bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolving collaboration, dependencies, and use in the Rust Open Source Software ecosystem
Authors: Schueller William , Wachs Johannes , Servedio Vito D. P. , Thurner Stefan , Loreto Vittorio 
Published: November 2022

AbstractOpen Source Software (OSS) is widely spread in industry, research, and government. OSS represents an effective development model because it harnesses the decentralized efforts of many developers in a way that scales. As OSS developers work independently on interdependent modules, they create a larger cohesive whole in the form of an ecosystem, leaving traces of their contributions and collaborations. Data harvested from these traces enable the study of large-scale decentralized collaborative work. We present curated data on the activity of tens of thousands of developers in the Rust ecosystem and the evolving dependencies between their libraries. The data covers eight years of developer contributions to Rust libraries and can be used to reconstruct the ecosystem’s development history, such as growing developer collaboration networks or dependency networks. These are complemented by data on downloads and popularity, tracking dynamics of use, visibility, and success over time. Altogether the data give a comprehensive view of several dimensions of the ecosystem.
High-quality Japanese flounder genome aids in identifying stress-related genes using gene coexpression network
Authors: Xu Xi-wen , Zheng Weiwei , Yang Yingming , Hou Jilun , Chen Songlin 
Published: November 2022

AbstractThe Japanese flounder is one of the most economically important marine flatfish. However, due to the increased frequency of extreme weather events and high-density industrial farming, an increasing number of environmental stresses have become severe threats to the healthy development of the Japanese flounder culture industry. Herein, we produced a high-quality chromosome-scale Japanese flounder genome using PacBio Circular Consensus Sequencing technologies. The assembled Japanese flounder genome spanned 588.22 Mb with a contig N50 size of 24.35 Mb. In total, 105.89 Mb of repetitive sequences and 22,565 protein-coding genes were identified by genome annotation. In addition, 67 candidate genes responding to distinct stresses were identified by gene coexpression network analysis based on 16 published stress-related RNA-seq datasets encompassing 198 samples. A high-quality chromosome-scale Japanese flounder genome and candidate stress-related gene set will not only serve as key resources for genomics studies and further research on the underlying stress responsive molecular mechanisms in Japanese flounder but will also advance the progress of genetic improvement and comprehensive stress-resistant molecular breeding of Japanese flounder.
Systematic analysis of expression profiles and prognostic significance for MMDS-related iron–sulfur proteins in renal clear cell carcinoma
Authors: Yang Ling , Chen Yu-Xin , Li Ying-Ying , Liu Xiao-Juan , Jiang Yong-Mei , Mai Jia 
Published: November 2022

AbstractMitochondrial metabolism disorders play an important role in the occurrence and development of tumors, and iron–sulfur protein is an important molecule for maintaining the normal function of mitochondria. However, the relationship between the expression, prognostic value, and immune infiltration of MMDS-related iron–sulfur protein genes in kidney renal clear cell carcinoma (KIRC) remains unclear. Based on online databases bioinformatics analysis was performed to evaluate the expression differences, survival impacts, immune infiltration, and prognostic significance of multiple mitochondrial dysfunction syndrome (MMDS)-related iron–sulfur protein genes in KIRC patients. For example, the protein–protein interaction (PPI) network was constructed using STRING and GEPIA database; Survival impacts were constructed by TCGA database; Immune infiltration was analyzed using TIMER database. There were significant differences in the mRNA expression levels of ISCA1, ISCA2, C1ORF69 and NFU1 in KIRC among different tumor grades and individual cancer stages. Furthermore, KIRC with high transcription levels of ISCA1, ISCA2, C1ORF69 and NFU1 (p < 0.01) was significantly associated with long overall survival (OS) and disease-free survival (DFS). In addition, overexpression of four genes, NFU1, ISCA1, ISCA2, and C1ORF69 in KIRC indicated a better prognosis. Further studies showed that immune cells had a significantly positive correlation with iron–sulfur protein family genes, including CD8+ T cells, CD4+ T cells and B cells. More importantly, the results of immunohistochemistry showed that the expression of NFU1, ISCA1, ISCA2 and C1ORF69 in normal tissues was higher than that in renal clear cell carcinoma tissues. In this study, we systematically analyzed the expression and prognostic value of iron–sulfur protein family genes in KIRC. More importantly, NFU1, ISCA1, ISCA2, and C1ORF69 are expected to become potential therapeutic targets for KIRC, as well as potential prognostic markers for improving the survival rate and prognostic accuracy of KIRC.
Phase 1 safety trial of a natural product cocktail with antibacterial activity in human volunteers
Authors: Bruce Julie , Oyedemi Blessing , Parsons Nick , Harrison Freya 
Published: November 2022

