bluuebunny/crossref_metadata_2025 huggingface dataset:
Fundamental parameters and abundance analysis of the components in the SB2 system HD 60803
Authors: Ryabchikova T , Zvyagintsev S , Tkachenko A , Tsymbal V , Pakhomov Yu , Semenko E
Published: October 2021

We perform a detailed spectroscopic study of the SB2 system HD 60803 based on high-resolution spectra obtained with different spectrographs. The analysis was done using two independent methods: a) direct modelling of the observed binary spectrum by a sum of synthetic spectra with a varying set of free parameters and minimizing the difference between the observed and theoretical spectra; and b) spectrum disentangling and independent modelling of the individual components. When applied to binary spectra from different spectrographs, both methods converge to a consistent solution for the fundamental parameters of the HD 60803 components: Teff = 6 055 ± 70 K, log g = 4.08 ± 0.12, ξt = 1.45 ± 0.18 km s−1, [M/H] = 0.03 ± 0.06 (primary), and Teff = 6 069 ± 70 K, log g= 4.14 ± 0.09, ξt = 1.48 ± 0.18 km s−1, [M/H] = 0.03 ± 0.06 (secondary). Differential abundance analysis of the components does not reveal any significant difference in their chemical composition. Apart from Li, both components have solar atmospheric abundances. The Li abundance exceeds the solar value by ∼2 dex, but it agrees with the Li abundance in main-sequence late-F-type stars. Relative-to-solar abundances in both components slightly correlate with the condensation temperature in the same way as that found in the solar analogues with/without detected giant planets. The estimated age of the system is 5.5 ± 0.5 Gyr.
The distribution of [α/Fe] in the Milky Way disc
Authors: Vincenzo Fiorenzo , Weinberg David H , Miglio Andrea , Lane Richard R , Roman-Lopes Alexandre
Published: October 2021

Using a sample of red giant stars from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) Data Release 16, we infer the conditional distribution $p([\alpha /{\rm Fe}]\, |\, [{\rm Fe}/{\rm H}])$ in the Milky Way disk for the α-elements Mg, O, Si, S, and Ca. In each bin of [Fe/H] and Galactocentric radius R, we model p([α/Fe]) as a sum of two Gaussians, representing ‘low-α’ and ‘high-α’ populations with scale heights $z_1=0.45\, {\rm kpc}$ and $z_2=0.95\, {\rm kpc}$, respectively. By accounting for age-dependent and z-dependent selection effects in APOGEE, we infer the [α/Fe] distributions that would be found for a fair sample of long-lived stars covering all z. Near the Solar circle, this distribution is bimodal at sub-solar [Fe/H], with the low-α and high-α peaks clearly separated by a minimum at intermediate [α/Fe]. In agreement with previous results, we find that the high-α population is more prominent at smaller R, lower [Fe/H], and larger |z|, and that the sequence separation is smaller for Si and Ca than for Mg, O, and S. We find significant intrinsic scatter in [α/Fe] at fixed [Fe/H] for both the low-α and high-α populations, typically ∼0.04-dex. The means, dispersions, and relative amplitudes of this two-Gaussian description, and the dependence of these parameters on R, [Fe/H], and α-element, provide a quantitative target for chemical evolution models and a test for hydrodynamic simulations of disk galaxy formation. We argue that explaining the observed bimodality will probably require one or more sharp transitions in the disk’s gas accretion, star formation, or outflow history in addition to radial mixing of stellar populations.
G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities
Authors: He Xiaomei , Yuan Jun , Wang Yinsheng
Published: October 2021

RNA guanine quadruplexes (rG4) assume important roles in post-transcriptional regulations of gene expression, which are often modulated by rG4-binding proteins. Hence, understanding the biological functions of rG4s requires the identification and functional characterizations of rG4-recognition proteins. By employing a bioinformatic approach based on the analysis of overlap between peaks obtained from rG4-seq analysis and those detected in >230 eCLIP-seq datasets for RNA-binding proteins generated from the ENCODE project, we identified a large number of candidate rG4-binding proteins. We showed that one of these proteins, G3BP1, is able to bind directly to rG4 structures with high affinity and selectivity, where the binding entails its C-terminal RGG domain and is further enhanced by its RRM domain. Additionally, our seCLIP-Seq data revealed that pyridostatin, a small-molecule rG4 ligand, could displace G3BP1 from mRNA in cells, with the most pronounced effects being observed for the 3′-untranslated regions (3′-UTR) of mRNAs. Moreover, luciferase reporter assay results showed that G3BP1 positively regulates mRNA stability through its binding with rG4 structures. Together, we identified a number of candidate rG4-binding proteins and validated that G3BP1 can bind directly with rG4 structures and regulate the stabilities of mRNAs.
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database
Authors: Fu Weiwei , Wang Rui , Nanaei Hojjat Asadollahpour , Wang Jinxin , Hu Dexiang , Jiang Yu
Published: October 2021

