bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetic Aging and Rheumatoid Arthritis
Authors: Mukherjee Nandini , Harrison Tracie C
Published: September 2023

This is the first known comparative assessment of the associations of epigenetic age estimates with the prevalence of rheumatoid arthritis (RA). We used data available in Gene Expression Omnibus (GSE42861) from the Swedish Epidemiological Investigation of Rheumatoid Arthritis study. Information regarding RA diagnosis and 450K DNA methylation (DNAm) of 18- to 70-year-old participants was available. Utilizing Horvath’s online DNAm Age Calculator, we determined the DNAm estimate of Telomere length (DNAmTL), Hannum’s epigenetic age, Horvath’s 2013 and 2018 epigenetic ages, PhenoAge, GrimAge, and the respective age-acceleration measures. The association of RA prevalence with epigenetic age measures was assessed using linear regression, adjusting for sex and smoking status. The p values were corrected for multiple testing using a false discovery rate. We identified statistically significant associations of RA with Horvath 2013 age acceleration (estimate: −1.34; FDR p value: 1.0 × 10−2), Horvath 2018 age acceleration (estimate: −1.32; FDR p value: 4.0 × 10−5), extrinsic age acceleration (estimate: 1.34; FDR p value: 1.0 × 10−2), PhenoAge acceleration (estimate: 2.31; FDR p value: 1.1 × 10−5), GrimAge (estimate: 2.54; FDR p value: 1.0 × 10−2), and GrimAge acceleration (estimate: 3.15; FDR p-value: 1.7 × 10−17). Of note, the raw and age-adjusted GrimAge surrogate DNAm protein components were significantly higher in RA cases than controls. Interestingly, the first-generation measures were associated only with women. No sex-specific effects were identified for PhenoAge or GrimAge accelerations. In this cross-sectional assessment, the second-generation clocks show promise as markers of biological aging, with higher epigenetic age acceleration observed in RA cases compared with healthy controls.
Misunderstanding the margin? The reception of the ECtHR’s margin of appreciation at the national level
Authors: Brems Eva
Published: September 2023

This exploratory article focuses on the receiving end of the margin of appreciation doctrine of the European Court of Human Rights (ECtHR), that is to say, the response of national-level legislators and courts to ECtHR case law involving other states parties, that grants national authorities a wide margin of appreciation. The paper explores the risk that national authorities might misinterpret the margin of appreciation in such cases as a marker of human rights clearance of a rights-restrictive practice as such or as a prompt for domestic courts toward deference in their relationship with the legislative and executive powers. The paper finds anecdotal evidence of such misinterpretation by domestic legislators in the reception of SAS v. France. In addition, an examination of recent fundamental rights case law of the Belgian Constitutional Court illustrates the existence of a problem of misunderstanding the margin of appreciation at the level of domestic courts.
Who misunderstands the margin of appreciation? A reply to Eva Brems
Authors: Iglesias Vila Marisa
Published: September 2023

This reply offers some critical reflections that tie into the assumptions of Eva Brem’s interesting study of the risk of national authorities’ misunderstandings of the margin of appreciation conceded by the European Court of Human Rights (ECtHR). Taking on board a cooperative conception of the principle of subsidiarity, this reply first questions the adequacy of the distinction between a systemic and a normative dimension of the margin of appreciation as the proper basis for assessing the risk of domestic misunderstanding of the margin of appreciation. Next, it raises some objections to the analysis that Brems makes of the ECtHR judgment in S.A.S. v. France, particularly her application of the normative dimension of the margin of appreciation to this example of possible misunderstanding. The reply argues that Brems’s assumption that the ECtHR conducted a procedural rationality review of the French burqa ban minimizes Strasbourg’s own contribution to the risk that other states, in similar cases, may misunderstand how human rights are to be applied to avoid misinterpreting their national margin of appreciation.
Desalkylgidazepam blood concentrations in 63 forensic investigation cases
Authors: Mérette Sandrine A M , Kim Subin , Davis Michael D , Shapiro Aaron M
Published: September 2023

