bluuebunny/crossref_metadata_2025 huggingface dataset:
A New Source of Mutilating Hand Injuries: The Side-by-Side Utility-Terrain Vehicle
Authors: Mendenhall Shaun D. , Graham Emily M. , Memmott Stanley , Frederiksen Hunter , Rioux-Forker Dana , Wang Angela A. , Hutchinson Douglas T.
Published: March 2023

Purpose:

Rates of mutilating hand injuries are increasing from accidents caused by all-terrain vehicles (ATVs) and the recently popularized side-by-side utility-terrain vehicles (UTVs). Increasing surgeon familiarity with upper extremity (UE) injury patterns, severity, and outcomes following ATV and UTV accidents may improve patient care and advocacy.

Methods:

Retrospective comparisons of UE injury patterns, severity, hospital and intensive care unit (ICU) admission lengths, and number of surgeries were made between ATVs and UTVs. Findings were analyzed with Fisher’s exact tests, MANOVA, ANOVAs with post hoc analyses, and multiple linear regressions.

Results:

A total of 154 cases were identified for inclusion (ATV=87; UTV=67). Patient ages ranged from 4-89 years. The UTV group contained significantly more hand and finger injuries, and more of the fractures were open (p=0.005, p<0.001, p<0.001, respectively). Riders of UTVs had nearly three times as many mutilating hand injuries and a near ninefold increase in amputations compared to ATV riders (p<0.001 and p<0.001, respectively). On average, the UTV group spent 2.5 additional days in the hospital, 0.91 additional days in an ICU, and had 1.3 additional surgeries (p=0.001, p=0.007, p<0.001, respectively). Vehicle type was the only variable significantly correlated with days in the hospital, ICU, and number of UE surgeries (p=0.002, p=0.008, p<0.001, respectively).

Conclusions:

Hand surgeons are in a unique position to serve as forerunners for increasing public awareness of off-road vehicle risks and promoting rider safety. Collaborating with manufacturers, emergency care providers, and directing teaching initiatives may improve patient outcomes.
Diagnostic Efficacy of Renal 2-D Shear Wave Elastography in Familial Mediterranean Fever Disease
Authors: Albayrak Eda , Akbas Meral Gizem
Published: March 2023

The aims of this study were to evaluate the kidneys of patients with familial Mediterranean fever (FMF) noninvasively and quantitatively using 2-D shear wave elastography (SWE) and to reveal the diagnostic efficacy of SWE in FMF-induced renal involvement. Healthy controls, FMF patients, and FMF patients with proteinuria were included in the study, and differences in renal stiffness values between the groups were examined. In addition, a relationship between age, sex, height, weight, body mass index, serum erythrocyte sedimentation rate, C-reactive protein, glomerular filtration rate, and renal stiffness values was evaluated. A total of 120 subjects, including 60 controls, 41 FMF patients without proteinuria, and 19 FMF patients with proteinuria, were enrolled in the study. Renal stiffness values were found to be significantly higher in the group with FMF compared with the control group. In addition, the values in the proteinuria group were higher than both the control group and FMF patients without proteinuria (P < 0.001). A significant positive correlation was found between the renal stiffness value and C-reactive protein. According to receiver operating characteristic analysis, the mean renal stiffness value was 7.905 kPa or greater to determine FMF-induced proteinuria. The current study shows that renal stiffness values were higher in FMF patients compared with the normal population and the values showed further increase in the presence of proteinuria, which indicates a more advanced stage of renal involvement of the disease. These findings reveal that SWE can be used as a noninvasive diagnostic tool in the diagnosis, follow-up, and evaluating the severity of FMF.
Extraordinary Complication of COVID-19 Swab Testing: CSF Rhinorrhea
Authors: Uz Uzdan , Günhan Kivanç , Pabuşcu Yüksel , Mutlu Sabri , Kamiloğlu Uğur
Published: March 2023

