bluuebunny/crossref_metadata_2025_split huggingface dataset:
A flexible implant towards acute intrapancreatic electrophysiology
Authors: Pascual Domenic , Brauns Lisa , Domes Ruth , Tisler Matthias , Kögel Marco , Stumpf Angelika , Kirschniak Andreas , Rolinger Jens , Kraushaar Udo , Jones Peter D. 
Published: March 2023

AbstractMicroelectrode arrays (MEAs) have proven to be a powerful tool to study electrophysiological processes over the last decades with most technology developed for investigation of the heart or brain. Other targets in the field of bioelectronic medicine are the peripheral nervous system and its innervation of various organs. Beyond the heart and nervous systems, the beta cells of the pancreatic islets of Langerhans generate action potentials during the production of insulin. In vitro experiments have demonstrated that their activity is a biomarker for blood glucose levels, suggesting that recording their activity in vivo could support patients suffering from diabetes mellitus with long-term automated read-out of blood glucose concentrations.Here, we present a flexible polymer-based implant having 64 low impedance microelectrodes designed to be implanted to a depth of 10 mm into the pancreas. As a first step, the implant will be used in acute experiments in pigs to explore the electrophysiological processes of the pancreas in vivo. Beyond use in the pancreas, our flexible implant and simple implantation method may also be used in other organs such as the brain.
PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data
Authors: Romain Groux , Ioannis Xenarios , Emanuel Schmid-Siegert 
Published: March 2023

AbstractBackgroundCytosine followed by guanine (CpG) rich genomic regions are known important regulatory sequences among vertebrates. Their cytosines can be subjected to a variety of chemical modifications, one of which being 5-methylcytosine (5mC), usually coined CpG methylation. CpG methylation has been demonstrated to have a deep impact on the nearby regulated genes. The advent of single molecule real time sequencing methods have proven to be powerful enablers in this field of research because of the possibility to detect DNA chemical modification directly from the raw sequencing data. In this perspective, several 5mC detection methods have been proposed.ResultsIn this work we present PAPET - PacBio Prediction of Epigenetic Toolkit - a computational method to detect 5mC directly from PacBio SequelII raw sequencing data. We characterized the 5mC signatures in the raw data and proposed a framework to model them. We also assessed the effect of the DNA sequence alone on the signal and propose a normalization method to leverage this effect. From this, we designed a probabilistic approach to predict the presence of cytosine methylation from the sequencing kinetics and benchmarked it.ConclusionsWe apply this framework to predict CpG methylation from SequelII data and demonstrate that the classifiers compare equally with PacBio’s prediction method counterparts in terms of AUC and achieve very high specificity and precision.
Correlative Imaging of 3D Cell Culture on Opaque Bioscaffolds for Tissue Engineering Applications
Authors: Sawyer Monet , Eixenberger Joshua , Nielsen Olivia , Manzi Jacob , Montenegro-Brown Raquel , Subbaraman Harish , Estrada David 
Published: March 2023

AbstractThree-dimensional (3D) tissue engineering (TE) is a prospective treatment that can be used to restore or replace damaged musculoskeletal tissues such as articular cartilage. However, current challenges in TE include identifying materials that are biocompatible and have properties that closely match the mechanical properties and cellular environment of the target tissue, while allowing for 3D tomography of porous scaffolds as well as their cell growth and proliferation characterization. This is particularly challenging for opaque scaffolds. Here we use graphene foam (GF) as a 3D porous biocompatible substrate which is scalable, reproduceable, and a suitable environment for ATDC5 cell growth and chondrogenic differentiation. ATDC5 cells are cultured, maintained, and stained with a combination of fluorophores and gold nanoparticle to enable correlative microscopic characterization techniques, which elucidate the effect of GF properties on cell behavior in a three-dimensional environment. Most importantly, our staining protocols allows for direct imaging of cell growth and proliferation on opaque GF scaffolds using X-ray MicroCT, including imaging growth of cells within the hollow GF branches which is not possible with standard fluorescence and electron microscopy techniques.Abstract Figure
Characteristics of the rumen virome in Japanese cattle
Authors: Sato Yoshiaki , Takebe Hiroaki , Tominaga Kento , Yasuda Jumpei , Kumagai Hajime , Hirooka Hiroyuki , Yoshida Takashi 
Published: March 2023

