bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Seeding for Error-Prone Sequences with SubseqHash2
Authors: Li Xiang , Chen Ke , Shao Mingfu 
Published: June 2024

AbstractSeeding is an essential preparatory step for large-scale sequence comparisons. Substring-based seeding methods such as kmers are ideal for sequences with low error rates but struggle to achieve high sensitivity while maintaining a reasonable precision for error-prone long reads. SubseqHash, a novel subsequence-based seeding method we recently developed, achieves superior accuracy to substring-based methods in seeding sequences with high mutation/error rates, while the only drawback is its computation speed. In this paper, we propose SubseqHash2, an improved algorithm that can compute multiple sets of seeds in one run by definingkorders over all length-ksubsequences and identifying the optimal subsequence under each of thekorders in a single dynamic programming framework. The algorithm is further accelerated using SIMD instructions. SubseqHash2 achieves a 10-50×speedup over repeating SubseqHash while maintaining the high accuracy of seeds. We demonstrate that SubseqHash2 drastically outperforms popular substring-based methods including kmers, minimizers, syncmers, and Strobemers for three fundamental applications. In read mapping, SubseqHash2 can generate adequate seed-matches for aligning hard reads that minimap2 fails on. In sequence alignment, SubseqHash2 achieves high coverage of correct seeds and low coverage of incorrect seeds. In overlap detection, seeds produced by SubseqHash2 lead to more correct overlapping pairs at the same false-positive rate. With all the algorithmic breakthroughs of SubseqHash2, we clear the path for the wide adoption of subsequence-based seeds in long-read analysis. SubseqHash2 is available athttps://github.com/Shao-Group/SubseqHash2.
How Error Correction Affects PCR Deduplication: A Survey Based on UMI Datasets of Short Reads
Authors: Ping Pengyao , Lan Tian , Su Shuquan , Liu Wei , Li Jinyan 
Published: June 2024

AbstractNext-Generation Sequencing (NGS) data is widely utilised for various downstream applications in bioinformatics, and numerous techniques have been developed forPCR-deduplicationanderror-correctionto eliminate bias and errors introduced during the sequencing. This study first-time provides a joint overview of recent advances in PCR-deduplication and error-correction on short reads. In particular, we utilise UMI-based PCR-deduplication strategies and sequencing data to assess the performance of the solely-computational PCR-deduplication approaches and investigate how error correction affects the performance of PCR-deduplication. Our survey and comparative analysis reveal that the deduplicated reads generated by the solely-computational PCR-deduplication and error-correction methods exhibit substantial differences and divergence from the sets of reads obtained by the UMI-based deduplication methods. The existing solely-computational PCR-deduplication and error-correction tools can eliminate some errors but still leave hundreds of thousands of erroneous reads uncorrected. All the error-correction approaches raise thousands or more new sequences after correction which do not have any benefit to the PCR-deduplication process. Upon these discoveries, we offer practical suggestions to enhance the existing computational approaches for improving the quality of short-read sequencing data.
Development and Validation of the School in China REfusal EvaluatioN Scale (SCREEN): A Tool to Assess School Refusal in Chinese Adolescents
Authors: Xie Mingzhi , Bie Xiaoyuan , Sun Ye , Lu Guibin , Shu Peng , Wang Yingyu , Liu Mingming 
Published: June 2024

AbstractThe escalating phenomenon of school refusal (SR) in China has emerged as a significant psychological and educational crisis, with recent surveys revealing a disengagement rate exceeding 70% among students in primary and secondary education. This study introduces the novel School in China REfusal EvaluatioN Scale (SCREEN), specifically designed to assess the multifaceted nature of SR in the Chinese educational context, incorporating culturally relevant socio-psychological variables. Through a robust methodological framework, this research develops and validates the SCREEN, involving the generation and validation of an item pool followed by exploratory and confirmatory factor analyses. The reliability of the SCREEN was affirmed with a Cronbach’s alpha of 0.778, and its validity confirmed through satisfactory factor loadings across multiple dimensions of school engagement. The study’s findings highlight the prevalence and complexity of SR across various educational stages, emphasizing the necessity for holistic intervention strategies that address educational, familial, and societal contributors to SR. The SCREEN’s effectiveness in identifying specific psychological factors contributing to SR underscores the potential for targeted interventions and educational reforms tailored to the unique needs of Chinese students. This research not only contributes to the academic understanding of SR but also provides a practical tool for early detection and intervention, advocating for an integrated approach involving educators, psychologists, and families to mitigate this educational challenge. Future research should focus on longitudinal studies to evaluate intervention efficacy and further refine assessment tools for broader application.
An implantable biohybrid nerve model towards synaptic deep brain stimulation
Authors: Sifringer Léo , Fratzl Alex , Clément Blandine F. , Chansoria Parth , Mönkemöller Leah S. , Duru Jens , Ihle Stephan J. , Steffens Simon , Beltraminelli Anna , Ceylan Eylul , Hengsteler Julian , Maurer Benedikt , Weaver Sean M. , Tringides Christina M. , Vulić Katarina , Madduri Srinivas , Zenobi-Wong Marcy , Roska Botond , Vörös János , Ruff Tobias 
Published: June 2024

