bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multi-Modal Genomic Knowledge Distillation Framework for Drug Response Prediction
Authors: Ge Shuang , Sun Shuqing , Xu Huan , Cheng Qiang , Ren Zhixiang 
Published: October 2024

AbstractPrecision oncology utilizes genomic data to tailor treatment to individuals. Cancer drug sensitivity studies can predict the response levels of different drugs for the same cultured cancer cell line, which is beneficial for personalized medicine. Recent studies have demonstrated that integrating multi-modal genomic data, e.g., gene expression, mutation, copy number alteration, methylation, can provide comprehensive knowledge and improve drug response prediction. Although multimodal genomic profiles are generally available from public datasets, only gene expression data is commonly used in clinical settings. In this study, we propose a framework for privileged information knowledge distillation to transfer knowledge from a multi-modal genomic teacher network, using only gene expression for inference. Specifically, we train a teacher network by feature re-weighting based on inter-modality dependencies and align the inter-sample correlations through our proposed relation-aware differentiation distillation. Experiments on the Genomics of Drug Sensitivity in Cancer (GDSC) dataset demonstrate that our framework improves drug response prediction by about 6% compared to the baseline and outperforms state-of-the-art methods. Transferable studies performed on missing GDSC data and clinical datasets further confirm the feasibility of our model for predicting drug responses using only gene expression data.
Enhancing pigment production by a chromogenic bacterium (Exiguobacterium aurantiacum) using tomato waste extract: A Statistical approach
Authors: Zeleke Birhanu , Muleta Diriba , Dinka Hunduma , Tsegaye Dereje , Hassen Jemal 
Published: October 2024

AbstractThere is high demand for microbial pigments as promising alternative for synthetic pigments basically for safety and economic reasons. This study aimed at the optimization of yellowish-orange pigment production by Exiguobacterium aurantiacum using agro-waste extract as growth substrate. Air samples were collected using depositional method. Pure cultures of pigment producing bacteria were isolated by subsequent culturing on fresh nutrient agar medium and the potent isolate was identified using MALDI-TOF technique. Culture conditions were screened using Plackett-Burman design and the most three significant variables were optimized by response surface methodology. Fermentation was conducted in 150 mL agro-waste decoctions from which tomato waste extract was selected because of higher optical density of the culture compared to other agro-waste extracts. Pigment was extracted by solvent extraction method and the best solvent was selected based on its ability to dissolve the culture suspension. The pigment was characterized using spectroscopic and chromatographic techniques. Culture agitation rate, initial medium pH and concentration of yeast extract were identified as the most significant (p< 0.0001) variables affecting pigment production. At optimized conditions, 0.96 g/L of pigment was extracted from 4.73 g/L of culture biomass and the extracted pigment under optimized conditions was 1.6 times higher than the pigment extracted under un-optimized conditions. The spectroscopic and chromatographic analyses demonstrated the presence of different functional groups and carotenoids were identified as parts of the molecule responsible for the yellowish-orange pigmentation of the extract. This study demonstrated the potential for optimization of pigment production by bacteria using agro-waste extract as substrate. Hence, the current findings strongly encourage for further study at a large-scale level for industrial production.
Impact of media brand on cefiderocol disk diffusion results
Authors: DeMarco MG , Field AM , Donohue LE , Cox HL , Kidd TS , Barry KE , Mathers AJ 
Published: October 2024

