bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life
Authors: Figueroa III Jose L , Dhungel Eliza , Bellanger Madeline , Brouwer Cory R , White III Richard Allen 
Published: March 2024

Motivation
MetaCerberus is a massively parallel, fast, low memory, scalable annotation tool for inference gene function across genomes to metacommunities. MetaCerberus provides an elusive HMM/HMMER-based tool at a rapid scale with low memory. It offers scalable gene elucidation to major public databases, including KEGG (KO), COGs, CAZy, FOAM, and specific databases for viruses, including VOGs and PHROGs, from single genomes to metacommunities.

Results
MetaCerberus is 1.3× as fast on a single node than eggNOG-mapper v2 on 5× less memory using an exclusively HMM/HMMER mode. In a direct comparison, MetaCerberus provides better annotation of viruses, phages, and archaeal viruses than DRAM, Prokka, or InterProScan. MetaCerberus annotates more KOs across domains when compared to DRAM, with a 186× smaller database, and with 63× less memory. MetaCerberus is fully integrated for automatic analysis of statistics and pathways using differential statistic tools (i.e. DESeq2 and edgeR), pathway enrichment (GAGE R), and pathview R. MetaCerberus provides a novel tool for unlocking the biosphere across the tree of life at scale.

Availability and implementation
MetaCerberus is written in Python and distributed under a BSD-3 license. The source code of MetaCerberus is freely available at https://github.com/raw-lab/metacerberus compatible with Python 3 and works on both Mac OS X and Linux. MetaCerberus can also be easily installed using bioconda: mamba create -n metacerberus -c bioconda -c conda-forge metacerberus.
Ribotin: automated assembly and phasing of rDNA morphs
Authors: Rautiainen Mikko 
Published: March 2024

Abstract

Motivation
The ribosomal DNA (rDNA) arrays are highly repetitive and homogenous regions which exist in all life. Due to their repetitiveness, current assembly methods do not fully assemble the rDNA arrays in humans and many other eukaryotes, and so variation within the rDNA arrays cannot be effectively studied.

Results
Here, we present the tool ribotin to assemble full length rDNA copies, or morphs. Ribotin uses a combination of highly accurate long reads and extremely long nanopore reads to resolve the variation between rDNA morphs. We show that ribotin successfully recovers the most abundant morphs in human and nonhuman genomes. We also find that genome wide consensus sequences of the rDNA arrays frequently produce a mosaic sequence that does not exist in the genome.

Availability and implementation
Ribotin is available on https://github.com/maickrau/ribotin and as a package on bioconda.
A simple, clinically usable whole-body MRI system of joint assessment in adolescents and young people with juvenile idiopathic arthritis
Authors: Choida Varvara , Bray Timothy J P , van Vucht Niels , Abbasi Maaz Ali , Bainbridge Alan P , Parry Thomas , Mallett Sue , Ciurtin Coziana , Hall-Craggs Margaret A 
Published: March 2024

Abstract

Objectives
To introduce and evaluate a simple method for assessing joint inflammation and structural damage on whole-body MRI (WBMRI) in juvenile idiopathic arthritis (JIA), which is usable in clinical practice.

Methods
The proposed system utilizes post-contrast Dixon WBMRI scans. Joints are assessed for synovitis (grade 0–2) and structural damage (present/absent) at 81 sites. The synovitis grading is based on features including above-normal intensity synovial enhancement, synovial hypertrophy, joint effusion, subarticular bone marrow oedema and peri-articular soft tissue oedema.
This system was evaluated in a prospective study of 60 young people (47 patients with JIA and 13 controls with non-inflammatory musculoskeletal pain) who underwent a WBMRI. Three readers (blinded to diagnosis) independently reviewed all images and re-reviewed 20 individual scans. The intra- and inter-reader overall agreement (OA) and the intra- and inter-reader Gwet’s agreement coefficients 2 (GAC2) were measured for the detection of a) participants with ≥1 joint with inflammation or structural damage and b) joint inflammation or structural damage for each joint.

Results
The inter-reader OA for detecting patients with ≥1 joint with inflammation, defined as grade 2 synovitis (G2), and ≥1 joint with structural damage were 80% and 73%, respectively. The intra-reader OA for readers 1–3 was 80–90% and 75–90%, respectively. The inter-reader OA and GAC2 for joint inflammation (G2) at each joint were both ≥85% for all joints but were lower if grade 1 synovitis was included as positive.

Conclusion
The intra- and inter-reader agreements of this WBMRI assessment system are adequate for assessing objective joint inflammation and damage in JIA.
Decision for Carpal Tunnel Surgery: High-deductible Health Plans versus Traditional Health Plans
Authors: Sanders Hayley M. , Tong Yanlin , Hooper Rachel C. , Wang Lu , Chung Kevin C. 
Published: March 2024

Background:
Delay in surgical treatment for carpal tunnel syndrome (CTS) may result in long-term decreased functional outcomes. Few investigators have examined the relationship between type of health insurance plan and time to definitive treatment of CTS following diagnosis. We investigated the relationship between insurance type, treatment decision, and the time between diagnosis and surgery across groups.