AbstractRestoring functional vision in blind patients lacking a healthy optic nerve requires bypassing retinal circuits, ideally, by directly stimulating the visual thalamus. However, available deep brain stimulation electrodes do not provide the resolution required for vision restoration. We developed an implantable biohybrid nerve model designed for synaptic stimulation of deep brain targets. The interface combines a stretchable stimulation array with an aligned microfluidic axon guidance system seeded with neural spheroids to facilitate the development of a 3 mm long nerve-like structure. A bioresorbable hydrogel nerve conduit was used as a bridge between the tissue and the biohybrid implant. We demonstrated stimulation of spheroids within the biohybrid structurein vitroand used high-density CMOS microelectrode arrays to show faithful activity conduction across the device. Finally, implantation of the biohybrid nerve onto the mouse cortex showed that neural spheroids grow axonsin vivoand remain functionally active for more than 22 days post-implantation.
Present and future suitability of invasive and urban vectors through an environmentally-driven Mosquito Reproduction Number
Authors: Pardo-Araujo Marta , Eritja Roger , Alonso David , Bartumeus Frederic 
Published: June 2024

1AbstractTemperature and water availability significantly influence mosquito population dynamics. We’ve devised a method, integrating experimental data with insights from mosquito and thermal biology, to calculate the basic reproduction number (RM) for urban mosquito species,Aedes albopictusandAedes aegypti.RMrepresents the number of female mosquitoes produced by one female during her lifespan, indicating suitability for growth. Environmental conditions, including temperature, rainfall and human density influenceRMby altering key mosquito life cycle traits. Validation using data from Spain and Europe confirms the approach’s reliability. Our analysis suggests that temperature increases may not uniformly benefitAe. albopictusproliferation but could boostAe. aegyptiexpansion. We suggest using vectorRMmaps, leveraging climate and environmental data, to predict areas susceptible to invasive mosquito population growth. These maps aid in resource allocation for intervention strategies, supporting effective vector surveillance and management efforts.
Distinct Excitability Properties of Cardiac Calbindin Neurons: Identifying a Unique Neuronal Population
Authors: Lizot G. , Bescond J. , De Koninck Y. , Chahine M. , Bois P. , Faivre J-F. , Chatelier A. 
Published: June 2024

AbstractThe intrinsic cardiac nervous system is a complex system that plays a critical role in the regulation of cardiac physiological parameters and has been shown to contribute to cardiac arrhythmias. To date, several types of neurons with distinct neurochemical and electrophysiological phenotypes have been identified. However, no study has correlated the neurochemical phenotype to a specific electrophysiological behavior. Calbindin-D28k, a calcium binding protein, is expressed in numerous cardiac neurons. Given that changes in neuronal excitability have been associated with arrhythmia susceptibility and that calbindin expression has been associated with modulations of neuronal excitability, our objective is to assess whether the cardiac calbindin neuronal population has specific properties that could be involved in cardiac modulation and arrhythmias. By using a Cre-Lox mouse model to specifically target calbindin neurons with a fluorescent reporter, we characterized the neurochemical and the electrophysiological phenotype of this cardiac neuronal population. Calbindin neurons exhibit a specific neurochemical profile and a larger soma with shorter neurite length compared to other neurons. This was combined with a distinct electrophysiological signature characterized by a lower excitability with a predominantly phasic profile associated to a lower N-type calcium current density. These properties resemble to the cardiac neuronal remodeling observed in pathologies such as type II diabetes and heart failure. Therefore, we believe that this specific neuronal population deserves investigations in the context of these pathologies.
Coral hosts actively accumulate inorganic carbon for Symbiodiniaceae to maintain symbiotic relationships
Authors: Zhang Boya , Tang Si , Liu Lu , Xu Meiting , Liu Yaqing , Zhu Jianming , Xiao Weimin , Bi Hongsheng , Zhou Jin , Benfield Mark C. , Cai Zhonghua 
Published: June 2024