ABSTRACTIntroductionCefiderocol is a siderophore cephalosporin that utilizes iron transport systems to cross cell membranes. This unique strategy complicates antimicrobial susceptibility testing (AST) due to variable iron content in media. While guidance for using iron-depleted media exists for broth microdilution (BMD), disk diffusion (DD) with commercial media is a common AST method in the clinical laboratory. We investigated cefiderocol DD result variability using multiple Mueller-Hinton agar (MHA) brands.MethodsDD results using Remel (Thermo Fisher Scientific, San Diego, CA), Hardy (Hardy Diagnostics, Springboro, OH), and BBL (Becton Dickenson, East Rutherford, NJ) MHA were compared to BMD using iron-depleted cation-adjusted Mueller-Hinton broth. BMD reproducibility, BMD trailing endpoints, and DD intra- and inter-brand variability in zones of inhibition were investigated.ResultsForty-seven multidrug-resistant clinical isolates and three Antibiotic Resistance bank isolates composed ofPseudomonas aeruginosa, carbapenemase (CP-) and non-carbapenemase-producing (non-CP-) carbapenem-resistant Enterobacterales (CRE),Acinetobacter baumanniicomplex,Stenotrophomonas maltophilia, andBurkholderia cepaciacomplex were tested. Categorical agreement (CA) ≥90% was only demonstrated using CLSI breakpoints with BBL agar. Intra- and inter-brand variability in DD were greatest forP. aeruginosaand CRE, with 30% (6/20) and 16.7% (3/18) exhibiting discrepant AST interpretations, respectively. Isolates not susceptible to cefiderocol via BMD were commonly associated with AST interpretation errors and lower CA.ConclusionsUsing commercial MHA for DD resulted in frequent AST interpretation discrepancies, particularly for isolates that were not susceptible to cefiderocol by BMD. Methods and quality control may need to be revisited to ensure the reliability of DD for cefiderocol AST.IMPORTANCE STATEMENTThe novel mechanism of action of cefiderocol overcomes a variety of resistance mechanisms associated with gram-negative bacteria and positions the agent as an attractive option for infections involving multidrug-resistant pathogens. The availability of accurate, timely antimicrobial susceptibility testing methods for cefiderocol in clinical microbiology laboratories is critical as cefiderocol-resistant isolates have been described and may contribute to treatment failure. Iron-depleted broth microdilution testing may not be feasible for many clinical laboratories. While disk diffusion is an appealing, practical method to implement, our data demonstrate reproducibility issues across agar brands, most notably for organisms that do not test susceptible to cefiderocol via broth microdilution. Discrepant errors and misclassifications of resistant isolates as susceptible, and susceptible isolates as resistant, may mislead clinicians and compromise treatment efficacy. More work is needed to standardize practical yet reproducible methods for cefiderocol antimicrobial susceptibility testing.
Modulation of heteromeric glycine receptor function through high concentration clustering
Authors: Yu Hailong , Wang Weiwei 
Published: October 2024

SummaryIon channels are targeted by many drugs for treating neurological, musculoskeletal, renal and other diseases. These drugs bind to and alter the function of individual channels to achieve desired therapeutic effects. However, many ion channels function in high concentration clusters in their native environment. It is unclear if and how clustering modulates ion channel function. Human heteromeric glycine receptors (GlyRs) are the major inhibitory neurotransmitter receptors in the spinal cord and are active targets for developing chronic pain medications. We show that the α2β heteromeric GlyR assembles with the master postsynaptic scaffolding gephyrin (GPHN) into micron-sized clustered at the plasma membrane after heterologous expression. The inhibitory trans- synaptic adhesion protein neuroligin-2 (NL2) further increases both the cluster sizes and GlyR concentration. The apparent glycine affinity increases monotonically as a function of GlyR concentration but not with cluster size. We also show that ligand re-binding to adjacent GlyRs alters kinetics but not chemical equilibrium. A positively charged N- terminus sequence of the GlyR β subunit was further identified essential for glycine affinity modulation through clustering. Taken together, we propose a mechanism where clustering enhances local electrostatic potential, which in turn concentrates ions and ligands, modulating the function of GlyR. This mechanism is likely universal across ion channel clusters found ubiquitously in biology and provides new perspectives in possible pharmaceutical development.
A major disease-related point mutation in spastin alters dramatically the dynamics and allostery of the motor
Authors: Kahawatte Shehani , Macke Amanda C. , Clair Carter St. , Dima Ruxandra I. 
Published: October 2024

