bluuebunny/crossref_metadata_2025 huggingface dataset:
Anthropology of Science
Authors: Krauss Alexander
Published: November 2024

Anthropology of science is the cross-cultural study of humanity which retraces how we have developed science, from the past to the present. So how did we get from being hunters and gatherers using axes, basic observation and numerical reasoning, to being scientists hunting explanations and gathering data using systematic controls and mathematical methods? How did we get from being nomads running in the savannahs and conducting trial and error, to being scientists running sophisticated experiments and conducting statistical analysis? Here we trace the history of how our species has reasoned more complexly over time. This ranges from how hunter-gatherer groups developed plant-based medicines and controlled parts of their environment through agriculture and livestock, to the ancient Chinese who developed, as the first or independently, effective immunisation techniques, magnetic compasses, negative numbers, astronomical observations of novae, seismographs and quantitative cartography, as well as papermaking and printing that fostered the spread of knowledge. Such innovations required complex understanding of causal relationships and making predictions. What made the work of 17th-century scientists possible is a cumulative process of greater technological advances and greater awareness of the methods already widely used for such advancements, namely more systematic observation, measurement and experimentation to create increasingly sophisticated technologies.
Philosophy of Science
Authors: Krauss Alexander
Published: November 2024

What science is and its foundation have been explored by philosophers for centuries, including Bacon, Hume and Popper, and what knowledge is and its foundation for over two and a half millennia, including Plato, Aristotle and Wittgenstein. Philosophers have addressed central questions of science of science longer than researchers in any other subfield of science of science. Major debates that have dominated philosophy of science include paradigm shifts, justification, induction, demarcation and realism. Paradigm shifts refer to fundamental changes in the theories of a scientific field. Justification deals with principles such as falsification and verification to justify our theories of the world. Induction addresses the question of whether observations we make can or cannot justify generalising about the observations in other contexts or in the future. Demarcation involves defining criteria for what is and is not science. Realism concerns whether scientific theories provide a reliable approximation and true description of reality, for observable and not directly observable phenomena. We can also better understand science by comprehending the metaphysical aspects underlying science: causal and mechanistic explanations, measurement of causes, the nature of scientific regularities and laws, and the metaphysical assumptions of science inherent in research, namely in methods, definitions, concepts and theories.
Science of Science: An Integrated Field Grounded in the New-Methods-Drive-Science Theory
Authors: Krauss Alexander
Published: November 2024

Establishing the field of science of science requires providing not only an empirical foundation but also a theoretical foundation for understanding science. The new-methods-drive-science theory presented here can offer a unifying theory and foundation for the field that is grounded in the powerful role of scientific methods which is the common thread among this scientific community. The theory can integrate and unify the disparate fields studying science as our methods and instruments are connected to all features of science. Our evolved methodological abilities of the mind and sophisticated methods and instruments we develop using our mind (such as novel statistical techniques and telescopes) are the main mechanism that directly enables us to develop knowledge and science, by expanding our present cognitive, sensory and methodological reach to the world. The theory describes how our methods and tools have driven the origins, foundations and present limits of science.
Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP
Authors: Su Chen , Pastor William A , Emad Amin
Published: November 2024

Deciphering the underlying gene regulatory networks (GRNs) that govern early human embryogenesis is critical for understanding developmental mechanisms yet remains challenging due to limited sample availability and the inherent complexity of the biological processes involved. To address this, we developed InPheRNo-ChIP, a computational framework that integrates multimodal data, including RNA-seq, transcription factor (TF)–specific ChIP-seq, and phenotypic labels, to reconstruct phenotype-relevant GRNs associated with endoderm development. The core of this method is a probabilistic graphical model that models the simultaneous effect of TFs on their putative target genes to influence a particular phenotypic outcome. Unlike the majority of existing GRN inference methods that are agnostic to the phenotypic outcomes, InPheRNo-ChIP directly incorporates phenotypic information during GRN inference, enabling the distinction between lineage-specific and general regulatory interactions. We integrated data from three experimental studies and applied InPheRNo-ChIP to infer the GRN governing the differentiation of human embryonic stem cells into definitive endoderm. Benchmarking against a scRNA-seq CRISPRi study demonstrated InPheRNo-ChIP’s ability to identify regulatory interactions involving endoderm markers FOXA2, SMAD2, and SOX17, outperforming other methods. This highlights the importance of incorporating the phenotypic context during network inference. Furthermore, an ablation study confirms the synergistic contribution of ChIP-seq, RNA-seq, and phenotypic data, highlighting the value of multimodal integration for accurate phenotype-relevant GRN reconstruction.
mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data
Authors: Wrobel Julia , Soupir Alex C , Hayes Mitchell T , Peres Lauren C , Vu Thao , Leroux Andrew , Fridley Brooke L
Published: November 2024

Technologies that produce spatial single-cell (SC) data have revolutionized the study of tissue microstructures and promise to advance personalized treatment of cancer by revealing new insights about the tumor microenvironment. Functional data analysis (FDA) is an ideal analytic framework for connecting cell spatial relationships to patient outcomes, but can be challenging to implement. To address this need, we present mxfda, an R package for end-to-end analysis of SC spatial data using FDA. mxfda implements a suite of methods to facilitate spatial analysis of SC imaging data using FDA techniques.

