bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual counterpart intuitionistic logic
Authors: Cantor Anthony , Stump Aaron 
Published: September 2023

Abstract
We introduce dual counterpart intuitionistic logic (or DCInt): a constructive logic that is a conservative extension of intuitionistic logic, a sublogic of bi-intuitionistic logic, has the logical duality property of classical logic, and also retains the modal character of its interpretation of the connective dual to intuitionistic implication. We define its Kripke semantics along with the corresponding notion of a bisimulation, and then prove that it has both the disjunction property and (its dual) the constructible falsity property. Also, for any class $ {\mathcal{C}}$ of Kripke frames from our semantics, we identify a condition such that $ {\mathcal{C}}$ will have the disjunction property if it satisfies the condition. This provides a method for generating extensions of DCInt that retain the disjunction property.
Clinical Intentions in Music Therapy Termination Processes: A Qualitative Inquiry
Authors: Abbott Elaine A 
Published: September 2023

Abstract
ABSTRACT: Given the limited literature on the specific termination practices of music therapists in multiple clinical settings, clinicians were asked to participate in open-ended interviews to address the following research questions: What are the current termination practices of music therapists? What types of termination practices might they describe? and What processes do they move through in their termination practices? Thematic analysis of the interview data was used to identify several themes, one of which is described in the present paper: clinical intentions. Four clinical intentions are described in the results: preparing the person for termination, considering the person’s context, framing the therapeutic structure, and implementing the termination process. Comparison of the results to the termination-related music therapy literature showed that general guidelines for termination are not universally applicable. A model for self/peer-supervision and decision-making for termination was presented for three purposes: (a) to provide an approach for students and clinicians to consider the specific termination-related circumstances in which they find themselves, (b) to provide an approach for them to consider how they might most effectively attend to the needs of the persons they serve, and (c) to provide an approach for them to consider their own needs for self-care.
Assessing base-resolution DNA mechanics on the genome scale
Authors: Jiang Wen-Jie , Hu Congcong , Lai Futing , Pang Weixiong , Yi Xinyao , Xu Qianyi , Wang Haojie , Zhou Jialu , Zhu Hanwen , Zhong Chunge , Kuang Zeyu , Fan Ruiqi , Shen Jing , Zhou Xiaorui , Wang Yu-Juan , Wong Catherine C L , Zheng Xiaoqi , Wu Hua-Jun 
Published: September 2023

Abstract
Intrinsic DNA properties including bending play a crucial role in diverse biological systems. A recent advance in a high-throughput technology called loop-seq makes it possible to determine the bendability of hundred thousand 50-bp DNA duplexes in one experiment. However, it's still challenging to assess base-resolution sequence bendability in large genomes such as human, which requires thousands of such experiments. Here, we introduce ‘BendNet’—a deep neural network to predict the intrinsic DNA bending at base-resolution by using loop-seq results in yeast as training data. BendNet can predict the DNA bendability of any given sequence from different species with high accuracy. To explore the utility of BendNet, we applied it to the human genome and observed DNA bendability is associated with chromatin features and disease risk regions involving transcription/enhancer regulation, DNA replication, transcription factor binding and extrachromosomal circular DNA generation. These findings expand our understanding on DNA mechanics and its association with transcription regulation in mammals. Lastly, we built a comprehensive resource of genomic DNA bendability profiles for 307 species by applying BendNet, and provided an online tool to assess the bendability of user-specified DNA sequences (http://www.dnabendnet.com/).
MetaTransformer: deep metagenomic sequencing read classification using self-attention models
Authors: Wichmann Alexander , Buschong Etienne , Müller André , Jünger Daniel , Hildebrandt Andreas , Hankeln Thomas , Schmidt Bertil 
Published: September 2023