Coronavirus disease 2019 (COVID-19) is a highly contagious disease that has reached pandemic status. The diagnosis of COVID-19 is made using the polymerase chain reaction test to evaluate a swab taken from the naso/oro-pharyngeal area. Since COVID-19 is still a pandemic, it is thought that the use of this diagnostic test will be on the agenda for a while. A patient with COVID-19 symptoms presented with unilateral cerebrospinal fluid rhinorrhea after a nasopharyngeal swab test. Although nasopharyngeal swabs are taken very frequently, the complication rate is very low. However, life-threatening complications can be observed on rare occasions, and care should be taken.
Motor Evoked Potential—A Pilot Study Looking at Reliability and Clinical Correlations in Multiple Sclerosis
Authors: Jacques F.H. , Apedaile B.E. , Danis I , Sikati-Foko V , Lecompte M , Fortin J
Published: March 2023

Purpose:

Multiple sclerosis (MS) is a clinically heterogeneous disease. Biomarkers that can assess pathological processes that are unseen with conventional imaging remain an unmet need in MS disease management. Motor evoked potentials (MEPs) could be such a biomarker. To determine and follow longitudinal MEP reliability and correlations with clinical measures in MS patients.

Methods:

This is a single-center study in alemtuzumab-treated MS patients to evaluate temporal reliability of MEPs, identify MEP minimum detectible differences, and explore correlations with existing clinical scales. Ten MS patients recently treated with alemtuzumab were evaluated every 6 months over 3 years. Clinical evaluations consisted of expanded disability status scale, timed 25-foot walk, 6-minute walk, and nine-hole peg test. MEPs were measured twice, 2 weeks apart, every 6 months.

Results:

Eight patients completed all 3 years of study. The intraclass correlation coefficient for MEP parameters ranged from 0.76 to 0.98. TA latency and amplitude with facilitation significantly and strongly correlated with all clinical measures, whereas the MEP duration modestly correlated. Biceps latency with facilitation significantly and moderately correlated with 9-hole peg test. Longitudinal correlations demonstrated good predictive values for either clinical deterioration or improvement.

Conclusions:

MEPs have excellent intrapatient and intrarater reliability, and TA MEPs significantly and strongly correlated with expanded disability status scale, 6-minute walk, and timed 25-foot walk, whereas biceps MEPs significantly and moderately correlated with nine-hole peg test. Further studies using larger cohorts of MS patients are indicated.

Clinical trial registration:

ClinicalTrials.gov, Identifier: NCT02623946.
Insulambacter thermoxylanivorax sp. nov., a thermophilic xylanolytic bacterium isolated from compost
Authors: Chhe Chinda , Uke Ayaka , Baramee Sirilak , Tachaapaikoon Chakrit , Pason Patthra , Waeonukul Rattiya , Ratanakhanokchai Khanok , Kosugi Akihiko
Published: March 2023

We isolated and analysed a Gram-negative, facultatively thermophilic, xylan-degrading bacterium that we designated as strain DA-C8T. The strain was isolated from compost from Ishigaki Island, Japan, by enrichment culturing using beech wood xylan as the sole carbon source. The strain showed high xylan degradation ability under anaerobic growth conditions. The isolate grew at 37–60 °C (optimum, 55 °C) and pH 4.0–11.0 (optimum, pH 9.0). As well as xylan, strain DA-C8T could use polysaccharides such as arabinoxylan and galactan as carbon sources. Comparison of 16S rRNA gene sequences indicated that strain DA-C8T was most closely related to

Paenibacillus cisolokensis

LC2-13AT (93.9 %) and

Paenibacillus chitinolyticus

HSCC596 (93.5 %). In phylogenetic analysis, strain DA-C8T belonged to the same lineage as

Xylanibacillus composti

K13T (92.5 %), but there was less statistical support for branching (70 %). Digital DNA–DNA hybridization, average nucleotide identity values and average amino acid sequence identity between strain DA-C8T and

P. cisolokensis

LC2-13AT were 21.8, 68.3 and 58.2 %, respectively. Those between strain DA-C8T and

