bluuebunny/crossref_metadata_2025_split huggingface dataset:
HOCl-producing Electrochemical Bandages for TreatingPseudomonas aeruginosa-Infected Murine Wounds
Authors: Fleming Derek , Bozyel Ibrahim , Ozdemir Dilara , Otero Judith Alvarez , Karau Melissa J. , Islam Anoy Md Monzurul , Koscianski Christina , Schuetz Audrey N. , Greenwood-Quaintance Kerryl E. , Mandrekar Jayawant N. , Beyenal Haluk , Patel Robin 
Published: September 2023

AbstractA novel electrochemical bandage (e-bandage) delivering low-level hypochlorous acid (HOCl) was evaluated againstPseudomonas aeruginosamurine wound biofilms. 5 mm skin wounds were created on the dorsum of Swiss-Webster mice and infected with 106colony forming units (CFU) ofP. aeruginosa. Biofilms were formed over two days, after which e-bandages were placed on the wound beds and covered with Tegaderm™. Mice were administered Tegaderm-only (control), non-polarized e-bandage (no HOCl production), or polarized e-bandage (using an HOCl-producing potentiostat), with or without concurrently administered systemic amikacin. Purulence and wound areas were measured before and after treatment. After 48 hours, animals were sacrificed, and wounds were harvested for bacterial quantification. Forty-eight hours of polarized e-bandage treatment resulted in mean biofilm reductions of 1.4 log10CFUs/g (9.0 vs 7.6 log10; p = 0.0107)vsnon-polarized controls, and 2.2 log10CFU/g (9.8 vs 7.6 log10; p = 0.004)vsTegaderm only controls. Systemic amikacin improved CFU reduction in Tegaderm-only (p = 0.0045) and non-polarized control groups (p = 0.0312), but not in the polarized group (p = 0.3876). Compared to the Tegaderm only group, there was more purulence reduction in the polarized group (p = 0.009), but not in the non-polarized group (p = 0.064). Wound closure was not impeded or improved by either polarized or non-polarized e-bandage treatment. Concurrent amikacin did not impact wound closure or purulence. In conclusion, an HOCl-producing e-bandage reducedP. aeruginosain wound biofilms with no impairment in wound healing, representing a promising antibiotic-free approach for addressing wound infections.
Selectivity to acoustic features of human speech in the auditory cortex of the mouse
Authors: Mohn Jennifer L. , Baese-Berk Melissa M. , Jaramillo Santiago 
Published: September 2023

AbstractA better understanding of the neural mechanisms of speech processing can have a major impact in the development of strategies for language learning and in addressing disorders that affect speech comprehension. Technical limitations in research with human subjects hinder a comprehensive ex-ploration of these processes, making animal models essential for advancing the characterization of how neural circuits make speech perception possible. Here, we investigated the mouse as a model organism for studying speech processing and explored whether distinct regions of the mouse auditory cortex are sensitive to specific acoustic features of speech. We found that mice can learn to categorize frequency-shifted human speech sounds based on differences in formant transitions (FT) and voice onset time (VOT). Moreover, neurons across various auditory cortical regions were selective to these speech features, with a higher proportion of speech-selective neurons in the dorso-posterior region. Last, many of these neurons displayed mixed-selectivity for both features, an attribute that was most common in dorsal regions of the auditory cortex. Our results demonstrate that the mouse serves as a valuable model for studying the detailed mechanisms of speech feature encoding and neural plasticity during speech-sound learning.
Cold-induced skin darkening does not protect amphibian larvae from UV-associated DNA damage
Authors: Hird Coen , Flanagan Emer , Franklin Craig E. , Cramp Rebecca L. 
Published: September 2023

AbstractMany amphibian declines are correlated with increasing levels of ultraviolet radiation (UVR). While disease is often implicated in declines, environmental factors such as temperature and UVR play an important role in disease epidemiology.The mutagenic effects of UVR exposure on amphibians are worse at low temperatures. Amphibians from cold environments may be more susceptible to increasing UVR. However, larvae of some species demonstrate cold acclimation, reducing UV-induced DNA damage at low temperatures. Understanding of the mechanisms underpinning this response is lacking.We rearedLimnodynastes peroniilarvae in cool (15°C) or warm (25°C) waters before acutely exposing them to 1.5 h of high intensity (80 μW cm-2) UVBR. We measured the colour of larvae and mRNA levels of a DNA repair enzyme. We reared larvae at 25°C in black or white containers to elicit a skin colour response, and then measured DNA damage levels in the skin and remaining carcass following UVBR exposure.Cold acclimated larvae were darker and displayed lower levels of DNA damage than warm-acclimated larvae. There was no difference in CPD-photolyase mRNA levels between cold- and warm-acclimated larvae. Skin darkening in larvae did not reduce larval accumulation of DNA damage following UVR exposure.Our results showed that skin darkening alone does not explain cold-induced reductions in UV-associated DNA damage inL. peroniilarvae. Beneficial cold-acclimation is more likely underpinned by increased CPD-photolyase abundance and/or increased photolyase activity at low temperatures.Research HighlightsL. peroniiilarvae darken when exposed to cold temperaturesDarker larvae were not protected from the effects of UV on DNA damageCold acclimation of larvae when exposed to UV is likely driven by DNA repair enzymes not melanin
Beadex, theDrosophilaLIM only protein, is required for the growth of the larval neuromuscular junction and sensorimotor activities
Authors: Chitre Kripa , Kairamkonda Subhash , Dwivedi Manish Kumar , Yadav Saumitra , Kumar Vimlesh , Sikdar Sujit K. , Nongthomba Upendra 
Published: September 2023

