bluuebunny/crossref_metadata_2025_split huggingface dataset:
gmcoda: Graphical model for multiple compositional vectors in microbiome studies
Authors: Fang Huaying 
Published: November 2023

Abstract

Motivation
Microbes are essential components in the ecosystem and participate in most biological procedures in environments. The high-throughput sequencing technologies help researchers directly quantify the abundance of microbes in a natural environment. Microbiome studies explore the construction, stability, and function of microbial communities with the aid of sequencing technology. However, sequencing technologies only provide relative abundances of microbes, and this kind of data is called compositional data in statistics. The constraint of the constant-sum requires flexible statistical methods for analyzing microbiome data. Current statistical analysis of compositional data mainly focuses on one compositional vector such as bacterial communities. The fungi are also an important component in microbial communities and are always measured by sequencing internal transcribed spacer instead of 16S rRNA genes for bacteria. The different sequencing methods between fungi and bacteria bring two compositional vectors in microbiome studies.

Results
We propose a novel statistical method, called gmcoda, based on an additive logistic normal distribution for estimating the partial correlation matrix for cross-domain interactions. A majorization–minimization algorithm is proposed to solve the optimization problem involved in gmcoda. Through simulation studies, gmcoda is demonstrated to work well in estimating partial correlations between two compositional vectors. Gmcoda is also applied to infer cross-domain interactions in a real microbiome dataset and finds potential interactions between bacteria and fungi.

Availability and implementation
Gmcoda is open source and freely available from https://github.com/huayingfang/gmcoda under GNU LGPL v3.
Second term improvement to generalized linear mixed model asymptotics
Authors: Maestrini Luca , Bhaskaran Aishwarya , Wand Matt P 
Published: November 2023

Abstract
A recent article by Jiang et al. (2022) on generalized linear mixed model asymptotics derived the rates of convergence for the asymptotic variances of maximum likelihood estimators. If m denotes the number of groups and n is the average within-group sample size then the asymptotic variances have orders m−1 and (mn)−1, depending on the parameter. We extend this theory to provide explicit forms of the (mn)−1 second terms of the asymptotically harder-to-estimate parameters. Improved accuracy of statistical inference and planning are consequences of our theory.
The role of governance in rewilding the United States to stem the biodiversity crisis
Authors: Carlson Shelby C , Vucetich John A , Elbroch L Mark , Perry Shelby , Roe Lydia A , Butler Tom , Bruskotter Jeremy T 
Published: November 2023

Abstract
A critical but underattended feature of the biodiversity crisis is the contraction of geographic range experienced by most studied terrestrial vertebrates. In the United States, the primary policy tool for mitigating the biodiversity crisis is a federal law, the Endangered Species Act (ESA). For the past two decades, the federal agencies that administer the ESA have interpreted the act in a manner that precludes treating this geographic element of the crisis. Therefore, the burden of mitigating the biodiversity crisis largely falls on wildlife agencies within state government, which are obligated to operate on behalf of the interests of their constituents. We present survey research indicating that most constituents expect state agencies to prioritize species restoration over other activities, including hunting. This prioritization holds even among self-identified hunters, which is significant because state agencies often take the provisioning of hunting opportunity as their top priority. By prioritizing rewilding efforts that restore native species throughout portions of their historic range, state agencies could unify hunting and nonhunting constituents while simultaneously stemming the biodiversity crisis.
Towards a ‘Social Model’ of Mental Capacity for Social Work
Authors: Brown Clare 
Published: November 2023

