bluuebunny/crossref_metadata_2025 huggingface dataset:
Combined effects of supplementation of amino acids and immunocastration in first antler growth of farmed fallow deer (Dama dama)
Authors: Ceacero Francisco , Ny Veit , Kotrba Radim , Bartoň Luděk , Čupić Stipan , Bureš Daniel , Turek Jiři , Komárková Martina , Needham Tersia
Published: January 2023

Context Amino acid supplementation and immunocastration are two husbandry practices with an increasing interest in the worldwide growing industry of deer farming. Amino acids (AAs) optimise nutrition and feed costs and improve the quality of products such as venison, velvet or antlers. Immunocastration (IC) reduces agonistic behaviours, which produce carcass damage and reduced growth. Thus, both treatments have positive effects on body growth, but may interfere with hormonal regulation, subsequently affecting antler growth. Aims This study aimed to evaluate the combined use of both practices and their impact on body and antler growth. Methods Forty-four yearling male fallow deer, approximate 10 months old, were subjected to the following four combinations based on both treatments: control–control, AA–control, IC–control, and AA–IC. Immunocastration treatment started in March 2020 and was repeated after 50 and 130 days. All groups received 250 g per animal and day of grains, and those under AA supplementation received ruminally protected lysine 6.3 g and ruminally protected methionine 2.1 g per animal and day. Biometric data, antlers and metatarsus were collected at slaughter in November. Antlers and metatarsus were analysed through computer-tomography scanning and mineral spectrometry. Key results Supplementation of AAs scarcely affected antler growth, although an indirect effect through improved body condition cannot be rejected. Immunocastration showed significant but not dramatic effects: IC animals had lighter antlers, with a lower amount of cortical bone and less mineralisation (density and calcium and phosphorus concentrations) in the base of the antler than did control animals. In contrast, the effects were scarce at the top of the antler and the metatarsus. Conclusions The results suggest a reduction but not total suppression of testosterone, with almost negligible effects on body growth and internal bones, thus not raising animal welfare issues. Implications Both techniques can be used simultaneously in deer farming, especially in farms with venison-production goals. Future research should focus on optimising the vaccination schedule for the main farmed deer species to ensure that the welfare benefits are well balanced with productivity.
Beneficial effects of instrumental music on the production performance of Xiandao green-shell layers housed under different stocking densities
Authors: Cao Shiwen , Yang Fengping , Wu Ruiyong , Zhang Xueyu , Ye Manhong , Wei Wanhong
Published: January 2023

Context Egg production rate (EPR) is the main criteria for egg producers and egg quality is important for consumers. Exposed to music, layers kept at appropriate stocking density could display optimal production performance without compromising egg quality. Aims This study aimed to investigate the possibility of employing instrumental music stimulus and regulating stocking density to maximise egg production performance and improve egg quality in Xiandao green-shell layers. Methods In total, 378 30-week-old layers were randomly distributed into nine treatments across three types of sound sources (natural sound, instrumental music, or mixed road noise) × three different stocking densities (4, 7 and 10 birds/cage corresponding to low, medium, and high density respectively), with six replicates per treatment. The 24-day experimental period was equally divided into four phases. EPR, average egg weight, and serum IgG concentration were determined at the end of each phase. Egg quality and organ indices were determined at the end of experiment. Results Hens exposed to music had a significantly higher EPR and laid eggs of better quality than did hens subjected to mixed road noise. Across all parameters, hens exposed to music did not significantly differ from hens exposed to natural sound. Stocking density had significant impacts on EPR, relative eggshell weight, and serum IgG concentration, with hens kept at high stocking density (357 cm2/hen) exhibiting the lowest values. Hens kept at medium density (510 cm2/hen) and low density (892 cm2/hen) showed no significant differences in tested parameters except that the former produced eggs with a significantly higher relative eggshell weight. Significant interactions between sound and density were observed in EPR, relative yolk weight, and spleen index, with hens exposed to music and kept at low density displaying the highest values. Conclusions Music and low stocking density had favourable effects on improving egg production and egg quality, while road noise and high stocking density exerted negative influences on them. Implications Xiandao green-shell layers are recommended to be kept at medium density to maximise the production benefits. The integration of music playback into management practices will not compromise layers’ production potential displayed under natural sound exposure.
Birth Weight, Gestational Age, and Risk of Cardiovascular Disease in Early Adulthood: Influence of Familial Factors
Authors: Lu Donghao , Yu Yongfu , Ludvigsson Jonas F , Oberg Anna Sara , Sørensen Henrik Toft , László Krisztina D , Li Jiong , Cnattingius Sven
Published: January 2023