AbstractThe appropriate growth of the neurons, accurate organization of their synapses, and successful neurotransmission are indispensable for sensorimotor activities. These processes are highly dynamic and tightly regulated. Extensive genetic, molecular, physiological, and behavioural studies have identified many molecular players and investigated their roles in various neuromuscular processes. In this paper, we show that Beadex (Bx), theDrosophilaLIM only (LMO) protein, is required for motor activities and neuromuscular growth ofDrosophila.Bx7, a null allele, adult flies are flightless, with reduced walking and jumping activities. The larvae ofBx7, and the RNAi-mediated neuronal-specific knockdown ofBxshow drastically reduced crawling behaviour, a diminished synaptic span of the neuromuscular junctions and an increased spontaneous neuronal firing with altered motor patterns in the central pattern generators (CPGs). Microarray studies identified multiple targets of Beadex that are involved in different cellular and molecular pathways, including those associated with the cytoskeleton and mitochondria, that could be responsible for the observed neuromuscular defects. With genetic interaction studies, we further show thatHighwire(Hiw), a negative regulator of synaptic growth at the NMJs, negatively regulatesBx, as the latter’s deficiency was able to rescue the phenotype of theHiwnull mutant,HiwDN. Thus, our data indicates that Beadex functions downstream of Hiw to regulate the larval synaptic growth and physiology.
Hospital-Acquired Acute Kidney Injury in Non-critical Medical Patients in a Developing Country Tertiary Hospital: Incidence and Predictors
Authors: Mekonnen Nahom Dessalegn , Leulseged Tigist Workneh , Hassen Buure Ayderuss , Yemaneberhan Kidus Haile , Berhe Helen Surafeal , Mera Nebiat Adane , Beyene Anteneh Abera , Getachew Lidiya Zenebe , Habtezgi Birukti Gebreyohannes , Abriha Feven Negasi 
Published: September 2023

ABSTRACTBackgroundAcute kidney injury (AKI) is a frequent complication in critical patients leading to worse prognosis. Although the consequences of AKI are worse among critical patients, AKI is also associated with less favorable outcomes in non-critical patients. Hence, understanding the magnitude of the problem in these patients is crucial, yet there is a scarcity of evidence in non-critical settings, especially in resource limited countries. Hence, the study aimed at determining the incidence and predictors of hospital acquired acute kidney injury (HAAKI) in non-critical medical patients who were admitted at a large tertiary hospital in Ethiopia.MethodsA retrospective chart review study was conducted among 232 hospitalized non-critical medical patients admitted to St. Paul’s Hospital Millennium Medical College between January 2020 and January 2022. Data was characterized using frequency and median with interquartile range. To identify predictors of HAAKI, a log binomial regression model was fitted at a p value of ≤ 0.05. The magnitude of association was measured using adjusted relative risk (ARR) with its 95% CI.ResultsDuring the median follow-up duration of 11 days (IQR, 6-19 days), the incidence of HAAKI was estimated to be 6.0 per 100 person-day observation (95% CI= 5.5 to 7.2). Significant predictors of HAAKI were found to be having type 2 diabetes mellitus (ARR=2.36, 95% CI= 1.03, 5.39, p-value=0.042), and taking vancomycin (ARR=3.04, 95% CI= 1.38, 6.72, p-value=0.006) and proton pump inhibitors (ARR=3.80, 95% CI = 1.34,10.82, p-value=0.012).ConclusionsHAAKI is a common complication in hospitalized non-critical medical patients, and is associated with a common medical condition and commonly prescribed medications. Therefore, it is important to remain vigilant in the prevention and timely identification of these cases and to establish a system of rational prescribing habits.
Statistical analysis of three data sources for Covid-19 monitoring in Rhineland-Palatinate, Germany
Authors: Pilz Maximilian , Küfer Karl-Heinz , Mohring Jan , Münch Johanna , Wlazło Jarosław , Leithäuser Neele 
Published: September 2023

AbstractIn Rhineland-Palatinate, Germany, a system of three data sources has been established to track the Covid-19 pandemic. These sources are the number of Covid-19-related hospitalizations, the Covid-19 genecopies in wastewater, and the prevalence derived from a cohort study. This paper presents an extensive comparison of these parameters. It is investigated whether wastewater data and a cohort study can be valid surrogate parameters for the number of hospitalizations and thus serve as predictors for coming Covid-19 waves. We observe that this is possible in general for the cohort study prevalence, while the wastewater data suffer from a too large variability to make quantitative predictions by a purely data-driven approach. However, the wastewater data as well as the cohort study prevalence are able to detect hospitalizations waves in a qualitative manner. Furthermore, a detailed comparison of different normalization techniques of wastewater data is provided.
A monoclonal antibody collection forC. difficiletyping
Authors: Hunault Lise , England Patrick , Barbut Frédéric , Iannascoli Bruno , Godon Ophélie , Déjardin François , Thomas Christophe , Dupuy Bruno , Guo Chunguang , Macdonald Lynn , Gorochov Guy , Sterlin Delphine , Bruhns Pierre 
Published: September 2023

