bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustainable living: Alternative green structure module design for home self-food production
Authors: Mahmud Nasrul-Arif , Sabil Azmal , Hisham Nadiyah Noor , Siraj Suhailah , Adnan Nor Azizah , Md Amin Noor Dina 
Published: July 2023

Abstract
Due to the increased food price volatility during the 2007-2008 food price crisis and its aftereffects, food self-sufficiency has been one of the policy priorities in various nations, including Senegal, India, the Philippines, Qatar, Bolivia, and Russia. In addition, the United Nations predicts that the global population will reach 9.7 billion by 2050, and that half of the land that may be utilised for crops and agriculture worldwide would be unusable for farming owing to climate change, soil degradation, and poverty. The world’s population is growing rapidly, and so is the demand for food. This highlights the importance of food self-sufficiency and the need to investigate and develop a comprehensive plan. This study explores food self-sufficiency and the concept of creating a modular and flexible self-produced food system that might potentially generate safe food from organic plants using environmentally aware farming practises and free of pesticide residues without the usage of arable land. The analysis phase comprises categorising the challenges, while the synthesis stage is when the efforts culminate in the creation of a remedy. Hence, more individuals may start growing their own food, with hydroponics being a popular choice.
Indoor level of BTEX and health risk assessment at science laboratories in a university
Authors: Hamid H H A , Nadzir M S M , Lee K E , Ayatillah A , Latif M T , Othman M 
Published: July 2023

Abstract
The levels of volatile organic compounds (VOCs) such as Benzene, Toluene, Ethylbenzene, and Xylene isomers (BTEX) are important parameters for an indoor air quality assessment. Exposure to BTEX in science laboratories in a university can potentially cause health risks to workers. Active sampling was carried out using Tenax® GR sorbent tubes and analyzed with thermal desorption gas chromatography-mass spectrometry (TD-GCMS) to measure the BTEX levels at selected indoor areas. The average concentration of individual BTEX at the laboratories complex were as follows: Benzene (1.76 ± 0.44 μg/m3), Toluene (8.15 ± 2.99 μg/m3), Ethylbenzene (3.75 ± 0.69 μg/m3), m, p-Xylene (6.07 ± 1.19 μg/m3) and o-Xylene (4.84 ± 0.43 μg/m3). The distribution of the BTEX components varied depending on the floor level, laboratory activities, laboratory size, and interior furniture. Non-cancer risk estimates based on hazard quotient value for BTEX were < 1, indicating unlikely non-cancer risk. Lifetime cancer risk estimates for Benzene were in the range of 1.16 × 10-6 – 2.54 × 10-6 indicating possible cancer risk at the sampled indoor locations. Therefore, science laboratories can potentially pose a health risk to workers from long-term exposure to BTEX.
Low energy ion-solid interactions: a quantitative experimental verification of binary collision approximation simulations
Authors: Hofsäss Hans , Junge Felix , Kirscht Patrick , van Stiphout Koen 
Published: July 2023

Abstract
Ultra-low energy ion implantation has become an attractive method for doping of two-dimensional materials and ultra-thin films. The new dynamic Monte Carlo program IMINTDYN based on the binary collision approximation allows a reliable prediction of low energy implantation profiles and target compositional changes, as well as efficient simulation of high energy light ion scattering. To demonstrate the quality of these predictions and simulations, we present a model case experiment where we implanted W ions into tetrahedral amorphous carbon with low (10 keV) and ultra-low (20 eV) ion energies and analyzed the W implantation profiles with high resolution Rutherford backscattering spectrometry (HR-RBS). This experiment is compared with a complete simulation of all aspects of ion-solid-interactions of the experiment using the new IMINTDYN program. A unique novel simulation option, also relevant for implantation into 2D materials, is the inclusion of the vacancy as target species with dynamic vacancy generation and annihilation. Whereas simulations neglecting vacancy formation cannot reproduce the measured implantation profiles, we find excellent agreement between simulated and measured HR-RBS spectra. We also demonstrate the important role of simultaneous weak collisions in the binary collision approximation at low projectile energies.
Comprehensive evaluation of deep and graph learning on drug–drug interactions prediction
Authors: Lin Xuan , Dai Lichang , Zhou Yafang , Yu Zu-Guo , Zhang Wen , Shi Jian-Yu , Cao Dong-Sheng , Zeng Li , Chen Haowen , Song Bosheng , Yu Philip S , Zeng Xiangxiang 
Published: July 2023

