bluuebunny/crossref_metadata_2025_split huggingface dataset:
A proof-of-concept investigation into predicting follicular carcinoma on ultrasound using topological data analysis and radiomics
Authors: Thomas Andrew M , Lin Ann C , Deng Grace , Xu Yuchen , Ranvier Gustavo Fernandez , Taye Aida , Matteson David S , Lee Denise 
Published: October 2023

AbstractAimsSonographic risk patterns identified in established risk stratification systems (RSS) may not accurately stratify follicular carcinoma from adenoma, which share many similar US characteristics. The purpose of this study is to investigate the performance of a multimodal machine learning model utilizing radiomics and topological data analysis (TDA) to predict malignancy in follicular thyroid neoplasms on ultrasound.MethodsThis is a retrospective study of patients who underwent thyroidectomy with pathology confirmed follicular adenoma or carcinoma at a single academic medical center between 2010–2022. Features derived from radiomics and TDA were calculated from processed ultrasound images and high-dimensional features in each modality were projected onto their first two principal components. Logistic regression with L2 penalty was used to predict malignancy and performance was evaluated using leave-one-out cross-validation and area under the curve (AUC).ResultsPatients with follicular adenomas (n=7) and follicular carcinomas (n=11) with available imaging were included. The best multimodal model achieved an AUC of 0.88 (95% CI: [0.85, 1]), whereas the best radiomics model achieved an AUC of 0.68 (95% CI: [0.61, 0.84]).ConclusionsWe demonstrate that inclusion of topological features yields strong improvement over radiomics-based features alone in the prediction of follicular carcinoma on ultrasound. Despite low volume data, the TDA features explicitly capture shape information that likely augments performance of the multimodal machine learning model. This approach suggests that a quantitative based US RSS may contribute to the preoperative prediction of follicular carcinoma.
Biomarkers of bleeding and venous thromboembolism in patients with acute leukemia
Authors: Hisada Yohei , Archibald Sierra J. , Bansal Karan , Chen Yanjun , Dai Chen , Dwarampudi Sindhu , Balas Nora , Hageman Lindsey , Key Nigel S. , Bhatia Smita , Bhatia Ravi , Mackman Nigel , Gangaraju Radhika 
Published: October 2023

AbstractBackgroundCoagulopathy and associated bleeding and venous thromboembolism (VTE) are major causes of morbidity and mortality in patients with acute leukemia. The underlying mechanisms of these complications have not been fully elucidated.ObjectivesTo evaluate the associations between biomarker levels and bleeding and VTE in acute leukemia patients.Patients/MethodWe examined plasma levels of activators, inhibitors and biomarkers of the coagulation and fibrinolytic pathways in patients ≥18 years with newly diagnosed acute leukemia compared to healthy controls. Multivariable regression models were used to examine the association of biomarkers with bleeding and VTE in acute leukemia patients. The study included 358 patients with acute leukemia (29 acute promyelocytic leukemia [APL], 253 non-APL acute myeloid leukemia [AML] and 76 acute lymphoblastic leukemia [ALL]), and 30 healthy controls.ResultsPatients with acute leukemia had higher levels of extracellular vesicle (EV) tissue factor (TF) activity, phosphatidylserine-positive EVs, plasminogen activator inhibitor-1 (PAI-1), plasmin-antiplasmin complexes, cell-free DNA and lower levels of citrullinated histone H3-DNA complexes compared to healthy controls. APL patients had the highest levels of EVTF activity and the lowest levels of tissue plasminogen activator among the acute leukemia patients. There were 41 bleeding and 37 VTE events in acute leukemia patients. High EVTF activity was associated with increased risk of bleeding (sHR 2.30, 95%CI 0.99-5.31) whereas high PAI-1 was associated with increased risk of VTE (sHR 3.79, 95%CI 1.40-10.28) in these patients.ConclusionsOur study shows alterations in several biomarkers in acute leukemia and identifies biomarkers associated with risk of bleeding and VTE.EssentialsThe mechanisms of acute leukemia-associated bleeding and thrombosis have not been elucidated.We measured plasma biomarkers of coagulation and fibrinolysis in acute leukemia patients.Biomarkers of the coagulation and fibrinolytic pathways are altered in acute leukemia patients.EVTF activity is associated with bleeding, and PAI-1 is associated with VTE in acute leukemia.
RVOT Reconstruction in d-Transposition of the Great Arteries with Ventricular Septal Defect and Pulmonary Obstruction: Male-Female Differences in Clinical and Homograft Function
Authors: Wang Xu , Bennink Isabelle M. , Veen Kevin M. , van de Woestijne Pieter C. , van der Ven Carlijn C. E. M. , Bogers Ad J. J. C. , Andrinopoulou Eleni-Rosalina , Helbing Wim. A. , Takkenberg Johanna J.M. 
Published: October 2023