Ruminant Genome Database (RGD; http://animal.nwsuaf.edu.cn/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; ∼8 600 000 conserved elements; and ∼1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.
VThunter: a database for single-cell screening of virus target cells in the animal kingdom
Authors: Chen Dongsheng , Tan Cong , Ding Peiwen , Luo Lihua , Zhu Jiacheng , Jiang Xiaosen , Ou Zhihua , Ding Xiangning , Lan Tianming , Zhu Yixin , Jia Yi , Wei Yanan , Li Runchu , Qin Qiuyu , Sun Chengcheng , Zhao Wandong , Lv Zhiyuan , Wang Haoyu , Wu Wendi , Yuan Yuting , Pu Mingyi , Li Yuejiao , Zhang Yanan , Chang Ashley , Guo Guoji , Bai Yong , Jin Xin , Liu Huan
Published: October 2021

Viral infectious diseases are a devastating and continuing threat to human and animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing viral receptors is fundamental for understanding the potential tissue tropism or host range of these pathogens. The rapid advancement of single-cell RNA sequencing (scRNA-seq) technology has paved the way for studying the expression of viral receptors in different tissues of animal species at single-cell resolution, resulting in huge scRNA-seq datasets. However, effectively integrating or sharing these datasets among the research community is challenging, especially for laboratory scientists. In this study, we manually curated up-to-date datasets generated in animal scRNA-seq studies, analyzed them using a unified processing pipeline, and comprehensively annotated 107 viral receptors in 142 viruses and obtained accurate expression signatures in 2 100 962 cells from 47 animal species. Thus, the VThunter database provides a user-friendly interface for the research community to explore the expression signatures of viral receptors. VThunter offers an informative and convenient resource for scientists to better understand the interactions between viral receptors and animal viruses and to assess viral pathogenesis and transmission in species. Database URL: https://db.cngb.org/VThunter/.
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center
Authors: Amos Beatrice , Aurrecoechea Cristina , Barba Matthieu , Barreto Ana , Basenko Evelina Y , Bażant Wojciech , Belnap Robert , Blevins Ann S , Böhme Ulrike , Brestelli John , Brunk Brian P , Caddick Mark , Callan Danielle , Campbell Lahcen , Christensen Mikkel B , Christophides George K , Crouch Kathryn , Davis Kristina , DeBarry Jeremy , Doherty Ryan , Duan Yikun , Dunn Michael , Falke Dave , Fisher Steve , Flicek Paul , Fox Brett , Gajria Bindu , Giraldo-Calderón Gloria I , Harb Omar S , Harper Elizabeth , Hertz-Fowler Christiane , Hickman Mark J , Howington Connor , Hu Sufen , Humphrey Jay , Iodice John , Jones Andrew , Judkins John , Kelly Sarah A , Kissinger Jessica C , Kwon Dae Kun , Lamoureux Kristopher , Lawson Daniel , Li Wei , Lies Kallie , Lodha Disha , Long Jamie , MacCallum Robert M , Maslen Gareth , McDowell Mary Ann , Nabrzyski Jaroslaw , Roos David S , Rund Samuel S C , Schulman Stephanie Wever , Shanmugasundram Achchuthan , Sitnik Vasily , Spruill Drew , Starns David , Stoeckert Christian J , Tomko Sheena Shah , Wang Haiming , Warrenfeltz Susanne , Wieck Robert , Wilkinson Paul A , Xu Lin , Zheng Jie
Published: October 2021

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
Proteome-pI2.0: proteome isoelectric point database update
Authors: Kozlowski Lukasz Pawel
Published: October 2021

Proteome-pI 2.0 is an update of an online database containing predicted isoelectric points and pKa dissociation constants of proteins and peptides. The isoelectric point—the pH at which a particular molecule carries no net electrical charge—is an important parameter for many analytical biochemistry and proteomics techniques. Additionally, it can be obtained directly from the pKa values of individual charged residues of the protein. The Proteome-pI 2.0 database includes data for over 61 million protein sequences from 20 115 proteomes (three to four times more than the previous release). The isoelectric point for proteins is predicted by 21 methods, whereas pKa values are inferred by one method. To facilitate bottom-up proteomics analysis, individual proteomes were digested in silico with the five most commonly used proteases (trypsin, chymotrypsin, trypsin + LysC, LysN, ArgC), and the peptides’ isoelectric point and molecular weights were calculated. The database enables the retrieval of virtual 2D-PAGE plots and customized fractions of a proteome based on the isoelectric point and molecular weight. In addition, isoelectric points for proteins in NCBI non-redundant (nr), UniProt, SwissProt, and Protein Data Bank are available in both CSV and FASTA formats. The database can be accessed at http://isoelectricpointdb2.org.
Targeting 3′ and 5′ untranslated regions with antisense oligonucleotides to stabilize frataxin mRNA and increase protein expression
Authors: Li Yanjie , Li Jixue , Wang Jun , Lynch David R , Shen Xiulong , R. Corey David , Parekh Darshan , Bhat Balkrishen , Woo Caroline , Cherry Jonathan J , Napierala Jill S , Napierala Marek
Published: October 2021