The association between intrauterine growth restriction and cardiovascular disease (CVD) later in life might be confounded by familial factors. We conducted a binational register-based cohort study to assess associations of birth weight for gestational age (GA), a proxy for intrauterine growth restriction, and GA with CVD risk in early adulthood, before and after addressing familial factors via sibling comparison. We included 3,410,334 live nonmalformed singleton births from Sweden (1973–1996) and Denmark (1978–1998). During a median follow-up period of 10 years from age 18 years onwards, 29,742 individuals developed incident CVD (hypertension, ischemic heart disease, or cerebrovascular disease). Compared with individuals born with appropriate birth weight for GA (AGA; 10th–90th percentiles) or full term (39–40 gestational weeks), individuals born severely small for GA (SGA; ≤3rd percentile) or preterm (22–36 weeks) were at increased risk of CVD (hazard ratio (HR) = 1.38 (95% confidence interval (CI): 1.32, 1.45) and HR = 1.31 (95% CI: 1.25, 1.38), respectively). The association was attenuated when comparing individuals born SGA with their AGA siblings (HR = 1.11, 95% CI: 0.99, 1.25) but remained robust when comparing individuals born preterm with their term siblings (HR = 1.21, 95% CI: 1.07, 1.37). Our findings suggest that both SGA and preterm birth are associated with CVD risk in early adulthood, with greater familial confounding noted for SGA birth.
Invited Commentary: Some Social Epidemiologic Lessons From the COVID-19 Pandemic
Authors: Schnake-Mahl Alina S , Bilal Usama
Published: January 2023

In their recent article, Dimitris et al. (Am J Epidemiol. 2022;191(6):980–986) presented a series of challenges modern epidemiology has faced during the coronavirus disease 2019 (COVID-19) pandemic, including challenges around the scientific progress, epidemiologic methods, interventions, equity, team science, and training needed to address these issues. Here, 2 social epidemiologists who have been working on COVID-19 inequities reflect on further lessons with an added year of perspective. We focus on 2 key challenges: 1) dominant biomedical individualistic narratives around the production of population health, and 2) the role of profit in policy-making. We articulate a need to consider social epidemiologic approaches, including acknowledging the importance of considering how societal systems lead to health inequities. To address these challenges, future (and current) epidemiologists should be trained in theories of population health distribution and political structures of governance. Last, we close with the need for better investment in public health infrastructure as a crucial step toward achieving population health equity.
Epidemiologic Utility of a Framework for Partition Number Selection When Dissecting Hierarchically Clustered Genetic Data Evaluated on the Intestinal Parasite Cyclospora cayetanensis
Authors: Barratt Joel L N , Plucinski Mateusz M
Published: January 2023

Comparing parasite genotypes to inform parasitic disease outbreak investigations involves computation of genetic distances that are typically analyzed by hierarchical clustering to identify related isolates, indicating a common source. A limitation of hierarchical clustering is that hierarchical clusters are not discrete; they are nested. Consequently, small groups of similar isolates exist within larger groups that get progressively larger as relationships become increasingly distant. Investigators must dissect hierarchical trees at a partition number ensuring grouped isolates belong to the same strain; a process typically performed subjectively, introducing bias into resultant groupings. We describe an unbiased, probabilistic framework for partition number selection that ensures partitions comprise isolates that are statistically likely to belong to the same strain. We computed distances and established a normalized distribution of background distances that we used to demarcate a threshold below which the closeness of relationships is unlikely to be random. Distances are hierarchically clustered and the dendrogram dissected at a partition number where most within-partition distances fall below the threshold. We evaluated this framework by partitioning 1,137 clustered Cyclospora cayetanensis genotypes, including 552 isolates epidemiologically linked to various outbreaks. The framework was 91% sensitive and 100% specific in assigning epidemiologically linked isolates to the same partition.
Implementation and expansion of inpatient and ambulatory pharmacist credentialing and privileging at an academic medical center
Authors: Dawson Courtney , Pham Aaron , Shipman Colleen , Lau Gary , Pham Yen
Published: January 2023

Purpose

This article highlights one academic medical center’s effort to implement a complete credentialing and privileging (C&P) process for both inpatient and ambulatory clinical pharmacists.

The C&P process offers a recognized method to advance pharmacy practice. Credentialing is defined as a process whereby an individual is deemed qualified in a specific subject matter area. Privileging is the process whereby an institution grants authority to an individual to perform services based on credentials. Federal guidelines permit pharmacists to obtain the same level of privileges as professional medical staff, such as physicians, if relevant state laws allow for the corresponding pharmacist scope of practice. States establish laws and regulations that specify the scope of practice for various types of licensed healthcare professionals, including pharmacists. Many health systems have attempted pharmacist C&P practices in both the inpatient and ambulatory care setting with varying degrees of success and reach. Privileged pharmacists provide established benefits and value to other members of the healthcare team. Oregon Health & Science University (OHSU) pursued C&P for both inpatient and ambulatory clinical pharmacists. Initiation and implementation processes were complex and accompanied by a variety of challenges.

Conclusion

OHSU operates with advanced pharmacy practice integrated into the interdisciplinary patient care team. Pharmacist C&P allows pharmacists to demonstrate significant clinical benefits and quality improvement in patient care delivery in both inpatient and ambulatory settings.
Exposure Monitoring Strategies for Applying Low-Cost PM Sensors to Assess Flour Dust in Industrial Bakeries
Authors: Ruiter Sander , Bard Delphine , Ben Jeddi Hasnae , Saunders John , Snawder John , Warren Nick , Gorce Jean-Philippe , Cauda Emanuele , Kuijpers Eelco , Pronk Anjoeka
Published: January 2023