AbstractThe rumen microbiome is a highly complex ecosystem that includes bacteria, archaea, protozoa, fungi, and viruses. Viruses have a high potential to modify the rumen digestion of feeds via infection and cell lysis of prokaryotes in the rumen; however, understanding of the rumen virome is substantially less advanced due to limitations of the reference genome database. In this study, we conducted metagenomic sequencing of virus-like particles (VLPs) in the rumens of 22 Japanese cattle to construct a reference viral genome catalog of the rumen and uncover the rumen virome characteristics. We succeeded in construction of 8 232 nonredundant viral genomes (≥5 kb length and ≥50% completeness). Among them, putative hosts of 1 223 virus genomes were predicted, and 1 053 virus genomes were taxonomically classified, mainly Siphoviridae, Myoviridae, and Podoviridae. Additionally, 2 764 putative auxiliary metabolic genes (AMGs) were identified in the viral genomes. Importantly, 22 viral genomes associated with archaea in the rumen were identified. Some archaeal viruses have AMGs related to DNA synthesis, suggesting that archaeal viruses control archaeal populations in the rumen and affect methane production from the rumen. Furthermore, we revealed that most rumen viruses were highly rumen-and individual-specific and related to rumen-specific prokaryotes. Overall, the rumen viral catalog and findings of this study will help future analyses to uncover the roles of rumen viruses in feed digestion, productivity, and methane production.
Altered co-expression patterns of synovial fluid proteins related to the immune system and extracellular matrix organization in late stage OA, compared to non-OA controls
Authors: Lönsjö Jenny , Rydén Martin , Turkiewicz Aleksandra , Hughes Velocity , Tjörnstand Jon , Önnerfjord Patrik , Englund Martin , Ali Neserin 
Published: March 2023

AbstractObjectiveSynovial fluid contains proteins that may have been released from surrounding tissues, our aim was to gain new insights into the proteomic profiles of human synovial fluid in knees with and without osteoarthritis (OA).MethodsWe used synovial fluid from 11 patients with end-stage medial compartment knee OA, aspirated during total knee replacement, and from 13 deceased donors who had no prior history of knee OA (healthy controls). These samples were analyzed using high-multiplex immunoassays Olink®. The differential expression of proteins between the groups was analyzed using a linear mixed effects model. The linear associations between pairs of protein expressions were estimated with a linear regression model.ResultsWe found that almost half of the detected proteins were differentially expressed between the OA and non-OA controls. The proteins that were most elevated in the OA group compared to controls were tartrate-resistant acid phosphatase type 5 (fold change 10.6, 95% CI [6.6-17.0]), coagulation factor XI (4.3 [2.6-6.8]) and urokinase-type plasminogen activator (4.3 [2.3-6.8]). The proteins with lower levels in OA compared to controls were fatty acid-binding protein, adipocyte (0.03 [0.02-0.05]), myocilin (0.05 [0.03-0.08]) and carbonic anhydrase 3 (0.14 [0.09-0.23]). The protein-protein co-expression analysis suggests an overall lower number of protein pairs that show co-expression in OA.ConclusionThere is a substantial change in protein abundance in synovial fluid in end-stage knee OA, suggesting that global joint homeostasis is severely deranged. Our findings suggest altered co-expression between the immune response and extracellular matrix organization in end-stage knee OA, in comparison to non-OA controls.
Long non-coding RNAs contribute to DNA damage resistance inArabidopsis thaliana
Authors: Durut Nathalie , Kornienko Aleksandra E. , Schmidt Heiko A. , Lettner Nicole , Donà Mattia , Nordborg Magnus , Scheid Ortrun Mittelsten 
Published: March 2023

