bluuebunny/crossref_metadata_2025_split huggingface dataset:
The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules
Authors: Zhang Chuwen , Fang Yun-Xin , Yin Xiuran , Lai Hongfei , Kuang Zenggui , Zhang Tianxueyu , Xu Xiang-Po , Wegener Gunter , Wang Jiang-Hai , Dong Xiyang 
Published: March 2023

AbstractBackgroundGas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization.ResultsComparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons.ConclusionsThese findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes.
Computational network analysis of host genetic risk variants of severe COVID-19
Authors: Alsaedi Sakhaa B. , Mineta Katsuhiko , Gao Xin , Gojobori Takashi 
Published: March 2023

Abstract
Background
Genome-wide association studies have identified numerous human host genetic risk variants that play a substantial role in the host immune response to SARS-CoV-2. Although these genetic risk variants significantly increase the severity of COVID-19, their influence on body systems is poorly understood. Therefore, we aim to interpret the biological mechanisms and pathways associated with the genetic risk factors and immune responses in severe COVID-19. We perform a deep analysis of previously identified risk variants and infer the hidden interactions between their molecular networks through disease mapping and the similarity of the molecular functions between constructed networks.

Results
We designed a four-stage computational workflow for systematic genetic analysis of the risk variants. We integrated the molecular profiles of the risk factors with associated diseases, then constructed protein–protein interaction networks. We identified 24 protein–protein interaction networks with 939 interactions derived from 109 filtered risk variants in 60 risk genes and 56 proteins. The majority of molecular functions, interactions and pathways are involved in immune responses; several interactions and pathways are related to the metabolic and cardiovascular systems, which could lead to multi-organ complications and dysfunction.

Conclusions
This study highlights the importance of analyzing molecular interactions and pathways to understand the heterogeneous susceptibility of the host immune response to SARS-CoV-2. We propose new insights into pathogenicity analysis of infections by including genetic risk information as essential factors to predict future complications during and after infection. This approach may assist more precise clinical decisions and accurate treatment plans to reduce COVID-19 complications.
TransCode: Uncovering COVID-19 transmission patterns via deep learning
Authors: Ren Jinfu , Liu Mutong , Liu Yang , Liu Jiming 
Published: March 2023

Abstract
Background
The heterogeneity of COVID-19 spread dynamics is determined by complex spatiotemporal transmission patterns at a fine scale, especially in densely populated regions. In this study, we aim to discover such fine-scale transmission patterns via deep learning.

Methods
We introduce the notion of TransCode to characterize fine-scale spatiotemporal transmission patterns of COVID-19 caused by metapopulation mobility and contact behaviors. First, in Hong Kong, China, we construct the mobility trajectories of confirmed cases using their visiting records. Then we estimate the transmissibility of individual cases in different locations based on their temporal infectiousness distribution. Integrating the spatial and temporal information, we represent the TransCode via spatiotemporal transmission networks. Further, we propose a deep transfer learning model to adapt the TransCode of Hong Kong, China to achieve fine-scale transmission characterization and risk prediction in six densely populated metropolises: New York City, San Francisco, Toronto, London, Berlin, and Tokyo, where fine-scale data are limited. All the data used in this study are publicly available.

Results
The TransCode of Hong Kong, China derived from the spatial transmission information and temporal infectiousness distribution of individual cases reveals the transmission patterns (e.g., the imported and exported transmission intensities) at the district and constituency levels during different COVID-19 outbreaks waves. By adapting the TransCode of Hong Kong, China to other data-limited densely populated metropolises, the proposed method outperforms other representative methods by more than 10% in terms of the prediction accuracy of the disease dynamics (i.e., the trend of case numbers), and the fine-scale spatiotemporal transmission patterns in these metropolises could also be well captured due to some shared intrinsically common patterns of human mobility and contact behaviors at the metapopulation level.