Abstract
The statutory social work role in England and Wales regularly involves assessment and ‘best interests’ decision making under the Mental Capacity Act (MCA) 2005. Legal frameworks that permit substitute decision making have, however, been challenged as a contravention of the human rights of people with disabilities. This article aims to answer the question: ‘Can mental capacity be theorised for social work assessment in England and Wales in a way that is compatible with social work ethics and values?’ Findings are that mental capacity is a complex and disputed concept best described using a constructivist ‘social model’ which situates it as a property of an individual’s relationships. Such a model suggests that assessments are a joint endeavour and that the quality of the relationship between assessor and assessed is crucial. The present legal framework disincentivises but does not prevent capacity assessment based on a social model. The existing literature suggests that further research might identify ways in which social work capacity assessment could enhance rather than diminish the autonomy of the people involved. These findings have implications for social work research, education and post qualification training.
Impaired cholinergic integrity of the colon and pancreas in dementia with Lewy bodies
Authors: Okkels Niels , Horsager Jacob , Fedorova Tatyana D , Knudsen Karoline , Skjærbæk Casper , Andersen Katrine B , Labrador-Espinosa Miguel , Vestergaard Karsten , Mortensen Janne K , Klit Henriette , Møller Mette , Danielsen Erik H , Johnsen Erik L , Bekan Goran , Hansen Kim V , Munk Ole L , Damholdt Malene F , Kjeldsen Pernille L , Hansen Allan K , Gottrup Hanne , Grothe Michel J , Borghammer Per 
Published: November 2023

Abstract
Dementia with Lewy bodies is characterized by a high burden of autonomic dysfunction and Lewy pathology in peripheral organs and components of the sympathetic and parasympathetic nervous system. Parasympathetic terminals may be quantified with 18F-fluoroetoxybenzovesamicol, a PET tracer that binds to the vesicular acetylcholine transporter in cholinergic presynaptic terminals. Parasympathetic imaging may be useful for diagnostics, improving our understanding of autonomic dysfunction and for clarifying the spatiotemporal relationship of neuronal degeneration in prodromal disease. Therefore, we aimed to investigate the cholinergic parasympathetic integrity in peripheral organs and central autonomic regions of subjects with dementia with Lewy bodies and its association with subjective and objective measures of autonomic dysfunction. We hypothesized that organs with known parasympathetic innervation, especially the pancreas and colon, would have impaired cholinergic integrity.
To achieve these aims, we conducted a cross-sectional comparison study including 23 newly diagnosed non-diabetic subjects with dementia with Lewy bodies (74 ± 6 years, 83% male) and 21 elderly control subjects (74 ± 6 years, 67% male). We obtained whole-body images to quantify PET uptake in peripheral organs and brain images to quantify PET uptake in regions of the brainstem and hypothalamus. Autonomic dysfunction was assessed with questionnaires and measurements of orthostatic blood pressure.
Subjects with dementia with Lewy bodies displayed reduced cholinergic tracer uptake in the pancreas (32% reduction, P = 0.0003) and colon (19% reduction, P = 0.0048), but not in organs with little or no parasympathetic innervation. Tracer uptake in a region of the medulla oblongata overlapping the dorsal motor nucleus of the vagus correlated with autonomic symptoms (rs = −0.54, P = 0.0077) and changes in orthostatic blood pressure (rs = 0.76, P &lt; 0.0001). Tracer uptake in the pedunculopontine region correlated with autonomic symptoms (rs = −0.52, P = 0.0104) and a measure of non-motor symptoms (rs = −0.47, P = 0.0230).
In conclusion, our findings provide the first imaging-based evidence of impaired cholinergic integrity of the pancreas and colon in dementia with Lewy bodies. The observed changes may reflect parasympathetic denervation, implying that this process is initiated well before the point of diagnosis. The findings also support that cholinergic denervation in the brainstem contributes to dysautonomia.
miR-1304 targets KLK11 to regulate gastric cancer cell proliferation through the mTOR signaling pathway
Authors: Ding Yi , Wang Zehua , Chen Chen , Li Dongyu , Wang Wenjia , Jia Yongxu , Qin Yanru 
Published: November 2023

Abstract

Objective
Gastric cancer (GC) is prevalent worldwide but has a dismal prognosis, and its molecular and pathogenic pathways remain unknown. Kallikrein 11 (KLK11) has a reduced expression in GC and may be a promising biomarker.