Abstract
Deep learning has emerged as a paradigm that revolutionizes numerous domains of scientific research. Transformers have been utilized in language modeling outperforming previous approaches. Therefore, the utilization of deep learning as a tool for analyzing the genomic sequences is promising, yielding convincing results in fields such as motif identification and variant calling. DeepMicrobes, a machine learning-based classifier, has recently been introduced for taxonomic prediction at species and genus level. However, it relies on complex models based on bidirectional long short-term memory cells resulting in slow runtimes and excessive memory requirements, hampering its effective usability. We present MetaTransformer, a self-attention-based deep learning metagenomic analysis tool. Our transformer-encoder-based models enable efficient parallelization while outperforming DeepMicrobes in terms of species and genus classification abilities. Furthermore, we investigate approaches to reduce memory consumption and boost performance using different embedding schemes. As a result, we are able to achieve 2× to 5× speedup for inference compared to DeepMicrobes while keeping a significantly smaller memory footprint. MetaTransformer can be trained in 9 hours for genus and 16 hours for species prediction. Our results demonstrate performance improvements due to self-attention models and the impact of embedding schemes in deep learning on metagenomic sequencing data.
Long-term study (1987–2023) on the distribution of 137Cs in soil following the Chernobyl nuclear accident: a comparison of temporal migration measurements and compartment model predictions
Authors: Kaissas Ioannis , Clouvas Alexandros , Postatziis Marios , Xanthos Stelios , Omirou Michalakis 
Published: September 2023

Abstract
After the Chernobyl accident, a designated area of ~1000 m2 within the University farm of Aristotle University of Thessaloniki in Northern Greece was utilized as a test ground for radioecological measurements. The profile of 137Cs in the soil was monitored from 1987 to 2023, with soil samples collected in 5-cm-thick slices (layers) down to a depth of 30 cm. The mean total deposition of 137Cs in the area, backdated to the time of the Chernobyl accident, was determined to be 18.6 ± 1.8 kBq m−2 based on four follow-up profile measurements of 137Cs in the soil for the years 2022 and 2023. It is noteworthy that this value is similar the total deposition at the site, which was independently measured to be about 20 kBq m−2 during the first year after the Chernobyl accident. The fractional contribution of each soil layer (e.g., 0–5 cm, 5–10 cm, 10–15 cm, etc.) to the total deposition of 137Cs (0–30 cm) is presented and analyzed. A compartment model was utilized to forecast the temporal evolution of fractional contributions of the different soil layers to the total deposition of 137Cs (0–30 cm). In this model, each soil layer is represented as a separate compartment. The model assumes that the transfer rates between adjacent compartments are equal. The agreement between the measured fractional contributions and the model predictions suggests that the compartment model with equal transfer rates can capture the broad patterns of 137Cs migration within the soil layers over the long period of 1987–2023. However, the use of a second compartment model with increasing transfer rates between consecutive soil layers did not align with the observed outcomes. This indicates that diffusion may not be the primary migration mechanism over the 36-y period covered by our study.
Methylome and proteome integration in human skeletal muscle uncover group and individual responses to high‐intensity interval training
Authors: Jacques Macsue , Landen Shanie , Romero Javier Alvarez , Hiam Danielle , Schittenhelm Ralf B. , Hanchapola Iresha , Shah Anup D. , Voisin Sarah , Eynon Nir 
Published: September 2023