AbstractSpastin is a microtubule-severing AAA+ ATPase that is highly expressed in neu-ronal cells and plays a crucial role in axonal growth, branching, and regeneration. This machine oligomerizes into hexamers in the presence of ATP and the microtubule carboxy-terminal tails (CTTs). Conformational changes in spastin hexamers, pow-ered by ATP hydrolysis, apply forces on the microtubule, ultimately leading to the severing of the filament. Mutations disrupt the normal function of spastin, impair-ing its ability to sever microtubules effectively and leading to abnormal microtubule dynamics in neurons characteristic for the set of neurodegenerative disorders called hereditary spastic paraplegias (HSP). Experimental studies have identified the HSP-related R591S (Drosophila melanogasternumbering) mutation as playing a crucial role in spastin. Given its significant role in HSP, we employed a combination of molecular dynamics simulations with machine learning and graph network based approaches to identify and quantify the perturbations caused by the R591S HSP mutation on spastin’s dynamics and allostery with functional implications. We found that the functional hex-amer, upon the HSP-related mutation, loses the ability to execute the primary motion associated with the severing action. The study of allosteric changes upon the mutation showed that the regions that are most perturbed are those involved in the formation of the inter-protomer contacts. The mutation induces rigidity in the allosteric networks of the motor making it more likely to experience loss of function as any applied per-turbations could not be easily dissipated by passing through a variety of alternative paths as in the wild-type (WT) spastin.
Ketogenesis protects against MASLD-MASH progression through mechanisms that extend beyond overall fat oxidation rate
Authors: Queathem Eric D. , Stagg David B. , Nelson Alisa B. , Chaves Alec B. , Crown Scott B. , Fulghum Kyle , Andre d’Avignon D. , Ryder Justin R. , Bolan Patrick J. , Hayir Abdirahman , Gillingham Jacob R. , Jannatpour Shannon , Rome Ferrol I. , Williams Ashley S. , Muoio Deborah M. , Ikramuddin Sayeed , Hughey Curtis C. , Puchalska Patrycja , Crawford Peter A. 
Published: October 2024

AbstractThe progression of metabolic-dysfunction-associated steatotic liver disease (MASLD) to metabolic-dysfunction-associated steatohepatitis (MASH) involves complex alterations in both liver-autonomous and systemic metabolism that influence the liver’s balance of fat accretion and disposal. Here, we quantify the relative contribution of hepatic oxidative pathways to liver injury in MASLD-MASH. Using NMR spectroscopy, UHPLC-MS, and GC-MS, we performed stable-isotope tracing and formal flux modeling to quantify hepatic oxidative fluxes in humans across the spectrum of MASLD-MASH, and in mouse models of impaired ketogenesis. We found in humans with MASH, that liver injury correlated positively with ketogenesis and total fat oxidation, but not with turnover of the tricarboxylic acid cycle. The use of loss-of-function mouse models demonstrated that disruption of mitochondrial HMG-CoA synthase (HMGCS2), the rate-limiting step of ketogenesis, impairs overall hepatic fat oxidation and induces a MASLD-MASH-like phenotype. Disruption of mitochondrial β-hydroxybutyrate dehydrogenase (BDH1), the terminal step of ketogenesis, also impaired fat oxidation, but surprisingly did not exacerbate steatotic liver injury. Taken together, these findings suggest that quantifiable variations in overall hepatic fat oxidation may not be a primary determinant of MASLD-to-MASH progression, but rather, that maintenance of hepatic ketogenesis could serve a protective role through additional mechanisms that extend beyond quantified overall rates of fat oxidation.
Visualizing developmental dynamics of nuclear morphology and transport machinery inDrosophila
Authors: Shindo Yuki , Balachandra Shruthi , Amodeo Amanda A. 
Published: October 2024