X. composti

K13 were 23.7, 67.7 and 57.6 %, respectively. The whole-genome DNA G+C content of strain DA-C8T was 52.3 mol%. The major cellular fatty acids were C16 : 0 (42.9 %), anteiso-C15 : 0 (20.0 %) and anteiso-C17 : 0 (16.7 %), the major quinone was menaquinone 7, and the major polar lipids were unidentified glycolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, a novel genus is proposed—Insulambacter gen. nov.—for the novel species Insulambacter thermoxylanivorax sp. nov. The type strain is DA-C8T (=JCM 34211T=DSM 111723T).
Lacticaseibacillus parakribbianus sp. nov., isolated from a pig farm faeces dump
Authors: Bai Lu , Paek Jayoung , Shin Yeseul , Kim Hongik , Kim Si Hyun , Shin Jeong Hwan , Kook Joong-Ki , Chang Young Hyo
Published: March 2023

A lactic acid bacterium isolated from pig faeces was characterized using a polyphasic approach. The strain was Gram-stain-positive, rod-shaped, and facultative anaerobic. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus

Lacticaseibacillus

. The multi-locus sequence tree revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus kribbianus. The main fatty acids were C16 : 0 and C18 : 1ω9c. The average nucleotide identity value, average amino acid identity, and genome-to-genome distance for YH-lacS6T and its most closely related strain, L. kribbianus, were 85.4, 85.2 and 29.2 %, respectively. The G+C content of the genomic DNA was 61.6 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lacS6T (=KCTC 21186T=JCM 34954T) represents a novel species. The name Lacticaseibacillus parakribbianus sp. nov. is proposed.
Rapid emergence and transmission of virulence-associated mutations in the oral poliovirus vaccine following vaccination campaigns
Authors: Walter Katharine S. , Altamirano Jonathan , Huang ChunHong , Carrington Yuan J. , Zhou Frank , Andrews Jason R. , Maldonado Yvonne
Published: March 2023

There is an increasing burden of circulating vaccine-derived polioviruses (cVDPVs) due to the continued use of oral poliovirus vaccine (OPV). However, the informativeness of routine OPV VP1 sequencing for the early identification of viruses carrying virulence-associated reversion mutations has not been directly evaluated in a controlled setting. We prospectively collected 15,331 stool samples to track OPV shedding from vaccinated children and their contacts for ten weeks following an immunization campaign in Veracruz State, Mexico and sequenced VP1 genes from 358 samples. We found that OPV was genetically unstable and evolves at an approximately clocklike rate that varies across serotypes and by vaccination status. Alarmingly, 28% (13/47) of OPV-1, 12% (14/117) OPV-2, and 91% (157/173) OPV-3 of Sabin-like viruses had ≥1 known reversion mutation. Our results suggest that current definitions of cVDPVs may exclude circulating virulent viruses that pose a public health risk and underscore the need for intensive surveillance following OPV use.
MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes
Authors: Mar Daniel , Babenko Ilona M. , Zhang Ran , Noble William Stafford , Denisenko Oleg , Vaisar Tomas , Bomsztyk Karol
Published: March 2023

Background

The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or “omes,” measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding (FFPE) are two common ways to store tissues, and these practices have generated vast biospecimen repositories. However, these biospecimens have been underutilized for multi-omic analysis due to the low throughput of current analytical technologies that impede large-scale studies.

Methods

Tissue sampling, preparation, and downstream analysis were integrated into a 96-well format multi-omics workflow, MultiomicsTracks96. Frozen mouse organs were sampled using the CryoGrid system, and matched FFPE samples were processed using a microtome. The 96-well format sonicator, PIXUL, was adapted to extract DNA, RNA, chromatin, and protein from tissues. The 96-well format analytical platform, Matrix, was used for chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), methylated RNA immunoprecipitation (MeRIP), and RNA reverse transcription (RT) assays followed by qPCR and sequencing. LC-MS/MS was used for protein analysis. The Segway genome segmentation algorithm was used to identify functional genomic regions, and linear regressors based on the multi-omics data were trained to predict protein expression.

