bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevention of the Occupational Silicosis Epidemic in Australia: What Do Those Who Assess Workplace Health Risk Think Should Be Done Now?
Authors: Cole Kate , Glass Deborah , Bence Tracey , Pisaniello Dino , Knott Peter , Rowett Shelley , Johnson Sharann 
Published: September 2022

Abstract
An Australian National Dust Disease Taskforce was established to address the re-emergence of occupational lung disease, in particular silicosis. Exposure to respirable crystalline silica (RCS) occurs in various industries in Australia. We asked occupational hygienists about their practical experiences and perspectives on RCS exposure and regulatory action. A total of 105 members of the Australian Institute of Occupational Hygienists completed an anonymous questionnaire, which addressed individual characteristics, experience, perceived level of employer awareness, effectiveness of current regulation, and recommendations for improvement, across three main industrial sectors. Based on professional experience, 71% were concerned about the potential for RCS over-exposure. Barriers to adequate exposure control included lack of management commitment and financial resources. The employment of specialist occupational hygiene inspectors was considered to be the most effective regulatory strategy. Given the large number of exposed workers in the construction industry, with only a moderate awareness, there is the potential for significant cost shifting of the burden of occupational lung disease from employers on to individuals and the public health system. A nationally consistent approach to RCS exposure control across all industrial sectors is now recommended, with an increased focus on measuring and controlling exposure.
SBbadger: biochemical reaction networks with definable degree distributions
Authors: Kochen Michael A , Wiley H Steven , Feng Song , Sauro Herbert M 
Published: September 2022

Abstract

Motivation
An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis.

Results
In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software.

Availability and implementation
SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images
Authors: Hu Jin-Xian , Yang Yang , Xu Ying-Ying , Shen Hong-Bin 
Published: September 2022

Abstract

Motivation
Recognition of protein subcellular distribution patterns and identification of location biomarker proteins in cancer tissues are important for understanding protein functions and related diseases. Immunohistochemical (IHC) images enable visualizing the distribution of proteins at the tissue level, providing an important resource for the protein localization studies. In the past decades, several image-based protein subcellular location prediction methods have been developed, but the prediction accuracies still have much space to improve due to the complexity of protein patterns resulting from multi-label proteins and the variation of location patterns across cell types or states.

Results
Here, we propose a multi-label multi-instance model based on deep graph convolutional neural networks, GraphLoc, to recognize protein subcellular location patterns. GraphLoc builds a graph of multiple IHC images for one protein, learns protein-level representations by graph convolutions and predicts multi-label information by a dynamic threshold method. Our results show that GraphLoc is a promising model for image-based protein subcellular location prediction with model interpretability. Furthermore, we apply GraphLoc to the identification of candidate location biomarkers and potential members for protein networks. A large portion of the predicted results have supporting evidence from the existing literatures and the new candidates also provide guidance for further experimental screening.

Availability and implementation
The dataset and code are available at: www.csbio.sjtu.edu.cn/bioinf/GraphLoc.

Supplementary information
Supplementary data are available at Bioinformatics online.
Messaging Should Reflect the Nuanced Relationship between Land Change and Zoonotic Disease Risk
Authors: Mader André D , Waters Neil A , Kawazu Erin C , Marvier Michelle , Monnin Noémie , Salkeld Daniel J 
Published: September 2022

AbstractA hallmark of the media publicity surrounding COVID-19 has been the message that land change causes zoonotic diseases to spill over from wild animals to humans. The secondary peer-reviewed literature sends a similar message. However, as indicated in the primary peer-reviewed literature, the complexity of interacting variables involved in zoonotic disease spillover makes it unlikely for such a claim to be universally applicable. The secondary peer-reviewed literature and the mainstream media also differ markedly from the primary peer-reviewed literature in their lack of nuance in messaging about the relationship between land change and spillover risk. We advocate accurate, nuanced messaging for the sake of the local communities at greatest risk from zoonotic disease, for the sake of scientific credibility, and so that proportionate attention may be given to other possible drivers of spillover risk.
Ideologies, Power and the Politics of Punishment: The Case of the British Conservative Party
Authors: Guiney Thomas 
Published: September 2022