AbstractCommunication between the cytoplasm and the nucleus requires a continuous exchange of molecules across the nuclear envelope (NE). The nuclear pore complex (NPC) is the gateway embedded in the NE through which cargo moves, while transport receptors mediate the passage of macromolecules through the NPC. Although their essential role as the components of the nuclear transport machinery has been extensively studied, how these factors respond to developmental and environmental cues has been underexplored. Here we tag the nucleoporin Nup96 and the transport receptor Impβ with mEGFP and mScarlet-I at their endogenous loci inDrosophila. We demonstrate the functionality of these markers in multiple tissues and offer new options for better visualization of nuclear morphology in densely packed, complex tissues. Then, we characterize the spatiotemporal dynamics of these markers in multiple developmental contexts. We find that Nup96 and Impβ form cytoplasmic puncta, whose size, numbers, and co-localization patterns change dynamically during oogenesis and early embryogenesis. Moreover, we find that the abundance of NPCs per nucleus decreases during early embryogenesis, complementing the emerging model in which NPCs play a regulatory role in development. The tools and observations described here will be useful in understanding the dynamic regulation of nuclear morphology and transport machinery in development.
Contour deformations for nonholomorphic actions
Authors: Lawrence Scott , Valgushev Semeon , Xiao Jianan , Yamauchi Yukari 
Published: October 2024

We show how contour deformations may be used to control the sign problem of lattice Monte Carlo calculations with nonholomorphic Boltzmann factors. Such actions arise naturally in quantum mechanical scattering problems. The approach is demonstrated in conjunction with the holomorphic gradient flow. As our central example we compute the real-time evolution of a particle in a one-dimensional analog of the Yukawa potential.

Published by the American Physical Society
2024
Advocating a place-space duality for an accounting research agenda
Authors: Yang ChunLei , Scapens Robert W. , Humphrey Christopher 
Published: October 2024

PurposeThe paper proposes a place-space duality, rather than a dualism, for accounting research.Design/methodology/approachThe discussion is informed by the literature in human geography, which, while developing the concept of space, has made an important distinction between abstract space and place as a site of experiential learning and memory.FindingsThe lack of a concept of place is a serious omission in the accounting literature and perpetuates an abstract sense of space, which can restrict the scope of accounting research.Research limitations/implicationsThe paper calls for further research to study accounting in place and to explore both the collective and individual senses of place, as well as conscious and unconscious place associations. We recognise that there is limited prior accounting research on this topic and that there are challenges in conducting such interdisciplinary research, especially as there is a lack of common ground between research in human geography and accounting and little integration of the two literatures.Practical implicationsThe paper proposes an accounting research agenda based on a place-space duality, which reflects the strength of people-place relationships, including place identities, place attachment and place dependence.Originality/valueThe paper provides a critique of the conceptualisation of space in accounting research, identifies place-space as a duality (rather than a dualism) and suggests a novel distinction between studying accounting in context and in place.
Work-related factors affecting mental well-being of young construction workers in South Australia
Authors: Tennakoon Tennakoon Mudiyanselage Maheshi Pabasara , Ranasinghe Udara , Samaraweera Aparna , Rameezdeen Raufdeen , Gallage Sasanka , Newman William Robert , White Benjamin James , Lim Delvin Noel Tze Wei 
Published: October 2024

PurposeMany work-related factors particularly affect the mental well-being of young construction workers and subsequently affect their productivity at work. Young construction workers in South Australia are more vulnerable than other workers because they consider the distress arising from work-related factors to be part of adapting to a new work life. Therefore, this study seeks to draw out the work-related factors that affect the mental well-being of young construction workers.Design/methodology/approachThe study employed a sequential mixed method approach including a preliminary qualitative case study and a quantitative survey. Around 20 interviews across two organisations were conducted in the initial case study and content analysis was used to contextualise the factors and identify new factors. Then, the outcome of the case study was fed into a questionnaire survey for further analysis. The survey received 43 valid responses. Principal component analysis (PCA) was performed on the survey outcome to assess and categorise the work-related factors.FindingsThe findings indicate ten prominent work-related factors contributing to poor mental well-being of young construction workers related to three main categories of factors, namely “nature of work”, “task-related stress” and “unsupportive behaviour”. The work-related factors that have the greatest impact on mental well-being are the machoism culture of industry, work overload and workplace bullying.Originality/valueThe outcome from this study enhances the understanding of key work-related factors affecting the mental well-being of young construction workers. Research findings would also help inform the development of clear, industry-informed initiatives tailored to protect and support young construction workers.
Unsafe behavior identification on construction sites by combining computer vision and knowledge graph–based reasoning
Authors: Mei Xinyu , Xu Feng , Zhang Zhipeng , Tao Yu 
Published: October 2024