Abstract
Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug–drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, natural language processing based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction.
Characterizing proteomic and transcriptomic features of missense variants in amyotrophic lateral sclerosis genes
Authors: Dilliott Allison A , Kwon Seulki , Rouleau Guy A , Iqbal Sumaiya , Farhan Sali M K 
Published: July 2023

Abstract
Within recent years, there has been a growing number of genes associated with amyotrophic lateral sclerosis (ALS), resulting in an increasing number of novel variants, particularly missense variants, many of which are of unknown clinical significance. Here, we leverage the sequencing efforts of the ALS Knowledge Portal (3864 individuals with ALS and 7839 controls) and Project MinE ALS Sequencing Consortium (4366 individuals with ALS and 1832 controls) to perform proteomic and transcriptomic characterization of missense variants in 24 ALS-associated genes.
The two sequencing datasets were interrogated for missense variants in the 24 genes, and variants were annotated with gnomAD minor allele frequencies, ClinVar pathogenicity classifications, protein sequence features including Uniprot functional site annotations, and PhosphoSitePlus post-translational modification site annotations, structural features from AlphaFold predicted monomeric 3D structures, and transcriptomic expression levels from Genotype-Tissue Expression. We then applied missense variant enrichment and gene-burden testing following binning of variation based on the selected proteomic and transcriptomic features to identify those most relevant to pathogenicity in ALS-associated genes.
Using predicted human protein structures from AlphaFold, we determined that missense variants carried by individuals with ALS were significantly enriched in β-sheets and α-helices, as well as in core, buried or moderately buried regions. At the same time, we identified that hydrophobic amino acid residues, compositionally biased protein regions and regions of interest are predominantly enriched in missense variants carried by individuals with ALS. Assessment of expression level based on transcriptomics also revealed enrichment of variants of high and medium expression across all tissues and within the brain. We further explored enriched features of interest using burden analyses and identified individual genes were indeed driving certain enrichment signals. A case study is presented for SOD1 to demonstrate proof-of-concept of how enriched features may aid in defining variant pathogenicity.
Our results present proteomic and transcriptomic features that are important indicators of missense variant pathogenicity in ALS and are distinct from features associated with neurodevelopmental disorders.
Skin thermal recovery following cryotherapy: a comparison of liquid nitrogen and liquid nitrous oxide
Authors: Erdmann Sophie A B , Wokes James 
Published: July 2023

Abstract
Cryotherapy is a common technique used in the management of superficial skin lesions, with current advice on the correct timing for freeze–thaw cycles based on nonscientific visual skin appearances. We investigated the effect of cryotherapy on thermal thawing times by creating a porcine skin model in a laboratory setting maintained at normal skin temperature and comparing liquid nitrogen and liquid nitrous oxide. Thermal assessment was performed using a thermal camera attached to an iPhone 11Pro® smartphone. Liquid nitrogen reduced skin temperature to –60 °C after 5 s of application, recovering to 0 °C after 70 s. Liquid nitrous oxide reduced skin temperature to –34.8 °C after 5 s but had a faster recovery to 0 °C after only 20 s. Both cryogens required a thawing period of 5 min to recover to normal skin temperature. We therefore suggest that optimum cellular degradation should allow for 5-min freeze–thaw cryotherapy cycles; a slower thawing period than is in current common practice.
A global pause generates nonselective response inhibition during selective stopping
Authors: Wadsley Corey G , Cirillo John , Nieuwenhuys Arne , Byblow Winston D 
Published: July 2023