AbstractExercise is a major beneficial contributor to muscle metabolism, and health benefits acquired by exercise are a result of molecular shifts occurring across multiple molecular layers (i.e., epigenome, transcriptome, and proteome). Identifying robust, across‐molecular level targets associated with exercise response, at both group and individual levels, is paramount to develop health guidelines and targeted health interventions. Sixteen, apparently healthy, moderately trained (VO2 max = 51.0 ± 10.6 mL min−1 kg−1) males (age range = 18–45 years) from the Gene SMART (Skeletal Muscle Adaptive Responses to Training) study completed a longitudinal study composed of 12‐week high‐intensity interval training (HIIT) intervention. Vastus lateralis muscle biopsies were collected at baseline and after 4, 8, and 12 weeks of HIIT. DNA methylation (~850 CpG sites) and proteomic (~3000 proteins) analyses were conducted at all time points. Mixed models were applied to estimate group and individual changes, and methylome and proteome integration was conducted using a holistic multilevel approach with the mixOmics package. A total of 461 proteins significantly changed over time (at 4, 8, and 12 weeks), whilst methylome overall shifted with training only one differentially methylated position (DMP) was significant (adj.p‐value < .05). K‐means analysis revealed cumulative protein changes by clusters of proteins that presented similar changes over time. Individual responses to training were observed in 101 proteins. Seven proteins had large effect‐sizes >0.5, among them are two novel exercise‐related proteins, LYRM7 and EPN1. Integration analysis showed bidirectional relationships between the methylome and proteome. We showed a significant influence of HIIT on the epigenome and more so on the proteome in human muscle, and uncovered groups of proteins clustering according to similar patterns across the exercise intervention. Individual responses to exercise were observed in the proteome with novel mitochondrial and metabolic proteins consistently changed across individuals. Future work is required to elucidate the role of these proteins in response to exercise.
Zinc finger protein ZBTB17 controls cellular senescence via interacting with nuclear receptor RXRA and its downstream calcium signaling
Authors: Wang Chaofan , Gao Yue , Luan Changjiao , Sun Wentao , Ge Sumin , Li Yaru , Xu Lei , Du Qiu , Liu Weili , Lu Guotao , Gong Weijuan , Ma Xingjie 
Published: September 2023

AbstractCellular senescence is broadly known as a stable cell cycle arrest accompanied by a senescence‐associated secretory phenotype (SASP). In the past decades, calcium signaling has emerged as a key mediator of cellular senescence. However, the transcriptional regulation of calcium signaling during cellular senescence remains partially understood. We have previously identified the nuclear receptor RXRA as a key senescence repressor through inhibiting the endoplasmic reticulum (ER) calcium release channel inositol 1,4,5‐trisphosphate receptor, type 2 (ITPR2) mediated intracellular calcium signaling. Nevertheless, as a transcriptional recruiter, the mechanism by which RXRA inhibits ITPR2 during cellular senescence remains unclear. Here we identified the zinc finger protein ZBTB17 can interact with RXRA. Interestingly, knockdown of ZBTB17 induces a cascade of RXRA‐dependent intracellular calcium signaling, mitochondrial membrane potential (MMP), reactive oxygen species (ROS) accumulation, DNA damages, and ultimately cellular senescence. Moreover, the signaling and senescence phenotype induced by knocking down of ZBTB17 can also be abolished after silencing ITPR2. Altogether, our work provides a new mechanism controlling intracellular calcium signaling and cellular senescence and unveils novel insight toward the role of zinc finger proteins.
Using Focus Groups to Identify Nutrition Education Needs and Implementation Strategies for the Wildland Firefighter
Authors: Holubetz Heidi , Brown Ann F. , Domitrovich Joseph W. , Roe Annie J. 
Published: September 2023

Abstract
Wildland firefighters (WLFFs) often participate in sustained, mental and physical efforts throughout the work shift, resulting in high daily total energy expenditure. Meeting nutritional needs is necessary for the health and well-being of WLFFs. However, nutrition education is limited in standardized training.

Objectives
The aims of the study are to describe the current state, identify topics of importance, and suggest implementation strategies for tailored nutrition education for the WLFFs.

Methods
Focus groups were conducted and survey data was collected to gather qualitative and quantitative data from a sample of WLFFs. Constant comparative strategy was used to generate themes from transcripts.

Results
Wildland firefighters showed interest in early-introduced, multimodal, and specific nutrition education tailored to the demands of the WLFF.

Conclusions:
Study findings provide nutrition topics of interest and importance to WLFFs and may be used to develop educational materials.
Epidemiology, clinical characteristics, diagnosis, and complications of scrub typhus infection in Nepal: a systematic review
Authors: Lamichhane Pratik , Pokhrel Kailash M. , Alghalyini Baraa , Zaidi Abdul Rehman Zia , Alshehery Maied Z. , Khanal Kapil , Bhattarai Madhur , Yadav Alisha 
Published: September 2023

Introduction:
Scrub typhus (ST) is a neglected tropical disease of serious concern in Nepal. This systematic review aims to describe the burden of disease, clinical presentation, and complications of ST infection in Nepal.

