bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRS: a method for determining transcript termini from RNAtag-seq sequencing data
Authors: Bar Amir , Argaman Liron , Eldar Michal , Margalit Hanah 
Published: November 2023

AbstractIn bacteria, determination of the 3’ termini of transcripts plays an essential role in regulation of gene expression, affecting the functionality and stability of the transcript. Several experimental approaches were developed to identify the 3’ termini of transcripts, however, these were applied only to a limited number of bacteria and growth conditions. Here we present a straightforward approach to identify 3’ termini from widely available RNA-seq data without the need for additional experiments. Our approach relies on the observation that the RNAtag-seq sequencing protocol results in overabundance of reads mapped to transcript 3’ termini. We present TRS (Termini by Read Starts), a computational pipeline exploiting this property to identify 3’ termini in RNAtag-seq data, and show that the identified 3’ termini are highly reliable. Since RNAtag-seq data are widely available for many bacteria and growth conditions, our approach paves the way for studying bacterial transcription termination in an unprecedented scope.
Dermis resident macrophages orchestrate localized ILC2 eosinophil circuitries to promote non-healing cutaneous leishmaniasis
Authors: Lee Sang Hun , Kang Byunghyun , Kamenyeva Olena , Ferreira Tiago Rodrigues , Cho Kyoungin , Khillan Jaspal S. , Kabat Juraj , Kelsall Brian L. , Sacks David L. 
Published: November 2023

AbstractTissue-resident macrophages are critical for tissue homeostasis and repair. We previously showed that dermis-resident macrophages produce CCL24 which mediates their interaction with IL-4+ eosinophils, required to maintain their M2-like properties in the TH1 environment of the Leishmania major infected skin. Here, we show that thymic stromal lymphopoietin (TSLP) and IL-5+ type 2 innate lymphoid cells are also required to maintain dermis-resident macrophages and promote infection. Single cell RNA sequencing reveals the dermis-resident macrophages as the sole source of TSLP and CCL24. Generation of Ccl24-cre mice permits specific labeling of dermis-resident macrophages and interstitial macrophages from other organs. Selective ablation of TSLP in dermis-resident macrophages reduces the numbers of IL-5+ type 2 innate lymphoid cells, eosinophils and dermis-resident macrophages, and ameliorates infection. Our findings demonstrate that dermis-resident macrophages are self-maintained as a replicative niche for L. major by orchestrating localized type 2 circuitries with type 2 innate lymphoid cells and eosinophils.
Mechanisms of synthetic lethality between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta targeting
Authors: Ronson George E. , Starowicz Katarzyna , Anthony Elizabeth J. , Piberger Ann Liza , Clarke Lucy C. , Garvin Alexander J. , Beggs Andrew D. , Whalley Celina M. , Edmonds Matthew J. , Beesley James F. J. , Morris Joanna R. 
Published: November 2023

AbstractA synthetic lethal relationship exists between disruption of polymerase theta (Polθ), and loss of either 53BP1 or homologous recombination (HR) proteins, including BRCA1; however, the mechanistic basis of these observations are unclear. Here we reveal two distinct mechanisms of Polθ synthetic lethality, identifying dual influences of 1) whether Polθ is lost or inhibited, and 2) the underlying susceptible genotype. Firstly, we find that the sensitivity of BRCA1/2- and 53BP1-deficient cells to Polθ loss, and 53BP1-deficient cells to Polθ inhibition (ART558) requires RAD52, and appropriate reduction of RAD52 can ameliorate these phenotypes. We show that in the absence of Polθ, RAD52 accumulations suppress ssDNA gap-filling in G2/M and encourage MRE11 nuclease accumulation. In contrast, the survival of BRCA1-deficient cells treated with Polθ inhibitor are not restored by RAD52 suppression, and ssDNA gap-filling is prevented by the chemically inhibited polymerase itself. These data define an additional role for Polθ, reveal the mechanism underlying synthetic lethality between 53BP1, BRCA1/2 and Polθ loss, and indicate genotype-dependent Polθ inhibitor mechanisms.
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms
Authors: Carrión Ornella , Li Chun-Yang , Peng Ming , Wang Jinyan , Pohnert Georg , Azizah Muhaiminatul , Zhu Xiao-Yu , Curson Andrew R. J. , Wang Qing , Walsham Keanu S. , Zhang Xiao-Hua , Monaco Serena , Harvey James M. , Chen Xiu-Lan , Gao Chao , Wang Ning , Wang Xiu-Juan , Wang Peng , Giovanonni Stephen J. , Lee Chih-Ping , Suffridge Christopher P. , Zhang Yu , Luo Ziqi , Wang Dazhi , Todd Jonathan D. , Zhang Yu-Zhong 
Published: November 2023

AbstractDimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase ‘Ddd’ or ‘Alma’ enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.
Customisable IT tool for on-field assessments to support disaster management
Authors: Grimaz Stefano , Malisan Petra , Zorzini Fabio , Grimaz Loris , Bettuzzi Mauro 
Published: November 2023

AbstractInformation and technology (IT) based tools are widely used in all phases of the disaster management cycle (DMC), improving the effectiveness of the prevision-prevention, preparedness, response, and recovery phases. The availability of on-field collected data provides an answer to the need to represent the scenario in which decision-makers will intervene. In this context, disaster management experience has shown that in many cases the users of on-field assessment outcomes (i.e., decision-makers) need: a data collection tool quickly and simply adaptable to better respond to specific and conditional needs; the automated elaboration of situation results; and the ability to exchange the information between the different phases of the DMC. This paper illustrates the IT tool, called "SPRINT-Engine", which was developed to meet these requirements. The SPRINT-Engine has been specifically developed and improved to permit easy and rapid customizability, even in near real-time. The paper presents some applications in real cases of on-field assessment managed by SPRINT-Lab researchers in support of institutions in various activities and projects at different scales and in different phases of the DMC.
Cellular dynamics as a marker of normal-to-cancer transition in human cells
Authors: Marques M. P. M. , de Carvalho A. L. M. Batista , Martins C. B. , Silva J. D. , Sarter M. , García Sakai V. , Stewart J. R. , de Carvalho L. A. E. Batista 
Published: November 2023

AbstractNormal-to-cancer (NTC) transition is known to be closely associated to cell´s biomechanical properties which are dependent on the dynamics of the intracellular medium. This study probes different human cancer cells (breast, prostate and lung), concomitantly to their healthy counterparts, aiming at characterising the dynamical profile of water in distinct cellular locations, for each type of cell, and how it changes between normal and cancer states. An increased plasticity of the cytomatrix is observed upon normal-to-malignant transformation, the lung carcinoma cells displaying the highest flexibility followed by prostate and breast cancers. Also, lung cells show a distinct behaviour relative to breast and prostate, with a higher influence from hydration water motions and localised fast rotations upon NTC transformation. Quasielastic neutron scattering techniques allowed to accurately distinguish the different dynamical processes taking place within these highly heterogeneous cellular systems. The results thus obtained suggest that intracellular water dynamics may be regarded as a specific reporter of the cellular conditions—either healthy or malignant.
Association between serum vitamin D levels and lipid profiles: a cross-sectional analysis
Authors: Gholamzad Amir , Khakpour Niloofar , Kabipour Tina , Gholamzad Mehrdad 
Published: November 2023