AbstractRecent scholarship has underscored the limitations of a theoretical repertoire that reduces the politics of punishment to debates over punitiveness, neoliberalism or penal exceptionalism. In this paper I argue that greater understanding of the dynamic interplay between ideologies and power can provide a richer account of the complex and contradictory landscapes of contemporary penal politics. I seek to show that political parties occupy a prominent position within representative systems of government and this mediating role, at the intersection between ideology and power, is closely associated with the production of penal policy outcomes. Reflecting upon the recent history of the British Conservative Party, I conclude that the politics of punishment is shaped, not only by inter-party competition (and consensus), but the dynamics of intra-party conflict.
Coal Criminals: Crimes of the Powerful, Extractivism and Historical Harm in the Global South
Authors: Atiles Jose , Rojas-Páez Gustavo 
Published: September 2022

AbstractThis article provides a criminological analysis of the extraction, consumption, and disposal of coal in the Caribbean and the global south. It looks at how the transnational corporation Applied Energy System (AES) and its 454-megawatt coal-fired electric power plant in Puerto Rico has manufactured a transnational network of environmental harm and violence. The paper aims to demonstrate how coloniality, law, and state-corporate deviance enable the coal sector- a habitual environmental offender- to engage in systemic harm across different jurisdictions and states of the global south. To do so, we engage with the work of scholars in the green criminology (treadmill of production), state-corporate crimes (crimes of development), and crimes of the powerful (Ecocide and Carbon Criminal) traditions. Furthermore, this article briefly describes the stories of resistance taking place in Puerto Rico. In doing so, the article describes the criminogenic practices behind this fossil fuel industry, and how it has taken advantage of colonial practices, thus enhancing the historical harm manufactured by modernity and replicated within the neoliberal economy.
Robot-assisted surgery in total knee arthroplasty: trauma maker or trauma savior? A prospective, randomized cohort study
Authors: Xu Zhonghua , Li Hua , Liu Zaiyang , Li Jie , Zhang Jun , Wang Min , Zhang Yuan 
Published: September 2022

Abstract

Background
Robotic assistance has been increasingly employed to improve the operative precision in modern knee surgery. The purpose of the study was to evaluate the trauma effect of one of the first domestically developed orthopedic surgical robots in China in a clinical trial of robot-assisted total knee arthroplasty (RA-TKA).

Methods
A total of 33 patients who underwent unilateral TKA for end-stage osteoarthritis were randomized to receive RA-TKA (17 cases) or conventional manual TKA (CM-TKA) in our institution in 2020. The trauma effects of the 4 main indicators with 48 sub-indicators in terms of subsectional operative time, inflammation and coagulation markers, physical and radiographical analyses of osteotomy deviation, and postoperative comfort were analyzed.

Results
Subsectional operative time analysis showed that the times for bone cutting and gap balancing with RA-TKA were 5.3 and 2.2 min shorter than those with CM-TKA (p = 0.010, p = 0.02), respectively. Arterial blood gas indicators (partial pressure of carbon dioxide, partial pressure of oxygen and SO2) 24 h after RA-TKA, as well as the white blood cell count and neutrophil ratio, were significantly lower than those after CM-TKA (p &lt; 0.05). Inflammatory markers at 72 h after surgery showed the increments of C-reactive protein, erythrocyte sedimentation rate and D-dimer of RA-TKA declined by 180.7, 22.0 and 1050.0% (p &lt; 0.05), respectively, referenced to the preoperative baseline values, as compared to CM-TKA. Mechanical deviation distribution exhibited percentages of region I errors for RA-TKA and CM-TKA of 76.5% and 27.1% (p = 0.000), respectively, and the success rates of one-time osteotomy were 94.1% and 62.5% (p = 0.039), respectively. Radiographical verification showed RA-TKA was more conducive to achieving mechanical alignment and ideal tibial component azimuths. Postoperative efficacy showed that patients were more comfortable after RA-TKA in terms of reduced administration of tranexamic acid, hydrocortisone and the utilization rate of temporary intensive opioid analgesics. No statistical difference in patient-reported outcome measures and complications were recorded between the two groups during continuous observation.

Conclusions
Compared with CM-TKA, RA-TKA decreases rather than increases trauma. It might shorten the time required for bone cutting and gap balancing, reduce mechanical errors related to the osteotomy and prosthesis position, and improve the accuracy of the mechanical alignment reconstruction. RA-TKA is also favorable in promoting postoperative comfort and minimizing inflammatory response and drug consumption.