ABSTRACTBackgroundThis study investigated male-female differences in clinical and homograft outcomes in dextro-transposition of the great arteries (d-TGA) patients, with ventricular septal defect (VSD) and pulmonary stenosis/atresia (PS/PA), who underwent right ventricular outflow tract (RVOT) reconstruction with a homograft.MethodsAll d-TGA with VSD and PS/PA patients receiving a homograft for RVOT reconstruction at our center from 1986 to 2021 were included. Time-to-event analyses were used for time-related clinical outcomes and mixed-effects models to characterize homograft function.ResultsTwenty-four patients (16 males) in whom 38 homografts were implanted over time were included. Median age at the first homograft implantation was 2.56 years [IQR: 1.26-11.31] and 2.06 years [IQR: 1.28-8.13] for males and females. Two early death (both males) and five late deaths (2 males) were observed. Twenty-two RVOT reinterventions (19/3 in males/females) occurred in follow-up (males/females:345.72/173.35 patient-years). The 10-year survival probability was 87.5% (95% CI: 67.3-100) for females and 87.1% (95% CI: 71.8-100) for males. Freedom from RVOT reintervention at 10-year was 87.5% (95% CI: 67.3-100) for females and 64.9% (95% CI: 47.9-88.0) for males. RVOT peak gradient increase rate was associated with body growth rate (7.27 [95% CI: 2.08-12.45], P=0.0133).ConclusionsSubstantial male-female differences in clinical and homograft outcomes were found in d-TGA with VSD and PS/PA patients receiving a homograft for RVOT reconstruction. Male patients had a higher RVOT reintervention rate and faster progression to homograft stenotic failure compared to females. Oversized homografts might benefit children for the strong association between rates of homograft stenosis and body growth.Clinical PerspectiveWhat is new?Male patients diagnosed with d-TGA, VSD, and PS/PA demonstrated a significantly higher rate of RVOT homograft reinterventions and a more rapid progression toward homograft stenotic failure when compared with their female counterparts.The male-female differences in clinical outcomes and homograft function may be attributed, in part, to the faster body growth observed in male children, especially given the strong association between rates of homograft stenosis and body growth.What are the clinical implications?For rapidly growing young children, opting for a suitably oversized homograft might serve as a more effective solution in reducing the rate of homograft stenotic failure.By exploring the relationship between homograft stenosis rate and individual body growth rate for each child, a personalized approach can be adopted during the homograft selection process, optimizing the sizing strategy for a better clinical outcome.
Theta and alpha oscillations in human hippocampus and medial parietal cortex support the formation of location-based representations
Authors: Satish Akul , Keller Vanessa G. , Raza Sumaiyah , Fitzpatrick Shona , Horner Aidan J. 
Published: October 2023

AbstractOur ability to navigate in a new environment depends on learning new locations. Mental representations of locations are quickly accessible during navigation and allow us to know where we are regardless of our current viewpoint. Recent fMRI research using pattern classification has shown that these location-based representations emerge in the retrosplenial cortex and parahippocampal gyrus, regions theorised to be critically involved in spatial navigation. However, little is currently known about the oscillatory dynamics that support the formation of location-based representations. We used MEG to investigate region-specific oscillatory activity in a task where participants could form location-based representations. Participants viewed videos showing that two perceptually distinct scenes (180° apart) belonged to the same location. This “overlap” video allowed participants to bind the two distinct scenes together into a more coherent location-based representation. Participants also viewed control “non-overlap” videos where two distinct scenes from two different locations were shown, where no location-based representation could be formed. In a post-video behavioural task, participants successfully matched the two viewpoints shown in the overlap videos, but not the non-overlap videos, indicating they successfully learned the locations in the overlap condition. Comparing oscillatory activity between the overlap and non-overlap videos, we found greater theta and alpha/beta power during the overlap relative to non-overlap videos, specifically at time-points when we expected scene integration to occur. These oscillations localised to regions in the medial parietal cortex (precuneus and retrosplenial cortex) and the medial temporal lobe, including the hippocampus. Therefore, we find that theta and alpha/beta oscillations in the hippocampus and medial parietal cortex are likely involved in the formation of location-based representations.
DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images
Authors: Schwab Johannes , Kimanius Dari , Burt Alister , Dendooven Tom , Scheres Sjors H.W. 
Published: October 2023