AbstractNew antibiotics are urgently needed to reduce the health burden of antibiotic-resistant bacterial infection. Natural products (NPs) derived from plants and animals are a current focus of research seeking to discover new antibacterial molecules with clinical potential. A cocktail of NPs based on a medieval remedy for eye infection eliminated biofilms of several highly antibiotic-resistant bacterial species in laboratory studies, and had a promising safety profile in vitro and in a mouse model. A necessary prelude to refining this remedy into a defined, synthetic mixture suitable for testing with wound infections is to firstly establish safety when applied to healthy human skin. We aimed to assess skin-related outcomes of the preparation in a sample of healthy volunteers. This prospective, single arm, non-randomised Phase I clinical trial consisted of a single patch test intervention with 48-h follow-up. Volunteers were staff, students and members of the public recruited from the University of Warwick and surrounding locality. Adults aged 18–79 years, with no history of severe immunity-related disease, diabetes, recent infection, or known pregnancy were eligible. A 100 µl application of a filter-sterilised NP mixture, comprising ground garlic, onion, white wine and bovine bile, was applied to skin on the upper arm and covered with a dressing. The primary outcome was skin-related adverse events over 48 h. Digital photographs were captured where bothersome, salve-related events were reported. 109 volunteers, aged 18–77 years, were recruited between June and July 2021. Sample mean age was 37.6 (SD 16.1) years, and 63 (58%) participants were female. Outcome data were obtained for 106/109 (97%); two participants were lost to follow-up and one removed the skin patch after nine hours due to a bothersome garlic odour. Twenty-one (19.8%) participants reported any patch-test related sign or symptom; of these 14 (13.2%) participants reported minor events related to the salve, including itchiness, redness, or garlic odour. No serious events were reported. We found no evidence of serious skin-related adverse events related to the NP preparation.Trial registration: International Standard Randomised Controlled Trial Number (ISRCTN10773579). Date registered: 08/01/2021.
Multiomics analysis couples mRNA turnover and translational control of glutamine metabolism to the differentiation of the activated CD4+ T cell
Authors: Matheson Louise S. , Petkau Georg , Sáenz-Narciso Beatriz , D’Angeli Vanessa , McHugh Jessica , Newman Rebecca , Munford Haydn , West James , Chakraborty Krishnendu , Roberts Jennie , Łukasiak Sebastian , Díaz-Muñoz Manuel D. , Bell Sarah E. , Dimeloe Sarah , Turner Martin 
Published: November 2022