Conclusions
The fine-scale transmission patterns due to the metapopulation level mobility (e.g., travel across different districts) and contact behaviors (e.g., gathering in social-economic centers) are one of the main contributors to the rapid spread of the virus. Characterization of the fine-scale transmission patterns using the TransCode will facilitate the development of tailor-made intervention strategies to effectively contain disease transmission in the targeted regions.

Graphical Abstract
Eating disorders in sexual minority adolescents and young adults: examining clinical characteristics and psychiatric co-morbidities in an inpatient medical setting
Authors: Chaphekar Anita V. , Downey Amanda , Garber Andrea K. , Kuykendall Mikayla , Bojorquez-Ramirez Paola , Ganson Kyle T. , Buckelew Sara M. , Nagata Jason M. 
Published: March 2023

Abstract
Background
Sexual minority adolescents and young adults are at higher risk of eating disorders compared to heterosexual peers. However, little is known about the clinical and psychiatric presentation of this population requiring inpatient medical stabilization. Given the increased risk for eating disorder behaviors in sexual minority individuals amidst increased rates of medical hospitalizations secondary to eating disorders, it is important to understand presenting characteristics of this population. The objectives of this study were to (1) describe the clinical characteristics of sexual minority adolescents and young adults with eating disorders admitted for medical instability and (2) compare psychiatric co-morbidities and suicidality of sexual minority adolescents and young adults to heterosexual peers.

Methods
A retrospective chart review was conducted of 601 patients admitted to a large inpatient eating disorders medical stabilization unit between 2012 and 2020. Data collected included demographics, medical data including vital signs, and psychiatric characteristics. Chi square or t-tests were used to examine potential differences in clinical characteristics and psychiatric co-morbidities between groups. Modified Poisson regression was used to assess associations between sexual orientation and psychiatric co-morbidities.

Results
Over one fifth (21.1%, n = 103) of our inpatient sample identified as a sexual minority individual. The average age of participants was 15.6 years (2.7). Sexual minority adolescents and young adults had higher percent median body mass index compared to heterosexual peers and yet equally severe vital sign instability on admission. Sexual minority adolescents and young adults were almost 1.5 times more likely to have a psychiatric comorbidity with higher rates of depression, anxiety, and post-traumatic stress disorder. Sexual minority adolescents and young adults were approximately two times more likely to have a history of self-injurious behaviors and/or suicidality.

Conclusions
Sexual minority adolescents and young adults with eating disorders have equally severe vital sign instability despite higher percent median body mass index on admission for medical stabilization. Sexual minority adolescents and young adults hospitalized for medical complications of eating disorders are far more likely to have an additional mental health disorder and a history of self-harm and/or suicidality, which may portend a less favorable long-term prognosis.
Impact of implementation interventions to improve substance use service delivery on recidivism among justice-involved youth
Authors: Robertson Angela A. , Gardner Sheena , Dembo Richard , Dennis Michael , Pankow Jennifer , Wilson Khirsten J. 
Published: March 2023

AbstractSubstance use disorders (SUD) are prevalent among justice-involved youth (JIY) and are a robust predictor of re-offending. Only a fraction of JIY with substance use problems receive treatment. This paper describes the impacts of system-level efforts to improve identification and referral to treatment on recidivism of JIY. A cluster randomized trial involving 20 county juvenile justice agency sites across 5 states was used to implement an organizational intervention (Core vs Enhanced) to juvenile justice staff and community-based treatment providers, working with 18,698 JIY from March 2014 to August 2017. Recidivism rates over four study time periods were examined. Logistic regression was used to predict recidivism as a function of site, need for SUD services, level of supervision, time, organizational intervention, and time x intervention interaction terms. Results indicated that Enhanced sites showed decreased levels of recidivism compared to Core-only sites, where it increased over time. Additionally, need for SU services, level of supervision, and site were significant predictors of reoffending. Findings suggest the potential value of facilitation of juvenile justice agency efforts to increasing identification of and referral to SUD services of JIY in need of such services for reducing further contact with the legal system.
Neutrophil extracellular traps primed intercellular communication in cancer progression as a promising therapeutic target
Authors: Shang Bingqing , Cui Honglei , Xie Ruiyang , Wu Jie , Shi Hongzhe , Bi Xingang , Feng Lin , Shou Jianzhong 
Published: March 2023