Low-cost particulate matter (PM) sensors provide new methods for monitoring occupational exposure to hazardous substances, such as flour dust. These devices have many possible benefits, but much remains unknown about their performance for different exposure monitoring strategies in the workplace. We explored the performance of PM sensors for four different monitoring strategies (time-weighted average and high time resolution, each quantitative and semi-quantitative) for assessing occupational exposure using low-cost PM sensors in a field study in the industrial bakery sector. Measurements were collected using four types of sensor (PATS+, Isensit, Airbeam2, and Munisense) and two reference devices (respirable gravimetric samplers and an established time-resolved device) at two large-scale bakeries, spread over 11 participants and 6 measurement days. Average PM2.5 concentrations of the low-cost sensors were compared with gravimetric respirable concentrations for 8-h shift periods and 1-min PM2.5 concentrations of the low-cost sensors were compared with time-resolved PM2.5 data from the reference device (quantitative monitoring strategy). Low-cost sensors were also ranked in terms of exposure for 8-h shifts and for 15-min periods with a shift (semi-quantitative monitoring strategy). Environmental factors and methodological variables, which can affect sensor performance, were investigated. Semi-quantitative monitoring strategies only showed more accurate results compared with quantitative strategies when these were based on shift-average exposures. The main factors that influenced sensor performance were the type of placement (positioning the devices stationary versus personal) and the company or workstation where measurements were collected. Together, these findings provide an overview of common strengths and drawbacks of low-cost sensors and different ways these can be applied in the workplace. This can be used as a starting point for further investigations and the development of guidance documents and data analysis methods.
Knowing the past to conserve the future: a commentary on ‘Evolutionary history of marginal habitats regulates the diversity of tree communities in the Atlantic Forest’
Authors: Rezende Vanessa L , de Miranda Pedro L Silva , Pontara Vanessa
Published: January 2023

This article comments on:

Jhonny Capichoni Massante, and Markus Gastauer. Evolutionary history of marginal habitats regulates the diversity of tree communities in the Atlantic Forest, Annals of Botany, Volume 131, Issue 2, 1 February 2023, Pages 261–274, https://doi.org/10.1093/aob/mcac111
Comparison of Various Metrics of Repetitive Head Impact Exposure And Their Associations With Neurocognition in Collegiate-Aged Athletes
Authors: Amadon Grace K , Goeckner Bryna D , Brett Benjamin L , Meier Timothy B
Published: January 2023

Objective

Characterize the levels of various metrics of repetitive head impacts (RHI) in contact (CS) and non-contact (NCS) sport athletes and determine the extent to which they are associated with fluid cognition.

Methods

Collegiate-aged athletes (n = 176) completed semi-structured interviews about participation in contact sport. RHI was operationalized based on current sport (CS/NCS), the cumulative number of years of participation, age at first exposure (AFE), and based on recently proposed traumatic encephalopathy syndrome (TES) categories. The NIH Toolbox Cognition Battery assessed fluid cognition. General linear models compared RHI metrics between CS and NCS athletes and tested associations of RHI measures with fluid cognition.

Results

CS athletes had more years of RHI exposure, higher rates of “extensive” exposure based on TES criteria, and were more likely to have AFE before age 12 relative to NCS (ps < .001). A subset of NCS athletes, however, reported prior RHI at levels categorized as being “extensive” based on TES criteria (5%), while a larger minority had AFE before 12 (34%). No adverse associations of RHI and fluid cognition were observed (ps > .05). Across all RHI metrics, more or earlier RHI was associated with better episodic memory (ps ≤ .05). Secondary analyses showed this effect was driven by women.

Conclusions

Current results find no evidence that RHI in collegiate-aged athletes is associated with worse neurocognition. Although there was extensive overlap among RHI measures, results demonstrate that categorizing athletes based on their current sport undercounts the lifetime RHI exposure in many NCS athletes.
Active Vitamin D3 (Calcitriol) Increases Adipose Graft Retention in a Xenograft Model
Authors: Loder Shawn , Wang Sheri , Amurgis Charles , DeSanto Marisa , Stavros Alexander G , Patadji Stell , Olevian Dane , Lee Phoebe , Guerrero David , Gusenoff Jeffrey A , Peter Rubin J , Kokai Lauren E
Published: January 2023

Background

Autologous fat grafting, although broadly indicated, is limited by unsatisfactory retention and often requires multiple procedures to achieve durable outcomes. Graft survival is strongly influenced by the magnitude and duration of post-engraftment ischemia. Calcitriol is a pleiotropic, safe nutrient with cell-specific influence on viability and metabolic flux.

Objectives

Evaluate the efficacy of activated vitamin D3 (calcitriol) in improving grafting outcomes and examine its mechanisms.

Methods

Lipoaspirate was collected for ex vivo culture (7 unique donors), in vitro bioenergetic analysis (6 unique donors), and in vivo transplantation (5 unique donors). Ex vivo samples were incubated for up to 2 weeks before extraction of the stromal vascular fraction (SVF) for viability or flow cytometry. SVF was collected for Seahorse (Agilent; Santa Clara, CA) analysis of metabolic activity. Human endothelial cell lines were utilized for analyses of endothelial function. In vivo, samples were implanted into athymic mice with calcitriol treatment either (1) once locally or (2) 3 times weekly via intraperitoneal injection. Grafts were assessed photographically, volumetrically, and histologically at 1, 4, and 12 weeks. Hematoxylin and eosin (H&E), Sirius red, perilipin, HIF1α, and CD31 tests were performed.

Results

Calcitriol-treated lipoaspirate demonstrated dose-dependent increases in SVF viability and metabolic reserve during hypoxic stress. Calcitriol treatment enhanced endothelial mobility ex vivo and endothelial function in vitro. In vivo, calcitriol enhanced adipocyte viability, reduced fibrosis, and improved vascularity. Continuous calcitriol was sufficient to improve graft retention at 12 weeks (P < .05).