Desalkylgidazepam, also known as bromonordiazepam, is the latest designer benzodiazepine to appear in postmortem blood samples in British Columbia. Our laboratory was first alerted to the presence of desalkylgidazepam in seized drug samples in May 2022, and the analyte was added to an in-house library shortly thereafter. Previously acquired spectra from routine death investigation cases were reprocessed using the updated library with the first presumptive identification of desalkylgidazepam occurring in a sample received in April 2022. A standard addition method for the quantitation of desalkylgidazepam in blood samples (from femoral, iliac, jugular and subclavian veins) was validated and consequently used to confirm presence and concentrations of the drug in 63 cases, with an average concentration of 42.2 ± 44.0 ng/mL (median concentration: 24.5 ng/mL; range: 3.7–220.6 ng/mL). Similar to detections of other novel benzodiazepines, co-occurrence of desalkylgidazepam with opioids and/or stimulants was common. To our knowledge, this paper is the first to report desalkylgidazepam concentrations in postmortem blood samples.
A 10-Year Single-Burn Center Review of Free Tissue Transfer for Burn-Related Injuries
Authors: Alessandri Bonetti Mario , Jeong Tiffany , Stofman Guy M , Egro Francesco M
Published: September 2023

Skin grafting is the mainstay treatment in burn patients. However, in the scenario of soft tissue deficit along with exposure of critical structures, free flap is the only reconstructive option to provide adequate coverage. The aim of the study is to review indications and surgical outcomes of burn patients requiring free tissue transfer. A retrospective cohort study was conducted to review all patients who underwent free tissue transfer for burn-related injuries between March 2012 and June 2023. A total of 13 patients required a free flap for their reconstruction. Eleven flaps were performed during the acute care and 2 were performed for delayed reconstruction. Patients were 69% males and 31% females, with a mean age of 45.5 ± 16 years and a mean BMI of 25.4 ± 6.5. The mean follow-up was 13.5 ± 13.9 months. Indications for free tissue transfer were bone exposure (92%) and severe neck burn contracture (8%). Overall complications rate was 54%. Complications included free flap loss (15%), hematoma (15%), vein thrombosis of the anastomosis (15%), infection (8%), amputation (8%), and wound healing issues (23%). Overall, 38% of the patients required re-operations including venous anastomosis revision, hematoma evacuation, debridement, skin grafting, and debulking. Although sometimes free flap remains the only reconstructive option in severe burn-related injuries, it is only rarely used. However, they carry a high risk of complications and should be considered only as the last resort for limb or life-threatening situations.
Outcomes in Stevens–Johnson Syndrome/Toxic Epidermal Necrolysis Patients Treated With a Medicine-Led Multidisciplinary Approach
Authors: Lewcun Joseph A , Vagonis Alex , Kontzias Christina , Newsom Megan , Drake Mack , Feldman Michael J
Published: September 2023

Patients with Stevens–Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) have traditionally been treated in burn centers. Our burn center’s approach differs by admitting these patients to a medicine service, with support from the burn team. The aim of this study was to determine whether SJS/TEN patients cared for with our system, with burn involvement but not burn admission, demonstrate equivalent outcomes. We conducted a retrospective review of all SJS/TEN patients admitted to the medicine service at a single academic medical center from 2009 to 2021. Outcome measures such as mortality, length of ICU stay, and total length of hospitalization were collected. The Severity-of-Illness Score for Toxic Epidermal Necrolysis (SCORTEN) was used to calculate expected mortality rates within the cohort. The observed mortality rates were then compared to the expected mortality rates. One hundred and twenty-six patients who were admitted for SJS/TEN were included (70 SJS, 40 SJS/TEN overlap, 16 TEN). The mortality rate for the entire cohort was 10.32% as compared to a 22.33% expected mortality rate (P = .010). The observed and expected mortality rates for SJS, SJS/TEN overlap, and TEN subgroups were 1.43% observed versus 10.22% expected (P = .029), 20.00% observed versus 35.83% expected (P = .133), and 25.00% observed version 44.06% expected (P = .264), respectively. Mortality rates in SJS/TEN patients admitted to medicine units are equivalent or decreased as compared to SCORTEN-predicted mortality rates. Admission of SJS/TEN patients to a medicine unit is appropriate providing there is burn team involvement in their care.
Access to Certified Burn Centers in the United States: The Geospatial and Transport Cost of Transfer
Authors: Edwards Shelley R , Chamoun Gabrielle , Hecox Emily , Brown Madyson I , Hoppe Ian C , Arnold Peter B , Humphries Laura S
Published: September 2023