AbstractThe ZFP36 family of RNA-binding proteins acts post-transcriptionally to repress translation and promote RNA decay. Studies of genes and pathways regulated by the ZFP36 family in CD4+ T cells have focussed largely on cytokines, but their impact on metabolic reprogramming and differentiation is unclear. Using CD4+ T cells lacking Zfp36 and Zfp36l1, we combined the quantification of mRNA transcription, stability, abundance and translation with crosslinking immunoprecipitation and metabolic profiling to determine how they regulate T cell metabolism and differentiation. Our results suggest that ZFP36 and ZFP36L1 act directly to limit the expression of genes driving anabolic processes by two distinct routes: by targeting transcription factors and by targeting transcripts encoding rate-limiting enzymes. These enzymes span numerous metabolic pathways including glycolysis, one-carbon metabolism and glutaminolysis. Direct binding and repression of transcripts encoding glutamine transporter SLC38A2 correlated with increased cellular glutamine content in ZFP36/ZFP36L1-deficient T cells. Increased conversion of glutamine to α-ketoglutarate in these cells was consistent with direct binding of ZFP36/ZFP36L1 to Gls (encoding glutaminase) and Glud1 (encoding glutamate dehydrogenase). We propose that ZFP36 and ZFP36L1 as well as glutamine and α-ketoglutarate are limiting factors for the acquisition of the cytotoxic CD4+ T cell fate. Our data implicate ZFP36 and ZFP36L1 in limiting glutamine anaplerosis and differentiation of activated CD4+ T cells, likely mediated by direct binding to transcripts of critical genes that drive these processes.
Integrative network analysis interweaves the missing links in cardiomyopathy diseasome
Authors: Chauhan Pankaj Kumar , Sowdhamini Ramanathan 
Published: November 2022

AbstractCardiomyopathies are progressive disease conditions that give rise to an abnormal heart phenotype and are a leading cause of heart failures in the general population. These are complex diseases that show co-morbidity with other diseases. The molecular interaction network in the localised disease neighbourhood is an important step toward deciphering molecular mechanisms underlying these complex conditions. In this pursuit, we employed network medicine techniques to systematically investigate cardiomyopathy’s genetic interplay with other diseases and uncover the molecular players underlying these associations. We predicted a set of candidate genes in cardiomyopathy by exploring the DIAMOnD algorithm on the human interactome. We next revealed how these candidate genes form association across different diseases and highlighted the predominant association with brain, cancer and metabolic diseases. Through integrative systems analysis of molecular pathways, heart-specific mouse knockout data and disease tissue-specific transcriptomic data, we screened and ascertained prominent candidates that show abnormal heart phenotype, including NOS3, MMP2 and SIRT1. Our computational analysis broadens the understanding of the genetic associations of cardiomyopathies with other diseases and holds great potential in cardiomyopathy research.
The effects of mindfulness meditation versus CBT for anxiety on emotional distress and attitudes toward seeking mental health treatment: a semi-randomized trial
Authors: Aisenberg-Shafran Daniela , Shturm Liav 
Published: November 2022

AbstractOlder adults often avoid seeking psychological treatment, thus challenging their ability to cope effectively with anxiety, stress, and depression. The current study aimed to compare the effects of a mindfulness intervention with cognitive behavioral therapy (CBT) on measures of emotional distress and attitudes toward seeking mental health treatment among older adults. Twenty-four seniors were assigned to three groups: (1) Mindfulness-based intervention for seniors (MBIS), (2) CBT for anxiety, or (3) a care-as-usual control group. Participants in the two intervention groups of eight weekly sessions were randomly assigned. Results showed that attitudes toward seeking psychological treatment and depression, anxiety, and worry levels were evaluated before and after the interventions. Following both interventions, participants considered the prospect of utilizing psychological treatment more positively, whereas no changes were observed in the control group. Interestingly, worry levels were eased only in the MBIS group, and anxiety levels were eased only in the CBT group. Our findings support the understanding that cognitive group interventions can effectively achieve their intended aim (decreasing worry or anxiety) and positively impact attitudes toward psychological treatment.Trial registration: clinicaltrials, NCT04165005, 15/11/19.
Au@Ag nanostructures for the sensitive detection of hydrogen peroxide
Authors: Yeh I-Hsiu , Tadepalli Sirimuvva , Liu Keng-Ku 
Published: November 2022