AbstractHigh primary productivity of coral reefs is widely attributed to the mutualistic symbiosis between coral hosts and their microalgal partners (Symbiodiniaceae). Although the mechanisms maintaining this symbiosis have been considerable investigated, how the symbiont microalgae within coral get sufficient CO2for photosynthesis still remains inadquately explored. Here, we hypothesized that corals may actively accumulate dissolved inorganic carbon (DIC) for microalgae to maintain the symbiosis. Carbon (HCO3-and glucose) supply and consumption were evaluated in the scleractinian coral (Goniopora lobata) and its symbiont under light and dark conditions. Results suggest that Symbiodiniaceae were high DIC consumers, requiring about 2-3 fold more DIC than free-living species. The corals were high DIC producers, with internal concentrations up to 4.2 fold higher than in the surrounding seawater. In the absence of microalgae utilization, the excess DIC they produced appeared detrimental to their own growth. Moreover, transcriptomic analysis identified several DIC enrichment pathways are evolved in corals to attact the Symbiodiniaceae, including CO2concentrating mechanisms, respiration, calcification and phosphoenolpyruvate carboxylase. Increased the CO2dosage in seawater may induce coral symbiosis bleaching. Our findings can deeper reveal on the mechanisms sustaining coral symbiosis, and may help to predict how some corals respond to DIC imbalance under climate changes.
AKT2 modulates astrocytic nicotine responsesin vivo
Authors: Lombardi Andrew M. , Wong Helen , Bower Myra E. , Milstead Ryan , Borski Curtis , Schmitt Emily , Griffioen Mina , LaPlante Lauren , Ehringer Marissa A. , Stitzel Jerry , Hoeffer Charles A. 
Published: June 2024

AbstractA better understanding of nicotine neurobiology is needed to reduce or prevent chronic addiction, ameliorate the detrimental effects of nicotine withdrawal, and increase successful cessation of use. Nicotine binds and activates two astrocyte-expressed nicotinic acetylcholine receptors (nAChRs), α4β2 and α7. We recently found thatProtein kinase B-β (Pkb-β orAkt2) expression is restricted to astrocytes in mice and humans. To determine if AKT2 plays a role in astrocytic nicotinic responses, we generated astrocyte-specificAkt2conditional knockout (cKO) and fullAkt2KO mice forin vivoandin vitroexperiments. Forin vivostudies, we examined mice exposed to chronic nicotine for two weeks in drinking water (200 μg/mL) and following acute nicotine challenge (0.09, 0.2 mg/kg) after 24 hrs. Ourin vitrostudies used cultured mouse astrocytes to measure nicotine-dependent astrocytic responses. We validated our approaches using lipopolysaccharide (LPS) exposure inducing astrogliosis. Sholl analysis was used to measure glial fibrillary acidic protein responses in astrocytes. Our data show that wild-type (WT) mice exhibit increased astrocyte morphological complexity during acute nicotine exposure, with decreasing complexity during chronic nicotine use, whereasAkt2cKO mice showed increased astrocyte morphology complexity. In culture, we found that 100μM nicotine was sufficient for morphological changes and blocking α7 or α4β2 nAChRs prevented observed morphologic changes. Finally, we performed conditioned place preference (CPP) inAkt2cKO mice and found that astrocytic AKT2 deficiency reduced nicotine preference compared to controls. These findings show the importance of nAChRs andAkt2signaling in the astrocytic response to nicotine.Main PointsNicotine regulates astrogliosisin vivo: acute exposure boosts complexity; chronic exposure diminishes it.AKT2, expressed in astroglia, modulates morphological changes in response to nicotine and nicotine-dependent conditioned place preference.
Phase-separating MoSpa2 Complex Organizes Actin Nucleation Center forM.oryzaePlant Infection
Authors: He Danxia , Li Yuanbao , Ma Qianqian , Han Libo , Tang Dingzhong , Miao Yansong 
Published: June 2024