Friedreich’s ataxia (FRDA) is a severe multisystem disease caused by transcriptional repression induced by expanded GAA repeats located in intron 1 of the Frataxin (FXN) gene encoding frataxin. FRDA results from decreased levels of frataxin; thus, stabilization of the FXN mRNA already present in patient cells represents an attractive and unexplored therapeutic avenue. In this work, we pursued a novel approach based on oligonucleotide-mediated targeting of FXN mRNA ends to extend its half-life and availability as a template for translation. We demonstrated that oligonucleotides designed to bind to FXN 5′ or 3′ noncoding regions can increase FXN mRNA and protein levels. Simultaneous delivery of oligonucleotides targeting both ends increases efficacy of the treatment. The approach was confirmed in several FRDA fibroblast and induced pluripotent stem cell-derived neuronal progenitor lines. RNA sequencing and single-cell expression analyses confirmed oligonucleotide-mediated FXN mRNA upregulation. Mechanistically, a significant elongation of the FXN mRNA half-life without any changes in chromatin status at the FXN gene was observed upon treatment with end-targeting oligonucleotides, indicating that transcript stabilization is responsible for frataxin upregulation. These results identify a novel approach toward upregulation of steady-state mRNA levels via oligonucleotide-mediated end targeting that may be of significance to any condition resulting from transcription downregulation.
Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8
Authors: Czernecki Dariusz , Hu Haidai , Romoli Filippo , Delarue Marc
Published: October 2021

All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3′-5′ exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.
Inferring primase-DNA specific recognition using a data driven approach
Authors: Soffer Adam , Eisdorfer Sarah A , Ifrach Morya , Ilic Stefan , Afek Ariel , Schussheim Hallel , Vilenchik Dan , Akabayov Barak
Published: October 2021

DNA–protein interactions play essential roles in all living cells. Understanding of how features embedded in the DNA sequence affect specific interactions with proteins is both challenging and important, since it may contribute to finding the means to regulate metabolic pathways involving DNA–protein interactions. Using a massive experimental benchmark dataset of binding scores for DNA sequences and a machine learning workflow, we describe the binding to DNA of T7 primase, as a model system for specific DNA–protein interactions. Effective binding of T7 primase to its specific DNA recognition sequences triggers the formation of RNA primers that serve as Okazaki fragment start sites during DNA replication.
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study
Authors: Cao Chen , Wang Jianhua , Kwok Devin , Cui Feifei , Zhang Zilong , Zhao Da , Li Mulin Jun , Zou Quan
Published: October 2021

The development of transcriptome-wide association studies (TWAS) has enabled researchers to better identify and interpret causal genes in many diseases. However, there are currently no resources providing a comprehensive listing of gene-disease associations discovered by TWAS from published GWAS summary statistics. TWAS analyses are also difficult to conduct due to the complexity of TWAS software pipelines. To address these issues, we introduce a new resource called webTWAS, which integrates a database of the most comprehensive disease GWAS datasets currently available with credible sets of potential causal genes identified by multiple TWAS software packages. Specifically, a total of 235 064 gene-diseases associations for a wide range of human diseases are prioritized from 1298 high-quality downloadable European GWAS summary statistics. Associations are calculated with seven different statistical models based on three popular and representative TWAS software packages. Users can explore associations at the gene or disease level, and easily search for related studies or diseases using the MeSH disease tree. Since the effects of diseases are highly tissue-specific, webTWAS applies tissue-specific enrichment analysis to identify significant tissues. A user-friendly web server is also available to run custom TWAS analyses on user-provided GWAS summary statistics data. webTWAS is freely available at http://www.webtwas.net.
MVIP: multi-omics portal of viral infection
Authors: Tang Zhidong , Fan Weiliang , Li Qiming , Wang Dehe , Wen Miaomiao , Wang Junhao , Li Xingqiao , Zhou Yu
Published: October 2021

Virus infections are huge threats to living organisms and cause many diseases, such as COVID-19 caused by SARS-CoV-2, which has led to millions of deaths. To develop effective strategies to control viral infection, we need to understand its molecular events in host cells. Virus related functional genomic datasets are growing rapidly, however, an integrative platform for systematically investigating host responses to viruses is missing. Here, we developed a user-friendly multi-omics portal of viral infection named as MVIP (https://mvip.whu.edu.cn/). We manually collected available high-throughput sequencing data under viral infection, and unified their detailed metadata including virus, host species, infection time, assay, and target, etc. We processed multi-layered omics data of more than 4900 viral infected samples from 77 viruses and 33 host species with standard pipelines, including RNA-seq, ChIP-seq, and CLIP-seq, etc. In addition, we integrated these genome-wide signals into customized genome browsers, and developed multiple dynamic charts to exhibit the information, such as time-course dynamic and differential gene expression profiles, alternative splicing changes and enriched GO/KEGG terms. Furthermore, we implemented several tools for efficiently mining the virus-host interactions by virus, host and genes. MVIP would help users to retrieve large-scale functional information and promote the understanding of virus-host interactions.
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data
Authors: Reimer Lorenz Christian , Sardà Carbasse Joaquim , Koblitz Julia , Ebeling Christian , Podstawka Adam , Overmann Jörg
Published: October 2021