AbstractEfficient repair of DNA lesions is essential for faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged youngArabidopsis thalianaplants with two different types of genotoxic stress and performedde novoassembly and transcriptome analysis. We identified three long non-coding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. To understand their potential role in DNA repair, we generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in theBrassicaceaegroup. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for a mechanistic analysis of their role.
Bacterial c-di-GMP plays a key role in the evolution of host-association
Authors: Obeng Nancy , Czerwinski Anna , Schütz Daniel , Michels Jan , Leipert Jan , Bansept Florence , Schultheiß Thekla , Kemlein Melinda , Fuß Janina , Tholey Andreas , Traulsen Arne , Schulenburg Hinrich 
Published: March 2023

AbstractMost microbes evolve faster than their hosts and should therefore drive evolution of host-microbe interactions1–3. However, relatively little is known about the characteristics that define the adaptive path of microbes to host-association. In this study we have identified microbial traits that mediate adaptation to hosts by experimentally evolving the bacteriumPseudomonas luridawith the nematodeCaenorhabditis elegans. We repeatedly observed the evolution of beneficial host-specialist bacteria with improved persistence in the nematode, achieved by mutations that uniformly upregulate the universal second messenger c-di-GMP. We subsequently upregulated c-di-GMP in differentPseudomonasspecies, consistently causing increased host-association. Comparison of Pseudomonad genomes from various environments revealed that c-di-GMP underlies adaptation to a variety of hosts, from plants to humans, suggesting that it is fundamental for establishing host-association.
Hexokinase 1 forms rings that constrict mitochondria during energy stress
Authors: Pilic Johannes , Gottschalk Benjamin , Bourgeois Benjamin , Habisch Hansjörg , Koshenov Zhanat , Oflaz Furkan E. , Erdogan Yusuf C. , Shoshan-Barmatz Varda , Madl Tobias , Graier Wolfgang F. , Malli Roland 
Published: March 2023

SummaryMetabolic enzymes can adapt during energy stress, but the precise mechanisms and consequences of these adaptations remain understudied. Here, we discovered that hexokinase 1 (HK1), a key glycolytic enzyme, clusters into ring-like structures around mitochondria during energy stress. These HK1-rings constrict mitochondria at contact sites with the endoplasmic reticulum (ER) and prevent mitochondrial fission by displacing the dynamin-related protein 1 (Drp1) from mitochondrial constriction sites. Mechanistically, we identified that the lack of ATP and glucose-6-phosphate (G6P) promotes the clustering of HK1. Moreover, we found several mutations that are critical for the formation of HK1-rings. Utilizing these mutations, we could show that HK1-rings keep mitochondria connected and rewire cellular metabolism during energy stress. Our findings highlight that HK1 is a robust energy stress sensor that regulates the shape, connectivity and metabolic activity of mitochondria. Thus, the formation of HK1-rings may affect mitochondrial function in energy stress-related pathologies.
Dietary factors and hypertension risk in West Africa: A systematic review and meta-analysis of observational studies
Authors: Batubo Nimisoere P. , Moore J. Bernadette , Zulyniak Michael A. 
Published: March 2023