AbstractHow to deal with continuously flexing molecules is one of the biggest outstanding challenges in single-particle analysis of proteins from cryo-EM images. Here, we present DynaMight, a new software tool that estimates a continuous space of conformations in a cryo-EM data set by learning 3D deformations of a Gaussian pseudo-atomic model of a consensus structure for every particle image. Inversion of the learnt deformations is then used to obtain an improved reconstruction of the consensus structure. We illustrate the performance of DynaMight for several experimental cryo-EM data sets. We also show how error estimates on the deformations may be obtained by independently training two variational autoencoders (VAEs) on half sets of the cryo-EM data, and how regularisation of the 3D deformations through the use of atomic models may lead to important artefacts due to model bias. DynaMight is distributed as free, open-source software, as part of RELION-5.
Stress-induced nucleoid remodeling inDeinococcus radioduransis associated with major changes in HU abundance and dynamics
Authors: Vauclare Pierre , Wulffelé Jip , Lacroix Françoise , Servant Pascale , Confalonieri Fabrice , Kleman Jean-Philippe , Bourgeois Dominique , Timmins Joanna 
Published: October 2023

ABSTRACTBacteria have developed a wide range of strategies to respond to stress, one of which is the rapid large-scale reorganization of their nucleoid, which is often associated with a major reprogramming of the gene expression profile. Nucleoid associated proteins (NAPs) are believed to be major actors in this process, but the molecular mechanisms underlying stress-induced nucleoid remodeling remain poorly understood. Here, using the radiation resistant bacterium,D. radiodurans, as a model, and advanced fluorescence microscopy approaches, we examined the changes in nucleoid morphology and compaction induced by either entry into stationary phase or exposure to UV-C light, and characterized the associated changes in abundance and dynamics of the major NAP inD. radiodurans, the heat-unstable (HU) protein. While both types of stress induced a similar macroscopic rearrangement of the nucleoid into a more compact structure, HU diffusion was significantly reduced in stationary phase cells, but was instead dramatically increased following exposure to UV-C, suggesting that the underlying mechanisms of remodeling are distinct. Furthermore, a detailed comparison of the cellular response to sublethal and lethal doses of UV-C light revealed that UV-induced nucleoid remodeling involves a rapid nucleoid condensation step associated with increased HU diffusion and abundance, followed by a slower decompaction phase to restore normal nucleoid morphology and HU dynamics, before cell growth and division can resume. Together, these findings shed light on the diversity and complexity of stressed-induced nucleoid remodeling processes in bacteria.
UGGT1-mediated reglucosylation ofN-glycan competes with ER-associated degradation of unstable and misfolded glycoproteins
Authors: Ninagawa Satoshi , Matsuo Masaki , Ying Deng , Oshita Shuichiro , Aso Shinya , Matsushita Kazutoshi , Taniguchi Mai , Fueki Akane , Yamashiro Moe , Sugasawa Kaoru , Saito Shunsuke , Imami Koshi , Kizuka Yasuhiko , Sakuma Tetsushi , Yamamoto Takashi , Yagi Hirokazu , Kato Koichi , Mori Kazutoshi 
Published: October 2023