Methods:
This was a retrospective cohort study using the MarketScan Commercial Claims and Encounters Database 2011–2020. We used χ2 tests, linear regression, and logistic regression models to analyze demographic data and the time lag interval between CTS diagnosis and treatment.

Results:
Overall, 28% of high-deductible health plan (HDHP) patients underwent carpal tunnel release, compared with 20% of traditional insurance patients (P < 0.001). HDHPs are defined by the internal revenue service as a deductible of $1400 for an individual or $2800 for a family per year. The odds of undergoing surgery versus no treatment for HDHP patients were 47% higher than traditional patients (P < 0.001). Among the patients who underwent surgery, HDHP patients underwent surgery 65 days earlier on average following diagnosis compared with traditional patients (P < 0.001).

Conclusions:
Patients with HDHPs who receive a diagnosis of CTS are more likely to undergo surgery, with a shorter time lag between diagnosis and surgery. The results from this study call attention to differences in surgical decision-making between patients enrolled in different insurance plans.
Designing a minimum dataset for autism spectrum disorder registry in Iran
Authors: Shayestehfar Monir , Jahandideh Pardis , Hariri Rabeeh , Shayestehfar Malihe , Memari Amirhossein 
Published: March 2024

Introduction:
The reported prevalence of autism spectrum disorders (ASDs) has been showing a marked increase over the past 20 years. Therefore, a uniform data gathering system for ASD registration could prominently enhance plans for managing ASD worldwide. So, in the current investigation the authors aimed to design and validate the Persian version of a minimum dataset (MDS) for being administered in the national ASD registries.

Methods:
The current study is a mixed-method study with both quantitative and qualitative methods providing and validating a form of MDS in four phases according to Delphi method. The proposed MDS consisted of 11 categories containing coding responses. Content validity (CV) was evaluated based on 20 expert’s suggestions and opinions. Item-CV Index (I-CVI) and Scale-CVI were administered to evaluate and validate the items and questions in the proposed MDS.

Results:
Twenty researchers from different disciplines scored each question and item. By taking into account the scores, the validity appraisal was provided for each item by computing the I-CVI value. Results showed that 41 out of 76 items had the value I-CVI less than 0.78 and were kept as relevant; 35 items were eliminated due to a value below 0.70. The Scale-CVI /Ave of the relevance for the entire form was 0.9396.

Conclusion:
The Persian version of MDS for ASD registry was found to be valid. Such MDS can be utilitarian for health cares and policymaking purposes by gathering and updating standard data for developing local and national registries.
Analysis of 358 histopathological reports of oral and maxillofacial lesions in elderly patients from Tanzania: a cross-sectional study
Authors: Sohal Karpal S. , Kalyanyama Boniphace M. , Agbor Ashu M. 
Published: March 2024

Background and Objective:
In Tanzania, roughly 6% of the total population is elderly, which is the age group that is vulnerable to several diseases in the orofacial region. This study aimed to determine the incidence of oral and maxillofacial lesions in elderly Tanzanian patients.

Material and Methods:
This was a cross-sectional study of histopathological results of patients with oral and maxillofacial lesions attended at Muhimbili National Hospital. All patients aged 60 years and above diagnosed with oral and maxillofacial lesions between 2016 and 2021 were included in the study. The information gathered included the age and sex of the patients, histopathological diagnosis, and anatomical location of the lesion. The Statistical Package for the Social Sciences, version 26 computer program was used for data analysis.

Results:
A total of 348 histopathological reports of 348 elderly patients with oral and maxillofacial lesions were obtained. There was an equal distribution by sex. Majority (78.2%) of the lesions were malignant, followed by benign ones (12.6%). The frequently affected site was the tongue (18.1%) and the mandible (15.4%). Squamous cell carcinoma was the most (60.3%) frequently encountered lesion. Others included adenoid cystic carcinoma (5.5%) and ameloblastoma (3.7%).

