bluuebunny/crossref_metadata_2025_split huggingface dataset:
By What Criteria Are Pictorial Styles Individuated?
Authors: Lim Hoyeon 
Published: October 2021

Abstract
In this article, I argue that pictorial styles are individuated in terms of different degrees of determinacy. For example, Morandi’s still-life etchings and Monet’s cathedral paintings embody different styles in that in the former, shape properties are differentiated in a fine-grained manner, and in the latter, coarse grained. I develop this view by critically examining John Kulvicki’s analysis of how we interpret pictures. According to Kulvicki, we rarely interpret pictures as differing in terms of features that belong to the vehicle of representation—that is, the design-content relation. Rather, he thinks that we individuate pictorial styles in terms of the content that each picture represents. Contra Kulvicki, I argue that we interpret the vehicular features of pictures in light of our knowledge of picture production, and that the diversity of pictorial styles involves both content and vehicle.
On the Estimation of POD and LOD of Qualitative Microbiological Assays from a Multi-Laboratory Validation Study
Authors: Wang Shizhen S , Ihrie John 
Published: October 2021

Abstract

Background
Jarvis et al. in 2019 (J. AOAC Int. 102: 1617–1623) estimated the mean laboratory effect (µ), standard deviation of laboratory effects (σ), probability of detection (POD), and level of detection (LOD) from a multi-laboratory validation study of qualitative microbiological assays using a random intercept complementary log–log model. Their approach estimated σ based on a Laplace approximation to the likelihood function of the model, but estimated µ from a fixed effectmodel due to a limitation in the MS Excel spreadsheet which was used by the authors to develop a calculation tool.

Objective
We compared the estimates of µ and σ from three approaches (the Laplace approximation that estimates µ and σ simultaneously from the random intercept model, adaptive Gauss–Hermite quadrature (AGHQ), and the method of Jarvis et al.) and introduced an R Shiny app to implement the AGHQ using the widely used “lme4” R package.

Methods
We conducted a simulation study to compare the accuracy of the estimates of µ and σ from the three approaches and compared the estimates of µ, σ, LOD, etc. between the R Shiny app and the spreadsheet calculation tool developed by Jarvis et al. for an example dataset.

Results
Our simulation study shows that, while the three approaches produce similar estimates of σ, the AGHQ has generally the best performance for estimating µ (and hence mean POD and LOD). The differences in the estimates between the R Shiny app and the spreadsheet were demonstrated using the example dataset.

Conclusion
The AGHQ is the best method for estimating µ, POD, and LOD.

Highlights
The user-friendly R Shiny app provides a better alternative to the spreadsheet.
Water and forage intake, diet digestibility, and blood parameters of beef cows and heifers consuming water with varying concentrations of total dissolved salts
Authors: Moehlenpah Alexandra N , Ribeiro Luana P S , Puchala Ryszard , Goetsch Arthur Louis , Beck Paul , Pezeshki Adel , Gross Megan A , Holder Amanda L , Lalman David L 
Published: October 2021