AbstractHydrogen peroxide (H2O2) is an important molecule in biological and environmental systems. In living systems, H2O2 plays essential functions in physical signaling pathways, cell growth, differentiation, and proliferation. Plasmonic nanostructures have attracted significant research attention in the fields of catalysis, imaging, and sensing applications because of their unique properties. Owing to the difference in the reduction potential, silver nanostructures have been proposed for the detection of H2O2. In this work, we demonstrate the Au@Ag nanocubes for the label- and enzyme-free detection of H2O2. Seed-mediated synthesis method was employed to realize the Au@Ag nanocubes with high uniformity. The Au@Ag nanocubes were demonstrated to exhibit the ability to monitor the H2O2 at concentration levels lower than 200 µM with r2 = 0.904 of the calibration curve and the limit of detection (LOD) of 1.11 µM. In the relatively narrow range of the H2O2 at concentration levels lower than 40 µM, the LOD was calculated to be 0.60 µM with r2 = 0.941 of the calibration curve of the H2O2 sensor. This facile fabrication strategy of the Au@Ag nanocubes would provide inspiring insights for the label- and enzyme-free detection of H2O2.
CO2 conversion to formamide using a fluoride catalyst and metallic silicon as a reducing agent
Authors: Wang Ruopeng , Nakao Kaiki , Manaka Yuichi , Motokura Ken 
Published: November 2022

AbstractMetallic silicon could be an inexpensive, alternative reducing agent for CO2 functionalization compared to conventionally used hydrogen or hydrosilanes. Here, metallic silicon recovered from solar panel production is used as a reducing agent for formamide synthesis. Various amines are converted to their corresponding amides with CO2 and H2O via an Si-H intermediate species in the presence of a catalytic amount of tetrabutylammonium fluoride. The reaction system exhibits a wide substrate scope for formamide synthesis. Spectroscopic analysis, including in situ Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), N2 adsorption/desorption analyses, and isotopic experiments reveal that the fluoride catalyst effectively oxidizes Si atoms on both surface and interior of the powdered silicon particles. The solid recovered after catalysis contained mesopores with a high surface area. This unique behavior of the fluoride catalyst in the presence of metallic silicon may be extendable to other reductive reactions, including those with complex substrates. Therefore, this study presents a potential strategy for the efficient utilization of abundant resources.
High-frequency chaotic bursts in laser diode with optical-feedback
Authors: Malica Tushar , Bouchez Guillaume , Wolfersberger Delphine , Sciamanna Marc 
Published: November 2022

AbstractThe diversity of observed nonlinear dynamics in laser diodes subjected to optical feedback shows promise as an excellent candidate for chaos-based commercial applications. Thus, works in the last decade have primarily focused on system performances, geometric configurations, and balancing their trade-offs. We demonstrate an optical feedback system operating on phase-conjugate feedback exhibiting state-of-the-art chaos bandwidth values reaching ≈ 30 GHz. We report numerous high-frequency, spatiotemporally complex, chaotic dynamics undocumented in the past four decades. We highlight the underlying physics involving a three-tier temporal interaction mechanism between laser relaxation oscillations, phase-conjugate feedback induced external cavity modes, and chaotic bursts repeating each delay time in the extended cavity. We show supporting real-time high-definition system outputs captured by modern large bandwidth oscilloscopes. The presented work shows to our knowledge, the highest bandwidth and complexity entropy to-date in an optical chaos from a single laser, thereby proving the unnecessary need for further complexity using cascading lasers.
Microwave-irradiated rapid synthesis of antimicrobial pyrazine derivatives in reactive eutectic media
Authors: Schneider Helen , Merbouh Nabyl , Keerthisinghe Sandra , Antonietti Markus , Filonenko Svitlana 
Published: November 2022

The influence of dilution with water on the efficiency of reactive eutectic media from ammonium formate and monosaccharides for synthesis of hydroxyalkylpyrazines via microwave irradiation.
Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders
Authors: Hanson Britt , Scotchman Elizabeth , Chitty Lyn S. , Chandler Natalie J. 
Published: November 2022

Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (&lt;500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
A superimposed current based busbar protection scheme using slope degree of grey incidence analysis model
Authors: Joband M. , Homayounifar S. , Sarlak M. 
Published: November 2022

AbstractSuperimposed current components contain effective information, which can be employed to enhance the dependability and security of busbar protection relays. This study aims to investigate the use of the slope degree of grey incidence analysis model to design a methodology for busbar protection. A grey‐based busbar protection criterion has been established to inspect the similarities of the superimposed currents measured by nearby CTs inside busbar protection zone. It is concluded that fault is internal if all of the superimposed currents are similar, otherwise, fault is external. It is shown that in all of the simulated cases, the authors’ methodology can make reliable discrimination between internal and external faults. Moreover, the results demonstrated that the protection indexes of the proposed scheme including security, dependability, sensitivity, and selectivity, are satisfactory for different conditions including fault type, fault resistance (to 500 Ω), fault inception angle, simultaneous faults, evolving faults, faults during transformer energization, CT saturation and normal operating switchings and white noise. Besides, the improvements noted in our algorithm are achieved with a low computational burden and sampling rate. Also, the scheme can be implemented in digital relays. It means that the existing busbar protection scheme can be replaced by the proposed scheme.
„Negativdruck-Lungenödem“ und „alveoläre Hämorrhagie“ als Komplikationen einer oberen Atemwegsobstruktion
Authors: Koehler Ulrich , Hildebrandt Olaf , Conradt Regina , Koehler Julian , Kesper Karl 
Published: November 2022

ZusammenfassungNegativdruck-Lungenödem und alveoläre Hämorrhagie sind lebensbedrohliche Komplikationen infolge einer akuten oberen Atemwegsobstruktion. Durch die Obstruktion im Larynx-/Pharynbereich kommt es zu hohen negativen Intrapleuraldrucken, die sich, durch unterschiedliche Faktoren bedingt, auf die Integrität der alveolo-kapillären Membran auswirken. In der Übersichtsarbeit werden klinische Symptome, Ätiologie, die Pathophysiologie sowie die therapeutischen Optionen beschrieben. Ziel ist es, den Kliniker mit den Krankheitsbildern und den Komplikationen vertraut zu machen.
Quantitative Evaluation of Brain Echogenicity in Hypoxic-Ischemic
Encephalopathy in Term Neonates Compared with Controls
Authors: Gonçalves Fabrício Guimarães , Freeman Colbey , Khrichenko Dmitry , Hwang Misun 
Published: November 2022

Abstract
Purpose Neurosonography evaluation of neonatal hypoxic-ischemic
encephalopathy (HIE) is mainly qualitative. We aimed to quantitatively compare
the echogenicity of several brain regions in patients with HIE to healthy
controls.
Materials and Methods 20 term neonates with clinical/MRI evidence
of HIE and 20 term healthy neonates were evaluated. Seven brain regions were
assessed [frontal, parietal, occipital, and perirolandic white matter (WM),
caudate nucleus head, lentiform nucleus, and thalamus]. The echogenicity of the
calvarial bones (bone) and the choroid plexus (CP) was used for ratio
calculation. Differences in the ratios were determined between neonates with HIE
and controls.
Results Ratios were significantly higher for HIE neonates in each region
(p<0.05). The differences were greatest for the perirolandic WM, with CP
and bone ratios being 0.23 and 0.22 greater, respectively, for the HIE compared
to the healthy neonates (p<0.001). The perirolandic WM had a high AUC,
at 0.980 for both the CP and bone ratios. The intra-observer reliability for all
ratios was high, with the caudate to bone ratio being the lowest at 0.832 and
the anterior WM to CP ratio being the highest at 0.992.
Conclusion When coupled with internal controls, quantitative
neurosonography represents a potential tool to identify early neonatal HIE
changes. Larger cohort studies could reveal whether a quantitative approach can
discern between degrees of severity of HIE. Future neurosonography protocols
should be tailored to evaluate the perirolandic region, which requires posterior
coronal scanning.