Conclusions:
The burden of oral and maxillofacial lesions among the elderly Tanzanian population was substantial. There was no sex predilection. A majority of the lesions were malignant, and the tongue was the frequently involved site.
Global supply chains security: a comparative analysis of emerging threats and traceability solutions
Authors: Gokkaya Betul , Karafili Erisa , Aniello Leonardo , Halak Basel 
Published: March 2024

PurposeThe purpose of this study is to increase awareness of current supply chain (SC) security-related issues by providing an extensive analysis of existing SC security solutions and their limitations. The security of SCs has received increasing attention from researchers, due to the emerging risks associated with their distributed nature. The increase in risk in SCs comes from threats that are inherently similar regardless of the type of SC, thus, requiring similar defence mechanisms. Being able to identify the types of threats will help developers to build effective defences.Design/methodology/approachIn this work, we provide an analysis of the threats, possible attacks and traceability solutions for SCs, and highlight outstanding problems. Through a comprehensive literature review (2015–2021), we analysed various SC security solutions, focussing on tracking solutions. In particular, we focus on three types of SCs: digital, food and pharmaceutical that are considered prime targets for cyberattacks. We introduce a systematic categorization of threats and discuss emerging solutions for prevention and mitigation.FindingsOur study shows that the current traceability solutions for SC systems do not offer a broadened security analysis and fail to provide extensive protection against cyberattacks. Furthermore, global SCs face common challenges, as there are still unresolved issues, especially those related to the increasing SC complexity and interconnectivity, where cyberattacks are spread across suppliers.Originality/valueThis is the first time that a systematic categorization of general threats for SC is made based on an existing threat model for hardware SC.
Market approach to provision of housing to low-income households in urban Malawi: a panacea or further dispossession?
Authors: Zuka Sane 
Published: March 2024

Purpose
The purpose of this study is to examine the effects of market-based approach to provision of housing to low-income households in urban Malawi.

Design/methodology/approach
This study was conducted in Blantyre, Malawi, between 2019 and 2022 and used both quantitative (household survey) and qualitative (in-depth interviews and document study) methods of data collection. Interviews were conducted with key players and investors in the housing sector. Household survey data were analyzed through descriptive statistics, which allowed the generation of descriptive housing valuables, whereas qualitative data were analyzed through content analysis.

Findings
This paper demonstrates that, rather than ameliorating the housing problems facing low-income households, the market approach to provision of housing in Malawi has worsened the housing situation in the country. This is so because the market approach to the provision of housing in Malawi is not only enforcing the logic of capitalistic accumulation in the housing sector but also supporting mechanisms of exclusion based on economic stratification within the community.

Research limitations/implications
Completeness of data over time as there is no market data bank available in the country.

Practical implications
The findings from this study suggest that some degree of state intervention in addressing the housing problem in Malawi is required.

Social implications
The study findings suggest that a market approach to the provision of housing can increase social inequality as low-income households face challenges in accessing housing.

Originality/value
There is a paucity of research on the effects of the market approach on the provision of affordable housing to low-income households in Malawi. This paper assesses this important policy gap and provides significant policy directions.
Managing quality assurance at community colleges in Ontario, Canada: experiences and perspectives of front-line quality managers
Authors: Jarrell Laura , Kirby Dale 
Published: March 2024

Purpose
This paper aims to examine the roles of quality managers at community colleges, their experiences balancing accountability and improvement and their insights into the future of quality assurance.

Design/methodology/approach
This phenomenological, qualitative study used semi-structured interviews with eight community college quality managers to investigate their roles, experiences and perspectives. A reflexive thematic approach was used to analyze the interview data.

Findings
Four themes were identified from participant responses: quality managers frame and enable program quality, quality managers drive program change, quality managers cultivate a culture of quality and quality managers seek system change. The findings illustrate the roles played by quality managers as they work to improve college education at program, institution and system-wide levels.

Research limitations/implications
The decision of participants to accept the recruitment invitation might reflect particular attitudes, perspectives or experiences.

Practical implications
Quality assurance has emerged as a key mechanism for ensuring postsecondary programs are current, relevant and meeting the evolving needs of students and employers. This study advances the understanding of how quality assurance processes play out at the operational level and explores the experiences of quality managers as they navigate various quality tensions.

Originality/value
Quality managers play key roles in leading, evaluating and influencing quality assurance processes in postsecondary education yet they are underrepresented in the literature. The findings of this study shed new light on the aspirational and influential roles they play in advancing quality assurance.
Deciding where to put them: Sensitivity tests and independent evaluation are critical when using species distribution models to inform conservation translocations
Authors: Finn Kaegan J. , Bergman Jayna C. , Lee‐Yaw Julie A. 
Published: March 2024

Abstract

Conservation translocations are an important tool for combating species declines and population losses. Species distribution models (SDMs) can facilitate the selection of suitable release sites for translocation programs. However, these models can be sensitive to several modelling decisions.

In this study, we explore the impacts of three key modelling decisions on Maxent models developed to inform reintroductions of the long‐toed salamander (Ambystoma macrodactylum) in southwestern Alberta. We specifically test the sensitivity of model predictions to (1) the type of environmental variables used to generate models, (2) whether the background points used to calibrate the models reflects the potential bias in the input locality records and (3) the choice of geographic study extent. We use independent presence‐absence data from an extensive field survey to test the accuracy of models based on different decisions.