ABSTRACTHow the fate (folding versus degradation) of glycoproteins is determined in the endoplasmic reticulum (ER) is an intriguing question. Monoglucosylated glycoproteins are recognized by lectin chaperones to facilitate their folding, whereas glycoproteins exposing well-trimmed mannoses are subjected to glycoprotein ER-associated degradation (gpERAD); we have elucidated how mannoses are sequentially trimmed by EDEM family members (George et al., 2020, 2021 eLife). Although reglucosylation by UGGT was previously reported to have no effect on substrate degradation, here we directly tested this notion using cells with genetically disrupted UGGT1/2. Strikingly, the results showed that UGGT1 delayed the degradation of misfolded substrates and unstable glycoproteins including ATF6α. An experiment with a point mutant of UGGT1 indicated that the glucosylation activity of UGGT1 was required for the inhibition of early glycoprotein degradation. These and overexpression-based competition experiments suggested that the fate of glycoproteins is determined by a tug-of-war between structure formation by UGGT1 and degradation by EDEMs. We further demonstrated the physiological importance of UGGT1, since ATF6α cannot function properly without UGGT1. Thus, our work strongly suggests that UGGT1 is a central factor in ER protein quality control via regulation of both glycoprotein folding and degradation.
Dose-dependent effects of histone methyltransferase NSD2 on site-specific double-strand break repair
Authors: Iwasaki Koh , Tojo Akari , Kobayashi Haruka , Kamimura Yoshitaka , Horikoshi Yasunori , Fukuto Atsuhiko , Sun Jiying , Yasui Manabu , Honma Masamitsu , Okabe Atsushi , Fujiki Ryoji , Kaneda Atsushi , Tashiro Satoshi , Sassa Akira , Ura Kiyoe 
Published: October 2023

AbstractHistone modifications are catalyzed and recognized by specific proteins to regulate dynamic DNA metabolism processes. NSD2 is a histone H3 lysine 36 (H3K36)-specific methyltransferase that associates both with various transcription regulators and DNA repair factors. Specifically, it has been implicated in the repair of DNA double-strand breaks (DSBs); however, the role of NSD2 during DSB repair remains enigmatic. Here, we show that NSD2 does not accumulate at DSB sites and that the localization of NSD2 at chromatin is maintained even after DSB formation. Using three different DSB repair reporter systems, which contained the endonuclease site in the active thymidine kinase gene (TK) locus, we demonstrated separate dose-dependent effects of NSD2 on HR, canonical-NHEJ (c-NHEJ), and non-canonical-NHEJ (non-c-NHEJ). Endogenous NSD2 has a role in repressing non-c-NHEJ, without affecting DSB repair efficiency by HR or total NHEJ. Furthermore, overexpression of NSD2 promotes c-NHEJ repair suppressing HR repair. Therefore, we propose that NSD2 has functions in chromatin integrity at the active regions during DSB repair.
UPL3 Promotes BZR1 Degradation, Growth Arrest, and Seedling Survival under Starvation Stress inArabidopsis
Authors: Zhang Zhenzhen , Zhang Hongliang , Gonzalez Efren , Grismer Tarabryn , Xu Shou-Ling , Wang Zhi-Yong 
Published: October 2023

AbstractBRASSINAZONE RESISTANT 1 (BZR1) is a key transcription factor of the brassinosteroid signaling pathway but also a signaling hub that integrates diverse signals that modulate plant growth. Previous studies have shown that starvation causes BZR1 degradation, but the underlying mechanisms are not understood. Here we performed quantitative proteomic analysis of BZR1 interactome under starvation conditions and identified two BZR1-interacting ubiquitin ligases, BAF1 and UPL3. Compared to the wild type, theupl3mutants show long hypocotyl and increased BZR1 levels when grown under sugar starvation conditions but not when grown on sugar-containing media, indicating a role of UPL3 in BZR1 degradation specifically under starvation conditions. Theupl3mutants showed a reduced survival rate after starvation treatment, supporting the importance of UPL3-mediated BZR1 degradation and growth arrest for starvation survival. Treatments with inhibitors of TARGET of RAPAMYCIN (TOR) and autophagy altered BZR1 level in the wild type but were less effective inupl3, suggesting that UPL3 mediates the TOR-regulated and autophagy-dependent degradation of BZR1. Further, the UPL3 protein level is increased posttranscriptionally by starvation but decreased by sugar treatment. Our study identifies UPL3 as a key component that mediates sugar regulation of hormone signaling pathways, important for optimal growth and survival in plants.IN A NUTSHELLBackgroundThe coordination between signaling pathways that monitor the levels of photosynthate and growth hormones is crucial for optimizing growth and survival, but the underlying mechanisms are not fully understood. When the sugar level is low, the BZR1 transcription factor of the brassinosteroid (BR) signaling pathway is degraded, and hence growth is attenuated to prevent starvation and enhance survival. When sugar is sufficient, sugar signaling inhibits BZR1 degradation and enables BR promotion of plant growth. The key component that mediates starvation-induced BZR1 degradation remains unknown.QuestionWhat proteins interact with BZR1 and mediate its degradation under sugar starvation?FindingWe performed immunoprecipitation mass spectrometry analysis of BZR1 in starvation-treated Arabidopsis and identified many BZR1-interacting proteins, including two E3 ligases UPL3 and BAF1. Genetic analysis showed that UPL3 plays a specific and prominent role in promoting autophagy-dependent BZR1 degradation and plant survival under sugar-starvation conditions.Next stepHow sugar-TOR signaling regulates UPL3 level remains to be studied in the future.
Modulation by NPYR underlies experience-dependent, sexually dimorphic learning
Authors: Peedikayil-Kurien Sonu , Haque Rizwanul , Gat Asaf , Oren-Suissa Meital 
Published: October 2023