Method
Herein, the function of KLK11 in GC and its regulatory mechanism was studied. Gene sequencing and quantitative reverse transcription-polymerase chain reaction were used to determine the expression of KLK11 in GC and precancerous lesions. Cell function tests and flow cytometry were conducted to determine the proliferative capacity and cell cycle of GC cells, respectively. A luciferase reporter test confirmed the interaction between RNA molecules. The mTOR/4E-BP1 signaling pathway was analyzed using western blotting.

Result
KLK11 has a suppressed expression in GC samples. KLK11 decreased the proliferative capacity of GC cells, by inhibiting the degree of mTOR/4E-BP1 phosphorylation. In contrast, miR-1304 increased GC cell proliferation by inhibiting KLK11. Moreover, KLK11 was able to limit in vivo GC cell proliferation.

Conclusion
These findings reveal a promising strategy to prevent and treat GC by targeting the KLK11-mediated mTOR/4E-BP1 cascade.
Exploring the effectiveness of node attacks based on combined centrality measures in scale-free networks
Authors: Divya P B , Johnson T P , Balakrishnan Kannan , Azad N 
Published: November 2023

Abstract
This article introduces a novel method for targeting complex networks that involves using a hybrid centrality score to rank nodes and carry out attacks. Unlike previous studies that have focused on using individual centrality measures, this approach takes into consideration the varying significance of nodes across different centrality measures. The study utilizes simulations on scale-free networks to demonstrate that the proposed strategy can be highly effective in inducing network failure, and certain combinations of centrality measures can result in greater attack severity than using individual measures alone. Overall, the research offers valuable insights into improving node-attack strategies for complex networks, which are typically resilient to random failures but susceptible to targeted attacks.
Dose Escalation of Biologics in Biologic-Naïve Patients With Ulcerative Colitis: Outcomes From the ODESSA-UC Study
Authors: Ghosh Sabyasachi , Kathe Niranjan , Umashankar Kandavadivu , Mirchandani Kirti , Hait Arunima , Paul Riyanka , Candela Ninfa , Fan Tao 
Published: November 2023

Abstract

Background
Dose escalation of biologics may regain treatment response in patients with ulcerative colitis (UC). However, dose escalation rates and associated outcomes and costs are not well characterized in biologic-naïve patients receiving antitumor necrosis factor-alpha (anti–TNF-α) treatments, such as infliximab or adalimumab or vedolizumab.

Methods
ODESSA-UC, a retrospective cohort study investigating dose escalation in patients with UC who had received first-line biologics, used data from IBM MarketScan databases. Adults with UC and ≥1 claim for an index drug (adalimumab, infliximab, or vedolizumab) were eligible. A Cox proportional hazards model was used to evaluate the adjusted rate of dose escalation. Logistic regression was used to evaluate the odds of experiencing adverse outcomes (corticosteroid use, infection, sepsis, or inflammatory bowel disease–related hospitalization) and incurring index drug costs.

Results
A year after the start of maintenance, a lower proportion of patients experienced dose escalation with vedolizumab (22.3%) than adalimumab (43.0%). The dose escalation risk was significantly higher for infliximab (hazard ratio [HR], 1.894; 95% confidence interval [CI], 1.486–2.413) and adalimumab (HR, 2.120; 95% CI, 1.680–2.675) than for vedolizumab. The odds of experiencing an adverse outcome after dose escalation were higher for anti–TNF-α treatments than for vedolizumab (odds ratio, 2.052; 95% CI, 1.200–3.507). Index drug costs after dose escalation were lowest for vedolizumab.

Conclusions
Patients with UC receiving vedolizumab had a lower risk of dose escalation and lower subsequent costs than patients receiving anti–TNF-α treatments. Our study demonstrates the possible clinical and economic implications of dose escalation.
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium
Authors: Clarke Jennifer L , Cooper Laurel D , Poelchau Monica F , Berardini Tanya Z , Elser Justin , Farmer Andrew D , Ficklin Stephen , Kumari Sunita , Laporte Marie-Angélique , Nelson Rex T , Sadohara Rie , Selby Peter , Thessen Anne E , Whitehead Brandon , Sen Taner Z 
Published: November 2023