Both model predictions and performance were sensitive to these modelling decisions. Models developed using local study extents were more accurate than those based on range‐wide extents. Both study extent and type of background points impacted model predictions and performance more than the set of environmental variables included in the models for this species.

We further demonstrate the impacts of these decisions on the ranking of potential release sites and present a final set of recommendations that accounts for this uncertainty under both current and future climatic conditions. We specifically identify three sites that are expected to be suitable in both present and future time periods as potential release sites for salamander reintroductions in southwestern Alberta.

Synthesis and applications: Our study adds to our understanding of how different modelling decisions impact SDMs and the downstream conclusions from these models while simultaneously demonstrating a rigorous approach for the use of SDMs in conservation translocation planning.
Featured Cover
Authors: Li Xiaokai , Zeng Sha , Chen Li , Zhang Yu , Li Xuemin , Zhang Biwei , Su Duo , Du Qinjiao , Zhang Jiaman , Wang Haoming , Zhong Zhining , Zhang Jinwei , Li Penghao , Jiang Anan , Long Keren , Li Mingzhou , Ge Liangpeng 
Published: March 2024

The cover image is based on the Original Article An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long‐range loop formation by Xiaokai Li et al., https://doi.org/10.1111/cpr.13552.
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DHEA: a neglected biological signal that may affect fetal and child development
Authors: Bailey Natasha A. , Davis Elysia Poggi , Sandman Curt A. , Glynn Laura M. 
Published: March 2024

BackgroundThe stress‐sensitive maternal hypothalamic–pituitary–adrenal (HPA) axis through the end‐product cortisol, represents a primary pathway through which maternal experience shapes fetal development with long‐term consequences for child neurodevelopment. However, there is another HPA axis end‐product that has been widely ignored in the study of human pregnancy. The synthesis and release of dehydroepiandosterone (DHEA) is similar to cortisol, so it is a plausible, but neglected, biological signal that may influence fetal neurodevelopment. DHEA also may interact with cortisol to determine developmental outcomes. Surprisingly, there is virtually nothing known about human fetal exposure to prenatal maternal DHEA and offspring neurodevelopment. The current study examined, for the first time, the joint impact of fetal exposure to prenatal maternal DHEA and cortisol on infant emotional reactivity.MethodsParticipants were 124 mother–infant dyads. DHEA and cortisol were measured from maternal hair at 15 weeks (early gestation) and 35 weeks (late gestation). Observational assessments of positive and negative emotional reactivity were obtained in the laboratory when the infants were 6 months old. Pearson correlations were used to examine the associations between prenatal maternal cortisol, prenatal maternal DHEA, and infant positive and negative emotional reactivity. Moderation analyses were conducted to investigate whether DHEA might modify the association between cortisol and emotional reactivity.ResultsHigher levels of both early and late gestation maternal DHEA were linked to greater infant positive emotional reactivity. Elevated late gestation maternal cortisol was associated with greater negative emotional reactivity. Finally, the association between fetal cortisol exposure and infant emotional reactivity was only observed when DHEA was low.ConclusionsThese new observations indicate that DHEA is a potential maternal biological signal involved in prenatal programming. It appears to act both independently and jointly with cortisol to determine a child's emotional reactivity. Its role as a primary end‐product of the HPA axis, coupled with the newly documented associations with prenatal development shown here, strongly calls for the inclusion of DHEA in future investigations of fetal programming.
Social Learning and Monetary Policy at the Effective Lower Bound
Authors: ARIFOVIC JASMINA , GRIMAUD ALEX , SALLE ISABELLE , VERMANDEL GAUTHIER 
Published: March 2024

AbstractThis paper develops a model that jointly accounts for the missing disinflation in the wake of the Great Recession and the subsequently observed inflation‐less recovery. The key mechanism works through heterogeneous expectations that may durably lose their anchoring to the central bank (CB)'s target and coordinate on particularly persistent below‐target paths. The welfare cost associated with persistent low inflation may be reduced if the CB announces to the agents its target or its own inflation forecasts, as communication helps coordinate expectations. However, the CB may lose its credibility whenever its announcements become decoupled from actual inflation.
Artificial replication cohort: Leveraging AI‐fabricated data for genetic studies
Authors: Smyk Wiktor , Adrych Krystian , Krawczyk Marcin 
Published: March 2024

AbstractRecent advancements in artificial intelligence (AI) present both opportunities and challenges within the scientific community. This study explores the capability of AI to replicate findings from genetic research, focusing on findings from prior work. Using an AI model without exposing any raw data, we created a dataset that closely mirrors the results of our original study, illustrating the ease of fabricating datasets with authenticity. This approach highlights the risks associated with AI misuse in scientific research. The study emphasizes the critical importance of maintaining the integrity of scientific inquiry in an era increasingly influenced by advanced AI technologies.