AbstractVitamin D is an essential nutrient that plays a crucial role in calcium homeostasis and bone health. Recent research suggests that vitamin D may also have an impact on lipid metabolism, specifically the level of circulating lipids in the blood. We aim to investigate it role among healthy participate. We conducted a cross-sectional study of 15,600 patients who were referred to the laboratories of university hospitals. We measured the serum levels of Vitamin D as well as triglycerides, total cholesterol, LDL, and HDL using ELISA. We found that the mean serum level of Vitamin D was 40.31 ± 20.79 ng/mL. Of the participants, 16.7% had a serum level of Vitamin D less than 20 ng/mL, 57.7% had a level between 21 and 40 ng/mL, and 13.5% had a level between 41 and 60 ng/mL. Additionally, 12.2% had a level greater than 60 ng/mL. We performed a one-way analysis of variance and found that as the serum level of Vitamin D increased, the mean LDL level decreased significantly. Our study provides evidence of a significant relationship between serum levels of Vitamin D and LDL levels in patients. The findings suggest that vitamin D status may play a role in regulating lipid metabolism and may have implications for the prevention and treatment of cardiovascular disease. Further research is needed to elucidate the underlying mechanisms of this relationship and to determine optimal levels of vitamin D intake for maintaining lipid profiles.
Opportunistic assessment of ischemic heart disease risk using abdominopelvic computed tomography and medical record data: a multimodal explainable artificial intelligence approach
Authors: Zambrano Chaves Juan M. , Wentland Andrew L. , Desai Arjun D. , Banerjee Imon , Kaur Gurkiran , Correa Ramon , Boutin Robert D. , Maron David J. , Rodriguez Fatima , Sandhu Alexander T. , Rubin Daniel , Chaudhari Akshay S. , Patel Bhavik N. 
Published: November 2023

AbstractCurrent risk scores using clinical risk factors for predicting ischemic heart disease (IHD) events—the leading cause of global mortality—have known limitations and may be improved by imaging biomarkers. While body composition (BC) imaging biomarkers derived from abdominopelvic computed tomography (CT) correlate with IHD risk, they are impractical to measure manually. Here, in a retrospective cohort of 8139 contrast-enhanced abdominopelvic CT examinations undergoing up to 5 years of follow-up, we developed multimodal opportunistic risk assessment models for IHD by automatically extracting BC features from abdominal CT images and integrating these with features from each patient’s electronic medical record (EMR). Our predictive methods match and, in some cases, outperform clinical risk scores currently used in IHD risk assessment. We provide clinical interpretability of our model using a new method of determining tissue-level contributions from CT along with weightings of EMR features contributing to IHD risk. We conclude that such a multimodal approach, which automatically integrates BC biomarkers and EMR data, can enhance IHD risk assessment and aid primary prevention efforts for IHD. To further promote research, we release the Opportunistic L3 Ischemic heart disease (OL3I) dataset, the first public multimodal dataset for opportunistic CT prediction of IHD.
Breathing sounds analysis system for early detection of airway problems in patients with a tracheostomy tube
Authors: Kim Hyunbum , Koh Daeyeon , Jung Yohan , Han Hyunjun , Kim Jongbaeg , Joo Younghoon 
Published: November 2023

AbstractTo prevent immediate mortality in patients with a tracheostomy tube, it is essential to ensure timely suctioning or replacement of the tube. Breathing sounds at the entrance of tracheostomy tubes were recorded with a microphone and analyzed using a spectrogram to detect airway problems. The sounds were classified into three categories based on the waveform of the spectrogram according to the obstacle status: normal breathing sounds (NS), vibrant breathing sounds (VS) caused by movable obstacles, and sharp breathing sounds (SS) caused by fixed obstacles. A total of 3950 breathing sounds from 23 patients were analyzed. Despite neither the patients nor the medical staff recognizing any airway problems, the number and percentage of NS, VS, and SS were 1449 (36.7%), 1313 (33.2%), and 1188 (30.1%), respectively. Artificial intelligence (AI) was utilized to automatically classify breathing sounds. MobileNet and Inception_v3 exhibited the highest sensitivity and specificity scores of 0.9441 and 0.9414, respectively. When classifying into three categories, ResNet_50 showed the highest accuracy of 0.9027, and AlexNet showed the highest accuracy of 0.9660 in abnormal sounds. Classifying breathing sounds into three categories is very useful in deciding whether to suction or change the tracheostomy tubes, and AI can accomplish this with high accuracy.
1,3-Diphenylureido hydroxamate as a promising scaffold for generation of potent antimalarial histone deacetylase inhibitors
Authors: Tavares Maurício T. , Krüger Arne , Yan Sun L. Rei , Waitman Karoline B. , Gomes Vinícius M. , de Oliveira Daffiny Sumam , Paz Franciarli , Hilscher Sebastian , Schutkowski Mike , Sippl Wolfgang , Ruiz Claudia , Toledo Mônica F. Z. J. , Hassimotto Neuza M. A. , Machado-Neto João A. , Poso Antti , Cameron Michael D. , Bannister Thomas D. , Palmisano Giuseppe , Wrenger Carsten , Kronenberger Thales , Parise-Filho Roberto 
Published: November 2023