Availability and implementation

The mxfda R package is freely available at https://cran.r-project.org/package=mxfda and has detailed documentation, including four vignettes, available at http://juliawrobel.com/mxfda/.
Conditional flux balance analysis toolbox for python: application to research metabolism in cyclic environments
Authors: Páez-Watson Timothy , Hernández Medina Ricardo , Vellekoop Loek , van Loosdrecht Mark C M , Wahl S Aljoscha
Published: November 2024

We present py_cFBA, a Python-based toolbox for conditional flux balance analysis (cFBA). Our toolbox allows for an easy implementation of cFBA models using a well-documented and modular approach and supports the generation of Systems Biology Markup Language models. The toolbox is designed to be user-friendly, versatile, and freely available to non-commercial users, serving as a valuable resource for researchers predicting metabolic behaviour with resource allocation in dynamic-cyclic environments.

Availability and implementation

Extensive documentation, installation steps, tutorials, and examples are available at https://tp-watson-python-cfba.readthedocs.io/en/. The py_cFBA python package is available at https://pypi.org/project/py-cfba/.
A framework for developing generic implant safety procedures for scanning patients with medical implants and devices in MRI
Authors: Ashmore Jonathan P , Prescott Sarah J , McLean John , Wilson Daniel J , Charles-Edwards Geoff , Wright Peter , Grainger David , Barker Gareth J , Lipton Alexandra J , Watt Rachel , Gopalan Deepa , Radon Mark R
Published: November 2024

UK guidelines for MR safety recommend that MRI departments refer to the implant manufacturer for advice regarding the MRI safety of scanning patients with an implantable medical device prior to scanning. This process of assuring safety can be time consuming, leading to delays and potential cancellations of a patient’s MRI. Furthermore, at times the implant cannot be identified, or the implant manufacturers cannot provide up to date MRI safety information. The purpose of generic implant safety procedures is to define a process for managing patients with certain types of implants where the risk from scanning is low. This process incorporates scope for an evidence-based risk-benefit decision to scan some groups of patients under locally approved conditions, without seeking to identify the exact make and model of the implant and subsequent assurance of MR safety from the implant manufacturer. This publication provides best practice recommendations from a multi-professional working group for the development of these procedures. It is supported by The Institute of Physics and Engineering in Medicine, The Society of Radiographers, The Royal College of Radiologists, The British Institute of Radiology, The British Association of MR Radiographers, The International Society of Magnetic Resonance in Medicine British and Irish Chapter, and the NHS Scotland MRI Physics Group.
OGC SO30 - Radiological thoracic duct embolisation for post oesophagectomy chyle leak: A single centre retrospective review
Authors: Fernandes Shriya , Snook Rhea , Kynes Larissa , McDonnell Declan , Maher Ben , Noble Fergus , Byrne James , Underwood Tim , Kelly Jamie , White Michael
Published: November 2024

Background

Chyle leak is a recognised complication of oesophagectomy associated with increased length of hospital stay, morbidity and is potentially fatal. Chyle leak management is controversial, and lacks a standardised or validated approach. Interventional radiological approaches are well described and routinely able to identify and embolise these thoracic duct leaks reducing need for return to theatre. The aim is to retrospectively evaluate outcomes of lymphangio-embolisation and in patients post Ivor Lewis oesophagectomy for oesophageal carcinoma.

Method

Data was analysed retrospectively from 168 patients who underwent Ivor Lewis oesophagectomy for oesophageal carcinoma from June 2020 to June 2024, of which 15 patients had chyle leak post operatively. Chyle leak was suspected when chest drain output >500ml in 24 hours and confirmed by high biochemical levels of chylomicrons and triglycerides within the drain fluid. Conservative management involved keeping the patient nil by mouth, total parenteral nutrition and monitoring intercostal drain output. Thoracic duct lymphangiogram was carried out to confirm location of chyle leak-embolisation was carried out using the femoral approach with lipidiol and/or microcoils and/or glue.

Results

15 out of 168 (9%) patients had post operative chyle leaks. Four resolved with conservative management within <14 days. 11 chyle leaks persisted after a median of 17 days (range 14-30 days) conservative management and went onto have thoracic duct embolisation. Of those embolised, six chyle leaks resolved within three days post procedure. Two resolved 5-7 days post embolization. One had repeat embolization seven days post primary embolisation. Two patients required thoracoscopic ligation of thoracic duct, due to obesity making embolisation technically impossible and lack of interventional radiology capacity respectively. No patients had adverse outcomes.