AbstractIn addition to the anti-infection response, neutrophils are linked to tumor progression through the secretion of inflammation components and neutrophil extracellular traps (NETs) formation. NET is a web-like structure constituted by a chromatin scaffold coated with specific nuclear and cytoplasmic proteins, such as histone and granule peptides. Increasing evidence has demonstrated that NETs are favorable factors to promote tumor growth, invasion, migration, and immunosuppression. However, the cell–cell interaction between NETs and other cells (tumor cells and immune cells) is complicated and poorly studied. This work is the first review to focus on the intercellular communication mediated by NETs in cancer. We summarized the complex cell–cell interaction between NETs and other cells in the tumor microenvironment. We also address the significance of NETs as both prognostic/predictive biomarkers and molecular targets for cancer therapy. Moreover, we presented a comprehensive landscape of cancer immunity, improving the therapeutic efficacy for advanced cancer in the future.
An integrated genetic analysis of epileptogenic brain malformed lesions
Authors: Fujita Atsushi , Kato Mitsuhiro , Sugano Hidenori , Iimura Yasushi , Suzuki Hiroharu , Tohyama Jun , Fukuda Masafumi , Ito Yosuke , Baba Shimpei , Okanishi Tohru , Enoki Hideo , Fujimoto Ayataka , Yamamoto Akiyo , Kawamura Kentaro , Kato Shinsuke , Honda Ryoko , Ono Tomonori , Shiraishi Hideaki , Egawa Kiyoshi , Shirai Kentaro , Yamamoto Shinji , Hayakawa Itaru , Kawawaki Hisashi , Saida Ken , Tsuchida Naomi , Uchiyama Yuri , Hamanaka Kohei , Miyatake Satoko , Mizuguchi Takeshi , Nakashima Mitsuko , Saitsu Hirotomo , Miyake Noriko , Kakita Akiyoshi , Matsumoto Naomichi 
Published: March 2023

AbstractFocal cortical dysplasia is the most common malformation during cortical development, sometimes excised by epilepsy surgery and often caused by somatic variants of the mTOR pathway genes. In this study, we performed a genetic analysis of epileptogenic brain malformed lesions from 64 patients with focal cortical dysplasia, hemimegalencephy, brain tumors, or hippocampal sclerosis. Targeted sequencing, whole-exome sequencing, and single nucleotide polymorphism microarray detected four germline and 35 somatic variants, comprising three copy number variants and 36 single nucleotide variants and indels in 37 patients. One of the somatic variants in focal cortical dysplasia type IIB was an in-frame deletion in MTOR, in which only gain-of-function missense variants have been reported. In focal cortical dysplasia type I, somatic variants of MAP2K1 and PTPN11 involved in the RAS/MAPK pathway were detected. The in-frame deletions of MTOR and MAP2K1 in this study resulted in the activation of the mTOR pathway in transiently transfected cells. In addition, the PTPN11 missense variant tended to elongate activation of the mTOR or RAS/MAPK pathway, depending on culture conditions. We demonstrate that epileptogenic brain malformed lesions except for focal cortical dysplasia type II arose from somatic variants of diverse genes but were eventually linked to the mTOR pathway.
Knowledge of earthen heritage deterioration in dry areas of China: salinity effect on the formation of cracked surface crust
Authors: Zhang Yue 
Published: March 2023