The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms.
Association of serum globulin with all-cause mortality in incident hemodialysis patients
Authors: Pai Alex Y , Sy John , Kim Joseph , Kleine Carola-Ellen , Edward Jessica , Hsiung Jui-Ting , Kovesdy Csaba P , Kalantar-Zadeh Kamyar , Streja Elani
Published: October 2021

Background

Serum globulin is a major component of total protein and can be elevated in inflammatory disease states. While inflammation is common in hemodialysis patients and associated with mortality and morbidity, the association between serum globulin and mortality has never been examined in hemodialysis patients.

Methods

In a retrospective cohort of 104 164 incident hemodialysis patients treated by a large dialysis organization from 2007 to 2011, we explored the association between baseline serum globulin, albumin: globulin (A:G) ratio and serum protein levels and all-cause, cardiovascular and infection-related mortality with adjustments for demographic variables and laboratory markers of malnutrition and inflammation using Cox proportional hazards models.

Results

Patients with a globulin concentration >3.8 g/dL had a higher all-cause and infection-related mortality risk {hazard ratio [HR] 1.11 [95% confidence interval (CI) 1.06–1.16] and HR 1.28 [95% CI 1.09–1.51], respectively} in the fully adjusted model when compared with the reference group of 3.0– <3.2 g/dL. In addition, patients with an A:G ratio <0.75 had a 45% higher all-cause mortality hazard [HR 1.45 (95% CI 1.38–1.52)] and patients with total serum protein <5.5 g/dL had a 34% higher risk of death [1.34 (95% CI 1.27–1.42)] when compared with the reference (A:G ratio 1.05– <1.15 and total serum protein 6.5– <7 g/dL).

Conclusions

Among incident hemodialysis patients, a higher globulin level was associated with a higher mortality risk independent of other markers of malnutrition and inflammation, including albumin. A lower A:G ratio and serum protein was also associated with a higher mortality hazard. The mechanisms that contribute to elevated serum globulin should be further explored.
Application of species-specific primers to estimate the in situ diet of Bythotrephes [Cladocera, Onychopoda] in its native European range via molecular gut content analysis
Authors: Pichler Arthur , Walters Tina L , Frischer Marc E , Nejstgaard Jens C , Ptáčníková Radka
Published: October 2021

The study of invasive species often focuses on regions of recent introduction rather than native habitats. Understanding an invasive species in its natural environment, however, can provide important insights regarding the long-term outcome of invasions. In this study we investigated the diet of the invasive spiny water flea, Bythotrephes longimanus, in two Austrian perialpine lakes, where it is native. The gut contents of wild-caught Bythotrephes individuals were estimated by quantitative polymerase chain reaction, targeting species-specific fragments of the barcoding region of the cytochrome c oxidase I gene of potential prey. The observed prey spectrum of Bythotrephes in the study lakes consisted primarily of Eudiaptomus gracilis and Diaphanosoma brachyurum. The Daphnia longispina complex, Leptodora kindtii and Mesocyclops leuckarti also contributed to the diet. Results indicate that Bythotrephes is a generalist feeder with a preference for epilimnetic prey.
Impacts of bunk management on steer performance and ruminal hydrogen sulfide concentrations in steers fed modified distillers grains with solubles
Authors: Neville Bryan W , Lekatz Leslie A , Moore Rebecca L , Pickinpaugh Wayde J , Kassetas Cierrah J
Published: October 2021