Abstract
The objective of this study was to investigate the effects of water quality on water intake (WI), forage intake, diet digestibility, and blood constituents in beef cows and growing beef heifers. This was a replicated 5 × 5 Latin square with five drinking water treatments within each square: 1) fresh water (Control); 2) brackish water (100 BRW treatment) with approximately 6,000 mg/kg total dissolved solids (TDS); 3) same TDS level as 100 BRW achieved by addition of NaCl to fresh water (100 SLW); 4) 50% brackish water and 50% fresh water to achieve approximately 3,000 mg/kg TDS (50 BRW); and 5) same TDS level as 50 BRW achieved by addition of NaCl to fresh water (50 SLW). Each of the five 21-d periods consisted of 14 d of adaptation and 5 d of data collection. Animals were housed individually and fed mixed alfalfa (Medicago sativa) grass hay cubes. Feed and WI were recorded daily. Data were analyzed with animal as the experimental unit. Age, treatment, and age × treatment were fixed effects, and animal ID within age was the random variable for intake, digestibility, and blood parameter data. Water and feed intake were greater than expected, regardless of age or water treatment. No treatment × age interactions were identified for WI (P = 0.71), WI expressed as g/kg body weight (BW; P = 0.70), or dry matter intake (DMI; P = 0.21). However, there was an age × treatment tendency for DMI when scaled to BW (P = 0.09) in cows consuming 100 BRW compared with fresh water. No differences were found for the other three treatments. Heifers provided 50 SLW water consumed less (P &lt; 0.05) feed (g/kg BW) compared with heifers provided fresh water and 100 BRW. No differences (P &gt; 0.05) in water, DMI, feed intake, or diet digestibility were found due to water quality treatment. In conclusion, under these conditions, neither absolute WI, absolute DMI, nor diet digestibility was influenced by the natural brackish or saline water used in this experiment. These results suggest that further research is necessary to determine thresholds for TDS or salinity concentration resulting in reduced water and/or feed intake and diet digestibility.
Structural insights into the enhanced thermostability of cysteine substitution mutants of L-histidine decarboxylase from Photobacterium phosphoreum
Authors: Oda Yuki , Nakata Kunio , Miyano Hiroshi , Mizukoshi Toshimi , Yamaguchi Hiroki , Kashiwagi Tatsuki 
Published: October 2021

Abstract
Enzymatic amino acid assays are important in physiological research and clinical diagnostics because abnormal amino acid concentrations in biofluids are associated with various diseases. L-histidine decarboxylase from Photobacterium phosphoreum (PpHDC) is a pyridoxal 5′-phosphate-dependent enzyme and a candidate for use in an L-histidine quantitation assay. Previous cysteine substitution experiments demonstrated that the PpHDC C57S mutant displayed improved long-term storage stability and thermostability when compared with those of the wild-type enzyme. In this study, combinational mutation experiments of single cysteine substitution mutants of PpHDC were performed, revealing that the PpHDC C57S/C101V/C282V mutant possessed the highest thermostability. The stabilizing mechanism of these mutations was elucidated by solving the structures of PpHDC C57S and C57S/C101V/C282V mutants by X-ray crystallography. In the crystal structures, two symmetry-related PpHDC molecules form a domain-swapped homodimer. The side chain of S57 is solvent exposed in the structure, indicating that the C57S mutation eliminates chemical oxidation or disulfide bond formation with a free thiol group, thereby providing greater stability. Residues 101 and 282 form hydrophobic interactions with neighboring hydrophobic residues. Mutations C101V and C282V enhanced thermostability of PpHDC by filling a cavity present in the hydrophobic core (C101V) and increasing hydrophobic interactions.
Social Selection and the Evolution of Maladaptation
Authors: McGlothlin Joel W , Fisher David N 
Published: October 2021

AbstractEvolution by natural selection is often viewed as a process that inevitably leads to adaptation or an increase in population fitness over time. However, maladaptation, an evolved decrease in fitness, may also occur in response to natural selection under some conditions. Social selection, which arises from the effects of social partners on fitness, has been identified as a potential cause of maladaptation, but we lack a general rule identifying when social selection should lead to a decrease in population mean fitness. Here we use a quantitative genetic model to develop such a rule. We show that maladaptation is most likely to occur when social selection is strong relative to nonsocial selection and acts in an opposing direction. In this scenario, the evolution of traits that impose fitness costs on others may outweigh evolved gains in fitness for the individual, leading to a net decrease in population mean fitness. Furthermore, we find that maladaptation may also sometimes occur when phenotypes of interacting individuals negatively covary. We outline the biological situations where maladaptation in response to social selection can be expected, provide both quantitative genetic and phenotypic versions of our derived result, and suggest what empirical work would be needed to test it. We also consider the effect of social selection on inclusive fitness and support previous work showing that inclusive fitness cannot suffer an evolutionary decrease. Taken together, our results show that social selection may decrease population mean fitness when it opposes individual-level selection, even as inclusive fitness increases.
Outcomes of intensity-modulated radiation therapy for intermediate- or high-risk prostate cancer: a single-institutional study
Authors: Sasamura Kazuma , Soyano Takashi , Kozuka Takuyo , Yuasa Takeshi , Yamamoto Shinya , Yonese Junji , Oguchi Masahiko , Yoshimura Ryoichi , Yoshioka Yasuo 
Published: October 2021

Abstract

Background
There are few reports from Japan about the outcomes of intensity-modulated radiation therapy for localized prostate cancer. This study was aimed at assessing the efficacy and toxicity of intensity-modulated radiation therapy in patients with intermediate- or high-risk prostate cancer.