Specialized burn centers are critical to minimizing burn-associated morbidity and mortality. However, American Burn Association-verified burn centers are unequally distributed across the United States, and fewer centers are available for pediatric patients relative to adults. The economic burden of transporting patients to these centers contributes significantly to the high cost of burn care. This study quantifies inequitable burn care access in the contiguous United States due to age group and location as a function of physical proximity to a verified burn center and transportation cost. County-level distances to the nearest verified adult or pediatric burn center were determined and mapped. Distance calculations for each population were combined with transport cost data (2022 CMS Ambulance Fee Schedules) to estimate transportation costs for each population (adult vs pediatric, urban vs rural). Pediatric patients reside 30.5 miles further than adults from the nearest center, significantly increasing transportation costs. Ground and air transport costs also increased for rural versus urban patients. Notably, rural patients face almost double the cost of air transport. While physical proximity to burn care appears to differ only modestly across age and region, this marginal increase in distance is associated with significant economic impact. This study highlights physical and economic barriers to burn care access faced by rural and pediatric patients and underscores the critical need to improve equity in burn care access. Future studies should expand on this report’s findings to more fully characterize the additional costs associated with inequitable burn care access.
In-situ shearing process observation system for soft materials via transmission electron microscopy
Authors: Miyata Tomohiro , Wang Hsiao-Fang , Watanabe Daisuke , Kawagoe Yoshiaki , Okabe Tomonaga , Jinnai Hiroshi
Published: September 2023

We developed an in-situ shear test system suitable for transmission electron microscopy (TEM) observations, which enabled us to examine the shear deformation behaviours inside soft materials at nanoscale resolutions. This study was conducted on a nanoparticle-filled rubber to investigate its nanoscale deformation behaviour under a large shear strain. First, the shear deformation process of a large area in the specimen was accurately examined and proven to exhibit an almost perfect simple shear. At the nanoscale, voids grew along the maximum principal strain during shear deformation. In addition, the nanoscale regions with rubber and silica aggregates exhibited deformation behaviours similar to the global shear deformation of the specimen. Although the silica aggregates exhibited displacement along the shearing directions, rotational motions were also observed owing to the torque generated by the local shear stress. This in-situ shear deformation system for TEM enabled us to understand the nanoscale origins of the mechanical properties of soft materials, particularly polymer composites.

Graphical Abstract
Effect of chronic disease on racial difference in COVID-19–associated hospitalization among cancer patients
Authors: Wu Xiao-Cheng , Yu Qingzhao , Yi Yong , Maniscalco Lauren S , Hsieh Mei-Chin , Gruber DeAnn , Mendoza Lee , Subbiah Suki , Sokol Theresa , Shrestha Pratibha , Chen Vivien W , Mederos Eileen T , Ochoa Augusto
Published: September 2023

Background

Research indicates that Black cancer patients have higher rates of COVID-19 hospitalization than their White counterparts. However, the extent to which chronic diseases contribute to racial disparities remains uncertain. We aimed to quantify the effect of chronic diseases on racial disparity in COVID-19–associated hospitalization among cancer patients.

Methods

We linked Louisiana Tumor Registry’s data with statewide COVID-19 data and hospital in-patient discharge data to identify patients diagnosed with cancer in 2015-2019 who tested positive for COVID-19 in 2020 and those with COVID-19–associated hospitalization. Multivariable logistic regression and mediation methods based on linear structural equations were employed to assess the effects of the number of chronic diseases (0, 1-2, ≥3) and individual chronic diseases.

Results

Of 6381 cancer patients who tested positive for COVID-19, 31.6% were non-Hispanic Black cancer patients. Compared with non-Hispanic White cancer patients, non-Hispanic Black cancer patients had a higher prevalence of chronic diseases (79.5% vs 66.0%) and higher COVID-19–associated hospitalization (27.2% vs 17.2%). The odds of COVID-19–associated hospitalization were 80% higher for non-Hispanic Black cancer patients than non-Hispanic White cancer patients (odds ratio = 1.80, 95% confidence interval = 1.59 to 2.04). After adjusting for age, sex, insurance, poverty, obesity, and cancer type, number of chronic diseases explained 37.8% of the racial disparity in COVID-19–associated hospitalization, and hypertension, diabetes, and chronic renal disease were the top 3 chronic diseases explaining 9.6%, 8.9%, and 7.3% of the racial disparity, respectively.

Conclusion

Chronic diseases played a substantial role in the racial disparity in COVID-19–associated hospitalization among cancer patients, especially hypertension, diabetes, and renal disease. Understanding and addressing the root causes are crucial for targeted interventions, policies, and health-care strategies to reduce racial disparity.
The Japanese nationwide cohort data of proton beam therapy for liver oligometastasis in esophagogastric cancer patients
Authors: Yamaguchi Hisashi , Fukumitsu Nobuyoshi , Numajiri Haruko , Ogino Hiroyuki , Katoh Norio , Okimoto Tomoaki , Suzuki Motohisa , Sakurai Hideyuki
Published: September 2023