AbstractWe report a series of 1,3-diphenylureido hydroxamate HDAC inhibitors evaluated against sensitive and drug-resistant P. falciparum strains. Compounds 8a–d show potent antiplasmodial activity, indicating that a phenyl spacer allows improved potency relative to cinnamyl and di-hydrocinnamyl linkers. In vitro, mechanistic studies demonstrated target activity for PfHDAC1 on a recombinant level, which agreed with cell quantification of the acetylated histone levels. Compounds 6c, 7c, and 8c, identified as the most active in phenotypic assays and PfHDAC1 enzymatic inhibition. Compound 8c stands out as a remarkable inhibitor, displaying an impressive 85% inhibition of PfHDAC1, with an IC50 value of 0.74 µM in the phenotypic screening on Pf3D7 and 0.8 µM against multidrug-resistant PfDd2 parasites. Despite its potent inhibition of PfHDAC1, 8c remains the least active on human HDAC1, displaying remarkable selectivity. In silico studies suggest that the phenyl linker has an ideal length in the series for permitting effective interactions of the hydroxamate with PfHDAC1 and that this compound series could bind as well as in HsHDAC1. Taken together, these results highlight the potential of diphenylurea hydroxamates as a privileged scaffold for the generation of potent antimalarial HDAC inhibitors with improved selectivity over human HDACs.
Investigation on the organic–inorganic hybrid crystal [NH2(CH3)2]2CuBr4: structure, phase transition, thermal property, structural geometry, and dynamics
Authors: Na Changyub , Lim Ae Ran 
Published: November 2023

AbstractUnderstanding the physical properties of the organic–inorganic hybrid [NH2(CH3)2]2CuBr4 is essential to expand its applications. The single [NH2(CH3)2]2CuBr4 crystals were grown and their comprehensive properties were investigated. The crystals had a monoclinic structure with the space group P21/n and lattice constants of a = 8.8651 (5) Å, b = 11.9938 (6) Å, c = 13.3559 (7) Å, and β = 91.322°. The transition temperature from phase I to phase II was determined to be 388 K. Variations in the 1H nuclear magnetic resonance chemical shifts of NH2 and 14N NMR chemical shifts according to the temperature changes in the cation were attributed to vibrations of NH2 groups at their localization sites. The 1H and 13C spin–lattice relaxation times (T1ρ) in phase II changed significantly with temperature, indicating that these values are governed by molecular motion. The T1ρ values were much longer in phase I than in phase II, which means energy transfer was difficult. Finally, the activation energies for phases I and II were considered. According to the basic mechanism of [NH2(CH3)2]2CuBr4 crystals, organic–inorganic materials may have potential applications in various fields.
A multimodal screening system for elderly neurological diseases based on deep learning
Authors: Park Sangyoung , No Changho , Kim Sora , Han Kyoungmin , Jung Jin-Man , Kwon Kyum-Yil , Lee Minsik 
Published: November 2023

AbstractIn this paper, we propose a deep-learning-based algorithm for screening neurological diseases. We proposed various examination protocols for screening neurological diseases and collected data by video-recording persons performing these protocols. We converted video data into human landmarks that capture action information with a much smaller data dimension. We also used voice data which are also effective indicators of neurological disorders. We designed a subnetwork for each protocol to extract features from landmarks or voice and a feature aggregator that combines all the information extracted from the protocols to make a final decision. Multitask learning was applied to screen two neurological diseases. To capture meaningful information about these human landmarks and voices, we applied various pre-trained models to extract preliminary features. The spatiotemporal characteristics of landmarks are extracted using a pre-trained graph neural network, and voice features are extracted using a pre-trained time-delay neural network. These extracted high-level features are then passed onto the subnetworks and an additional feature aggregator that are simultaneously trained. We also used various data augmentation techniques to overcome the shortage of data. Using a frame-length staticizer that considers the characteristics of the data, we can capture momentary tremors without wasting information. Finally, we examine the effectiveness of different protocols and different modalities (different body parts and voice) through extensive experiments. The proposed method achieves AUC scores of 0.802 for stroke and 0.780 for Parkinson’s disease, which is effective for a screening system.
Patterns of host-parasite associations between marine meiofaunal flatworms (Platyhelminthes) and rhytidocystids (Apicomplexa)
Authors: Van Steenkiste Niels W. L. , Wakeman Kevin C. , Söderström Bill , Leander Brian S. 
Published: November 2023