AbstractOver the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as ‘databases’ throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means.Database URL: https://www.agbiodata.org/databases
Comparison of strategies for catheter ablation of left posterior fascicular ventricular tachycardia
Authors: Wei Hui-Qiang , Chen Wanwen , Luo Sini , Liao Zili , Fang Xianhong , Liao Hongtao , Sun Qi , Guo Xiao-Gang , Yang Jian-Du , Liang Jackson J , Wu Shulin , Xue Yumei , Ma Jian , Zhan Xianzhang 
Published: November 2023

Abstract

Aims
Traditional ablation strategies including targeting the earliest Purkinje potential (PP) during left posterior fascicular (LPF) ventricular tachycardia (VT) or linear ablation at the middle segment of LPF during sinus rhythm are commonly used for the treatment of LPF-VT. Catheter ablation for LPF-VT targeting fragmented antegrade Purkinje (FAP) potential during sinus rhythm is a novel approach. We aimed to compare safety and efficacy of different ablation strategies (FAP ablation vs. traditional ablation) for the treatment of LPF-VT.

Methods and results
Consecutive patients with electrocardiographically documented LPF-VT referred for catheter ablation received either FAP ablation approach or traditional ablation approach. Electrophysiological characteristics, procedural complications, and long-term clinical outcome were assessed. A total of 189 consecutive patients who underwent catheter ablation for LPF-VT were included. Fragmented antegrade Purkinje ablation was attempted in 95 patients, and traditional ablation was attempted in 94 patients. Acute ablation success with elimination of LPF-VT was achieved in all patients. Left posterior fascicular block occurred in 11 of 95 (11.6%) patients in the FAP group compared with 75 of 94 (79.8%) patients in the traditional group (P &lt; 0.001). Fragmented antegrade Purkinje ablation was associated with significant shorter procedure time (94 ± 26 vs. 117 ± 23 min, P = 0.03) and fewer radiofrequency energy applications (4.1 ± 2.4 vs. 6.3 ± 3.5, P = 0.003) compared with the traditional group. One complete atrioventricular block and one left bundle branch block were seen in the traditional group. Over mean follow-up of 65 months, 89 (93.7%) patients in the FAP group and 81 (86.2%) patients in the traditional group remained free of recurrent VT off antiarrhythmic drugs (P = 0.157).

Conclusion
Left posterior fascicular-ventricular tachycardia ablation utilizing FAP and traditional ablation approaches resulted in similar acute and long-term procedural outcomes. Serious His-Purkinje injury did occur infrequently during traditional ablation. The use of FAP ablation approach was associated with shorter procedure time and fewer radiofrequency energy applications, especially for non-inducible patients.
Divergence in theSaccharomycesSpecies’ Heat Shock Response Is Indicative of Their Thermal Tolerance
Authors: Fay Justin C , Alonso-del-Real Javier , Miller James H , Querol Amparo 
Published: November 2023

AbstractThe Saccharomyces species have diverged in their thermal growth profile. Both Saccharomyces cerevisiae and Saccharomyces paradoxus grow at temperatures well above the maximum growth temperature of Saccharomyces kudriavzevii and Saccharomyces uvarum but grow more poorly at lower temperatures. In response to thermal shifts, organisms activate a stress response that includes heat shock proteins involved in protein homeostasis and acquisition of thermal tolerance. To determine whether Saccharomyces species have diverged in their response to temperature, we measured changes in gene expression in response to a 12 °C increase or decrease in temperature for four Saccharomyces species and their six pairwise hybrids. To ensure coverage of subtelomeric gene families, we sequenced, assembled, and annotated a complete S. uvarum genome. In response to heat, the cryophilic species showed a stronger stress response than the thermophilic species, and the hybrids showed a mixture of parental responses that depended on the time point. After an initial strong response indicative of high thermal stress, hybrids with a thermophilic parent resolved their heat shock response to become similar to their thermophilic parent. Within the hybrids, only a small number of temperature-responsive genes showed consistent differences between alleles from the thermophilic and cryophilic species. Our results show that divergence in the heat shock response is mainly a consequence of a strain's thermal tolerance, suggesting that cellular factors that signal heat stress or resolve heat-induced changes are relevant to thermal divergence in the Saccharomyces species.
On the detection of upper mantle discontinuities with radon-transformed receiver functions (CRISP-RF)
Authors: Olugboji Tolulope , Zhang Ziqi , Carr Steve , Ekmekci Canberk , Cetin Mujdat 
Published: November 2023