A nationwide multicenter cohort study on particle therapy was launched by the Japanese Society for Radiation Oncology in Japan in May 2016. We analyzed the outcome of proton beam therapy (PBT) for liver oligometastasis of esophagogastric cancers. Cases in which PBT was performed at all PBT facilities in Japan between May 2016 and February 2019 were enrolled. The patients were selected based on the following criteria: controlled primary cancer, liver recurrence without extrahepatic tumors and no more than three liver lesions. Twenty-two males and two females with a median age of 69 (range, 52–80) years and 35 lesions were included. This study included 6 patients with esophageal and 18 patients with gastric cancer. The median lesion size, fraction size and biological effective dose (BED)10 were 32 (7–104) mm, 3.8 gray (relative biological effect)/fractions (Gy (RBE)/fr) (2–8 Gy (RBE)/fr) and 96.9 (88.8–115.2) Gy, respectively. The median follow-up period was 18 (4–47) months. The 1-, 2- and 3-year overall survival (OS) rates were 75, 51.8 and 45.3%, respectively, and the median OS was 25.3 months. The 1-, 2- and 3-year cumulative local recurrence (LR) rates were 3, 6 and 6%, respectively. Patients’ age (P < 0.01), performance status (P = 0.017) and tumor size (P = 0.024) were significant OS-related factors. No Grade 3 or higher adverse events (AEs) were observed. Owing to the low incidence of AEs and the low LR cumulative incidence, PBT is a feasible option for liver oligometastasis of esophagogastric cancers.
Supernumerary intranasal tooth: case report and review of the literature
Authors: Elgamri Alya Isam , Siddig Omer Elfatih Haj , Jobran Afnan W M
Published: September 2023

The supernumerary intranasal teeth are unusual phenomena. They may be asymptomatic or present with different signs and symptoms such as epistaxis, infection, and nasal obstruction. We report a case of a supernumerary intranasal tooth that erupted more than 2 years ago and was treated with surgical removal under local analgesia.
Ruʾūs al-Jibāl Arabic in Context: A Proposal for an Expanded Typology of Southeastern Arabian Dialects
Authors: Shockley Mark Daniel
Published: September 2023

This paper seeks to clearly outline the features that distinguish Ruʾūs al-Jibāl Arabic (also called Šiḥḥī Arabic, Musandam Arabic) spoken on the Omani peninsula from surrounding dialects. Comparison with nearby Arabic varieties yields a few areal features (in segmental phonology) that establish a dialect continuum from the coasts of northern Oman to Musandam. A large number of phonological similarities between Ruʾūs al-Jibāl Arabic and Dhofari Arabic are then documented here for the first time. This robust but discontinuous link re-frames many of the peculiarities of Ruʾūs al-Jibāl Arabic as vestiges of a coastal southern Arabian dialect group. This finding fits a wellknown ancient pattern of northward population movements out of south Arabia, and allows for a more effective delineation of innovations unique to Ruʾūs al-Jibāl . It also offers a direction forward for an expanded framework for the classification of the Arabic dialects of southeastern Arabia, incorporating Oman's peripheries at Dhofar and Musandam.
Joint Imputation of General Data
Authors: Robbins Michael W
Published: September 2023

High-dimensional complex survey data of general structures (e.g., containing continuous, binary, categorical, and ordinal variables), such as the US Department of Defense’s Health-Related Behaviors Survey (HRBS), often confound procedures designed to impute any missing survey data. Imputation by fully conditional specification (FCS) is often considered the state of the art for such datasets due to its generality and flexibility. However, FCS procedures contain a theoretical flaw that is exposed by HRBS data—HRBS imputations created with FCS are shown to diverge across iterations of Markov Chain Monte Carlo. Imputation by joint modeling lacks this flaw; however, current joint modeling procedures are neither general nor flexible enough to handle HRBS data. As such, we introduce an algorithm that efficiently and flexibly applies multiple imputation by joint modeling in data of general structures. This procedure draws imputations from a latent joint multivariate normal model that underpins the generally structured data and models the latent data via a sequence of conditional linear models, the predictors of which can be specified by the user. We perform rigorous evaluations of HRBS imputations created with the new algorithm and show that they are convergent and of high quality. Lastly, simulations verify that the proposed method performs well compared to existing algorithms including FCS.
Dual counterpart intuitionistic logic
Authors: Cantor Anthony , Stump Aaron
Published: September 2023

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: 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