Conclusion

Thoracic duct embolisation is an effective and safe approach for routine management of post oesophagectomy chyle leaks and may reduce return to theatre.
HPB SO37 - GTN Patch for Medical Relaxation of the Sphincter of Oddi: “A Safe and Effective Pre-ERCP Treatment for Controlled Bile Leak Post-Cholecystectomy"
Authors: Zino Samer , Thiagarajah Sai Viswan Karthigesu , Bakewell Zoe , Bright Euan
Published: November 2024

Background

Bile leak is a frequent complication following laparoscopic total, subtotal cholecystectomy, and bile duct exploration (BDE) with an incidence up to 2.8%. It can contributing significantly to postoperative morbidity and mortality. GTN has demonstrated efficacy in reducing papillary muscle contraction and Sphincter of Oddi pressure. Similarly GTN might promote healing and closure of bile leaks post total or subtotal cholecystectomy. This study aims to assess the safety and effectiveness of GTN in treating bile leaks post total, subtotal cholecystectomy or bile duct exploration.

Method

Data was prospectively collected from patients who developed bile leaks after total or subtotal cholecystectomy between June 2020 and June 2024. Inclusion criteria were patients with a bile leak post-surgery during this period. Exclusion criteria included unstable patients, uncontrolled bile leaks, the presence of biliary obstruction, or major bile duct injuries. Suitable patients were treated with a GTN patch as first line management before potential ERCP. A 5 mg GTN skin patch was applied every 24 hours, starting at least 48 hours post-surgery if drain output exceeded 100 ml/hour. Patients were consented about side effects including hypotension and headache.

Results

Seven patients were treated with GTN, with mean age of 51 years, four were females. Four cases were emergencies and four had subtotal cholecystectomies, one in the elective group. Bile leaks occurred after biloma drainage and one after removal of trans-cystic drain post trans-cystic BDE. All patients experienced significant drain output reduction the day after starting GTN. There were no complications during or after treatment. One required ERCP two months later for persistent low-volume bile leak of 5-10 ml per day. Headaches occurred in two cases, treatment was discontinued in one. The average time to GTN treatment was 3.4 days.

Conclusion

This study demonstrates GTN treatment's safety and effectiveness for managing bile leaks following total, subtotal cholecystectomy or BDE. We recommend GTN as the primary therapy for controlled bile leaks, barring biliary obstruction or major injury. Response can be evaluated within 24-48 hours through significant output reduction. Implementing local protocols can minimize variations in GTN treatment initiation times. GTN should be prioritized over ERCP to prevent complications like perforation, pancreatitis, and bleeding. We aim for this study to underscore GTN's efficacy to surgeons and promote multicentre research initiatives.
Factors associated with self-initiated moves during the formal eviction process
Authors: Nilsson Ida
Published: November 2024

Housing eviction is a common occurrence, affecting hundreds of thousands of Europeans annually. It is well known that it primarily impacts the most vulnerable groups in society and is associated with adverse outcomes. However, previous research heavily relies on enforced removals registered in official statistics, thus missing eviction outcomes that do not undergo or disrupt the formal eviction process. This exploratory study, based on unique national Swedish register data on evictions with a sample of over 60,000 individuals, examines self-initiated moves and contrasts them with enforced removals and lease regain. Results from univariable and multivariable multinomial logistic regression analyses indicate that economic hardship and living in a single household are associated with both self-initiated moves and enforced removals. However, distinct factors associated with self-initiated moves are aged under twenty-five, living as a couple with children, residing in a non-metropolitan municipality, and having a native background. Gender-stratified analysis highlights strong associations for young women and native-background women with self-initiated moves. The results underscore the significance of implementing preventive social services interventions that address the specific needs of this larger group of individuals who face evictions under a broader definition. Further implications for research, policy, and social work practice are discussed.
Concussion leads to opposing sensorimotor effects of habituation deficit and fatigue in zebrafish larvae
Authors: Köcher Laura , Beppi Carolina , Penner Marco , Meyer Samuel , Bögli Stefan Yu , Straumann Dominik
Published: November 2024

Concussion, or mild traumatic brain injury, is caused by sudden mechanical forces impacting the brain either directly or through inertial loading. This can lead to physical, behavioural and cognitive impairments. Despite concussion being a significant health issue, our understanding of the relationship between initial impact force and the subsequent neurological consequences is not well understood. Previously, we established a model of concussion in zebrafish larvae. Here, we further investigate concussions of varying severities in zebrafish larvae using linear deceleration. Using an acoustic assay to monitor the larval sensorimotor behaviour, we found that different parameters of the resulting escape behaviour are modulated by the impact force of the preceding concussive insult. To investigate the relative contributions of habituation performance and fatigue on the escape response behaviour, we constructed a neurocomputational model. Our findings suggest that a concussive impact initially affects habituation performance at first and, as the impact force increases, fatigue is induced. Fatigue then alters the escape response behaviour in an opposing manner.
Motor learning is modulated by dopamine availability in the sensorimotor putamen
Authors: Muehlberg Christoph , Goerg Sophia , Rullmann Michael , Hesse Swen , Sabri Osama , Wawrzyniak Max , Classen Joseph , Fricke Christopher , Rumpf Jost-Julian
Published: November 2024