Results

MultiomicsTracks96 was used to generate 8-dimensional datasets including RNA-seq measurements of mRNA expression; MeRIP-seq measurements of m6A and m5C; ChIP-seq measurements of H3K27Ac, H3K4m3, and Pol II; MeDIP-seq measurements of 5mC; and LC-MS/MS measurements of proteins. We observed high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles (ChIP-seq: H3K27Ac, H3K4m3, Pol II; MeDIP-seq: 5mC) was able to recapitulate and predict organ-specific super-enhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic expression profiles can be more accurately predicted by the full suite of multi-omics data, compared to using epigenomic, transcriptomic, or epitranscriptomic measurements individually.

Conclusions

The MultiomicsTracks96 workflow is well suited for high dimensional multi-omics studies – for instance, multiorgan animal models of disease, drug toxicities, environmental exposure, and aging as well as large-scale clinical investigations involving the use of biospecimens from existing tissue repositories.
Reduction of human Alzheimer’s disease risk and reversal of mouse model cognitive deficit with nucleoside analog use
Authors: Magagnoli Joseph , Yerramothu Praveen , Ambati Kameshwari , Cummings Tammy , Nguyen Joseph , Thomas Claire C. , Wang Shao-bin , Cheng Kaitlyn , Juraev Maksud , Dholkawala Roshni , Nagasaka Ayami , Ambati Meenakshi , Nagasaka Yosuke , Ban Ashley , Ambati Vidya L. , Sutton S. Scott , Gelfand Bradley D. , Ambati Jayakrishna
Published: March 2023

Innate immune signaling through the NLRP3 inflammasome has been implicated in the pathogenesis of Alzheimer’s disease (AD), the most prevalent form of dementia. We previously demonstrated that nucleoside reverse transcriptase inhibitors (NRTIs), drugs approved to treat HIV and hepatitis B infections, also inhibit inflammasome activation. Here we report that in humans, NRTI exposure was associated with a significantly lower incidence of AD in two of the largest health insurance databases in the United States. Treatment of aged 5xFAD mice (a mouse model of amyloid-β deposition that expresses five mutations found in familial AD) with Kamuvudine-9 (K-9), an NRTI-derivative with enhanced safety profile, reduced Aβ deposition and reversed their cognitive deficit by improving their spatial memory and learning performance to that of young wild-type mice. These findings support the concept that inflammasome inhibition could benefit AD and provide a rationale for prospective clinical testing of NRTIs or K-9 in AD.
MicroRNA-29 Differentially Mediates Preeclampsia-Dysregulated Cellular Responses to Cytokines in Female and Male Fetal Endothelial Cells
Authors: Zhou Chi , Freel Colman , Mills Olivia , Yang Xin-Ran , Yan Qin , Zheng Jing
Published: March 2023

Introduction

Preeclampsia (PE) differentially impairs female and male fetal endothelial cell function which is associated with the increased risks of adult-onset cardiovascular disorders in children born to mothers with PE. However, the underlying mechanisms are poorly defined. Wehypothesizethat dysregulation of microRNA-29a-3p and 29c-3p (miR-29a/c-3p) in PE disturbs gene expression and cellular responses to cytokines in fetal endothelial cells in a fetal sex-dependent manner.

Methods

RT-qPCR analysis of miR-29a/c-3p was performed on female and male unpassaged (P0) human umbilical vein endothelial cells (HUVECs) from normotensive (NT) and PE pregnancies. Bioinformatic analysis of an RNAseq dataset was performed to identify PE-dysregulated miR-29a/c-3p target genes in female and male P0-HUVECs. Gain- and loss-of-function assays were conducted to determine the effects of miR-29a/c-3p on endothelial monolayer integrity and proliferation in response to TGFβ1 and TNFα in NT and PE HUVECs at passage 1.