Abstract
Selective response inhibition may be required when stopping a part of a multicomponent action. A persistent response delay (stopping-interference effect) indicates nonselective response inhibition during selective stopping. This study aimed to elucidate whether nonselective response inhibition is the consequence of a global pause process during attentional capture or specific to a nonselective cancel process during selective stopping. Twenty healthy human participants performed a bimanual anticipatory response inhibition paradigm with selective stop and ignore signals. Frontocentral and sensorimotor beta-bursts were recorded with electroencephalography. Corticomotor excitability and short-interval intracortical inhibition in primary motor cortex were recorded with transcranial magnetic stimulation. Behaviorally, responses in the non-signaled hand were delayed during selective ignore and stop trials. The response delay was largest during selective stop trials and indicated that stopping-interference could not be attributed entirely to attentional capture. A stimulus-nonselective increase in frontocentral beta-bursts occurred during stop and ignore trials. Sensorimotor response inhibition was reflected in maintenance of beta-bursts and short-interval intracortical inhibition relative to disinhibition observed during go trials. Response inhibition signatures were not associated with the magnitude of stopping-interference. Therefore, nonselective response inhibition during selective stopping results primarily from a nonselective pause process but does not entirely account for the stopping-interference effect.
Digital PCR Partition Classification
Authors: Vynck Matthijs , Chen Yao , Gleerup David , Vandesompele Jo , Trypsteen Wim , Lievens Antoon , Thas Olivier , De Spiegelaere Ward 
Published: July 2023

Abstract

Background
Partition classification is a critical step in the digital PCR data analysis pipeline. A range of partition classification methods have been developed, many motivated by specific experimental setups. An overview of these partition classification methods is lacking and their comparative properties are often unclear, likely impacting the proper application of these methods.

Content
This review provides a summary of all available digital PCR partition classification approaches and the challenges they aim to overcome, serving as a guide for the digital PCR practitioner wishing to apply them. We additionally discuss strengths and weaknesses of these methods, which can further guide practitioners in vigilant application of these existing methods. This review provides method developers with ideas for improving methods or designing new ones. The latter is further stimulated by our identification and discussion of application gaps in the literature, for which there are currently no or few methods available.

Summary
This review provides an overview of digital PCR partition classification methods, their properties, and potential applications. Ideas for further advances are presented and may bolster method development.
PageRank centrality with non-local random walk-based teleportation
Authors: Bowater David , Stefanakis Emmanuel 
Published: July 2023

Abstract
PageRank is a popular measure of centrality that is often applied to rank nodes in real-world networks. However, in many cases, the notion of teleportation is counterintuitive because it implies that whatever is moving around the network will jump or ‘teleport’ directly from one node to any other, without considering how far apart the nodes are. To overcome this issue, we propose here a general measure of PageRank centrality whereby the teleportation probabilities depend, in some way, on the distance separating the nodes. We accomplish this by drawing upon recent advances in non-local random walks, which allow the proposed measure to be tailored for various real-world networks and applications. To illustrate the flexibility of the proposed measure and to demonstrate how it differs from PageRank centrality, we present and discuss experimental results for a selection of real-world spatial and social networks, including an air transportation network, a collaboration network and an urban street network.
Major Adverse Cardiovascular Events by Baseline Cardiovascular Risk in Patients with Ulcerative Colitis Treated with Tofacitinib: Data from the OCTAVE Clinical Programme
Authors: Schreiber Stefan , Rubin David T , Ng Siew C , Peyrin-Biroulet Laurent , Danese Silvio , Modesto Irene , Guo Xiang , Su Chinyu , Kwok Kenneth K , Jo Hyejin , Chen Yan , Yndestad Arne , Reinisch Walter , Dubinsky Marla C 
Published: July 2023

Abstract

Background and Aims
Patients with inflammatory bowel disease have increased risk of atherosclerotic cardiovascular [CV] disease [ASCVD]. Tofacitinib is an oral ﻿Janus kinase inhibitor for the treatment of ulcerative colitis [UC]. We report major adverse CV events [MACE] in the UC OCTAVE programme, stratified by baseline CV risk.

Methods
Rates of MACE were analysed by baseline [first tofacitinib exposure] CV risk profile: prior ASCVD, or 10-year ASCVD risk categories [low, borderline, intermediate, high].

