN. Methods Medline, Web of Science, Chinese Biomedical Medical, and Chinese National Knowledge Infrastructure databases were searched to acquire eligible studies published before September 30, 2019. The quality of the studies was evaluated by Quality Assessment of Diagnostic Accuracy Studies-2. Summary receiver operating characteristic curve and area under the curve were applied to summarize the overall diagnostic performances. The pooled sensitivity, specificity, and diagnostic odds ratio (DOR) were calculated with the fixed-effects model. RevMan 5.3, Stata 12.0, and Meta-disc 1.4 software were used. Results A total of 7 studies were included. Of these, 4 studies were available for comparison between SLE with and without LN, and 3 studies were for active and inactive LN. The total area under the curve was 0.8640, and DOR was 14.89 (95% confidence interval [CI], 7.95–27.86). For LN diagnosis, the pooled sensitivity, specificity, and DOR were 0.55 (95% CI, 0.47–0.63), 0.92 (95% CI, 0.86–0.96), and 16.54 (95% CI, 7.57–36.15), respectively. For assessing LN activity, the pooled sensitivity, specificity, and DOR were 0.91 (95% CI, 0.82–0.96), 0.70 (95% CI, 0.58–0.81), and 18.45 (95% CI, 7.45–45.87), respectively. Conclusions This meta-analysis indicated that uTWEAK has relatively moderate sensitivity and specificity for diagnosis and evaluating activity in LN, suggesting that uTWEAK can serve as a helpful biomarker for LN.
The Zn2+ and Ca2+‐binding S100B and S100A1 proteins: beyond the myths

The S100 genes encode a conserved group of 21 vertebrate‐specific EF‐hand calcium‐binding proteins. Since their discovery in 1965, S100 proteins have remained enigmatic in terms of their cellular functions. In this review, we summarize the calcium‐ and zinc‐binding properties of the dimeric S100B and S100A1 proteins and highlight data that shed new light on the extracellular and intracellular regulation and functions of S100B. We point out that S100B and S100A1 homodimers are not functionally interchangeable and that in a S100A1/S100B heterodimer, S100A1 acts as a negative regulator for the ability of S100B to bind Zn2+. The Ca2+ and Zn2+‐dependent interactions of S100B with a wide array of proteins form the basis of its activities and have led to the derivation of some initial rules for S100B recognition of protein targets. However, recent findings have strongly suggested that these rules need to be revisited. Here, we describe a new consensus S100B binding motif present in intracellular and extracellular vertebrate‐specific proteins and propose a new model for stable interactions of S100B dimers with full‐length target proteins. A chaperone‐associated function for intracellular S100B in adaptive cellular stress responses is also discussed. This review may help guide future studies on the functions of S100 proteins in general.
Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections

Background The gastrointestinal microbiome plays an important role in host health and there is increasing concern regarding the deleterious effects of pharmaceuticals on the fecal microbiome. The effect of anthelmintic therapy on the fecal microbiome in dogs has not yet been evaluated. The purpose of this study was to evaluate the effect of anthelmintic administration on the fecal microbiome of dogs with and without subclinical Giardia species and Cryptosporidium canis infections. Methodology/Principal findings Part 1: 6 healthy adult research beagles with subclinical giardiasis and cryptosporidiosis were administered a commercially available preparation of febantel combined with pyrantel and praziquantel (FPP) orally daily for three days. Part 2: 19 healthy staff-owned dogs without giardiasis or cryptosporidiosis were divided into a treatment group (n = 9) that was administered fenbendazole orally daily for five days and an untreated control group (n = 10). For both parts of the study, feces were collected at multiple time points before and after anthelmintic (FPP or fenbendazole) administration. Fecal DNA was extracted for Illumina sequencing of the bacterial 16S rRNA gene and qPCR assays. Neither FPP nor fenbendazole treatment caused a significant change in alpha or beta diversity or the relative abundance of bacterial species. Upon univariate statistical analysis neither FPP or fenbendazole caused minimal changes in the fecal microbiota. Conclusion FPP administration was associated with minimal alterations of the fecal microbiome of healthy research beagles with subclinical giardiasis and cryptosporidiosis. Fenbendazole administration was associated with minimal alterations of the fecal microbiome of healthy staff owned dogs.
Pitching shoulder passive flexibility: torque-angle analysis for external rotation and internal rotation