Successful motor skill acquisition requires the dynamic interaction of multiple brain regions, with the striatum playing a critical role in this network. Animal studies suggest that dopaminergic mechanisms are involved in the regulation of motor learning–associated striatal plasticity. In humans, however, the contribution of nigrostriatal dopaminergic transmission to motor learning remains elusive beyond its well-characterized role in initiation and fluent execution of movements. In this prospective observational study, we investigated motor sequence learning in individuals who had undergone 123I-N-ω-fluoropropyl-2β-carbomethoxy-3β-(4-iodophenyl)nortropane single-photon emission computed tomography for the differential diagnosis of Parkinson's disease (n = 41) and age-matched healthy controls (n = 20). We found that striatal dopamine transporter depletion exhibited distinct spatial patterns that were associated with impairments in motor sequence learning and the manifestation of Parkinsonian motor symptoms, respectively. Specifically, significant associations between striatal dopamine transporter depletion and impairments in motor sequence learning were confined to posterior putaminal regions, whereas significant associations of striatal dopamine transporter depletion with Parkinsonian motor symptom severity showed a widespread spatial pattern across the entire striatal volume with an anterior maximum. Normative functional connectivity analysis revealed that both behavioural domains shared largely overlapping connectivity patterns with the basal ganglia and supplementary motor area. However, apart from connectivity with more posterior parts of the supplementary motor area, significant functional connectivity with primary motor cortical areas was only present for striatal dopamine transporter availability–related modulation of online motor learning. Our findings indicate that striatal dopaminergic signalling plays a specific role in motor sequence learning beyond its influence on mere motor execution, implicating learning-related sensorimotor striatum recruitment and cortico-striatal plasticity as dopamine-dependent mechanisms.
Patient-reported outcome measures for life participation in patients with chronic kidney disease: a systematic review
Authors: Hughes Anastasia , Ju Angela , Cazzolli Rosanna , Howell Martin , Caskey Fergus J , Elliott Meghan J , Farragher Janine , Greenwood Sharlene , Levin Adeera , Manera Karine , Sluiter Amanda , Teixeira-Pinto Armando , Trimarchi Hernán , Wang Bill , Guha Chandana , Wu Rebecca , Jauré Allison
Published: November 2024

Background

The symptoms, comorbidities and treatment burden associated with chronic kidney disease (CKD) can be debilitating and limit life participation in patients with CKD not requiring kidney replacement therapy (KRT). The aim of this study was to identify the characteristics, content and psychometric properties of patient-reported outcome measures (PROMs) used to assess life participation in patients with CKD.

Methods

We searched MEDLINE, Embase, PsycINFO and CINAHL from database inception to February 2023 for all studies that reported life participation in patients with CKD (stages 1–5 not requiring kidney replacement therapy). We analysed the characteristics, dimensions of life participation and psychometric properties of the measures.

Results

From the 114 studies included, 20 (18%) were randomized trials, 3 (3%) were non-randomized trials and 91 (80%) were observational studies. Forty-one different measures were used to assess life participation, of which six (15%) were author-developed measures. Twelve (29%) measures assessed life participation specifically, while 29 (71%) measures assessed broader constructs such as quality of life, which included questions relevant to life participation. The 36-Item Short Form Health Survey (SF-36) and Kidney Disease Quality of Life Short Form (KDQOL-SF) were the most frequently used, in 39 (34%) and 24 (21%) studies, respectively. Many content domains for life participation were assessed, including physical activities (walking, running and sports), social activities, leisure activities, work or study and self-care. None of the measures for life participation were developed specifically for CKD. Four measures (EuroQol 5-dimension 3-level (EQ-5D-3L), Functional Assessment of Cancer Therapy - Anemia, Short Form 6-dimension and Short-From 36-dimension (SF-36)) had validation data collected in patients with CKD.

Conclusion

The measures for life participation used in patients with CKD vary in content, with few validated in the CKD population. There is a need for a validated measure to assess life participation in a meaningful and consistent way in all patients with CKD worldwide.
Liver dysfunction as a rare presentation of ICD lead-induced tricuspid regurgitation: a case report
Authors: Fleming Suzannah , Somarakis Konstantinos , Squire Gareth , Goldney Jonathan , Loke Ian
Published: November 2024

Background

Implanted cardiac devices with right ventricular leads can cause tricuspid regurgitation and subsequent heart failure. In these patients, congestive hepatopathy because of tricuspid regurgitation is well documented; however, the presentation of liver dysfunction without overt heart failure is rare.

Case summary

We report a case of a 56-year-old man with presumed hypertrophic cardiomyopathy, presenting with jaundice without signs of decompensated heart failure, 8 years post-implantation of dual-chamber implantable cardiac defibrillator (ICD). A workup for abnormal liver function, including a liver biopsy, determined congestive hepatopathy as the cause. Cardiac imaging revealed severe tricuspid regurgitation caused by right ventricular ICD lead causing tricuspid valve malposition. Management included both tricuspid valve replacement and extraction of ICD, and there was an excellent recovery.