AbstractThe evolutionary paths taken by each sex within a given species sometimes diverge, resulting in behavioral differences. Given their distinct needs, the mechanism by which each sex learns from a shared experience is still an open question. Here, we reveal sexual dimorphism in learning:C. elegansmales do not learn to avoid the pathogenic bacteria PA14 as efficiently and rapidly as hermaphrodites. Notably, neuronal activity following pathogen exposure was dimorphic: hermaphrodites generate robust representations, while males, in line with their behavior, exhibit contrasting representations. Transcriptomic and behavioral analysis revealed that the neuropeptide receptornpr-5, an ortholog of the mammalian NPY receptor, regulates male learning by modulating neuronal activity. Furthermore, we show the dependency of the males’ decision-making on their sexual status and demonstrate the pivotal role ofnpr-5as a modulator of incoming sensory cues. Taken together, we portray sex-specific plasticity in behavior toward a shared experience by modulating learning.
AI-enabled human capital management (HCM) software adoption using full consistency method (FUCOM): evidence from banking industry
Authors: Yadav Rama Shankar , Kaya Sema Kayapinar , Pant Abhay , Tiwari Anurag 
Published: October 2023

PurposeArtificial intelligence (AI)-based human capital management (HCM) software solutions represent a potentially effective way to leverage and streamline a bank’s human resources. However, despite the attractiveness of AI-based HCM solutions to improve banks’ effectiveness, to the best of the authors’ knowledge, there are no current studies that identify critical success factors (CSFs) for adopting AI-based HCM in the banking sector. This study aims to fill this gap by investigating CSFs for adopting AI-based HCM software solutions in the banking sector.Design/methodology/approachFull consistency method methodology and technology–organization–environment, economic and human framework are used for categorizing and ranking CSFs.FindingsThe study identifies the technological and environmental dimensions as the most and least important dimensions for AI-based HCM adoption in banks. Among specific CSFs, compatible technology facilities, sufficient privacy and security and relative advantages of technology over competing technologies were identified as the most important. Implementation of AI-based HCM solutions requires significant outlays of resources, both human and financial, for banks.Originality/valueThe study provides bank administrators a set of objective parameters and criterion to evaluate the feasibility of adopting a particular AI-based HCM solution in banks.
Information governance orientation, supply chain strategy type and performance outcomes
Authors: In Joonhwan , Bradley Randy , Bichescu Bogdan C. , Han Sumin 
Published: October 2023

PurposeThis study aims to examine the performance implications of an information governance (IG) framework for managing, controlling access to and securing information, focusing on (1) the performance benefits of an organization's IG orientation and (2) how the configuration of IG orientation and supply chain (SC) strategy type relate to performance outcomes.Design/methodology/approachThis study leverages multiple secondary sources for US hospitals, serving as the context for the study. It also employs cluster analysis to develop an SC strategy taxonomy, namely sophisticated and delivery-focused SC strategies. The proposed research model is tested using a robust regression to mitigate the influence of outliers and produce more accurate estimates.FindingsIG orientation is positively associated with financial performance and patient experience, and IG-oriented hospitals with a sophisticated SC strategy realize more financial benefits and achieve better patient care experiences compared to other configurations. Regardless of SC strategy type, IG-oriented hospitals offer better care experiences than non-IG-oriented hospitals.Practical implicationsThis paper offers empirical evidence that a hospital's IG orientation and SC strategy jointly affect financial outcomes and patient experience. For hospitals, an organization-wide framework for governing information streamlines both intra- and inter-organizational information flows and improves care delivery throughout a patient's care experience.Originality/valueThis is one of a few studies that empirically examine the performance implications of governance of information in the domain of supply chain management (SCM). This study also develops an SC strategy taxonomy for the healthcare context and offers a springboard for research in service SC strategy.