Methods:
A systematic search of PubMed, EMBASE, Google Scholar, and national databases was conducted for any literature published in English between January 2000 and January 2023. Any type of study design (observational studies, case series, and interventional studies) that reported laboratory-confirmed ST and was conducted in Nepal among patients of all age groups was included. The seroprevalence of ST among acute undifferentiated febrile illness (AUFI) cases, geographical distribution, monthly distribution, clinical presentations, complications, and treatment were assessed by the study.

Result:
A total of 15 studies with 10, 977 participants were included in the review. The seroprevalence of ST among the AUFI cases in Nepal was 19.31%. Young people at or below 20 years of age were mostly affected. The maximum number of cases were reported from Bagmati province (59.46%) and in the month of August (26.33%). Fever, headache, cough, shortness of breath, nausea, and abdominal pain were the clinical characteristics in decreasing order of occurrence. The most common complication was acute kidney injury, followed by respiratory problems, cardiac issues, and neurological manifestations. The case fatality rate of ST in Nepal was 2.56%.

Conclusion:
The authors findings showed a significant burden of ST among AUFI cases in Nepal. Improved surveillance, general public awareness, and early detection post-calamities could help reduce the disease burden and improve patient outcomes.
Increases in local skin temperature correlate with spontaneous foot lifting and heat hyperalgesia in both incisional inflammatory models of pain
Authors: Banik Ratan K. , Sia Twan , Ibrahim Mohab M. , Sivanesan Eellan , Uhelski Megan , Pena Adrian , Streicher John M. , Simone Donald A. 
Published: September 2023

Abstract

Background:
This study investigated if a localized increase in skin temperature in rat models of incisional and inflammatory pain correlates with the intensity of spontaneous and evoked pain behaviors.

Methods:
Anesthetized rats received either a 20-mm longitudinal incision made through the skin, fascia, and muscle of the plantar hind paw or an injection of complete Freund adjuvant into the plantar hind paw of anesthetized rats to induce local inflammation. Spontaneous and evoked pain behaviors were assessed, and changes in skin temperature were measured using a noncontact infrared thermometer.

Results:
There were no differences in skin temperature between the ipsilateral and contralateral hind paw before the incision or inflammation. Skin temperature increased at 2 hours after hind paw plantar incision or 1 day after inflammation of the affected paw, which gradually returned to baseline by the first day and fourth days after treatment, respectively. The increase in skin temperature correlated with the intensity of spontaneous pain behaviors and heat but not with mechanical allodynia.

Conclusions:
Our results suggest that a simple measurement of localized skin temperature using a noncontact infrared thermometer could measure the extent of spontaneous pain behaviors and heat hyperalgesia following plantar incision or inflammation in animals. In the absence of a reliable objective marker of pain, these results are encouraging. However, studies are warranted to validate our results using analgesics and pain-relieving interventions, such as nerve block on skin temperature changes.
Historical biogeography of New World Killifishes (Cyprinodontiformes: Funduloidea) recapitulates geographical history in the Gulf of México watershed
Authors: Hernández Sonia G. , Hoagstrom Christopher W. , Matamoros Wilfredo A. 
Published: September 2023