AbstractMicroturbellarians are abundant and ubiquitous members of marine meiofaunal communities around the world. Because of their small body size, these microscopic animals are rarely considered as hosts for parasitic organisms. Indeed, many protists, both free-living and parasitic ones, equal or surpass meiofaunal animals in size. Despite several anecdotal records of “gregarines”, “sporozoans”, and “apicomplexans” parasitizing microturbellarians in the literature—some of them dating back to the nineteenth century—these single-celled parasites have never been identified and characterized. More recently, the sequencing of eukaryotic microbiomes in microscopic invertebrates have revealed a hidden diversity of protist parasites infecting microturbellarians and other meiofaunal animals. Here we show that apicomplexans isolated from twelve taxonomically diverse rhabdocoel taxa and one species of proseriate collected in four geographically distinct areas around the Pacific Ocean (Okinawa, Hokkaido, and British Columbia) and the Caribbean Sea (Curaçao) all belong to the apicomplexan genus Rhytidocystis. Based on comprehensive molecular phylogenies of Rhabdocoela and Proseriata inferred from both 18S and 28S rDNA sequences, as well as a molecular phylogeny of Marosporida inferred from 18S rDNA sequences, we determine the phylogenetic positions of the microturbellarian hosts and their parasites. Multiple lines of evidence, including morphological and molecular data, show that at least nine new species of Rhytidocystis infect the microturbellarian hosts collected in this study, more than doubling the number of previously recognized species of Rhytidocystis, all of which infect polychaete hosts. A cophylogenetic analysis examining patterns of phylosymbiosis between hosts and parasites suggests a complex picture of overall incongruence between host and parasite phylogenies, and varying degrees of geographic signals and taxon specificity.
Warming affects routine swimming activity and novel odour response in larval zebrafish
Authors: Sourisse Jade M. , Bonzi Lucrezia C. , Semmelhack Julie , Schunter Celia 
Published: November 2023

AbstractTemperature is a primary factor affecting the physiology of ectothermic animals and global warming of water bodies may therefore impact aquatic life. Understanding the effects of near-future predicted temperature changes on the behaviour and underlying molecular mechanisms of aquatic animals is of particular importance, since behaviour mediates survival. In this study, we investigate the effects of developmental temperature on locomotory behaviour and olfactory learning in the zebrafish,Danio rerio. We exposed zebrafish from embryonic stage to either control (28 °C) or elevated temperature (30 °C) for seven days. Overall, warming reduced routine swimming activity and caused upregulation of metabolism and neuron development genes. When exposed to olfactory cues, namely catfish cue, a non-alarming but novel odour, and conspecifics alarming cue, warming differently affected the larvae response to the two cues. An increase in locomotory activity and a large transcriptional reprogramming was observed at elevated temperature in response to novel odour, with upregulation of cell signalling, neuron development and neuron functioning genes. As this response was coupled with the downregulation of genes involved in protein translation and ATP metabolism, novel odour recognition in future-predicted thermal conditions would require energetic trade-offs between expensive baseline processes and responsive functions. To evaluate their learning abilities at both temperatures, larvae were conditioned with a mixture of conspecifics alarm cue and catfish cue. Regardless of temperature, no behavioural nor gene expression changes were detected, reinforcing our findings that warming mainly affects zebrafish molecular response to novel odours. Overall, our results show that future thermal conditions will likely impact developing stages, causing trade-offs following novel olfactory detection in the environment.