Trial registration
The Chinese Clinical Trial Registry (ChiCTR2000031282) approved registration on 26 March 2020.
Digital technologies, gig work and labour share
Authors: Henley Andrew 
Published: September 2022

Abstract
Conflict over the functional income distribution, discussed and explained in Keith Cowling’s work in the 1980s, remains a feature of capitalist economies. In the twenty first century labour flexibilisation strategies have become a key tool in enabling monopoly capitalists to manipulate the functional distribution of income. Through the lens of institutional theory, this paper traces labour flexibilisation in the UK since the 1980s, in order to describe and evaluate how the use of digital technologies has become allied to non-standard contracting and ‘dependent’ self-employment in the growth of the gig economy. The paper argues that this provides employers with increased flexibility of the labour input at both extensive and intensive margins. Digital technology and gig working also position dominant internet platform businesses to apply downward pressure to labour share at a monopoly-monopsony nexus between individual consumers and new service sector workers. This has led to new ways in which employment contracts and the nature of organisations as an outcome of monopoly capitalist labour process are contested.
Digital platforms: monopoly capital through a classical-marxian lens
Authors: Vasudevan Ramaa 
Published: September 2022

Abstract
The classical-marxian conception of capitalist monopoly, based on restrictions to capital mobility arising from production conductions and property rights rather than oligopolistic market structure, is a fruitful way of approaching the implications of the pervasive spread of modern corporations—what has been termed the stage of Monopoly Capital. The relevance of the classical-marxian conception of ‘capitalist monopoly’ in the context of new technology is investigated by applying it to the monopoly exercised by contemporary digital platforms, with a specific focus on Google (Alphabet), Amazon and Facebook.
Benefit of Risk-stratified Prophylactic Treatment on Clinical Outcome in Postoperative Crohn’s Disease
Authors: Joustra Vincent , van Sabben Joris , van der does de Willebois Eline , Duijvestein Marjolijn , de Boer Nanne , Jansen Jeroen , van der Bilt Jarmila , Lameris Wytze , Bemelman Willem , Buskens Christianne , D’Haens Geert 
Published: September 2022

AbstractBackground and AimsWhereas immediate postoperative treatment has shown effectiveness in reducing endoscopic postoperative recurrence [POR], evidence regarding the clinical benefit is limited. We compared rates of clinical POR in Crohn’s disease [CD] patients receiving immediate prophylactic treatment with rates in patients receiving endoscopy-driven treatment.MethodsWe retrospectively collected data from 376 consecutive CD patients who underwent an ileocaecal resection with anastomosis between 2007 and 2018 with at least 3 years of follow-up at three sites. Subsequently, high- and low-risk patients categorised by established guidelines, who underwent endoscopy within 12 months postoperatively, were grouped according to a prophylactic- or endoscopy-driven approach and compared for incidence and time till endoscopic and clinical POR.ResultsProphylactic treatment reduced rates of and time till endoscopic POR within 1 year in high-risk (hazard ratio [HR] 0.48, 95% confidence interval [CI] 0.27-0.86, p = 0.04, number needed to treat [NNT] = 5) but not low-risk [HR 0.90, 95% CI 0.32-2.56, p = 0.85] patients. Conversely, no significant differences in clinical POR within 3 years between prophylactic- and endoscopy-driven low-risk [HR 1.17, 95% CI 0.41-3.29, p = 0.75] and high-risk patients were observed [HR 1.06, 95% CI 0.63-1.79, p = 0.82, NNT = 22]. However, a large numerical albeit not statistical significant difference in 3-year clinical POR [28.6% vs. 62.5%, p = 0.11] in a subset of high-risk patients with three or more ECCO-defined risk factors was observed, indicating a cumulative effect of having multiple risk factors.ConclusionOur observations favour step-up treatment guided by early endoscopic evaluation with prophylactic treatment reserved for carefully selected high-risk patients, in order to avoid potential overtreatment of a significant number of patients.
A case series of eosinophilic myocarditis: different faces of the same coin
Authors: Mengesha Bethlehem , Meir Karen , Gural Alexander , Asleh Rabea 
Published: September 2022

Abstract

Background
Eosinophilic myocarditis (EM) is a rare form of myocarditis with various aetiologies and dire consequences if not diagnosed and treated expeditiously.