Conclusions

Calcitriol increased fat graft retention in a xenograft model. Calcitriol has potential to be a simple, economical means of increasing fat graft retention and long-term outcomes.
Upregulation of MAP kinase HOG1 gene of white-rot fungus Phlebia sp. MG-60 inhibits the ethanol fermentation and mycelial growth
Authors: Motoda Taichi , Chen Fu-Chia , Tsuyama Taku , Tokumoto Yuji , Kijidani Yoshio , Kamei Ichiro
Published: January 2023

Wood biomass conversion for fossil resource replacement could result in the sustainable production of chemicals, although lignin represents an obstacle to efficient polysaccharide use. White-rot fungus Phlebia sp. MG-60 reportedly selectively and aerobically degrades lignin in hardwood, then it begins cellulose saccharification from the delignified wood to produce ethanol. Environmental conditions might change white-rot fungi-driven biomass conversion. However, how the environmental response sensor affects ethanol fermentation in white-rot fungi remains elusive. In this study, we focused on MGHOG1, the yeast Hog1 homolog in Phlebia sp. MG-60, a presumably important player in osmoresponse. We generated MGHOG1 overexpressing (OE) transformants in Phlebia sp. MG-60, exhibiting slower mycelial growth compared with the wild-type under salinity stress. MGHOG1 overexpressing liquid cultures displayed suppressed mycelial growth and ethanol fermentation. Therefore, MGHOG1 potentially influences ethanol fermentation and mycelial growth in Phlebia sp. MG-60. This study provides novel insights into the regulation of white-rot fungi-mediated biomass conversion.
Overexpression of a predicted transketolase gene and disruption of an α-1,3-glucan synthase gene inAspergillus oryzaeDGLA3 strain enhances the yield of free dihomo-γ-linolenic acid
Authors: Tamano Koichi , Nakai Shiori , Takayama Haruka , Imai Yasuhiko
Published: January 2023

Free dihomo-γ-linolenic acid (DGLA), a polyunsaturated free fatty acid (FFA), can potentially be used to produce eicosanoid pharmaceuticals, such as prostaglandin E1. Previously, we constructed an Aspergillus oryzae mutant strain, named DGLA3, which produced free DGLA at an increased yield by faaA gene disruption and cooverexpression of one elongase and two desaturase genes. In this study, we achieved a further increase. Since FFA production is increased by enhancing the pentose phosphate pathway, we overexpressed a predicted transketolase gene composing the pathway in DGLA3, which consequently increased the free DGLA yield by 1.9-fold to 403 mg/L. Additionally, we disrupted the α-1,3-glucan synthase gene agsB involved in cell-wall biosynthesis, which further increased it by 1.3-fold to 533 mg/L. Overall, the yield increased by 2.5-fold. Free DGLA productivity and biomass increased similarly, but residual glucose concentration decreased. Increased hyphal dispersion appeared to cause additional glucose consumption, resulting in an increase in biomass and yield.
Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism
Authors: Yang Bo , Chen Hailin
Published: January 2023

Recent studies have shown that the expression of circRNAs would affect drug sensitivity of cells and thus significantly influence the efficacy of drugs. Traditional biomedical experiments to validate such relationships are time-consuming and costly. Therefore, developing effective computational methods to predict potential associations between circRNAs and drug sensitivity is an important and urgent task. In this study, we propose a novel method, called MNGACDA, to predict possible circRNA–drug sensitivity associations for further biomedical screening. First, MNGACDA uses multiple sources of information from circRNAs and drugs to construct multimodal networks. It then employs node-level attention graph auto-encoders to obtain low-dimensional embeddings for circRNAs and drugs from the multimodal networks. Finally, an inner product decoder is applied to predict the association scores between circRNAs and drug sensitivity based on the embedding representations of circRNAs and drugs. Extensive experimental results based on cross-validations show that MNGACDA outperforms six other state-of-the-art methods. Furthermore, excellent performance in case studies demonstrates that MNGACDA is an effective tool for predicting circRNA–drug sensitivity associations in real situations. These results confirm the reliable prediction ability of MNGACDA in revealing circRNA–drug sensitivity associations.
Deleterious synonymous mutation identification based on selective ensemble strategy
Authors: Wang Lihua , Zhang Tao , Yu Lihong , Zheng Chun-Hou , Yin Wenguang , Xia Junfeng , Zhang Tiejun
Published: January 2023

Although previous studies have revealed that synonymous mutations contribute to various human diseases, distinguishing deleterious synonymous mutations from benign ones is still a challenge in medical genomics. Recently, computational tools have been introduced to predict the harmfulness of synonymous mutations. However, most of these computational tools rely on balanced training sets without considering abundant negative samples that could result in deficient performance. In this study, we propose a computational model that uses a selective ensemble to predict deleterious synonymous mutations (seDSM). We construct several candidate base classifiers for the ensemble using balanced training subsets randomly sampled from the imbalanced benchmark training sets. The diversity measures of the base classifiers are calculated by the pairwise diversity metrics, and the classifiers with the highest diversities are selected for integration using soft voting for synonymous mutation prediction. We also design two strategies for filling in missing values in the imbalanced dataset and constructing models using different pairwise diversity metrics. The experimental results show that a selective ensemble based on double fault with the ensemble strategy EKNNI for filling in missing values is the most effective scheme. Finally, using 40-dimensional biology features, we propose a novel model based on a selective ensemble for predicting deleterious synonymous mutations (seDSM). seDSM outperformed other state-of-the-art methods on the independent test sets according to multiple evaluation indicators, indicating that it has an outstanding predictive performance for deleterious synonymous mutations. We hope that seDSM will be useful for studying deleterious synonymous mutations and advancing our understanding of synonymous mutations. The source code of seDSM is freely accessible at https://github.com/xialab-ahu/seDSM.git.
From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies?
Authors: Defo Joel , Awany Denis , Ramesar Raj
Published: January 2023