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

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

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.
Viruses of Nitrogen-Fixing Mesorhizobium Bacteria in Globally Distributed Chickpea Root Nodules
Authors: Matsumoto Brandon L. , Sieradzki Ella T. , Greenlon Alex , Perilla-Henao Laura M. , Ter Horst Anneliek M. , Geonczy Sara E. , Cook Douglas R. , Emerson Joanne B.
Published: September 2023

Legume nodules are specialized environments on plant roots that are induced and dominated by nitrogen-fixing bacteria. Bacteriophages (phages) in these nodules could potentially provide top-down controls on the population size and, therefore, the function of nitrogen-fixing symbionts. Here we sought to characterize the diversity and biogeographical patterns of phages that infect nitrogen-fixing Mesorhizobium symbionts isolated from root nodules, leveraging 266 genomes of Mesorhizobium isolated from nodules and 648 nodule metagenomes collected from three species of chickpea plants ( Cicer spp.) under different agricultural management practices, spanning eight countries on five continents. We identified 106 phage populations (viral operational taxonomic units [vOTUs]) in Mesorhizobium draft genomes, 37% of which were confirmed as likely prophages. These vOTUs were detected in 64% of the Mesorhizobium-dominated nodule metagenomes and 58% of the Mesorhizobium isolates. Per metagenome, 1 to 16 putative Mesorhizobium vOTUs were detected, with more than half of the nodules containing only one such vOTU. The majority of vOTUs were detected exclusively in Ethiopia, followed by India and Morocco, with the lowest richness of putative Mesorhizobium phages in countries that applied industrial Mesorhizobium inoculants to crops. Two vOTUs were identified in five or more countries and in nodules dominated by different strains of Mesorhizobium, suggesting infection of diverse Mesorhizobium hosts and long-term interactions. Beta-diversity of these Mesorhizobium phage assemblages was significantly correlated with the dominant Mesorhizobium strain, but not with measured environmental parameters. Our findings indicate that nitrogen-fixing nodules in chickpea plants can contain distinct viral assemblages, with potential impacts on the nodule microbiome that bear further exploration.
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

Exercise 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

Cellular 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

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

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.
Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces
Authors: Waschulin Valentin , Borsetto Chiara , Corre Christophe , Wellington Elizabeth M.
Published: September 2023

γ-butyrolactone and related signalling systems are found in

Streptomyces

and other actinobacteria where they control the production of secondary or specialized metabolites such as antibiotics. Genetic manipulation of these regulatory systems therefore leads to changes in the secondary metabolite profile of a strain and has been used to activate previously silent secondary metabolite gene clusters. However, there is no easy way to assess the presence of γ-butyrolactone-like systems in

Streptomyces

strains without whole-genome sequencing. We have therefore developed and tested a PCR screen that is able to detect homologues of the commonly co-located butenolide synthase and γ-butyrolactone receptor genes. This PCR screen could be employed for the screening of strain libraries to detect signalling systems without the necessity for whole-genome sequencing.
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

We 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

Long-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

Aims/hypothesis

Pancreatic 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.

Methods

We 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.

Results

Based 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.

Conclusions

Here 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 availability

A 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).
Ancestral genomes and population sequencing data reveal strand- and context-specificity of polymorphic G4 sites
Authors: Lobo Thamar Jessurun , Guryev Victor
Published: September 2023

Recent studies highlight the important functional roles of non-canonical DNA conformations. One of such structures, G-quadruplex (G4), was shown to be involved in multiple processes within a cell such as telomere maintenance, gene regulation, protein translation and alternative splicing. On the other hand, DNA in non-double stranded context can hinder replication and repair processes and, indeed, a higher rate of polymorphisms was reported at G4 sites. However, strand-specificity, positional and nucleotide contexts of nucleotide substitutions at G4 sites are under-investigated.

Here, we combine ancestral genome data and DNA variants from large populational sequencing project to investigate substitution patterns within putative DNA quadruplexes. We confirm the overall elevated rate of base replacement except transitions at CpG sites, which are less likely than in the rest of the genome potentially due to hypomethylated status of G4s. Within G4 loops, there is a trend of replacing weak bases (A, T) with strong bases (G, C) that could promote DNA duplex stabilization. However, this trend is less pronounced when derived allele is rare in the human population. The most over-represented thymine to guanine replacement is about order of magnitude more frequent within G4 than in non-G4 regions. The analysis of nucleotide context of the substitutions shows clear difference between G-rich and C-rich of DNA quadruplexes implying that the strands of the quadruplex might have different mutation dynamics. Finally, we show that the observed deviations from random mutation accumulation result in a biased nucleotide composition of G4 loops rich in adenines. Future studies should reveal specific mutation and selection processes that shape the content of G4-associated DNA polymorphisms.