Methods
We conducted a review of the data, retrieved from our institutional database, of patients who had received intensity-modulated radiation therapy for localized prostate cancer at a radiation dose of 78 Gy in 39 fractions. Data of 201 patients with intermediate-risk prostate cancer and 311 patients with high-risk prostate cancer were analyzed.

Results
The median follow-up period after the completion of intensity-modulated radiation therapy was 100 months (range, 24–154). The rates of cause-specific survival, overall survival, metastasis-free survival and biochemical recurrence-free survival in the intermediate-risk patients were 99, 95, 95 and 94% at 5 years and 99, 91, 90 and 86% at 8 years, respectively; the corresponding rates in the high-risk patients were 100, 97, 91 and 84% at 5 years and 96, 92, 84 and 76% at 8 years, respectively. The crude incidence of late grade 2–3 genitourinary toxicity was 28.1%, and that of late grade 3 genitourinary toxicity was 2.0%. The crude incidence of late grade 2 gastrointestinal toxicity was 5.1%, and there were no cases of late grade 3 gastrointestinal toxicity.

Conclusions
Our data demonstrated that intensity-modulated radiation therapy is effective for patients with localized intermediate-risk or high-risk prostate cancer while having minimal toxicity.
Vancomycin: an overview on current alternative antibiotic therapy to vanquish
Authors: Elnour Asim Ahmed , Ramadan Azza 
Published: October 2021

Abstract

Objectives
For more than 60 years, vancomycin has continued to be in clinical use despite drug resistance. Therefore, finding alternative antibiotics to vancomycin is of great need and urgency. The main objective was to provide robust evidence for the clinical pros and cons of these alternatives.

Methods
A rigorous literature search was conducted for studies involving vancomycin and suitable alternatives such as teicoplanin, linezolid, tedizolid, dalbavancin, telavancin, daptomycin, tigecycline, quinupristin/dalfopristin (streptogramins) and ceftobiprole/ceftaroline (cephalosporins).

Key findings
This review explored the limitations associated with the clinical utility of vancomycin in day-to-day clinical practice. New remedies such as ceftaroline, ceftobiprole, tedizolid, dalbavancin and oritavancin with specific clinical utility are becoming available and offer enhanced tolerability profile, effective cure rate and minimum rates of resistance. However, these alternatives are not without limitations.

Conclusions
We objectively provide suitable alternatives to vancomycin that could be included in hospital formularies and guidelines. However, caution must be undertaken when utilizing these alternatives, given their limitations.
Mass-loading and non-spherical divergence in hot galactic winds: implications for X-ray observations
Authors: Nguyen Dustin D , Thompson Todd A 
Published: October 2021

ABSTRACT
Cool clouds are expected to be destroyed and incorporated into hot supernova-driven galactic winds. The mass-loading of a wind by the cool medium modifies the bulk velocity, temperature, density, entropy, and abundance profiles of the hot phase relative to an unmass-loaded outflow. We provide general equations and limits for this physics that can be used to infer the rate of cool gas entrainment from X-ray observations, accounting for non-spherical expansion. In general, mass-loading flattens the density and temperature profiles, decreases the velocity and increases the entropy if the Mach number is above a critical value. We first apply this model to a recent high-resolution galactic outflow simulation where the mass-loading can be directly inferred. We show that the temperature, entropy, and composition profiles are well matched, providing evidence that this physics sets the bulk hot gas profiles. We then model the diffuse X-ray emission from the local starburst M82. The non-spherical (more cylindrical) outflow geometry is directly taken from the observed X-ray surface brightness profile. These models imply a total mass-loading rate that is about equal to that injected in the starburst ≃ 10 M⊙ yr−1, and they predict an asymptotic hot wind velocity of $\sim 1000\, {\rm km \ s^{-1}}$, which is ∼1.5–2 times smaller than previous predictions. We also show how the observed entropy profile can be used to constrain the outflow velocity, making predictions for future missions like XRISM. We argue that the observed X-ray limb brightening may be explained by mass-loading at the outflow’s edges.
Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation inSchizosaccharomyces pombemitochondria
Authors: Herbert Christopher J , Labarre-Mariotte Sylvie , Cornu David , Sophie Cyrielle , Panozzo Cristina , Michel Thomas , Dujardin Geneviève , Bonnefoy Nathalie 
Published: October 2021

AbstractMitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles the human system by its mitochondrial DNA structure and physiology, most translational activators appear to be either lacking, or recruited for post-translational functions. By combining bioinformatics, genetic and biochemical approaches we identified two interacting factors, Cbp7 and Cbp8, controlling Cytb production in S. pombe. We show that their absence affects cytb mRNA stability and impairs the detection of the Cytb protein. We further identified two classes of Cbp7/Cbp8 partners and showed that they modulated Cytb or Cox1 synthesis. First, two isoforms of bS1m, a protein of the small mitoribosomal subunit, that appear mutually exclusive and confer translational specificity. Second, a complex of four proteins dedicated to Cox1 synthesis, which includes an RNA helicase that interacts with the mitochondrial ribosome. Our results suggest that S. pombe contains, in addition to complexes of translational activators, a heterogeneous population of mitochondrial ribosomes that could specifically modulate translation depending on the mRNA translated, in order to optimally balance the production of different respiratory complex subunits.
qPTMplants: an integrative database of quantitative post-translational modifications in plants
Authors: Xue Han , Zhang Qingfeng , Wang Panqin , Cao Bijin , Jia Chongchong , Cheng Ben , Shi Yuhua , Guo Wei-Feng , Wang Zhenlong , Liu Ze-Xian , Cheng Han 
Published: October 2021

AbstractAs a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.
Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus
Authors: Hill Chris H , Cook Georgia M , Napthine Sawsan , Kibe Anuja , Brown Katherine , Caliskan Neva , Firth Andrew E , Graham Stephen C , Brierley Ian 
Published: October 2021

Abstract
The 2A protein of Theiler's murine encephalomyelitis virus (TMEV) acts as a switch to stimulate programmed –1 ribosomal frameshifting (PRF) during infection. Here, we present the X-ray crystal structure of TMEV 2A and define how it recognises the stimulatory RNA element. We demonstrate a critical role for bases upstream of the originally predicted stem–loop, providing evidence for a pseudoknot-like conformation and suggesting that the recognition of this pseudoknot by beta-shell proteins is a conserved feature in cardioviruses. Through examination of PRF in TMEV-infected cells by ribosome profiling, we identify a series of ribosomal pauses around the site of PRF induced by the 2A-pseudoknot complex. Careful normalisation of ribosomal profiling data with a 2A knockout virus facilitated the identification, through disome analysis, of ribosome stacking at the TMEV frameshifting signal. These experiments provide unparalleled detail of the molecular mechanisms underpinning Theilovirus protein-stimulated frameshifting.
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer
Authors: Tang Gongyu , Cho Minsu , Wang Xiaowei 
Published: October 2021

Abstract
Large-scale multi-omics datasets, most prominently from the TCGA consortium, have been made available to the public for systematic characterization of human cancers. However, to date, there is a lack of corresponding online resources to utilize these valuable data to study gene expression dysregulation and viral infection, two major causes for cancer development and progression. To address these unmet needs, we established OncoDB, an online database resource to explore abnormal patterns in gene expression as well as viral infection that are correlated to clinical features in cancer. Specifically, OncoDB integrated RNA-seq, DNA methylation, and related clinical data from over 10 000 cancer patients in the TCGA study as well as from normal tissues in the GTEx study. Another unique aspect of OncoDB is its focus on oncoviruses. By mining TCGA RNA-seq data, we have identified six major oncoviruses across cancer types and further correlated viral infection to changes in host gene expression and clinical outcomes. All the analysis results are integratively presented in OncoDB with a flexible web interface to search for data related to RNA expression, DNA methylation, viral infection, and clinical features of the cancer patients. OncoDB is freely accessible at http://oncodb.org.
mBodyMap: a curated database for microbes across human body and their associations with health and diseases
Authors: Jin Hanbo , Hu Guoru , Sun Chuqing , Duan Yiqian , Zhang Zhenmo , Liu Zhi , Zhao Xing-Ming , Chen Wei-Hua 
Published: October 2021