Two experiments were conducted to evaluate the impacts of bunk management on dry matter intake (DMI), growth performance, carcass characteristic, and hydrogen sulfide (H2S) concentrations in beef steers fed modified distillers grains with solubles (MDGS; DM basis). In Experiment 1, 139 steers (440.4 ± 31.0 kg) were randomly assigned to one of 16 pens with pen randomly assigned to one of two treatments: 1) Control (CON, bunks managed to be devoid of feed prior to feeding), or 2) Over-fed (OVF, bunks managed to have minimum of 2.54 cm of feed remaining each morning) during adaptation. Following adaptation all steers in Experiment 1 were transitioned to CON bunks and followed to finishing. In Experiment 2, 126 steers (445.4 ± 40.63 kg) were randomly assigned to one of 16 pens. Treatments in Experiment 2 were arranged in a 2 × 2 factorial and include the two bunk management strategies utilized in Experiment 1 (OVF or CON) and either 25% MDGS or 50% MDGS (DM basis). Ruminal H2S was measured via rumenocentesis during dietary adaptation. There were no differences (P ≥ 0.13) observed in either experiment for growth performance due to bunk management. In Experiment 1, OVF steers had greater (P = 0.001) DMI during adaptation; however, overall DMI was not different (P = 0.14) between treatments. In Experiment 2, DMI (d 0 to 104) tended to decrease (P = 0.09) with greater MDGS inclusion. Hot carcass weight, ribeye area, marbling score, and quality grade were not affected (P ≥ 0.48) by either bunk management or MDGS inclusion. In Experiment 2, back fat (1.30 vs. 1.17 ± 0.042 cm) and yield grade (3.2 vs. 3.0 ± 0.11) were greater (P = 0.03) for CON steers compared with OVF but were not affected (P = 0.59) by MDGS inclusion. In Experiment 1, H2S tended (P = 0.07) to be greater in steers on OVF compared with CON. In Experiment 2, bunk management strategy did not impact (P = 0.82) H2S concentrations. There was a MDGS inclusion × day interaction for H2S with steers fed 50% MDGS having greater (P < 0.01) H2S concentrations compared with steers fed 25% MDGS on d 28 and 35. Bunk management strategy during adaptation did not impact growth performance but did reduce intake in Experiment 1. Yield grade decreased when OVF bunk management was applied throughout Experiment 2. Response of H2S concentrations in the rumen were variable and likely influenced by inconsistencies in bunk management and resulting DMI during the early portions of the feedlot study.
Performance of growing beef cattle consuming bahiagrass hay treated with calcium oxide and molasses
Authors: Ciriaco Francine M , Henry Darren D , Sanford Carla D , Canal Luara B , Dubeux Jose C B , DiLorenzo Nicolas
Published: October 2021

Two experiments were conducted to evaluate the effects of Pensacola bahiagrass (Paspalum notatum) hay treated with calcium oxide (CaO) and molasses on performance of growing beef cattle supplemented or not with cottonseed meal. In Exp. 1, growing Bos indicus influenced heifers (n = 59; 250 ± 29 kg body weight [BW]) and steers (n = 37; 256 ± 45 kg BW) were used. In Exp. 2, heifers (n = 56; 249 ± 26 kg BW) and steers (n = 8; 249 ± 20 kg BW) from Exp. 1 were used. Both experiments were randomized complete block designs and consisted of 56-d periods in which cattle were weighed every 14 d. On day 0, cattle were weighed after a 16-h water and feed withdrawal, stratified by sex, breed, and BW, and blocked by initial BW. Cattle were allotted to 24 and 16 dormant bahiagrass pastures (1.34 ha each) in Exp. 1 and Exp. 2, respectively. Pastures were located in two different areas within 0.52 km of each other and were stratified by location and randomly assigned (n = 8 pastures/treatment) to treatment. In Exp. 1 treatments were: 1) untreated dry hay (DH); 2) hay treated with 10% molasses (dry matter [DM] basis) + water (to 65% DM; MOL); or 3) hay treated with 5% CaO (DM basis) + 10% molasses (DM basis) + water (to 65% DM; CAO). In Exp. 2 only treatments MOL and CAO were applied, and cottonseed meal was provided at 0.3% of cattle BW/d (as fed basis). In both experiments, data were analyzed using pasture as the experimental unit. The model included the fixed effects of treatment, sex, and their interaction (Exp. 1). Location and block were included as random effects. In both experiments, initial and final BW were not affected by treatment (P ≥ 0.362 and P ≥ 0.283, respectively) or sex (P ≥ 0.512 and P ≥ 0.495, respectively) and no treatment × sex interaction was observed in Exp. 1 (P > 0.05). Additionally, no effects of treatment (P ≥ 0.515), sex (P ≥ 0.285), or treatment × sex interaction (Exp. 1; P = 0.582) were observed on average daily gain (average of −0.03 kg in Exp. 1 and 0.537 kg in Exp. 2). Bahiagrass hay treated with molasses alone or in combination with CaO failed to improve performance of growing beef cattle. However, when protein supplementation via cottonseed meal was provided, cattle did not experience weight loss.
Outcomes of Operatively Managed Lumbar and Sacral Facet Fractures in Pediatric Athletes: A Case Series
Authors: Nazareth Alexander , Andras Lindsay M. , Illingworth Kenneth D. , Miller Daniel J. , Cahill Patrick J. , Skaggs David L.
Published: October 2021

Background:

Facet fractures have been reported in a total of 6 young athletes in 4 previous publications. These injuries were not diagnosed on magnetic resonance imaging (MRI) or radiographs, and were identified on computed tomography (CT). Our purpose was to report a series of athletes with operatively managed facet fractures. This may be an under-recognized diagnosis.

Methods:

Retrospective review of pediatric patients with operatively managed isolated lumbar or sacral facet fractures from 3 tertiary pediatric hospitals from 2014 to 2019. Clinical records and imaging studies were reviewed.