Discussion

This is a rare case where severe tricuspid regurgitation and congestive hepatopathy secondary to an ICD lead presented with jaundice in the absence of signs of decompensated heart failure. In patients with an implanted cardiac device presenting with signs of liver dysfunction, congestive hepatopathy secondary to tricuspid regurgitation should be considered.
Response of the nephron arterial network and its interactions to acute hypertension: a simulation
Authors: Marsh Donald J , Holstein-Rathlou Niels-Henrik
Published: November 2024

We simulated the dynamics of a group of 10 nephrons supplied from an arterial network and subjected to acute increases in blood pressure. Arterial lengths and topology were based on measurements of a vascular cast. The model builds on a previous version exercised at a single blood pressure with 2 additional features: pressure diuresis and the effect of blood pressure on efferent arteriolar vascular resistance. The new version simulates autoregulation, and reproduces tubule pressure oscillations. Individual nephron dynamics depended on mean arterial pressure and the axial pressure gradient required to cause blood flow through the arteries. Rhythmic blood withdrawal into afferent arterioles caused blood flow fluctuations in downstream vessels. Blood pressure dependent changes in nephron dynamics affected synchronization metrics. The combination of vascular pressure gradients and oscillations created a range of arterial pressures at the origins of the 10 afferent arterioles. Because arterial blood pressure in conscious animals has 1/f dynamics, we applied an arterial pressure pattern with such dynamics to the model. Amplitude of tubule pressure oscillations were affected by the 1/f blood pressure fluctuations, but the oscillation frequencies did not change. The pressure gradients required to deliver blood to all afferent arterioles impose a complexity that affects nephrons according to their locations in the network, but other interactions compensate to ensure the stability of the system. The sensitivity of nephron response to location on the network, and the constancy of the tubular oscillation frequency provide a spatial and time context.
Network hub gene detection using the entire solution path information
Authors: Kuismin Markku , Sillanpää Mikko J
Published: November 2024

Gene co-expression networks typically comprise modules and their associated hub genes, which are regulating numerous downstream interactions within the network. Methods for hub screening, as well as data-driven estimation of hub co-expression networks using graphical models, can serve as useful tools for identifying these hubs. Graphical model-based penalization methods typically have one or multiple regularization terms, each of which encourages some favorable characteristics (e.g. sparsity, hubs, and power-law) to the estimated complex gene network. It is common practice to find a single optimal graphical model corresponding to a specific value of the regularization parameter(s). However, instead of doing this, one could aggregate information across several graphical models, all of which depend on the same data set, along the solution path in the hub gene detection process. We propose a novel method for detecting hub genes that utilizes the information available in the solution path. Our procedure is related to stability selection, but we replace resampling with a simple statistic. This procedure amalgamates information from each node of the data-driven graphical models into a single influence statistic, similar to Cook’s distance. We call this statistic the Mean Degree Squared Distance (MDSD). Our simulation and empirical studies demonstrate that the MDSD statistic maintains a good balance between false positive and true positive hubs. An R package MDSD is publicly available on GitHub under the General Public License https://github.com/markkukuismin/MDSD.
Double-diffusive layering during the evolution of planetary mantles
Authors: Dude Sabine , Hansen Ulrich
Published: November 2024

The degree of layering during planetary mantle evolution has been a key issue and is still heavily debated, especially since the observation of seismic discontinuities within the Earth mantle and their correlation to phase transitions within the mantle mineral assemblage and the detection of geochemical differences in mantle derived basalts (Mid Ocean Ridge Basalts and Ocean Island Basalts). We present the phenomenon of double-diffusive layering in a fluid with strongly temperature dependent viscosity, as relevant for planetary mantle material, to study the influence of an initial compositional gradient with regard to the thermal and chemical evolution of a planet. The numerical experiments show that in a wide parameter range distinct layers are formed self-organized from a continuously stratified state by dynamic fractionation and are thus likely to appear as a generic feature. Considering this as a plausible model for planetary mantle evolution it provides a dynamic explanation for the existence of distinct chemical reservoirs within the history of a planet’s mantle.
SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research
Authors: Li Jie , Ni Qingyang , He Guangqi , Huang Jiale , Chao Haoyu , Li Sida , Chen Ming , Hu Guoyu , Whelan James , Shou Huixia
Published: November 2024

Soybean is a globally important crop for food, feed, oil, and nitrogen fixation. A variety of multi-omics studies have been carried out, generating datasets ranging from genotype to phenotype. In order to efficiently utilize these data for basic and applied research, a soybean multi-omics database with extensive data coverage and comprehensive data analysis tools was established. The Soybean Omics Database (SoyOD) integrates important new datasets with existing public datasets to form the most comprehensive collection of soybean multi-omics information. Compared to existing soybean databases, SoyOD incorporates an extensive collection of novel data derived from the deep-sequencing of 984 germplasms, 162 novel transcriptomic datasets from seeds at different developmental stages, 53 phenotypic datasets, and more than 2500 phenotypic images. In addition, SoyOD integrates existing data resources, including 59 assembled genomes, genetic variation data from 3904 soybean accessions, 225 sets of phenotypic data, and 1097 transcriptomic sequences covering 507 different tissues and treatment conditions. Moreover, SoyOD can be used to mine candidate genes for important agronomic traits, as shown in a case study on plant height. Additionally, powerful analytical and easy-to-use toolkits enable users to easily access the available multi-omics datasets, and to rapidly search genotypic and phenotypic data in a particular germplasm. The novelty, comprehensiveness, and user-friendly features of SoyOD make it a valuable resource for soybean molecular breeding and biological research. SoyOD is publicly accessible at https://bis.zju.edu.cn/soyod.
Economic Insecurity during the COVID-19 Pandemic among Healthcare Workers by Educational Attainment
Authors: Mroz Tracy M , Dunlap Ben S , Frogner Bianca K
Published: November 2024