Abstract
Numerous important earthen heritage sites in northwestern China have survived until today because of the arid and semi-arid climate. However, most of them suffer from various types and degrees of deterioration, with many questions not answered. Scaling off is one of the main types of deterioration widely observed at the Site of Yar City. To clarify the underlying mechanisms of cracked surface crust formation, previous experimental achievements are reviewed in the framework of unsaturated soil mechanics in this paper. A series of laboratory tests on the properties of local soil during desiccation, including water retention, volumetric shrinkage, cracking and tensile strength, are presented and analyzed, with a particular emphasis on salinity effect. Results show that suction is the key factor controlling the soil behavior. With the decrease in water content, all suction components increased gradually. The presence of NaCl led to a large increase in total suction, but a negligible change in matric suction. The soil shrinkage characteristic curve, which can be divided into three zones, was not affected by NaCl. The suction-loading curve indicates that the change in void ratio was governed by matric suction. In addition, most of the drying shrinkage of soil took place in saturated and near-saturated conditions. According to the quantitative analysis of final crack patterns, the highly fragmented surface morphology tended to be induced in thinner, less salinized soil specimens. The soil tensile strength also increased during drying, which was further enhanced by the cementation of salt crystals between particles. These preliminary results can provide some insights in understanding the on-site deterioration of earthen heritage sites.
Perceived network bridging influences the career commitment decisions of early career teachers
Authors: Reid Joshua W. , Polizzi Samuel J. , Zhu Yicong , Jiang Siying , Ofem Brandon , Salisbury Sara , Beeth Michael , Mohr-Schroeder Margaret , Sheppard Keith , Roehrig Gillian , Rushton Gregory T. 
Published: March 2023

Abstract
Background
Retaining highly qualified science, technology, engineering, and mathematics (STEM) teachers is imperative for meeting demands of the twenty-first century STEM workforce. While multiple studies have revealed several factors that influence teacher retention, little work has examined how these factors interact with one another. This study explored the relationship between two critical factors that relate to teachers’ decisions to remain in the profession: teacher identity and communities of practice (CoP) networks.

Results
Drawing upon scholarship on science teacher identity, CoP, and social network theory, we demonstrate a quantitative relationship between perceived network bridging roles and career commitment, which is mediated through teacher identity.

Conclusions
The findings from this study have both implications for scholarship in teacher retention and science teacher identity development. Potential solutions for improving novice teachers’ self-image through providing opportunities to grow their professional networks both locally and regionally/nationally are suggested.
The WORMESH-II flatworm-like mesh robot with 2-DOF double joints
Authors: Rasanga Ganegoda V. C. , Hiraishi Kengo , Hodoshima Ryuichi , Kotosaka Shinya 
Published: March 2023

AbstractThis paper deals with the development of a flatworm-like mesh robot WORMESH-II, which is the second prototype in the WORMESH series inspired from a flattened and soft-bodied flatworm. The pedal locomotion is the primary locomotor of the flatworm that is continuous gliding propulsion along the bottom of the body. The significance of WORMESH series is use of multiple pedal waves to generate the locomotion. The WORMESH-II is a modular robot having a revolute joint system to interconnect two modules. Further, it contains two module types: control module (CM) and joint module (JM). Depending on their arrangements, WORMESH-II can be arranged in different module formations. First, this paper presents the design of WORMESH-II in which double joints capable of three-dimensional motion are introduced. Then, two locomotion gaits for translational and spinning locomotion are described for WORMESH-II in isotropic module formation. Three synchronized parallel pedal waves and one pedal wave loop by the new double joint mechanism were respectively utilized to generate translational and spinning motions of WORMESH-II for IMF. The proposed locomotion gaits were investigated by dynamics simulation and the experiment using the prototype of WORMESH-II. We have successfully demonstrated basic translational and spinning locomotion of WORMESH-II with the velocity of 2.8 mm/s and the angular velocity of 0.0043 rad/s, respectively.
Subconjunctival filtration in evolution: current evidence on MicroShunt implantation for treating patients with glaucoma
Authors: Ahmed Iqbal Ike K. , Sadruddin Omar , Panarelli Joseph F. 
Published: March 2023