ABSTRACT In this study, a custom device was developed to analyse the pitching shoulder’s external rotation (ER) and internal rotation (IR) passive flexibility. We analysed three novel measures: the resistance onset angle (ROA = angle where the shoulder begins stretching), rotational stiffness, and torque at the end range of motion (ROM). The purpose was to conduct a bilateral analysis to determine if there are significant differences between the throwing and non-throwing shoulder. Participants were 30 upper level pitchers (13 division I, 17 minor league). During testing, pitchers laid supine on a treatment table and the arm was secured to a rotational wheel with the shoulder abducted 90° and elbow flexed 90°. Dependent t-tests revealed significant (p < 0.01) and relatively extreme bilateral differences for all three variables. The throwing shoulder had: increased ER ROA (9°), decreased IR ROA (5.3°), increased ER stiffness (17%), increased IR stiffness (34%), increased ER torque (21%), and increased IR torque (30%). Secondary correlation analysis was completed to determine if the torque-angle variables were good predictors of the end ROM. Stiffness correlations were weak for ER (r = 0.35, p = 0.048) and IR (r = 0.42, p = 0.017) but ROA correlations were strong for ER (r = 0.85, p < 0.001) and IR (r = 0.86, p < 0.001).
Effects of Heating Temperature on the Properties of Bio-Board Manufactured by Using Soybean Straw

The objective of this paper is to effectively use soybean straw biomass resources and decrease the negative effects of using synthetic resin. Soybean straw was ground through a wet process then hot-pressed to make biodegradable fiberboard (bio-board) without any binder. The effect of heating temperature on mechanical properties and dimensional stability performance of produced bio-board was investigated. Bonding quality and chemical changes of the bio-board were also evaluated using scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy. The moisture content decreased from 12.5% to 3.4% with the increase of heating temperature. Meanwhile, most mechanical properties of bio-board improved. However, an excessive heating temperature, especially at 230 °C, did not significantly promote the improvement of most mechanical properties. However, the dimensional stability performance of the bio-board was greatly improved from 140 °C to 230 °C. Overall, the results showed that bio-board could be made by using soybean straw without any synthetic resin. Heating temperature plays a significant role in affecting the properties of bio-board. The refined bio-board is expected to be used as a packaging material, heat insulation in architecture, and mulch film for agricultural purposes.
RP-HPLC based method for the determination of Tamsulosin HCl in API, Prepared dosage form and spiked plasma.

An analytical method for measurement of tamsulosin HCl from its different life cycle stages was developed using RP-HPLC technique. The elution of tamsulsoin was studied using MediterraneaTM Sea 18 column (dimesions 250 × 4.6 mm and pore size 5μm) and mobile phase comprising of buffer (pH 5.4): Acetonitrile (ACN) at ratio 60:40. The tamsolusin HCl elution was also studied by varying the operating conditions including the composition and flow rate of mobile phase, stationary phase temperature and scanning wavelength. The optimal elution conditions include; a) mobile phase flow rate; 1ml/min, b) wavelength; 224nm and stationary phase temperature 30°C. Linearity was recorded in the absorption data over tamsulosin concentration range of 0.007 to 40μg/ml. The values of paramters LOD and LOQ noted for tamsulosin dissolved in mobile phase were 0.0014 and 0. 042μg/ml respectively, while for the counterpart in spiked plasma were 0.0017 and 0. 051μg/ml respectively. The analytical method was prompt, accurate, reproducible and suitable for analysis of tamsulosin HCl in different samples of interest at formulation, regulation and clinical evaluations.
Cyp1b1 directs Srebp-mediated cholesterol and retinoid synthesis in perinatal liver; Association with retinoic acid activity during fetal development