Prior to the COVID-19 pandemic, healthcare workers with less formal education (e.g., nursing assistants, home care aides) versus more formal education (e.g., physicians, nurses) were more likely to experience economic insecurity, the real and/or perceived risk of financial losses. Given the unprecedented impact of COVID-19 on healthcare workers, we sought to describe economic insecurity among these workers during the pandemic. Using data from the U.S. Census Bureau’s Household Pulse Survey from July 2021 to July 2023, we examined economic insecurity among healthcare workers by educational attainment. Higher proportions of healthcare workers with an associate degree or below reported difficulty paying usual expenses, food insufficiency, and being behind on rent/mortgage payments compared to healthcare workers with a bachelor’s degree or higher. Accounting for other sociodemographic characteristics, higher educational attainment was associated with significantly lower odds of economic insecurity. Since the public health emergency has ended and temporary policies to support low wage workers during the pandemic have sunsetted, targeted policies to promote economic security among financially vulnerable low wage workers are critical to enable recruitment and retention of these essential healthcare workers.
Non-government advocacy for health equity: evidence from Australia
Authors: Musolino Connie , Freeman Toby , Flavel Joanne , Baum Fran
Published: November 2024

The aim of this paper is to identify non-governmental organizations (NGOs) advocating for policy and practices to address rising health inequities in Australia. NGOs can play a critical role in shaping and influencing governance processes including public policy relating to the social and commercial determinants of health inequities. However, scholarship on who the NGOs are that are advocating to address health inequities in Australia and how they operate is sparse. Through desktop analysis in 2022, we searched NGO websites and documents for evidence of advocacy activities related to health inequities between 2017 and 2022. A database of the NGOs was compiled, noting the type of organization, function, advocacy activities and main issues their advocacy covered. A total of 137 NGOs were identified as engaging in activities advocating for change to address health inequities either directly (e.g. advocating directly to address health inequities) or indirectly (e.g. advocating on social determinants of health inequities such as housing and linking to their unequal health impacts). We noted the primary issues they advocated on, including topic categories: risk factor, disease-specific, broader health system, social determinants of health equity, and health workforce and service issues. The results indicate that Australian NGOs from multiple sectors are active in advocacy to address heath inequities on a variety of topics and through a variety of activities. This study provides a template for similar studies in other countries and suggests further research is needed to understand the role and impact of civil society advocacy to address growing health inequities.
Uplift of genetic diagnosis of rare respiratory disease using airway epithelium transcriptome analysis
Authors: Legebeke Jelmer , Wheway Gabrielle , Baker Lee , Wai Htoo A , Walker Woolf T , Thomas N Simon , Coles Janice , Jackson Claire L , Holloway John W , Lucas Jane S , Baralle Diana
Published: November 2024

Rare genetic respiratory disease has an incidence rate of more than 1:2500 live births in Northern Europe and carries significant disease burden. Early diagnosis improves outcomes, but many individuals remain without a confident genetic diagnosis. Improved and expanded molecular testing methods are required to improve genetic diagnosis rates and thereby improve clinical outcomes. Using primary ciliary dyskinesia (PCD) as an exemplar rare genetic respiratory disease, we developed a standardized method to identify pathogenic variants using whole transcriptome RNA-sequencing (RNA-seq) of nasal epithelial cells cultured at air-liquid interface (ALI). The method was optimized using cells from healthy volunteers, and people with rhino-pulmonary disease but no diagnostic indication of PCD. We validated the method using nasal epithelial cells from PCD patients with known genetic cause. We then assessed the ability of RNA-seq to identify pathogenic variants and the disease mechanism in PCD likely patients but in whom DNA genetic testing was inconclusive. The majority of 49 targeted PCD genes were optimally identified in RNA-seq data from nasal epithelial cells grown for 21 days at ALI culture. Four PCD-likely patients without a previous genetic diagnosis received a confirmed genetic diagnosis from the findings of the RNA-seq data. We demonstrate the clinical potential of RNA-seq of nasal epithelial cells to identify variants in individuals with genetically unsolved PCD. This uplifted genetic diagnosis should improve genetic counselling, enables family cascade screening, opens the door to potential personalised treatment and care approaches. This methodology could be implemented in other rare lung diseases such as cystic fibrosis.
Shedding light on trawl fishing activity in the Mediterranean Sea with remote sensing data
Authors: Marsaglia Luca , Parisi Antonio , Libralato Simone , Miller Nathan A , Davis Pete , Paolo Fernando S , Fiorentino Fabio , Garofalo Germana , Costantini Marco , Russo Tommaso
Published: November 2024