PurposeWorkers' unsafe behavior is the main cause of construction safety accidents, thereby highlighting the critical importance of behavior-based management. To compensate for the limitations of computer vision in tackling knowledge-intensive issues, semantic-based methods have gained increasing attention in the field of construction safety management. Knowledge graph provides an efficient and visualized method for the identification of various unsafe behaviors.Design/methodology/approachThis study proposes an unsafe behavior identification framework by integrating computer vision and knowledge graph–based reasoning. An enhanced ontology model anchors our framework, with image features from YOLOv5, COCO Panoptic Segmentation and DeepSORT integrated into the graph database, culminating in a structured knowledge graph. An inference module is also developed, enabling automated the extraction of unsafe behavior knowledge through rule-based reasoning.FindingsA case application is implemented to demonstrate the feasibility and effectiveness of the proposed method. Results show that the method can identify various unsafe behaviors from images of construction sites and provide mitigation recommendations for safety managers by automated reasoning, thus supporting on-site safety management and safety education.Originality/valueExisting studies focus on spatial relationships, often neglecting the diversified spatiotemporal information in images. Besides, previous research in construction safety only partially automated knowledge graph construction and reasoning processes. In contrast, this study constructs an enhanced knowledge graph integrating static and dynamic data, coupled with an inference module for fully automated knowledge-based unsafe behavior identification. It can help managers grasp the workers’ behavior dynamics and timely implement measures to correct violations.
Addressing diversity in flux: identity work, identity negotiation and intersectionality insights
Authors: Donmanige Iresha , Almeida Shamika , Frino Betty 
Published: October 2024

PurposeDiversity management literature is at a crossroads with limitations in producing novel insights due to its heavy reliance on the etic approach and surface-level diversity. This paper reviews identity work, identity negotiation and intersectionality to propose an interdisciplinary lens that offers new insights and suggestions for future research that will advance the diversity management literature.Design/methodology/approachOur paper advances methods in the diversity management literature by reviewing interdisciplinary research using a dual approach: a bibliometric analysis of the vast literature examining 323 papers published between 1987 and 2023, supplemented by a summary review of the identified thematic clusters.FindingsThis study identified seven thematic clusters around identity construction, transformation and navigation processes. The study highlights significant research gaps in (1) context-specificity, (2) deep-level forms of diversity, (3) lack of focus on meso-level stakeholders, and most importantly (4) lack of focus on the interplay of micro-level and meso-level interactions.Originality/valueThis paper contributes in three ways. Firstly, it pioneers a dual approach to comprehending the research landscape on identity work, identity negotiation and intersectionality, employing bibliometric analysis and summary review. Secondly, with its interdisciplinary reach, it advocates for a more inclusive diversity management approach, exploring micro-meso-level interaction through new lenses. Lastly, it offers theoretical and practical contributions by proposing an integrated multiple lens to better address the challenges and tensions of an increasing diversity of the workforce.
Microfinance institution and moneylenders in a segmented rural credit market
Authors: Das Abhirupa , Sinha Uday Bhanu 
Published: October 2024

Purpose
The effectiveness of microfinance institutions (MFIs) in rescuing poor borrowers from “clutches of” moneylenders has been a much-debated topic over the past few decades. This paper aims to contribute by presenting a model of competition between a socially motivated MFI and profit-maximizing moneylenders when market segmentation exists.

Design/methodology/approach
A principal–agent model is used to characterize equilibrium conditions under scenarios where only moneylenders operate, only MFI operates and when both co-exist to pose comparative results effectively.

Findings
The authors find unambiguous benefits arising when a welfare-maximizing MFI enters the market. However, there are benefits to having local agents like moneylenders on the ground who also have informational advantages.

Originality/value
To the best of authors’ knowledge, this study is the first to evaluate the competition between MFI and moneylenders under the framework of captive and noncaptive segments with a mandatory savings requirement.