Abstract
Background
Although traditional surgical procedures for glaucoma (such as trabeculectomy and tube-shunt implantation) can significantly reduce intraocular pressure (IOP), they are associated with numerous complications, some of which are vision-threatening, or involve prolonged recovery or a highly intensive postoperative course. Micro-invasive glaucoma surgery (MIGS) procedures have shown better safety but reduced efficacy in achieving target IOP. Combinations of these methods have led to the development of subconjunctival micro-invasive procedures with safety comparable to traditional surgery and greater efficacy than minimally invasive methods. This review describes the use of one of these devices, the poly(styrene-block-isobutylene-block-styrene) (SIBS)-based PreserFlo MicroShunt (Santen, Emeryville, CA), in the surgical treatment of patients with glaucoma.

Main text
The MicroShunt is an 8.5-mm tube made of an inert polymer with no endplate, an internal diameter of 70 μm, and fins intended to prevent peritubular flow and anchor the device within the sclera to prevent proximal migration into the eye. Following ab externo implantation, the tube provides a conduit for flow of aqueous humor from the anterior chamber into the subconjunctival/sub-Tenon space. Clinical trials to date have shown that, when paired with mitomycin C (MMC) treatment, MicroShunt implantation significantly reduced both IOP and the number of glaucoma medications. These IOP-lowering results were found both when surgery was performed alone and with phacoemulsification. The MicroShunt also showed a safety profile comparable to that of traditional filtering surgery.

Conclusions
The MicroShunt and other novel subconjunctival procedures have shown substantial IOP reductions while mitigating hypotony-related complications. MMC, which modulates fibrosis and scarring postoperatively, is essential to surgical success. Randomized, long-term clinical trials will further clarify the role of controlled micro-incisional device-assisted ab externo glaucoma filtering surgery in long-term glaucoma management.
An appraisal of the implementation of the national school feeding programme and its effect on enrolment and attendance in public primary schools in Southeast, Nigeria: perception of heads of schools
Authors: Agu Chibuike Innocent , Ossai Edmund Ndudi , Ogah Onwe Emeka , Agu Ifunaya Clara , Akamike Ifeyinwa , Ugwu George Onyemaechi , Edwin Nwobodo , Ewenyi Blessing Lucy , Azuogu Benedict N. 
Published: March 2023

Abstract
Introduction
The National Home Grown School Feeding Programme (NHGSFP) was re-launched in Nigeria in 2016, eleven years after it was first introduced in the country, with Enugu as one of the beneficiary States. The objectives of the programme are to improve the health of school children and aid in the realization of Universal Basic Education (UBE) goals. This study explored the opinions of heads of public primary schools on the implementation and policy benefits of NHGSFP in Enugu, southeast Nigeria.

Methods
This was a cross-sectional study conducted among 24 headmasters and headmistresses purposively selected from public primary schools in the Enugu metropolis. Qualitative data were collected through the use of a pretested Key Informant Interview (KII) guide, and analyzed using a thematic approach.

Results
All the participants were aware of the NHGSFP, which involved the provision of one mid-day meal per child per school day to the pupils, and all their schools were part of the programme. Most of the participants complained about the nutritional quality and quantity of the school meals which they felt were poor. None of the schools had a kitchen within the school premises, and all the participants admitted that deworming was not regularly carried out, as part of the programme. Most of the participants believed that the objectives of the feeding programme, including, reduced hunger among learners, increased school enrolment, attendance and enhanced participatory learning, were being met.

Conclusion
Although the NHGSFP was implemented in every school in Enugu metropolis, Enugu State, Nigeria, regular deworming of pupils was not carried out, and there were concerns about certain aspects of the implementation, such as inadequate funding and poor quality of school meals. Thus, there is a need for the introduction of deworming and more allocation of funds to the programme to improve the quantity and nutritional quality of school meals.