Genome-wide association studies (GWAS) have benefited greatly from enhanced high-throughput technology in recent decades. GWAS meta-analysis has become increasingly popular to highlight the genetic architecture of complex traits, informing about the replicability and variability of effect estimations across human ancestries. A wealth of GWAS meta-analysis methodologies have been developed depending on the input data and the outcome information of interest. We present a survey of current approaches from SNP to pathway-based meta-analysis by acknowledging the range of resources and methodologies in the field, and we provide a comprehensive review of different categories of Genome-Wide Meta-analysis methods employed. These methods highlight different levels at which GWAS meta-analysis may be done, including Single Nucleotide Polymorphisms, Genes and Pathways, for which we describe their framework outline. We also discuss the strengths and pitfalls of each approach and make suggestions regarding each of them.
Benchmarking differential abundance analysis methods for correlated microbiome sequencing data
Authors: Yang Lu , Chen Jun
Published: January 2023

Differential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Current microbiome studies frequently generate correlated samples from different microbiome sampling schemes such as spatial and temporal sampling. In the past decade, a number of DAA tools for correlated microbiome data (DAA-c) have been proposed. Disturbingly, different DAA-c tools could sometimes produce quite discordant results. To recommend the best practice to the field, we performed the first comprehensive evaluation of existing DAA-c tools using real data-based simulations. Overall, the linear model-based methods LinDA, MaAsLin2 and LDM are more robust than methods based on generalized linear models. The LinDA method is the only method that maintains reasonable performance in the presence of strong compositional effects.
Benchmarking of computational methods for predicting circRNA-disease associations
Authors: Lan Wei , Dong Yi , Zhang Hongyu , Li Chunling , Chen Qingfeng , Liu Jin , Wang Jianxin , Chen Yi-Ping Phoebe
Published: January 2023

Accumulating evidences demonstrate that circular RNA (circRNA) plays an important role in human diseases. Identification of circRNA-disease associations can help for the diagnosis of human diseases, while the traditional method based on biological experiments is time-consuming. In order to address the limitation, a series of computational methods have been proposed in recent years. However, few works have summarized these methods or compared the performance of them. In this paper, we divided the existing methods into three categories: information propagation, traditional machine learning and deep learning. Then, the baseline methods in each category are introduced in detail. Further, 5 different datasets are collected, and 14 representative methods of each category are selected and compared in the 5-fold, 10-fold cross-validation and the de novo experiment. In order to further evaluate the effectiveness of these methods, six common cancers are selected to compare the number of correctly identified circRNA-disease associations in the top-10, top-20, top-50, top-100 and top-200. In addition, according to the results, the observation about the robustness and the character of these methods are concluded. Finally, the future directions and challenges are discussed.
Metadata retrieval from sequence databases with ffq
Authors: Gálvez-Merchán Ángel , Min Kyung Hoi (Joseph) , Pachter Lior , Booeshaghi A Sina
Published: January 2023

Motivation

Several genomic databases host data and metadata for an ever-growing collection of sequence datasets. While these databases have a shared hierarchical structure, there are no tools specifically designed to leverage it for metadata extraction.

Results

We present a command-line tool, called ffq, for querying user-generated data and metadata from sequence databases. Given an accession or a paper’s DOI, ffq efficiently fetches metadata and links to raw data in JSON format. ffq’s modularity and simplicity make it extensible to any genomic database exposing its data for programmatic access.

Availability and implementation

ffq is free and open source, and the code can be found here: https://github.com/pachterlab/ffq.
Vaa3D-x for cross-platform teravoxel-scale immersive exploration of multidimensional image data
Authors: Liang Jiangshan , Deng Luchen , Chen Shize , Wang Yimin , Ruan Zongcai , Zhang Lingli
Published: January 2023

Vaa3D is a software package that has been widely used to visualize and analyze multidimensional microscopic images in a number of cutting edge bioimage informatics applications. However, due to many recent updates of both software development environments and operating systems, it was highly requested to maintain Vaa3D and disseminate it on latest operating systems. In addition, there has never been a showcase about how to use Vaa3D’s cross-platform visualization and immersive exploration functions for multidimensional and teravoxel-scale images. Here, we introduce a newly developed version of the software, called Vaa3D-x, to address all the above issues.

Availability and implementation

Vaa3D-x is released in both binary and Open-Source available at vaa3d.org and GitHub (https://github.com/Vaa3D).