ABSTRACTWe reconstructed the phylogenetic relationships of superfamily Funduloidea with a synthesis of its biogeographic history. We used DNA sequences from five genes for 135 species, with four fossil calibrations, to generate a time-calibrated phylogeny. We estimated diversification rates, ancestral areas (Nearctic or Neotropical), and ancestral habitat (coastal or upland), for each node. Our results suggest that Funduloidea originated in the Late Cretaceous and diversified from Late Paleocene to present at a uniform rate, except Cyprinodontidae expressed an accelerated rate of speciation ~11.02 Ma. Neither viviparity, marine-to-freshwater transition, consistently accelerated speciation. Funduloidea has a coastal origin, but invaded inland many times. Funduloidea phylogeny indicates, sea-level falls isolate coastal populations, but increase island accessibility and climatic cooling facilitates invasions of temperate species into the tropics. For continental lineages, ancient river drainages accord with lineage distributions, including enigmatic disjunctions in Goodeidae andFundulus. Niche shifts occurred from estuaries to open coasts and from forests to grasslands. Antiquity, adaptability, and dynamic geography can explain Funduloidea diversity. Combined environmental and phylogenetic data unveil the history of the Gulf of México watershed. Phylogeny suggests there was diversification by barrier displacement and coastal speciation pump. Overall, speciation time, transitions to freshwater, dispersal, vicariance, adaptive radiation, and viviparity contributed to total diversification.
Local read haplotagging enables accurate long-read small variant calling
Authors: Kolesnikov Alexey , Cook Daniel , Nattestad Maria , McNulty Brandy , Gorzynski John , Goenka Sneha , Ashley Euan A. , Jain Miten , Miga Karen H. , Paten Benedict , Chang Pi-Chuan , Carroll Andrew , Shafin Kishwar 
Published: September 2023

AbstractLong-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford nanopore technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced. In this work, we have developed a local haplotype approximate method that enables state-of-the-art variant calling performance with multiple sequencing platforms including PacBio Revio system, ONT R10.4 simplex and duplex data. This addition of local haplotype approximation makes DeepVariant a universal variant calling solution for long-read sequencing platforms.
Calcium-dependent transcriptional profiles of human pancreatic islet cells reveal functional diversity in islet subpopulations
Authors: Yoon Ji Soo , Sasaki Shugo , Velghe Jane , Zosel Katarina , Lee Michelle Y. Y. , Winata Helena , Nian Cuilan , Lynn Francis C. 
Published: September 2023

AbstractAims/hypothesisPancreatic islets depend on cytosolic calcium to trigger the secretion of glucoregulatory hormones and regulate the transcription of genes important for the response to stimuli. To date, there has not been an attempt to profile calcium-regulated gene expression in all islet cell types. Our aim was to construct a large single-cell transcriptomic dataset from human islets exposed to conditions that would acutely induce or inhibit intracellular calcium signalling, while preserving biological heterogeneity.MethodsWe exposed intact human islets from three donors to the following conditions: (1) 2.8 mM glucose; (2) 25 mM glucose and 40 mM KCl to maximally stimulate calcium signalling; and (3) 25 mM glucose, 40 mM KCl and 5 mM EGTA (calcium chelator) to inhibit calcium signalling, for 1 hour. We sequenced 43,909 cells from all islet cell types, and further subsetted the cells to form an endocrine cell-specific dataset of 32,486 cells expressingINS,GCG,SSTorPPY. We compared transcriptomes across conditions to determine the differentially expressed calcium-regulated genes in each endocrine cell type, and in each endocrine cell subcluster of alpha and beta cells.ResultsBased on the number of calcium-regulated genes, we found that each alpha and beta cell cluster had a different magnitude of calcium response. We also showed that a polyhormonal cluster expressingINS, GCG, andSSTis defined by calcium-regulated genes specific to this cluster. Finally, we identified the genePCDH7from the beta cell clusters that had the highest number of calcium-regulated genes, and showed that cells expressing cell surface PCDH7 protein have enhanced glucose-stimulated insulin secretory function.ConclusionsHere we use our single-cell dataset to show that human islets have cell-type-specific calcium-regulated gene expression profiles, some of them specific to subpopulations. In our dataset, we identifyPCDH7as a novel marker of beta cells having an increased number of calcium-regulated genes and enhanced insulin secretory function.Data availabilityA searchable and user-friendly format of the data in this study, specifically designed for rapid mining of single-cell RNA sequencing data, is available athttps://lynnlab.shinyapps.io/Hislet_2023/. The raw data files are available at NCBI Gene Expression Omnibus (GSE196715).