Results:

Ten patients with symptomatic lumbar or sacral facet fractures met inclusion criteria (mean age at presentation; 13.3±2.1 years, 70% Female). All patients reported competitive participation in sports. On physical examination, 10/10 (100%) of patients had lower back pain that was exacerbated with lumbar spine extension. Limited CT scans demonstrated facet fractures in 10/10 (100%) patients not detected on plain film or MRI. All patients experienced significant relief of pain following excision of the facet fracture fragment. At time of first postoperative visit, 9/10 (90%) patients were pain free while one had generalized back pain thought to be related to fibromyalgia and not facet pathology. At time of last follow-up, 2/10 (20%) of patients reported nonspecific back pain that was not localized in the area of the facet fracture, while 80% (8/10) remained pain free. All patients 100% (10/10) returned to full participation to sports. There were no complications noted in this series. Average follow-up was 27 months (range: 1 to 68 mo).

Conclusions:

Athletes with localized back pain exacerbated by spine extension may have a facet fracture. As facet fractures are usually not identified with radiographs or MRI, a limited CT scan should be considered in the evaluation of pediatric athletes with localized back pain exacerbated by extension. In this series, surgical excision of facet fracture fragments was safe and provided predictable pain relief.
Exploring Content Relationships Among Components of a Multisource Feedback Program
Authors: Roy Marguerite , Kain Nicole , Touchie Claire
Published: October 2021

Introduction:

A new multisource feedback (MSF) program was specifically designed to support physician quality improvement (QI) around the CanMEDS roles of Collaborator, Communicator, and Professional. Quantitative ratings and qualitative comments are collected from a sample of physician colleagues, co-workers (C), and patients (PT). These data are supplemented with self-ratings and given back to physicians in individualized reports. Each physician reviews the report with a trained feedback facilitator and creates one-to-three action plans for QI. This study explores how the content of the four aforementioned multisource feedback program components supports the elicitation and translation of feedback into a QI plan for change.

Methods:

Data included survey items, rater comments, a portion of facilitator reports, and action plans components for 159 physicians. Word frequency queries were used to identify common words and explore relationships among data sources.

Results:

Overlap between high frequency words in surveys and rater comments was substantial. The language used to describe goals in physician action plans was highly related to respondent comments, but less so to survey items. High frequency words in facilitator reports related heavily to action plan content.

Discussion:

All components of the program relate to one another indicating that each plays a part in the process. Patterns of overlap suggest unique functions conducted by program components. This demonstration of coherence across components of this program is one piece of evidence that supports the program's validity.
Physical Therapy Practice for Critically Ill Patients With COVID-19 in the Intensive Care Unit
Authors: Stolboushkin Catherine , Mondkar Rajashree , Schwing Terrence , Belarmino Bobby
Published: October 2021

Purpose:

To describe physical therapist (PT) practice for patients with COVID-19 in the intensive care unit (ICU) at a tertiary hospital and to describe a novel clinical decision-making algorithm (nCDM) and its use in enhancing clinical practice for this patient population.

Methods:

This is a single-center, retrospective chart review. An nCDM was formulated to assist with best practice. The Activity Measure for Post-Acute Care “6 clicks” (AM-PAC) score, highest level of mobility, discharge destination, and observed clinical complications at hospital discharge were collected.

Results:

Seventy-seven patients received ICU PT services. Of these, twenty-six patients were outside previously established parameters for initiating PT intervention and forty-four patients were on mechanical ventilation during the initial PT evaluation. All groups showed a statistically significant improvement in their respective AM-PAC scores from initial PT evaluation to ICU discharge.

Conclusion:

The authors have described our PT practice for this patient population in our setting. Patients who were outside previously established parameters for initiating PT intervention were able to participate with PT and showed functional improvement. This nCDM shows a promising use in enhancing clinical decision-making for PT practice while treating patients with COVID-19 in the ICU.
ACUTE MACULAR NEURORETINOPATHY AFTER COVID-19 VACCINATION
Authors: Zaheer Naima , Renju Mary P. , Chavan Randhir
Published: October 2021

Purpose:

To report a case of acute macular neuroretinopathy after the vaccination for coronavirus disease 2019.

Methods:

A 22-year-old White woman presented with symptoms of paracentral scotomas within a week of receiving coronavirus disease 2019 vaccination. Complete evaluation was performing using multimodal imaging techniques.

Results:

Spectral domain optical coherence tomography and near-infrared imaging showed characteristic features of acute macular neuroretinopathy.

Conclusion/Discussion:

To the best of our knowledge this is the first reported case of acute macular neuroretinopathy after coronavirus disease 2019 vaccination. Optical coherence tomography angiography did not reveal any signal attenuation, and multifocal electroretinogram and central visual fields were normal indicating that near-infrared imaging and spectral domain optical coherence tomography remain the gold standard in diagnosing this condition especially in smaller lesions.
Effect of Blue Light Filters on Tear and Contrast Sensitivity in Individuals Using Electronic Devices
Authors: Sánchez-González María Carmen , Madroñero María , García-Romera Marta C. , Silva-Viguera María-del-Carmen , Conejero-Domínguez Juan-Josè , Gargallo-Martínez Beatriz , De-Hita-Cantalejo Concepción , Bautista-Llamas María-José
Published: October 2021

Objectives:

To investigate the effect of contact lenses with blue light filters on contrast sensitivity and any alteration in tear quantity and quality.