This study uses Synthetic Aperture Radar (SAR) vessel detections and Automatic Identification System (AIS) to predict trawl fishing intensity and distribution of fishing activity in areas where public AIS data are not available. By processing SAR data, considering spatial and temporal autocorrelation, and building a General Additive Model, a statistical relationship between SAR vessel detections and AIS fishing activity was established. The study provides spatially explicit estimates of trawler fishing activity, compared with official fleet records published by the General Fisheries Commission of the Mediterranean, revealing the distribution and intensity of trawl fishing activity not previously publicly tracked. Fishing grounds in the Strait of Sicily along the coast of Tunisia and North of Egypt showed an intensity of trawl fishing activity similar to the Adriatic Sea. This area is historically known to be subject to the highest trawling pressure in the Mediterranean, and also as one of the most heavily trawled regions in the world. The study shows that the integration of remote sensing data, such as SAR, offers a promising avenue to overcome data gaps and improve fisheries management in the Mediterranean where only a portion of the fishing fleet is publicly tracked.
Medication shortage behaviour change with multidisciplinary clinician-designed digital notification intervention
Authors: Teo Melissa , Stretton Brandon , Booth Andrew E C , Satheakeerthy Shrirajh , Howson Sarah , Evans Shaun , Kovoor Joshua , Fu Sarah , McNeil Keith , Menz Bradley , Gupta Aashray , Gibson Kieran , Tan Sheryn , Chan Weng Onn , Maddison John , Gluck Samuel , Gilbert Toby , Bacchi Stephen
Published: November 2024

Objectives

To evaluate the effect of a clinician-designed digital notification system on the use of intravenous paracetamol during a medication shortage.

Methods

An in-house digital notification platform was designed through multidisciplinary collaboration. A 4-week pre- and post-implementation methodology was employed to evaluate the effect of the intervention.

Key findings

There was significantly lower use of intravenous paracetamol in the post-implementation period compared to the pre-implementation period (median 80 doses per day, interquartile range 58 to 93, vs 94, interquartile range 83 to 122, P < .001).

Conclusions

Multidisciplinary clinician-designed digital notification platforms may assist during times of medication shortage.
The first fossil chylizine fly (Diptera: Psilidae) with a discussion on the ages of related fossil Acalyptratae
Authors: Ross Andrew J , Zhou Jiale , Hoffeins Christel , Crighton Bill
Published: November 2024

The first fossil rust fly (Diptera: Psilidae) from the Insect Bed of the Bembridge Marls of the Isle of Wight is also the first known fossil record of the subfamily Chylizinae. It is late Eocene: Priabonian in age, 34.2 Ma. Chyliza colenutti Ross, Zhou, Hoffeins & Crighton, sp. nov. is compared with 30 extant species of Chyliza and differs from them in having a relatively long 2nd basal cell compared to the discal cell. Some other fossil Acalyptratae records are reviewed and their probable ages updated. The phylogenetic position of the Psilidae is currently uncertain so the family may have appeared anytime from 70–40 million years ago.
Use of echinocandins combined with clindamycin in Pneumocystis pneumonia: a case series of 14 patients
Authors: Bilbao Idoia , Pineda Abel de la Cruz Iñigo , de Asís Carmona-Torre Francisco , Rodríguez-Mateos Mariano , Yuste Ara José Ramón , del Pozo Jose L
Published: November 2024

Background

Pneumocystis jirovecii pneumonia (PcP) is an opportunistic infection for which the standard of care is co-trimoxazole. However, safety concerns and intolerance may compromise its utility.

Objectives

To evaluate the safety and efficacy of the combination of echinocandins and clindamycin to treat PcP.

Patients and methods

We investigated 14 patients treated with a co-trimoxazole-free combined regimen that included echinocandins and clindamycin.

Results

Clinical cure was achieved in 8 out of 14 patients, while 5 had a fatal outcome due to their primary disease; however, only one patient died due to PcP.

Conclusions

Echinocandin and clindamycin may be a safe and effective alternative treatment for patients who cannot be given co-trimoxazole for PcP.
Dynamics of blood Taurine concentration and its correlation with nutritional and physiological status during the fattening period of Japanese black cattle
Authors: Takai Shuntaro , Lee Huseong , Kim Minji , Torii Shinichiro , Nishihara Koki , Oh Joonpyo , Masaki Tatsunori , Ikuta Kentaro , Iwamoto Eiji , Masuda Kota , Uemoto Yoshinobu , Terada Fuminori , Haga Satoshi , Roh Sanggun
Published: November 2024