Results
Of 1157 patients [2814.4 patient-years of exposure; ≤7.8 years’ tofacitinib treatment], 4% had prior ASCVD and 83% had no prior ASCVD and low–borderline baseline 10-year ASCVD risk. Eight [0.7%] patients developed MACE; one had prior ASCVD. Incidence rates [unique patients with events/100 patient-years of exposure; 95% confidence intervals] for MACE were: 0.95 [0.02–5.27] in patients with prior ASCVD; and 1.81 [0.05–10.07], 1.54 [0.42–3.95], 0.00 [0.00–2.85], and 0.09 [0.01–0.32] in patients without prior ASCVD and with high, intermediate, ­borderline, and low baseline 10-year ASCVD risk, respectively. For the 5/7 patients with MACE and without prior ASCVD, 10-year ASCVD risk scores were numerically higher [&gt;1%] prior to MACE versus at baseline, primarily due to increasing age.

Conclusions
Most patients receiving tofacitinib in the UC OCTAVE programme had low baseline 10-year ASCVD risk. MACE were more frequent in patients with prior ASCVD and higher baseline CV risk. This analysis demonstrates potential associations between baseline CV risk and MACE in patients with UC, suggesting CV risk should be assessed individually in clinical practice.

ClinicalTrials.gov
NCT00787202; NCT01465763; NCT01458951; NCT01458574; NCT01470612.
Mediation analysis of the testosterone treatment effect to prevent type 2 diabetes in the Testosterone for Prevention of Type 2 Diabetes Mellitus trial
Authors: Robledo Kristy P , Marschner Ian C , Handelsman David J , Bracken Karen , Stuckey Bronwyn G A , Yeap Bu B , Inder Warrick , Grossmann Mathis , Jesudason David , Allan Carolyn A , Wittert Gary 
Published: July 2023

Abstract

Objective
To determine if testosterone treatment effect on glycaemia is mediated through changes in total fat mass, abdominal fat mass, skeletal muscle mass, non-dominant hand-grip, oestradiol (E2), and sex hormone-binding globulin (SHBG).

Design
Mediation analysis of a randomised placebo-controlled trial of testosterone.

Methods
Six Australian tertiary care centres recruited 1007 males, aged 50-74 years, with waist circumference ≥95 cm, serum total testosterone ≤14 nmol/L (immunoassay), and either impaired glucose tolerance or newly diagnosed type 2 diabetes on an oral glucose tolerance test (OGTT). Participants were enrolled in a lifestyle programme and randomised 1:1 to 3 monthly injections of 1000 mg testosterone undecanoate or placebo for 2 years. Complete data were available for 709 participants (70%). Mediation analyses for the primary outcomes of type 2 diabetes at 2 years (OGTT ≥ 11.1 mmol/L and change in 2-h glucose from baseline), incorporating potential mediators: changes in fat mass, % abdominal fat, skeletal muscle mass, non-dominant hand-grip strength, E2, and SHBG, were performed.

Results
For type 2 diabetes at 2 years, the unadjusted OR for treatment was 0.53 (95% CI:.35-.79), which became 0.48 (95% CI:.30-.76) after adjustment for covariates. Including potential mediators attenuated the treatment effect (OR 0.77; 95% CI:.44-1.35; direct effect) with 65% mediated. Only fat mass remained prognostic in the full model (OR: 1.23; 95% CI: 1.09-1.39; P &lt; .001).