Supplementary information

Supplementary data are available at Bioinformatics online.
Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers
Authors: Peng Xiyu , Dorman Karin S
Published: January 2023

Motivation

Amplicon sequencing is widely applied to explore heterogeneity and rare variants in genetic populations. Resolving true biological variants and quantifying their abundance is crucial for downstream analyses, but measured abundances are distorted by stochasticity and bias in amplification, plus errors during polymerase chain reaction (PCR) and sequencing. One solution attaches unique molecular identifiers (UMIs) to sample sequences before amplification. Counting UMIs instead of sequences provides unbiased estimates of abundance. While modern methods improve over naïve counting by UMI identity, most do not account for UMI reuse or collision, and they do not adequately model PCR and sequencing errors in the UMIs and sample sequences.

Results

We introduce Deduplication and Abundance estimation with UMIs (DAUMI), a probabilistic framework to detect true biological amplicon sequences and accurately estimate their deduplicated abundance. DAUMI recognizes UMI collision, even on highly similar sequences, and detects and corrects most PCR and sequencing errors in the UMI and sampled sequences. DAUMI performs better on simulated and real data compared to other UMI-aware clustering methods.

Availability and implementation

Source code is available at https://github.com/DormanLab/AmpliCI.

Supplementary information

Supplementary data are available at Bioinformatics online.
Upregulation of FOXA2 in uterine luminal epithelium and vaginal basal epithelium of epiERα−/− (Esr1fl/flWnt7aCre/+) mice
Authors: Hancock Jonathan Matthew , Li Yuehuan , Martin Taylor Elijah , Andersen Christian Lee , Ye Xiaoqin
Published: January 2023

Forkhead box protein A2 (FOXA2) is a pioneer transcription factor important for epithelial budding and morphogenesis in different organs. It has been used as a specific marker for uterine glandular epithelial cells (GE). FOXA2 has close interactions with estrogen receptor α (ERα). ERα binding to Foxa2 gene in the uterus indicates its regulation of Foxa2. The intimate interactions between ERα and FOXA2 and their essential roles in early pregnancy led us to investigate the expression of FOXA2 in the female reproductive tract of pre-implantation epiERα−/− (Esr1fl/flWnt7aCre/+) mice, in which ERα is conditionally deleted in the epithelium of reproductive tract. In the oviduct, FOXA2 is detected in the ciliated epithelial cells of ampulla but absent in the isthmus of day 3.5 post-coitum (D3.5) Esr1fl/fl control and epiERα−/− mice. In the uterus, FOXA2 expression in the GE appears to be comparable between Esr1fl/fl and epiERα−/− mice. However, FOXA2 is upregulated in the D0.5 and D3.5 but not PND25-28 epiERα−/− uterine luminal epithelial cells (LE). In the vagina, FOXA2 expression is low in the basal layer and increases toward the superficial layer of the D3.5 Esr1fl/fl vaginal epithelium, but FOXA2 is detected in the basal, intermediate, and superficial layers, with the strongest FOXA2 expression in the intermediate layers of the D3.5 epiERα−/− vaginal epithelium. This study demonstrates that loss of ERα in LE and vaginal basal layer upregulates FOXA2 expression in these epithelial cells during early pregnancy. The mechanisms for epithelial cell-type specific regulation of FOXA2 by ERα remain to be elucidated.
Inviting, Affording and Translating Harm: Understanding the Role of Technological Mediation in Technology-Facilitated Violence
Authors: Wood Mark A , Mitchell Matthew , Pervan Flynn , Anderson Briony , O’Neill Tully , Wood Jackson , Arpke-Wales Will
Published: January 2023

Technologies not only extend capabilities but also mediate experience and action. To date, however, research on technology-facilitated violence has tended not to focus on the role technological mediation plays in acts of violence facilitated through technology. Building on prior work in the field, this article develops a theoretical framework and typology for understanding the role technological mediation plays in producing technology-facilitated violence. First, drawing on postphenomenological theories of technology, we argue that technology-facilitated violence is best understood as a form of ‘harm translation,’ where a technology’s affordances and other properties ‘invite’ an individual to actualize harmful ends. Then, distinguishing between four modes of harm translation, we construct a typology for analysing the intersections between user intention and technological design that, together, facilitate violence. We argue that by attending to these distinctions our typology may help researchers and designers identify and address the specific causal dynamics involved in producing different kinds of technology-facilitated harm.
Secukinumab long-term efficacy and safety in psoriasis through to year 5 of treatment: results of a randomized extension of the phase III ERASURE and FIXTURE trials
Authors: Langley Richard G , Sofen Howard , Dei-Cas Ignacio , Reich Kristian , Sigurgeirsson Bardur , Warren Richard B , Paul Carle , Szepietowski Jacek C , Tsai Tsen-Fang , Hampele Isabelle , You Ruquan , Charef Pascal , Papavassilis Charis
Published: January 2023

Background

In the long-term extension study of the ERASURE and FIXTURE trials, the efficacy of secukinumab (a fully human anti-interleukin-17A monoclonal antibody) was demonstrated to have been maintained through to year 3 of treatment in moderate-to-severe plaque psoriasis.

Objectives

To assess the efficacy and safety of secukinumab through to year 5 of treatment in moderate-to-severe plaque psoriasis.