SUMMARYSeismic interrogation of the upper mantle from the base of the crust to the top of the mantle transition zone has revealed discontinuities that are variable in space, depth, lateral extent, amplitude and lack a unified explanation for their origin. Improved constraints on the detectability and properties of mantle discontinuities can be obtained with P-to-S receiver function (Ps-RF) where energy scatters from P to S as seismic waves propagate across discontinuities of interest. However, due to the interference of crustal multiples, uppermost mantle discontinuities are more commonly imaged with lower resolution S-to-P receiver function (Sp-RF). In this study, a new method called CRISP-RF (Clean Receiver-function Imaging using SParse Radon Filters) is proposed, which incorporates ideas from compressive sensing and model-based image reconstruction. The central idea involves applying a sparse Radon transform to effectively decompose the Ps-RF into its underlying wavefield contributions, that is direct conversions, multiples, and noise, based on the phase moveout and coherence. A masking filter is then designed and applied to create a multiple-free and denoised Ps-RF. We demonstrate, using synthetic experiment, that our implementation of the Radon transform using a sparsity-promoting regularization outperforms the conventional least-squares methods and can effectively isolate direct Ps conversions. We further apply the CRISP-RF workflow on real data, including single station data on cratons, common-conversion-point stack at continental margins and seismic data from ocean islands. The application of CRISP-RF to global data sets will advance our understanding of the enigmatic origins of the upper mantle discontinuities like the ubiquitous mid-lithospheric discontinuity and the elusive X-discontinuity.
Ovol2 promoter mutations in mice and human illuminate species-specific phenotypic divergence
Authors: Sunny Sweetu Susan , Lachova Jitka , Kasparek Petr , Palkova Marcela , Spoutil Frantisek , Prochazka Jan , Sedlacek Radislav , Liskova Petra , Kozmik Zbynek 
Published: November 2023

Abstract
Pathogenic variants in the highly conserved OVOL2 promoter region cause posterior polymorphous corneal dystrophy (PPCD) 1 by inducing an ectopic expression of the endothelial OVOL2 mRNA. Here we produced an allelic series of Ovol2 promoter mutations in the mouse model including the heterozygous c.-307T&gt;C variant (RefSeq NM_021220.4) causing PPCD1 in humans. Despite the high evolutionary conservation of the Ovol2 promoter, only some alterations of its sequence had phenotypic consequences in mice. Four independent sequence variants in the distal part of the Ovol2 promoter had no significant effect on endothelial Ovol2 mRNA level or caused any ocular phenotype. In contrast, the mutation c.-307T&gt;C resulted in increased Ovol2 expression in the corneal endothelium. However, only a small fraction of adult mice c.-307T&gt;C heterozygotes developed ocular phenotypes such as irido-corneal adhesions, and corneal opacity. Interestingly, phenotypic penetrance was increased at embryonic stages. Notably, c.-307T&gt;C mutation is located next to the Ovol1/Ovol2 transcription factor binding site. Mice carrying an allele with a deletion encompassing the Ovol2 binding site c.-307_-320del showed significant Ovol2 gene upregulation in the cornea endothelium and exhibited phenotypes similar to the c.-307T&gt;C mutation. In conclusion, although the mutations c.-307T&gt;C and -307_-320del lead to a comparably strong increase in endothelial Ovol2 expression as seen in PPCD1 patients, endothelial dystrophy was not observed in the mouse model, implicating species-specific differences in endothelial cell biology. Nonetheless, the emergence of dominant ocular phenotypes associated with Ovol2 promoter variants in mice implies a potential role of this gene in eye development and disease.