Conclusion
At least part of the testosterone treatment effect was found to be mediated by changes in fat mass, abdominal fat, skeletal muscle mass, grip strength, SHBG, and E2, but predominantly by changes in fat mass.
Digest: Trilobites to vertebrates: how development influences the evolution of segmental patterning
Authors: Verma Neeharika 
Published: July 2023

Abstract
How has the evolution of segment size patterning been developmentally regulated and what does the trilobite fossil record tell us about these ancestral control mechanisms? Nikolic et al. relate the evolutionary and developmental mechanisms of segmentation in extinct trilobites to those seen in extant arthropods and vertebrates to examine how ontogenic renovations are echoed in the phylogeny of segmental patterning.
Diversity and succession of chemolithoautotrophic microbial community along a recently deglaciation chronosequence on the Tibetan Plateau
Authors: Khan Ajmal , Kong Weidong , Khan Sardar , Nawab Javed , Khan Muhammad Israr 
Published: July 2023

Abstract
Glaciers in high-altitude mountain regions are retreating rapidly due to global warming, exposing deglaciated soils to extreme environmental conditions, and microbial colonization. However, knowledge about chemolithoautotrophic microbes, which play important roles in the development of oligotrophic deglaciated soils prior to plant colonization, remains elusive in deglaciated soils. Using real-time quantitative PCR and clone library methods, the diversity and succession of the chemolithoautotrophic microbial community harboring the cbbM gene across a 14-year deglaciation chronosequence on the Tibetan Plateau were determined. The abundance of the cbbM gene remained stable for the first 8 years after deglaciation and then increased significantly, ranging from 105 to 107 gene copies g−1 soil (P &lt; 0.001). Soil total carbon increased gradually to 5-year deglaciation and then decreased. While total nitrogen and total sulfur levels were low throughout the chronosequence. Chemolithoautotrophs were related to Gammaproteobacteria and Betaproteobacteria, with the former dominating early deglaciated soils and the latter dominating older deglaciated soils. The diversity of chemolithoautotrophs was high in mid-age deglaciated soils (6-year-old) and was low in early (3-year-old) and older deglaciated soils (12-year-old). Our findings revealed that chemolithoautotrophic microbes colonize deglaciated soils quickly and follow a clear successional pattern across recently deglaciated chronosequences.
Data management strategy for a collaborative research center
Authors: Mittal Deepti , Mease Rebecca , Kuner Thomas , Flor Herta , Kuner Rohini , Andoh Jamila 
Published: July 2023

Abstract
The importance of effective research data management (RDM) strategies to support the generation of Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience data grows with each advance in data acquisition techniques and research methods. To maximize the impact of diverse research strategies, multidisciplinary, large-scale neuroscience research consortia face a number of unsolved challenges in RDM. While open science principles are largely accepted, it is practically difficult for researchers to prioritize RDM over other pressing demands. The implementation of a coherent, executable RDM plan for consortia spanning animal, human, and clinical studies is becoming increasingly challenging. Here, we present an RDM strategy implemented for the Heidelberg Collaborative Research Consortium. Our consortium combines basic and clinical research in diverse populations (animals and humans) and produces highly heterogeneous and multimodal research data (e.g., neurophysiology, neuroimaging, genetics, behavior). We present a concrete strategy for initiating early-stage RDM and FAIR data generation for large-scale collaborative research consortia, with a focus on sustainable solutions that incentivize incremental RDM while respecting research-specific requirements.
Vietnam's prudent pivot to the rules-based international order
Authors: Do Thuy T 
Published: July 2023

Abstract
Vietnam's conceptualization of the international and regional orders has changed remarkably over the past decades. Previously an outsider if not a challenger of the western-crafted liberal order, Vietnam has in recent years increasingly leaned toward a rules-based international order. This article argues that the reason for Vietnam's changing perceptions about the liberal international order is largely threefold: domestic reform and modernization; deepened integration into the international political economy; as well as growing strategic concerns over great power coercion stemming from China's rise. Vietnam's pivot to the rules-based international order, however, is cautious given Hanoi's lingering worry over western intentions to undermine Vietnam's socialist orientation, the path dependence of Vietnam's relationships with its traditional partners as well as the occasional clashes between the old, conservative worldview and the new, open-minded thinking in shaping its foreign policy. As a result, Vietnam's vision for a rules-based international order emphasizes universally negotiated rules and institutions, rather than western-dominated ones, with a focus on the rules and norms promoted by the United Nations and ASEAN. Amid the current power shift, Vietnam supports an emerging multi-polar and multi-center order in which small and medium states like itself would have a bigger voice and greater agency.