Results

PE downregulated miR-29a/c-3p in male, but not female P0-HUVECs. PE dysregulated significantly more miR-29a/c-3p target genes in female vs. male P0-HUVECs. Many of these PE-differentially dysregulated miR-29a/c-3p target genes are associated with critical cardiovascular diseases and endothelial functions. We further demonstrated that miR-29a/c-3p knockdown specifically recovered the PE-abolished TGFβ1-induced strengthening of endothelial monolayer integrity in female HUVECs, while miR-29a/c-3p overexpression specifically enhanced the TNFα-promoted cell proliferation in male PE HUVECs.

Conclusions

PE differentially dysregulates miR-29a/c-3p and their target genes associated with cardiovascular diseases- and endothelial function in female and male fetal endothelial cells, possibly contributing to the fetal sex-specific endothelial dysfunction observed in PE.
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

Microelectrode 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

Background

Cytosine 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.

Results

In 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.

Conclusions

We 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

Three-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

The 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

Objective

Synovial 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).

Methods

We 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.

Results

We 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.

Conclusion

There 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

Efficient 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

Most 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

Metabolic 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

Background

Contrary 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.

Methods

PubMed, 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.

Results

3298 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.

Conclusion

High 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

Introduction

The 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 Analysis

Interventional 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 dissemination

An 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 limitations

We 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

Protein 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.
Genetically encoded, noise-tolerant, auxin biosensors in yeast facilitate metabolic engineering and directed evolution
Authors: Chaisupa Patarasuda , Rahman Md Mahbubur , Hildreth Sherry B , Moseley Saede , Gatling Chauncey , Helm Richard F. , Wright R. Clay
Published: March 2023

Auxins are important plant growth regulating compounds that are applied in vast quantities to crops across the globe to control weeds and improve crop quality and yield. Auxins are also produced by nearly every kingdom of life and control both organismal behavior as well as inter-kingdom interactions. Improving our understanding of auxin biosynthesis and signaling is critical to both improving crop plants and controlling symbiotic, commensal, and parasitic inter-kingdom relationships, many of which are critical to ecosystems from forests and oceans to the human microbiome. We present a suite of auxin biosensors that will advance our understanding of and ability to engineer auxin perception by plants and auxin production by fungi. We have developed genetically encoded, ratiometric auxin biosensors in the model yeast Saccharomyces cerevisiae, based on the mechanism plants use to perceive auxin. The ratiometric design of these biosensors improves measurements of auxin concentration by reducing clonal and growth phase variation. These biosensors are capable of measuring exogenous auxin in yeast cultures across five orders of magnitude, likely spanning the physiologically relevant range. We implement these biosensors to measure the production of auxin during different growth conditions and phases for S. cerevisiae. Finally, we demonstrate how these biosensors could be used to improve quantitative functional studies and directed evolution of plant auxin perception machinery. These genetically encoded auxin biosensors will enable future studies of auxin biosynthesis, transport, and signaling in a wide range of yeast species, as well as other fungi, and plants.
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

Although 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 abstract

Highlights

Sperm aster/mitotic apparatus centration occurs at entry into first mitosis

MT-based cortical pulling is active during interphase and switched off at mitotic entry

Loss of cortical pulling at mitosis entry facilitates centration of the aster

MT-based cytoplasmic pulling is active during both interphase and mitosis

Agent-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.
Bis[2-(thiophen-2-yl)quinoxaline-κN
4]silver(I) perchlorate
Authors: Crundwell Guy
Published: March 2023

The crystal of the title salt, [Ag(C12H8N2S)2]ClO4, has C2/c symmetry whereby the silver(I) atom sits on a twofold rotation axis, as does the perchlorate anion, which is disordered about this axis. The thienylquinoxaline ligand is nearly planar with the thienyl ring making a dihedral angle of 10.88 (8)° with respect to the quinoxaline moiety.
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.
Women’s crucible leadership experiences: through the lens of the four-frame organisational model
Authors: Bachnik Katarzyna , Howe-Walsh Liza , Critchley Lisa , Alicea Marisa , Guajardo Maria , Washington Christa Ellen
Published: March 2023

Purpose

This study aims to explore the individual lived crucible experiences of women leaders in higher education (HE) and business as the catalyst to investigate organisational inequality regimes that prevent women leaders from fully participating, contributing and flourishing at work. Drawing upon Bolman and Deal’s four-frame theoretical organisational model, this study analyses women’s lived crucible leadership experiences to better understand the organising processes and practices that render intersectionality invisible that reinforce and perpetuate inequality regimes.