AbstractPolarized actin cable from Spitzenkörper at the hyphal tip fuels filamentous growth in diverse biphasic fungal pathogens. This multi-component complex, featuring the actin nucleator Bni1 and other factors, initiates actin polymerization, guiding biphasic fungal growth and host infection. How dynamic assembly of Spitzenkörper and actin cable are achieved to support filamentous fungi that undergo multistage morphogenesis for host invasion remains unclear, includingMagnaporthe oryzae, which undergoes multistage morphological transition during rice infection. Here, we identified that the scaffolder MoSpa2 remodeling actin cable networks, in space and time, by assembling the polarisome complex via phase separation, supportingMagnaporthe oryzae’s polarized growth. Via N-terminal intrinsically disordered regions (IDRs), MoSpa2 first stimulates actin cable assembly through multivalent interactions with MoBni1 nucleator, and then also creates polarized actin cable bundles by F-actin association and a concurrent inhibition of cofilin-mediated F-actin depolymerization. MoSpa2 mutants exhibit impaired hyphal growth and reduced rice infection, underling its significance. This work elucidates the fundamental mechanisms underlying fungal morphogenesis, offering the potential for targeted interventions in pathogenesis.
Striatal cholinergic interneuron pause response requires Kv1 channels, is absent in dyskinetic mice, and is restored by dopamine D5 receptor inverse agonism
Authors: Tubert C , Paz RM , Stahl AM , Rela L , Murer MG 
Published: June 2024

AbstractStriatal cholinergic interneurons (SCIN) exhibit pause responses conveying information about rewarding events, but the mechanisms underlying them remain elusive. Thalamic inputs induce a pause mediated by intrinsic mechanisms and regulated by dopamine D2 receptors, though the underlying membrane currents are unknown. Moreover, the role of D5 receptors (D5R) has not been addressed so far. We performed ex vivo studies that show that glutamate released by thalamic inputs in the dorsolateral striatum induces a burst in SCIN, followed by the activation of a Kv1-dependent delayed rectifier current responsible for the pause. Endogenous dopamine promotes the pause through D2R stimulation, while pharmacological stimulation of D5R suppresses it. Remarkably, the pause response is absent in parkinsonian mice rendered dyskinetic by chronic L-DOPA treatment but can be reinstated acutely by the inverse D5R agonist clozapine. Blocking the Kv1 current eliminates the pause reinstated by the D5R inverse agonist. In conclusion, the pause response is mediated by delayed rectifier Kv1 channels, which are tonically blocked in dyskinetic mice by a mechanism depending on D5R ligand-independent activity. Targeting these alterations may have therapeutic value in Parkinson’s disease.HighlightsIn brain slices, thalamostriatal input triggers a burst followed by a pause in SCIN.Kv1, but not Kv7 or Kir2.2 channels, are necessary for the expression of the pause.D2R stimulation promotes, and D5R stimulation inhibits the pause.Thalamic bursts are not followed by a pause in SCIN from dyskinetic mice.D5R inverse agonism restores a Kv1-dependent pause response in dyskinetic mice.
Frequency of antimicrobial-resistant bloodstream infections in Thailand, 2022
Authors: Tuamsuwan Krittiya , Chamawan Panida , Boonyarit Phairam , Srisuphan Voranadda , Klaytong Preeyarach , Rangsiwutisak Chalida , Wannapinij Prapass , Fongthong Trithep , Stelling John , Turner Paul , Limmathurotsakul Direk 
Published: June 2024