Taurine, biosynthesized from methionine or cysteine in the liver, plays a crucial regulatory role in bile acid conjugation, antioxidant effects, and glucose and cholesterol metabolism. This may influence the metabolic changes associated with fat accumulation in beef cattle. However, the physiological role of taurine in this species has not been fully elucidated. In this study, we explored the physiological role of taurine in Japanese Black steers (Bos taurus) in different phases during the fattening period. To examine the correlation among plasma taurine concentrations, various physiological parameters, and genes related to taurine synthesis in the liver, we used biopsied liver tissues, blood samples, and rumen fluids collected from 21 steers at three different stages, i.e., early (T1; 13 mo of age), middle (T2; 20 mo of age), and late (T3; 28 mo of age) phases. Additionally, to investigate the regulatory mechanisms underlying the expression profile of taurine synthesis genes, primary bovine hepatocytes obtained from 4-wk-old Holstein calves were treated with palmitate, oleate, acetate, propionate, or β-hydroxybutyrate (BHBA). Plasma taurine and cholesterol concentrations significantly (P < 0.001) increased in the T2 phase, which is potentially attributable to increased energy intake and assimilation induced by increased intake of concentrated feed. Cysteine-sulfinic acid decarboxylase (CSAD) expression significantly increased (P < 0.01) in T2 than in other phases. The expression levels of cysteine dioxygenase type 1 (CDO1) and cholesterol 7 alpha-hydroxylase (CYP7A1) were significantly higher (P < 0.05) in T2 than in T3; moreover, the CDO1/glutamate-cysteine ligase catalytic subunit (GCLC) ratio was higher (P < 0.05) in T2 than in T1. Plasma taurine concentrations were positively correlated with plasma methionine (r = 0.51; P < 0.05) and total cholesterol (r = 0.56; P < 0.05) concentrations at T2. Relative CDO1 mRNA expression was upregulated in cultured bovine hepatocytes treated with oleate and propionate, whereas it was downregulated upon acetate treatment. These findings indicate that the increase in plasma taurine concentrations in the T2 phase is associated with changes in lipid and methionine metabolism in Japanese Black steers.
Sex hormone deficiency in male and female mice expressing the Alzheimer’s disease-associated risk-factor TREM2 R47H variant impacts the musculoskeletal system in a sex- and genotype-dependent manner
Authors: Pianeta Roquelina , Deosthale Padmini , Sanz Natasha , Kohler Rachel , Okpara Chiebuka , Arnett Matthew , Asad Iqra , Rogers Amber , Gerbig Madison , Essex Alyson , Liu Ziyue , Wallace Joseph M , Plotkin Lilian I
Published: November 2024

The R47H variant of the triggering receptor expressed on myeloid cells 2 (TREM2) is a risk factor for Alzheimer’s disease in humans and leads to lower bone mass accrual in female but not male 12-mo-old mice. To determine whether, as with aging, gonadectomy results in sex-specific musculoskeletal effects, gonad removal or SHAM surgery was performed in 4-mo-old TREM2R47H/+ mice and WT male and female littermates (n = 10-12/group), with sexes analyzed separately. Body weight was lower in males, but higher in females after gonadectomy, independently of their genotype. Gonadectomy also leads to decreased BMD in males at all sites and in the whole body (total) and spine in female mice for both genotypes. Total and femur BMD was lower in gonadectomized male mice 6-wk post-surgery, independently of the genotype. On the other hand, BMD was only lower in ovariectomized WT but not TREM2R47H/+ mice in all sites measured at this time point. Bone formation and resorption marker levels were not affected by orchiectomy, whereas CTX was higher 3 wk after surgery and P1NP showed a tendency toward lower values at the 6-wk time point only in ovariectomized WT mice. Micro-CT analyses showed no differences resulting from gonadectomy in structural parameters in femoral cortical bone for either sex, but lower tissue mineral density in males of either genotype 6-wk post-surgery. Nevertheless, biomechanical properties were overall lower in gonadectomized males of either genotype, and only for WT ovariectomized mice. Distal femur cancellous bone structure was also affected by gonadectomy in a genotype- and sex-dependent manner, with genotype-independent changes in males, and only in WT female mice. Thus, expression of the TREM2 R47H variant minimally alters the impact of gonadectomy in the musculoskeletal system in males, whereas it partially ameliorates the consequences of ovariectomy in female mice.
Building: a possibility for a post-critical perspective in educational research
Authors: Zamojski Piotr
Published: November 2024

The aim of this article is to give an example of how an exercise in post-critical educational research might be conceptualized. The example refers to an enquiry into building a public sphere around education in Poland. First, a post-critical approach in educational research is defined with reference to the two dominant perspectives of social research, namely the (neo)positivistic and the critical paradigm. Next, and following insights of Hannah Arendt and Jacques Rancière, the idea of building is presented in terms of the persistent introduction of a new beginning into a social reality through acting in line with an assumption (an axiom) that, from the point of view of critical knowledge about the current status quo, seems fictional (or impossible). Such a persistent verification of an impossible axiom aims at establishing a sphere of exception from the dominant social order, offering—through the ideas of Alain Badiou and Giorgio Agamben—a nondialectical logic of social transformation. Finally, in conclusion the article focuses on the phenomenon of condensation as one of the key results of the exemplary research project analysed throughout the text. This points to the kind of knowledge that post-critical research projects are able to bring about.