Abstract
mBodyMap is a curated database for microbes across the human body and their associations with health and diseases. Its primary aim is to promote the reusability of human-associated metagenomic data and assist with the identification of disease-associated microbes by consistently annotating the microbial contents of collected samples using state-of-the-art toolsets and manually curating the meta-data of corresponding human hosts. mBodyMap organizes collected samples based on their association with human diseases and body sites to enable cross-dataset integration and comparison. To help users find microbes of interest and visualize and compare their distributions and abundances/prevalence within different body sites and various diseases, the mBodyMap database is equipped with an intuitive interface and extensive graphical representations of the collected data. So far, it contains a total of 63 148 runs, including 14 401 metagenomes and 48 747 amplicons related to health and 56 human diseases, from within 22 human body sites across 136 projects. Also available in the database are pre-computed abundances and prevalence of 6247 species (belonging to 1645 genera) stratified by body sites and diseases. mBodyMap can be accessed at: https://mbodymap.microbiome.cloud.
Time-dependent evolution of IgG antibody levels after first and second dose of mRNA-based SARS-CoV-2 vaccination in haemodialysis patients: a multicentre study
Authors: Santos-Araújo Carla , Mota Veiga Pedro , Santos Mário João , Santos Lidia , Romãozinho Catarina , Silva Mónica , Lucas Carlos , Duarte Mary Luz , Haarhaus Mathias , Haase Michael , Macário Fernando 
Published: October 2021

ABSTRACT

Background
Vaccination programs are essential for the containment of the coronavirus disease 2019 pandemic, which has hit haemodialysis populations especially hard. Early reports suggest a reduced immunologic response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines in dialysis patients, in spite of a high degree of seroconversion. We aimed to identify risk factors for a reduced efficacy of an mRNA vaccine in a cohort of haemodialysis patients.

Method
In a multicentre study, including 294 Portuguese haemodialysis patients who had received two doses of BNT162b2 with a 3-week interval, immunoglobulin G-class antibodies against the SARS-CoV-2 spike protein were determined 3 weeks after the first dose (M1) and 6 weeks after the second dose (M2). The threshold for seroconversion was 10 UR/mL. Demographic and clinical data were retrieved from a quality registry. Adverse events were registered using a questionnaire.

Results
At M2, seroconversion was 93.1% with a median antibody level of 197.5 U/mL (1.2–3237.0) and a median increase of 180.0 U/mL (−82.9 to 2244.6) from M1. Age [beta −8.9; 95% confidence interval (95% CI) −12.88 to −4.91; P &lt; 0.0001], ferritin &gt;600 ng/mL (beta 183.93; 95% CI 74.75–293.10; P = 0.001) and physical activity (beta 265.79; 95% CI 30.7–500.88; P = 0.03) were independent predictors of SARS-CoV-2 antibody levels after two vaccine doses. Plasma albumin &gt;3.5 g/dL independently predicted the increase of antibody levels between both doses (odds ratio 14.72; 95% CI 1.38 to 157.45; P = 0.03). Only mild adverse reactions were observed in 10.9% of patients.

Conclusions
The SARS-CoV-2 vaccine BNT162b2 is safe and effective in haemodialysis patients. Besides age, iron status and nutrition are possible modifiable modulators of the immunologic response to SARS-CoV-2 mRNA vaccines. These data suggest the need for an early identification of populations at higher risk for diminished antibody production and the potential advantage of the implementation of oriented strategies to maximize the immune response to vaccination in these patients.