Methods:

This prospective longitudinal pilot study required three visits by each participant. Monocular visual acuity, contrast sensitivity, phenol red thread test, and tear breakup time were measured at each visit.

Results:

There were significant differences in logarithmic contrast sensitivity between the groups. The breakup time (BUT) was significantly lower after using video display terminals than before (P<0.05). No differences in BUT were found between groups video display terminals and contact lenses having the blue filter (P>0.05). However, higher mean values were observed in the group after video display terminal use with contact lenses having the blue filter than that with standard contact lenses (P>0.05 in both groups). Furthermore, the mean value of phenol red thread test on the group after video display terminal use with contact lenses having the blue filter was lower than the group before its use (P>0.05).

Conclusion:

The results establish a possible relationship between tear stability, improved contrast sensitivity, and the use of a blue filter in contact lenses.
Glaucoma Prevalence and Glaucoma Surgical Considerations in Prosthetic Replacement of the Ocular Surface Ecosystem Device Use
Authors: Duong Andrew T. , Ertel Monica K. , Van Tassel Sarah H.
Published: October 2021

Objectives:

The purpose of this study was to identify patients with glaucoma and corneal/ocular surface disease who have been fit with Prosthetic Replacement of the Ocular Surface Ecosystem (PROSE; BostonSight, Needham, MA) devices and to understand the PROSE device fit experience in patients with glaucoma at Weill Cornell Medicine (WCM).

Methods:

This is a retrospective chart review of patients older than 18 years who underwent PROSE device fitting at WCM. Records were reviewed for demographic information and ophthalmic variables. Descriptive statistics were performed.

Results:

Between 2011 and 2017, 281 patients underwent PROSE device fitting at WCM, of whom 24 patients (8.5%) had a glaucoma diagnosis and 17 patients (6.0%) were identified as glaucoma suspect. Ocular surface disease was the most common indication for PROSE device wear (58.3%). Five patients had a history of incisional glaucoma surgery in the eye undergoing PROSE device fitting: three valved glaucoma drainage implants and two trabeculectomies. Three of these eyes were successfully fit with PROSE devices.

Conclusions:

Patients fitted with Prosthetic Replacement of the Ocular Surface Ecosystem devices at WCM had a higher prevalence of glaucoma than in the general population. Among patients with incisional glaucoma surgery, PROSE device fitting was challenging, with a 40% failure rate.
A prospective cohort study of the presence of SARS-CoV-2 in clinical samples from multiple bodily sites: implications for transmission routes of COVID-19
Authors: Liu Meixian , Huang Huimin , Bian Xiqing , Zheng Zhiyuan , Li Na , Sun Baoqing , Wu Jian-Lin
Published: October 2021

Objective:

The coronavirus disease 2019 (COVID-19) epidemic resulting from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has still spread globally. The occurrence of the Delta variant, which is more infectious and spreads faster than earlier forms of the virus that causes COVID-19, makes infection prevention more challenging. Therefore, this study aimed to gain a comprehensive insight into the transmission routes of SARS-CoV-2 for curbing the propagation of SARS-CoV-2 in human populations.

Methods:

We studied a prospective cohort of 576 patients admitted consecutively to the First Affiliated Hospital of Guangzhou Medical University from January 21 to June 8, 2020. These patients were chosen based on their similar clinical phenotypes or imaging findings. There were 21 (3.6%) laboratory-confirmed COVID-19 patients (16 severe and 5 mild cases) and 555 non-COVID-19 patients. The antibody response and routes and duration of viral shedding were systematically evaluated in serial clinical specimens. Moreover, SARS-CoV-2 RNA was also detected in a mouth rinse, urine, and tear samples. This study was approved by the Medical Ethical Committee of The First Affiliated Hospital of Guangzhou Medical University (approval No. 2020-77).

Results:

SARS-CoV-2 mainly existed in sputum, nasal and throat swabs, and feces samples. Virus latency was longer in sputum and feces samples than in nasopharyngeal samples. IgG antibody response in respiratory samples was related to disease severity. Although droplets and aerosols are the major transmission routes for COVID-19, covert routes of transmission from asymptomatic patients, contaminated surfaces, and wastewater are also of interest.

Conclusion:

Our findings provide a solid foundation for developing prophylactic measures against SARS-CoV-2.
Staff Beliefs Toward Self-Injurious Behavior in Patients: A Study of Secure Services
Authors: Steene Lisa Maria Beethoven , Ireland Jane L. , Ireland Carol A.
Published: October 2021