Methods

Responders with ≥ 75% improvement in Psoriasis Area and Severity Index (PASI 75) from two core trials – ERASURE and FIXTURE – were randomized 2 : 1 at year 1 (end of core trials) to either the same dose (300 or 150 mg, continuous treatment) or placebo (treatment withdrawal) every 4 weeks, until year 3 or relapse (> 50% reduction in maximal PASI from core study baseline). Partial responders (achieving PASI 50 but not PASI 75) at year 1 continued at the same dose as in the core trials. At year 3, all patients received open-label secukinumab treatment, with those on secukinumab 300 mg continuing on their dose, while those on secukinumab 150 mg or placebo received secukinumab 150 or 300 mg based on the physician’s discretion. The study is registered on ClinicalTrials.gov with the identifier NCT01544595.

Results

Most patients randomized to placebo at year 1 relapsed, but the response was rapidly recaptured upon reinitiation of treatment. PASI responses were sustained with secukinumab through to year 5. The PASI responses for the 300 mg responders + partial responders group at year 1 (PASI 75/90/100: 86.8%/72.8%/45.9%) trended downwards until year 3 (PASI 75/90/100: 82.3%/58.4%/32.7%) and then remained stable through year 4 (PASI 75/90/100: 83.3%/60.1%/32.2%) until year 5 (PASI 75/90/100: 81.1%/62.8%/35.1%). Dermatology Life Quality Index showed sustained benefit up to year 5. Absolute PASI responses were maintained throughout the study. The most common adverse events (AEs) were infections and infestations, nasopharyngitis, and upper respiratory tract infections (URTIs). The overall exposure-adjusted incidence rate (EAIR; with 95% confidence interval) for all AEs was 139.9 (130.3–149.9). EAIRs for Crohn's disease and neutropenia were 0.1 (0.0–0.3) and 0.5 (0.3–0.8), respectively.

Conclusions

The 4-year extension of two pivotal phase III trials demonstrated that secukinumab treatment was effective through to year 5 and improved quality of life in patients with moderate-to-severe plaque psoriasis. The most common AEs were infections and infestations, nasopharyngitis, and URTIs. The safety profile was consistent with that in the secukinumab phase II/III clinical development programme.
British Association of Dermatologists guidelines for the management of people with cutaneous squamous cell carcinoma in situ (Bowen disease) 2022
Authors: Sharma Ashish , Birnie Andrew J , Bordea Cristina , Cheung Seau Tak , Mann Jasmine , Morton Colin A , Salim Asad , Hasan Zeeshaan-Ul , Hashme Maria , Mansour Kiaee Zahra , Mohd Mustapa M Firouz , Exton Lesley S
Published: January 2023

The overall objective of the guideline is to provide up-to-date, evidence-based recommendations for the management of squamous cell carcinoma in situ (SCC in situ). The document aims to: offer an appraisal of all relevant literature up to 13th August 2021, focusing on any key developments; address important, practical clinical questions relating to the primary guideline objective; provide guideline recommendations and if appropriate research recommendations.
Photoprotection for people with skin of colour: needs and strategies
Authors: Krutmann Jean , Piquero-Casals Jaime , Morgado-Carrasco Daniel , Granger Corinne , Trullàs Carles , Passeron Thierry , Lim Henry W
Published: January 2023

Skin of colour or pigmented skin has unique characteristics: it has a higher eumelanin-to-pheomelanin ratio, more mature melanosomes, an increased amount of melanin distributed in the upper layers of the epidermis, and more efficient DNA repair compared with lighter skin. However, individuals with skin of colour are at a significant risk of skin damage caused by ultraviolet radiation, including the development of photodermatoses and photoageing changes such as uneven skin tone, and are predisposed to pigmentary disorders. In fact, one of the most common conditions leading to dermatology consultations by patients with skin of colour is photoexacerbated pigmentary disorders. Unfortunately, individuals with skin of colour may be less prone to engage in photoprotective measures, including the use of sunscreens. Physicians are also less likely to prescribe sunscreens for them. There is thus a clear need for better education on photodamage and for more efficient and suitable photoprotection in populations with skin of colour. However, this need has thus far only partially been met, and the development of sunscreen products designed to provide optimal photoprotection for people with skin of colour remains a challenge. Targeted sunscreens for individuals with skin of colour require optimal cosmetic appeal (leaving no white residue and not disrupting skin tone). They should include broad-spectrum [ultraviolet (UV)B/UVA] protection with high sun protection factor, as well as protection against long-wave UVA (UVA1) and visible light, as these wavelengths are capable of inducing or augmenting pigmentary disorders. They may also contain depigmenting agents for patients with pigmentary disorders.
Severe tracheal involvement in type XVII collagen junctional epidermolysis bullosa
Authors: Bozonnat Alizée , Polivka Laura , Leclerc-Mercier Stéphanie , Luscan Romain , Charbit-Henrion Fabienne , Bodemer Christine , Lapillonne Alexandre , Hadj-Rabia Smail
Published: January 2023

In COLXVII-junctional epidermolysis bullosa, mucosal involvement remains inconsistent and is limited to the oral cavity and the oesophagus. We documented the observation of a patient presenting with tracheal damage.
Validation of novel diagnostic criteria for atopic dermatitis in an adult and elderly Chinese population
Authors: Yew Yik Weng , Apfelbacher Christian J
Published: January 2023

This is an invited commentary on the article titled “Validation of the main diagnostic criteria of atopic dermatitis and proposing a novel diagnostic criteria in adult and elderly Chinese populations: a multicenter, prospective, clinical setting-based study.”
DO WE USE ANTIBIOTICS CORRECTLY FOR THE TREATMENT OF ACUTE CHOLECYSTITIS?
Authors: Torroella Vallejo A , Carolina Caldera M C , Morales Sevillano X , Turrado Rodríguez V , Vidal O
Published: January 2023

Introduction

Adequate antibiotic therapy is one of the mainstays in treatment of acute cholecystitis. The Tokyo Guidelines 2018 (TG18) offer recommendations for the appropriate use of antimicrobials in clinical practice. This work evaluates whether antibiotic therapy in patients operated on for cholecystitis is in line with current recommendations.