Design/methodology/approach

A collaborative autoethnographic research method was selected for data collection. The research team members each selected one significant crucible moment from their professional career and used the Gibb’s six-part reflective cycle to document their narrative and reflect on their leadership experience. A reflexive thematic analysis was used based on Braun and Clarke’s six phases.

Findings

The study features the importance of creating a climate in organisations that acknowledges the need for greater equity, diversity and inclusion (EDI) to support women leaders. Four global themes emerged from the analysis of the leadership narratives: organisation, power dynamics, emotional distress and perseverance and intersectionality. These themes illuminate a greater understanding of organisational life for women and confirm the presence of inequality regimes of gender and race.

Originality/value

This is the first study to explore the impact of women leaders’ crucible experiences through the lens of the Bolman and Deal’s model that highlights the need to consider an EDI lens as the fifth frame.
Income inequality and polity – an empirical analysis of political Kuznets curve
Authors: Han Yongseung , Kim Myeong Hwan
Published: March 2023

Purpose

Faced with contradictory outcomes in empirical studies on the relation between democracy and income inequality, this paper attempts to provide empirical relations between democracy and income inequality. In particular, the authors seek to find if any curvilinear relation exists as in the Kuznets hypothesis.

Design/methodology/approach

Given elusiveness in empirical relations, the authors will consider several specifications using different estimation methods such as ordinary least squares (OLS), panel data estimation and performing statistical tests to determine the best specification for the relation between income inequality and democracy. Once the authors choose the specification, then the authors will apply this specification to the different groups of data to find any meaningful implications.

Findings

Using the unbalanced panel of 136 countries spanning from 1980 to 2018, the authors found an inverse U-shaped relation, called a political Kuznets curve – income inequality increases first and then decreases later as more democracy is achieved. By quantifying the curve, the authors find that the direct impact of democracy on income inequality is small and that the incremental impact of democracy on income inequality is smaller in a semi-democracy while relatively larger in a full democracy and autocracy.

Originality/value

From the study’s findings, the following policy implications can be considered. First, any change in income inequality caused by democratization should not be concerning as the impact of democracy on income inequality is measured to be very small. Second, the largest factor reducing income inequality is real GDP per capita. Third, the authors find that an impact of government expenditure on income inequality is also inversely U-shaped.
A picture paints a thousand words: supporting organizational learning in the emergency services with data visualization
Authors: Holdsworth David , Zagorecki Adam
Published: March 2023

Purpose

This study aims to examine the use of data visualization as a tool to support practitioner-led organizational learning within the emergency services. The authors investigate how data visualization can support visual communication and the analysis of emergency response data to promote system improvement.

Design/methodology/approach

The authors investigate if communication data, presented as node-link diagrams, can be understood and evaluated by firefighters. Objective understanding of the communication network is measured quantitatively, while subject judgement of the emergency response system is measured qualitatively and compared to prior system evaluation outcomes. The authors compare different data visualization layouts and assess their value in supporting practitioner evaluation of emergency response systems.

Findings

The authors find that while firefighters are largely unfamiliar with their use, data visualizations function as a tool for visual communication and analysis. The authors identify the importance of visualization design and the difficulty in representing characteristics of a dynamic network within static diagrams. The authors also find some correlation between layout design and how respondents interpret visual data.

Originality/value

Results demonstrate the value of data visualization to support practitioner-led organizational learning and suggest future work to support the development of emergency response management.