Staff beliefs toward patient self-harm in secure forensic services are explored, capturing forensic nurses and other clinical staff from four secure units from one National Health Service trust, comprising high through low and forensic learning disability. One hundred fifty-five respondents took part (overall completion rate: 61%). The Theory-Driven Measure of Self-Injurious Behavior and the Suicide Competency Assessment Form were completed. It was predicted that higher competency and increased levels of training would associate with beliefs toward patient self-harm. Beliefs differed in accordance to location; perceiving self-injurious behavior as planned and within patient control was endorsed more in high-security settings by forensic nurses, with nurses in high security also more likely to endorse the perception that patients engaging in such behaviors were able to cope and felt valued. Competence and training experience were identified as factors of relevance. The study offers suggestions for future research, including a focus on capturing the environment, exploring “endorsed beliefs” as opposed to “negative attitudes,” and proposing the concept of “professional exposure to self-harm” as an important variable.
Patients' Expressed Nursing Care Needs in a Forensic Psychiatric Setting
Authors: Åling Maria , Syrén Susanne , Strömberg Lars
Published: October 2021

The aim of this study was to describe the patients' nursing care needs in a forensic psychiatric setting in line with the NANDA-I classification. Ten patients sentenced to forensic psychiatric care were interviewed. Data were analyzed by means of directed content analysis with a deductive approach, where we used “served time” as a factor in the analysis, thus creating three categories: newly arrived patients with a length of stay of only a couple of years, patients with a length of stay of around 5 years, and patients with a length of stay of more than 5 years. Thirteen NANDA-I diagnoses were identified during the analyses, distributed on seven different domains. When distributing the given NANDA-I diagnoses according to the created categories, an explanatory pattern emerged, and three themes became apparent: denial, insight, and listlessness. Considering the differences in views, the patients' own recognition of what is a problem, a potential, or a risk could improve a “working relation” and, eventually, a recovery. NANDA-I nursing diagnoses may improve individualized and person-centered care as NANDA-I makes care continuously consistent over time.
Vestibular Aqueduct Size Correlates With the Degree of Cochlear Hydrops in Patients With and Without Menière's Disease
Authors: Grosser Desiree , Willenborg Kerstin , Dellani Paulo , Avallone Emilio , Götz Friedrich , Böthig Dietmar , Warnecke Athanasia , Lanfermann Heinrich , Lenarz Thomas , Giesemann Anja
Published: October 2021

Objective:

To correlate the CT imaging findings of the visibility and size of the vestibular aqueduct (VA) with the degree of the cochlear hydrops determined in MRI late imaging of the hydrops. Study Design: Retrospective study. Setting: Tertiary referral center. Patients: A total of 127 patients (62 women, 65 men, average age 55.6 yrs): 86 of these were diagnosed with Menière's disease (American Academy of Otolaryngology–Head and Neck Surgery [AAO-HNS] criteria; 67 unilateral, 19 bilateral).

Intervention(s):

Temporal bone CT and hydrops MRI were performed in all patients.

Main Outcome Measure(s):

Visibility/width of the VA in temporal bone CT and grade of cochlear hydrops evaluated by MRI.

Results:

The width of the VA is significantly smaller in patients diagnosed with Menière's disease (30% non-visible VA), compared with the patients who did not fulfill the diagnostic criteria of Menière's disease (12% non-visible VA) (double sided Spearman correlation, p < 0.001). In all ears of patients diagnosed with Menière's disease the width of the VA was significantly correlated with the degree of the cochlear hydrops (in cases of non-visible VA 65% [34/52] ears presented with hydrops grade 3 or 4; 13% [7/52] ears presented with hydrops grade 1 or 2 and 21% [11/52] ears showed no hydrops) (Spearman correlation p = 0.001/p < 0.01). This is also true for all ears that can be summarized as hydrophic ear disease (symptomatic ears that present with a hydrops in MRI).

Conclusions:

The results of our study could confirm the importance of the VA in the pathogenesis of the endolymphatic hydrops in vivo.
Validation of a Moroccan Arabic Version of the Tinnitus Handicap Inventory (THI-M)
Authors: Halily Sara , Ardhaoui Hamida , Zoukal Sofia , Abada Redallah larbi , Oukessou Youssef , Rouadi Sami , Roubal Mohamed , Mahtar Mohamed
Published: October 2021

Objective:

Cultural adaptation of the tinnitus handicap inventory questionnaire to the Moroccan dialect version.

Method:

We conducted a prospective study over a 3 years period (January 2017–January 2020) in the Otolaryngology Department of Casablanca University hospital. Translation was produced by a forward–backward procedure with analysis of the psychometric properties of the Moroccan version of the tinnitus handicap inventory.

Results:

The final Moroccan version of Tinnitus Handicap Inventory (THI) was given to 83 otosclerosis patients suffering from tinnitus. They filled the questionnaire twice before surgery and 1 year after surgery.

The item-total correlations are all statistically significant (p < 0.001) and vary between 0.279 (item 15) and 0.817 (item 12).

The internal consistency of the Moroccan version of THI, assessed through Cronbach's α, was found to be excellent at 0.953. The interclass correlation showed an excellent reliability for all subscales (0.999–1).

THI scores decreased significantly from baseline to 1-year postoperative follow-up on all subscale scores, indicating clinical improvement.

Conclusion:

The Moroccan version of THI has a good reliability comparable with translations in other languages and the original version. It is a valid tool to assess tinnitus improvement after otosclerosis surgery.