AbstractBackgroundContrary to North America and Europe, the prevalence of hypertension is rising in West Africa. Although diet is implicated as a contributor to this trend, nutritional guidelines in West Africa are not tailored to address this concern. This study aimed to address this limitation by investigating dietary factors common to West Africa and evaluating their association with hypertension.MethodsPubMed, Scopus, Web of Science, and Medline were searched to identify studies that investigated diet and hypertension in West African adults. All meta-analyses used a generic inverse-variance random effects model, with subgroup analyses by age, BMI, and study location, and were performed in R.Results3298 studies were identified, of which 31 (n=48,809 participants) satisfied inclusion criteria □ all cross-sectional. Meta-analyses of the association between dietary factors and hypertension included: dietary fat (OR=1.76; 95% CI:1.44,2.14; p<0.0001), red meat (OR=1.51; 95% CI: 1.04, 2.18; p = 0.03), junk-food (OR=1.41; 95% CI: 1.19, 1.67; p < 0.0001), dietary salt (OR= 1.25; 95% CI: 1.12, 1.40; p<0.0001), alcohol (OR= 1.17; 95% CI: 1.03, 1.32; p= 0.013), and ‘fruits and vegetables’ (OR=0.80; 95% CI: 0.24, 1.17; p < 0.0001). Subgroup analyses suggested that ‘fruit and vegetable’ consumption is less protective in the elderly.ConclusionHigh consumption of dietary salt, red meat, dietary fat, junk food, and alcohol are associated with increased odds of hypertension, whereas high fruit and vegetable appear protective. This region-specific evidence will support the development of nutritional assessment tools for clinicians, patients, and researchers aiming to reduce hypertension in West Africa.
Scalability of mobile technology interventions in the prevention and management of HIV among adolescents in low- and middle-income countries: protocol for a systematic review
Authors: Adebayo Emmanuel , Wang Dongqing , Olumide Adesola O. , Ogunniyi Adesola , Fawzi Wafaie 
Published: March 2023

AbstractIntroductionThe rate of new infection of HIV is still high among adolescents globally. Adolescents in low and middle-income countries (LMICs) who are least likely to have access to quality healthcare have the highest proportion of those living with HIV. Mobile technology has played an important role in providing access to information and services among adolescents within the region in recent years. This review aims to synthesise and summarise information that will be useful in planning, designing, and implementing future mHealth strategies within the region.Methods and AnalysisInterventional studies on the prevention and management of HIV among adolescents that used mobile technology in LMICs will be included. MEDLINE (via PubMed), EMBASE, Web of Science, CINAHL, and the Cochrane Library are the information sources that have been identified as relevant to the area of study. These sources will be searched from inception to March 2023. The risk of bias will be assessed using the Cochrane Risk of Bias tool. The scalability of each study will be assessed using the Intervention Scalability Assessment Tool (ISAT). Two independent reviewers will conduct the selection of studies, data extraction, assessment of the risk of bias, and scalability. A narrative synthesis of all the included studies will be provided through a table.Ethics and disseminationAn ethical approval was not necessary for this study. This is a systematic review of publicly available information and therefore ethical approval was not deemed necessary. The results of this review will be published in a peer reviewed journal and dataset will be presented in the main manuscript.Strengths and limitationsWe believe that the likelihood of missing any published article will be low because of the information sources we are considering.The scalability tool (ISAT) has not been used in any systematic review before.The evidence provided in this review will be limited to low-middle-income countries.The exclusion of studies not published in English is a limitation for this review.
A hierarchical strategy to decipher protein dynamicsin vivowith chemical cross-linking mass spectrometry
Authors: Zhang Beirong , Gong Zhou , Zhao Lili , An Yuxin , Gao Hang , Chen Jing , Liang Zhen , Liu Maili , Zhang Yukui , Zhao Qun , Zhang Lihua 
Published: March 2023