AbstractObjectivesTo evaluate the frequency of antimicrobial-resistant bloodstream infections (AMR BSI) in ThailandMethodsWe analyzed data from 2022, generated by 111 public hospitals in health regions 1 to 12, using the AutoMated tool for Antimicrobial resistance Surveillance System (AMASS) and submitted to the Ministry of Public Health, Thailand. Multilevel Poisson regression models were used.ResultsThe most common cause of community-origin AMR BSI was third-generation cephalosporin-resistantEscherichia coli(3GCREC, 65.6%; 5,101/7,773 patients) and of hospital-origin AMR BSI was carbapenem-resistantAcinetobacter baumannii(CRAB, 51.2%, 4,968/9,747 patients). The percentage of patients tested for BSI was negatively associated with the frequency of community-origin 3GCREC BSI and hospital-origin CRAB BSI. Hospitals in health regions 4 (lower central) had the highest frequency of community-origin 3GCREC BSI per 100,000 tested patients (adjusted incidence rate ratio, 2.06; 95% confidence interval: 1.52-2.97). Health regions were not associated with the frequency of hospital-origin CRAB BSI, although between-hospital variation was high even adjusting for hospital level and size.ConclusionThe high between-hospital variation of hospital-origin CRAB BSI suggests the importance of hospital-specific factors. Our approach and findings highlight health regions and hospitals where actions against AMR infection, including antimicrobial stewardship and infection control, should be prioritized.HighlightsThe frequency of AMR BSI in 111 public hospitals in Thailand in 2022 was studied.The frequency of community-origin 3GCREC BSI was different by regions.The frequency of hospital-origin CRAB BSI varied greatly among hospitals.Underuse of BC was associated with the higher frequency of AMR BSI per tested patients.Our findings contributed to actions against AMR at local and national levels.
Inferring genetic variant causal networks by leveraging pleiotropy
Authors: Tournaire Martin , Nouira Asma , Favre Moiron Mario , Rozenholc Yves , Verbanck Marie 
Published: June 2024

AbstractGenetic variants have been associated with multiple traits through genome-wide association studies (GWASs), but pinpointing causal variants and their mechanisms remains challenging. Molecular phenotypes, such as eQTLs, are routinely used to interpret GWAS results. However, much concern has recently been raised about their weak overlap. Taking the opposite approach with PRISM (Pleiotropic Relationships to Infer the SNP Model), we leverage pleiotropy to pinpoint direct effects and build variant causal networks. PRISM clusters variant-trait effects into trait-mediated, confounder-mediated, and direct effects, and builds individual variant causal networks by cross-referencing results from all traits. In simulations, PRISM demonstrated high precision in identifying direct effects and reconstructing causal networks. Applying PRISM to 61 traits and diseases from UK Biobank, we found that direct effects accounted for less than 13% of significant effects, yet were highly enriched in heritability. Multiple lines of evidence showed that PRISM causal networks are consistent with established biological mechanisms.
Nurses’ Support of Treatment Decision-Making for Patients with Cancer During the COVID-19 Pandemic in Japan
Authors: Yoshida Shiori , Sasaki Konosuke , Sato Fumiko 
Published: June 2024

AbstractDuring the COVID-19 pandemic, cancer patients became reluctant to come to the hospital, receive cancer treatment, and were willing to interrupt or postpone treatment due to concerns about infection. The purpose of this study was to discuss effective treatment strategy decision making support for cancer patients by nurses recognized during the COVID-19 pandemic. The study population comprised nurse of decision-making support at cancer care during COVID-19 from May to July 2021 at 49 the cancer care center hospitals were established in each prefecture, who had engaged 50% of their nursing care provided to patients with cancer.Data were collected on treatment strategy decision-making support using an online cross-sectional survey. Factors that influenced patients’ decision-making were identified using multivariable logistic regression analysis. A total of 182 (25.0%) were nurses engaged in decision making were enrolled in this study. Factors that influenced patients’ decision to receive treatment to their satisfaction were their resignation or compromise in accepting the decision due to the pandemic (odds ratio [OR] 0.44 (95% CI [0.22, 0.87]), videoconference follow-up (OR 0.17, 95% Cl [0.04, 0.66]), and infection prevention information provision (OR 3.82, 95% Cl [1.54,9.46]). Factors influencing patients’ decision to give up and accept the doctor’s recommendation even though they were not convinced included fear of disease progression (OR 2.51, 95% Cl [1.21, 5.22]), anger at not receiving the treatment they desired (OR 2.48, 95% Cl [1.17, 5.27]), and compromise with the pandemic situation (OR 3.15, 95% Cl [1.53, 6.50]). The factor that influenced patients’ continued treatment even though they were not convinced included the nurse listened to the patients’ thoughts (OR 0.07, 95% Cl [0.01, 0.51]). Treatment decision support of patients with cancer during COVID-19 included lifestyle guidance to prevent the spread of infection and listening to their concerns to help them find meaning in their choices.