Methods

Retrospective analysis of patients undergoing cholecystectomy for acute cholecystitis between 06/01/2021 and 12/31/2021. Demographic variables were collected, including risk factors (RRFF) for developing infectious complications or presenting multiresistant microorganisms, as well as SIRS criteria. Information was collected on antibiotic prophylaxis, empiric treatment, its duration, and adherence to both the guidelines and the results of the cultures. Finally, hospital stay and postoperative infectious complications were recorded.

Results

64 patients were operated upon. 51.6% had RRFF of presenting infectious complications, 29.7% had SIRS criteria, 17.2% had RRFF of multiresistant bacteria. According to the TG18, 62.5% were grade 2. Antibiotic prophylaxis was administrated in 82.8% of the cases. Empirical treatment was maintained in 76.6% of the patients, with a mean duration of 5.87±4.1 days. The empirical antibiotic was adapted to the antibiogram in 57.9% of the cases. In none of the cases in which it was not adapted was the antibiotic changed. Surgical site infection was 7.8%.

Conclusions

The concordance of the empirical antibiotic treatment and its duration according to the guidelines, as well as the adequacy of the type of antibiotic according to the cultures, is only fulfilled in a little more than half of the cases.
CONTRAST-ENHANCED ULTRASOUND IN PEDIATRIC ABDOMINAL TRAUMA
Authors: Núñez García B , Álvarez García N , Patricia Beltrán V , Romero Novo M I , Jiménez Gómez J , Santiago Martínez S , Esteva Miró C , Betancourth Alvarenga J E
Published: January 2023

Introduction

Evaluation of the use of contrast-enhanced ultrasound (CEUS) in patients with abdominal trauma.

Methods

Retrospective study of patients with grade III or higher abdominal trauma, according to the American Association of Surgical Association (AAST) severity scale. All patients underwent an initial CT scan, mode B ultrasound before discharge and a second-generation contrast-enhanced ultrasound (CEUS) one month after the trauma (contrast dose=0.03 ml/kg).

Results

From January 2017 to December 2021, a total of 36 patients (2–15 years) with abdominal trauma were collected. 18 hepatic, 8 splenic, 8 renal and 2 pancreatic traumas. Of these, 8 patients required urgent embolization due to active bleeding or pseudoaneurysm and 1 patient required urgent surgical intervention.

CEUS at 1 month showed: complete resolution in 22 patients, 2 residual hematomas, 1 patient with urinoma and devascularized area, 3 pseudoaneurysms, 7 with persistence of lacerations resolved at 2 weeks and 1 patient with 2 pancreatic cysts.

Conclusions

CEUS allows evaluation of parenchymal injuries of abdominal organs, as well as the presence of residual hematomas, active bleeding, pseudoaneurysms, urinomas and/or devascularized areas, therefore, it can be a useful tool for follow-up and monitoring of abdominal trauma.

The absence of irradiation and its great accessibility allow it to be repeated as often as desired; and the confirmation of resolution enables an earlier return to daily life.
ROBOTIC APPROACH IN 10 CASES OF CORPOROCAUDAL PANCREATECTOMY. INITIAL EXPERIENCE OF A BILIO-PANCREATIC UNIT
Authors: Sánchez-Bueno F , Gil Vazquez P J , Ferreras Martínez D , Gómez Pérez B , Gómez Boch F , Alcaraz Solano A , Cugat Andorra E
Published: January 2023

Introduction

The aim of this paper is to analyze the validity and safety of a new robotic approach implantation program in the corporocaudal pancreatectomy (PCC) in a Bilio-Pancreatic Unit, evaluating morbi-mortality and hospital stay.

Methods

Given the controversy of which is the best therapeutic option in distal pancreatectomy in clinical process surgery tributaries, we designed this prospective, non-randomized, single-center study of pancreatic resection with Robotic approach). Ten patients (7 women and 3 men) were included, with a mean age of 57.8 years, (range 36–73 years). In all patients, the body mass index was higher than 30 and the diagnosis was made with a preoperative computed tomography.

Results

The robotic approach was successful in all cases, performing a corporal-caudal pancreatectomy associated with splenectomy. Blood loss was minimal during intervention, not requiring any blood transfusion. The mean operative time was 135.8 minutes. Conversion to open surgery was not necessary. Three patients had postoperative complications when a CT scan diagnosed an intra-abdominal collection in the left hypocondrium. It was resolved by percutaneous radiological drainage. Median hospital stay was 4 days (3–15). There was not perioperative mortality at 90 days. Anatomopathological study showed 5 mucinous cystic neoplasms, 2 adenocarcinomas of the pancreas and 3 well-differentiated neuroendocrine tumors. Mean size of the lesions were 4.8 cm (2.4–9).

Conclusions

Robotic distal pancreatectomy is an effective and safe technique. In addition, postoperative morbidity and hospital stay decreases.