Background Cytochrome P450 1b1 (Cyp1b1) deletion and dietary retinol deficiency during pregnancy (GVAD) affect perinatal liver functions regulated by Srebp. Cyp1b1 is not expressed in perinatal liver but appears in the E9.5 embryo, close to sites of retinoic acid (RA) signaling. Hypothesis Parallel effects of Cyp1b1 and retinol on postnatal Srebp derive from effects in the developing liver or systemic signaling. Approach Cluster postnatal increases in hepatic genes in relation to effects of GVAD or Cyp1b1 deletion. Sort expression changes in relation to genes regulated by Srebp1 and Srebp2.Test these treatments on embryos at E9.5, examining changes at the site of liver initiation. Use in situ hybridization to resolve effects on mRNA distributions of Aldh1a2 and Cyp26a1 (RA homeostasis); Hoxb1 and Pax6 (RA targets). Assess mice lacking Lrat and Rbp4 (DKO mice) that severely limits retinol supply to embryos. Results At birth, GVAD and Cyp1b1 deletion stimulate gene markers of hepatic stellate cell (HSC) activation but also suppress Hamp. These treatments then selectively prevent the postnatal onset of genes that synthesize cholesterol (Hmgcr, Sqle) and fatty acids (Fasn, Scd1), but also direct cholesterol transport (Ldlr, Pcsk9, Stard4) and retinoid synthesis (Aldh1a1, Rdh11). Extensive support by Cyp1b1 is implicated, but with distinct GVAD interventions for Srebp1 and Srebp2. At E9.5, Cyp1b1 is expressed in the septum transversum mesenchyme (STM) with β-carotene oxygenase (Bco1) that generates retinaldehyde. STM provides progenitors for the HSC and supports liver expansion. GVAD and Cyp1b1-/- do not affect RA-dependent Hoxb1 and Pax6. In DKO embryos, RA-dependent Cyp26a1 is lost but Hoxb1 is sustained with Cyp1b1 at multiple sites. Conclusion Cyp1b1-/- suppresses genes supported by Srebp. GVAD effects distinguish Srebp1 and Srebp2 mediation. Srebp regulation overlaps appreciably in cholesterol and retinoid homeostasis. Bco1/Cyp1b1 partnership in the STM may contribute to this later liver regulation.
The impact of maternal supplementation during pregnancy and the first 6 months postpartum on the growth status of the next child born after the intervention period: Follow‐up results from Bangladesh and Ghana

Abstract Pregnancy and breastfeeding make demands on maternal nutrient stores. The extent of depletion and the degree to which nutrient stores are replenished between pregnancies has implications for a mother's nutritional status at conception of the subsequent child and therefore that child's birth outcomes and growth. Using follow‐up data collected several years after a randomized effectiveness trial conducted in rural Bangladesh and a randomized efficacy trial conducted in semiurban Ghana, we evaluated the impact of maternal supplementation with small‐quantity lipid‐based nutrient supplements (LNS) or multiple micronutrients (MMN) through pregnancy (the index pregnancy) and 6 months postpartum on the growth status of the next living younger sibling conceived and born after the index pregnancy. In both Bangladesh (n = 472 younger siblings) and Ghana (n = 327 younger siblings), there were no overall differences in the growth status or the prevalence of undernutrition among younger siblings whose mothers had received LNS (or MMN, Ghana only) during and after the index pregnancy compared with the younger siblings of mothers who had received iron plus folic acid (IFA) during the index pregnancy (Ghana) or during and for 3 months after the index pregnancy (Bangladesh). These findings do not indicate that preconception nutrition interventions do not improve child growth. Rather, they suggest that any benefits of maternal LNS or MMN supplementation during one pregnancy and for 6 months postpartum are unlikely to extend to the growth of her next child beyond any effects due to IFA alone.
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

Abstract Background Accurately identifying single-nucleotide polymorphisms (SNPs) from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP-calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia, and Klebsiella. Results We evaluated the performance of 209 SNP-calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic bacteria such as Escherichia coli but less dominant for clonal species such as Mycobacterium tuberculosis. Conclusions The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest-performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often used the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup, or Strelka.
Navigating the intricacies of molecular docking.

Computational molecular modeling refers to a collection of techniques used to explore and establish in silico models for the understanding of molecular interactions present in systems. These systems including those within the biological environment, and computational techniques have been in use since the 1980s [1,2]. Presently, computational chemistry techniques are at a level of unprecedented availability, with computational power and software availability making computational studies more feasible than ever before. In this way, computational chemistry has become a mainstay in the academic process of molecular design, and particularly in drug design as used in medicinal chemistry. In this editorial, we will focus on common software packages and techniques that can be performed on typical desktop computer systems available to any academic researcher for use.