AbstractProtein dynamics are essential for their various functions. Meanwhile, the intracellular environment would affect protein structural dynamics, especially for the intrinsically disordered proteins (IDPs). Chemical cross-linking mass spectrometry (CXMS) can unbiasedly capture the protein conformation information in cells and can also represent the protein dynamics. Here, we proposed a hierarchy deciphering strategy for protein dynamicsin vivo. With the prior structure from AlphaFold2, the steady local conformation can be extensively evaluated. On this basis, the full-length structure of multi-domain proteins with various dynamic features can be characterized using CXMS. Furthermore, the complementary strategy with unbiased sampling and distance-constrained sampling enables an objective description of the intrinsic motion of the IDPs. Therefore, the hierarchy strategy we presented herein could help us better understand the molecular mechanisms of protein functions in cells.
Reduction of cortical pulling at mitotic entry facilitates aster centration
Authors: Rosfelter Anne , Labbey Ghislain de , Chenevert Janet , Dumollard Rémi , Schaub Sebastien , Machaty Zoltan , Besnardeau Lydia , Hebras Céline , Turlier Hervé , Burgess David , McDougall Alex 
Published: March 2023

AbstractAlthough it has been studied for more than a century, the question of how one cell divides into two equal parts is still not fully resolved. Zygotes have provided much of the mechanistic insight into how the mitotic apparatus finds the center of the cell since the centrally-located mitotic apparatus is created from a large sperm aster that forms at the cortex and thus far from the zygote center. Here we show that in ascidians, the sperm aster extends throughout the cytoplasm during interphase yet remains located near the cortex and does not migrate towards the zygote center. It is only at mitotic entry, when the sperm aster has duplicated and the mitotic apparatus is being assembled, that most of the migration and centration occurs. This temporal pattern of centration behavior is mirrored by primate zygotes (including human). The current mechanisms of aster centration include cytoplasmic pulling that scale with microtubule (MT) length, MT pushing against the proximal cortex or MT-based cortical pulling. However, it is not yet known whether and how these 3 mechanisms are coordinated to prevent aster migration during interphase and trigger migration at mitotic entry. By monitoring quantitatively all three mechanisms (cytoplasmic pulling, pushing and cortical pulling) we have discovered that cortical pulling is switched off as the zygote enters mitosis while both cytoplasmic pulling and proximal cortical pushing remain active. Physical simulations could recapitulate both the static and migratory aspects of sperm aster and mitotic apparatus behavior. We therefore surmise that the reduction in cortical pulling at mitotic entry represents a switch that allows proximal cortical pushing forces and cytoplasmic pulling forces to center the nascent mitotic apparatus.Graphical abstractHighlightsSperm aster/mitotic apparatus centration occurs at entry into first mitosisMT-based cortical pulling is active during interphase and switched off at mitotic entryLoss of cortical pulling at mitosis entry facilitates centration of the asterMT-based cytoplasmic pulling is active during both interphase and mitosisAgent-based simulations advocate the need for cytoplasmic pulling, a switch in cortical pulling and a minor role of pushing for aster centration at mitotic entry.
Is COCOMO and Putnam relevant to e-Government? Software development efforts estimation in e-Government in the Indian state of Andhra Pradesh
Authors: Balakrishna Sundar 
Published: March 2023

Purpose
This paper aims to examine the process for estimation of efforts for software development and suggests a framework for estimating software development costs and ensuring quality of code in e-Government projects from the Indian state of Andhra Pradesh. With no established processes for estimation of efforts, the Government relied on open bids from the market to develop these e-Government applications.

Design/methodology/approach
The paper adopts an exploratory case study approach to analyze the e-Government applications in Andhra Pradesh. Using data from the information technology department of the Government of Andhra Pradesh, the paper evolves a framework to compute costs of software development, based on the software development life cycle.

Findings
The framework helps in arriving at a hurdle price before the tender process. The study has shown that an e-Government application in AP state would cost Rs. 224,000, or US$2,969.25, for a simple application, and Rs. 33,60,000, or US$44,538.71, for a complex application over a five-year period, depending on the complexity and size of the application. This information would be useful to the Government decision-makers for expanding e-Government.

Research limitations/implications
Further research may assess the utility of this framework for e-Government support activities like automation of data centers, video conferencing facilities and ushering in financial technologies for encouraging cashless payments.

Originality/value
The paper provides information that could be of value at a national level (for India) and at the same time providing a guide for other countries that would like to adopt this framework.