Case summary
We report three cases of EM at different stages of the disease with differing clinical manifestations. We highlight the diagnostic workup including the role of multimodality imaging and endomyocardial biopsy (EMB), and the treatment strategies.

Discussion
EM is an underdiagnosed and potentially life-threatening disease. Therefore, a high clinical suspicion for EM should arise when patients with signs and symptoms of cardiovascular disease develop hypereosinophilia or vice versa. Early identification of this condition using multimodality imaging and EMB is of paramount importance as the disease may progress to the irreversible late fibrotic stage if treatment is delayed.
Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load
Authors: Yue Yihong , Wang Fushun , Pan Jie , Chen Xue-Ping , Tang Yi , Yang Zhihong , Ma Jing , Li Meng , Yang Ming 
Published: September 2022

Abstract
Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.
Involvement of the Noncanonical Polyadenylation Polymerase Cid14 in Fungal Azole Resistance in the Pathogen Cryptococcus neoformans
Authors: Li Chenxi , Zhen Sihui , Ma Xiaoyu , Ma Lan , Wang Zhen , Zhang Ping , Zhu Xudong 
Published: September 2022

Abstract
The yeast noncanonical polyadenylation polymerase Cid14 was originally identified from fission yeast and plays a critical role in the TRAMP complex. This protein is a cytoplasmic cofactor and regulator of RNA-degrading exosomes. Cid14 is highly conserved from yeast to animals and has been demonstrated to play key roles in the regulation of RNA surveillance, nutrition metabolism, and growth in model organisms, but not yet in Cryptococcus neoformans (C. neoformans). Here, we report the identification of a gene encoding an equivalent Cid14 protein, named CID14, in the fungal pathogen C. neoformans. To obtain insights into the function of Cid14, we created a mutant strain, cid14Δ, with the CRISPR–Cas9 editing tool. Disruption of CID14 impaired cell membrane stability. Further investigations revealed the defects of the cid14Δ mutant in resistance to low carbohydrate levels. Meanwhile, significantly, the ability to grow under flucytosine stress was decreased in the cid14Δ mutant. More importantly, our results showed that the cid14Δ mutant does not affect yeast virulence but exhibits multidrug resistance to azole. Our work is the first to suggest that Cid14 plays critical roles in azole resistance by affecting Afr1, which is chiefly responsible for azole excretion in the ABC (ATP-binding cassette) transporter.
The “terminal line”: a novel sign for the identification of distal mesorectum end during TME for rectal cancer
Authors: Ghareeb Waleed M , Wang Xiaojie , Zhao Xiaozhen , Xie Meirong , Emile Sameh H , Shawki Sherief , Chi Pan 
Published: September 2022

Abstract

Background
Although the clinical importance of complete, intact total mesorectal excision (TME) is the widely accepted standard for decreasing local recurrence of rectal cancer, the residual mesorectum still represents a significant component of resection margin involvement. This study aimed to use a visible intraoperative sign to detect the distal mesorectal end to ensure complete inclusion of the mesorectum and avoid unnecessary over-dissection.

Methods
The distal mesorectum end was investigated retrospectively through a review of 124 operative videos at the Union Hospital of Fujian Medical University (Fujian, China) and Cleveland Clinic (Ohio, USA) by two independent surgeons who were blinded to each other. Furthermore, 28 cadavers and 44 post-operative specimens were prospectively examined by hematoxylin and eosin (H&E) staining and Masson's staining to validate and confirm the findings of the retrospective part. Univariate and multivariate analyses were carried out to detect the independent factors that can affect the visualization of the distal mesorectal end.

Results
The terminal line (TL) is the distal mesorectal end of the transabdominal and transanal TME (taTME) and appears as a remarkable pearly white fascial structure extending posteriorly from 2 to 10 o'clock. Histopathological examination revealed that the fascia propria of the rectum merges with the presacral fascia at the TL, beyond which the mesorectum ends, with no further downward extension. In the retrospective observation, the TL was seen in 56.6% of transabdominal TME and 56.0% of taTME operations. Surgical approach and tumor distance from the anal verge were the independent variables that directly influenced the detection of the TL (P = 0.03 and P = 0.01).

Conclusion
The TL is a visible sign where the transabdominal TME should end and the taTME should begin. Recognition of the mesorectal end may impact the certainty of complete mesorectum inclusion. Further clinical trials are needed to confirm the preliminary findings.