ABSTRACTClostridioides difficileis the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in adults. VariousC. difficilestrains circulate currently, associated with different outcomes and antibiotic resistance profiles. However, most studies still focus on the reference strain 630 that does not circulate anymore, partly due to the lack of immunological tools to study current clinically importantC. difficilePCR ribotypes. Herein, we immunized mice expressing human variable antibody genes with the Low Molecular Weight (LMW) subunit of the surface layer protein SlpA from variousC. difficilestrains. Monoclonal antibodies purified from hybridomas bound LMW with high-affinity and whole bacteria from currentC. difficileribotypes with different cross-specificities. This first collection of anti-C. difficilemAbs represent valuable tools for basic and clinical research.
Post-meiotic mechanism of facultative parthenogenesis in gonochoristic whiptail lizard species
Authors: Ho David V. , Tormey Duncan , Odell Aaron , Newton Aracely A. , Schnittker Robert R. , Baumann Diana P. , Neaves William B. , Schroeder Morgan R. , Sigauke Rutendo F. , Barley Anthony J. , Baumann Peter 
Published: September 2023

AbstractFacultative parthenogenesis (FP) has historically been regarded as rare in vertebrates, but in recent years incidences have been reported in a growing list of fish, reptile, and bird species. Despite the increasing interest in the phenomenon, the underlying mechanism and evolutionary implications have remained unclear. A common finding across many incidences of FP is a high degree of homozygosity at microsatellite loci. This has led to the proposal that first or second polar body fusion following the meiotic divisions restores diploidy and thereby mimics fertilization. Here we show that FP occurring in the gonochoristicAspidoscelisspeciesA. marmoratusandA. arizonaeresults in genome-wide homozygosity, an observation inconsistent with polar body fusion as the underlying mechanism of restoration. Instead, a high-quality reference genome forA. marmoratusand analysis of whole-genome sequencing from multiple FP and control animals reveals that a post-meiotic mechanism gives rise to homozygous animals from haploid, unfertilized oocytes. Contrary to the widely held belief that females need to be isolated from males to undergo FP, females housed with conspecific and heterospecific males produced unfertilized eggs that underwent spontaneous development. In addition, a mixture of offspring arising from fertilized eggs and parthenogenetic development was observed to arise from a single clutch. Strikingly, our data support a mechanism for facultative parthenogenesis that removes all heterozygosity in a single generation. Complete homozygosity exposes the genetic load and explains the high rate of congenital malformations and embryonic mortality associated with FP in many species. Conversely, FP constitutes strong purifying selection as non-functional alleles of all essential genes are purged in a single generation.
Natural variation of immune epitopes reveals intrabacterial antagonism
Authors: Stevens Danielle M. , Moreno-Pérez Alba , Weisberg Alexandra J. , Ramsing Charis , Fliegmann Judith , Zhang Ning , Madrigal Melanie , Martin Gregory , Steinbrenner Adam , Felix Georg , Coaker Gitta 
Published: September 2023

AbstractPlants and animals detect biomolecules termed Microbe-Associated Molecular Patterns (MAMPs) and induce immunity. Agricultural production is severely impacted by pathogens which can be controlled by transferring immune receptors. However, most studies use a single MAMP epitope and the impact of diverse multi-copy MAMPs on immune induction is unknown. Here we characterized the epitope landscape from five proteinaceous MAMPs across 4,228 plant-associated bacterial genomes. Despite the diversity sampled, natural variation was constrained and experimentally testable. Immune perception in bothArabidopsisand tomato depended on both epitope sequence and copy number variation. For example, Elongation Factor Tu is predominantly single copy and 92% of its epitopes are immunogenic. Conversely, 99.9% of bacterial genomes contain multiple Cold Shock Proteins and 46% carry a non-immunogenic form. We uncovered a new mechanism for immune evasion, intrabacterial antagonism, where a non-immunogenic Cold Shock Protein blocks perception of immunogenic forms encoded in the same genome. These data will lay the foundation for immune receptor deployment and engineering based on natural variation.Significance StatementPlants recognize pathogens as non-self using innate immune receptors. Receptors on the cell surface can recognize amino acid epitopes present in pathogen proteins. Despite many papers investigating receptor signaling, the vast majority use a single epitope. Here, we analyzed the natural variation across five different epitopes and experimentally characterized their perception in plants. We highlight the importance of analyzing all epitope copies within a pathogen genome. Through genetic and biochemical analyses, we revealed a mechanism for immune evasion, intrabacterial antagonism, where a non-immunogenic epitope blocks perception of immunogenic forms encoded in a single genome. These data can directly inform disease control strategies by enabling prediction of receptor utility and deployment for current and emerging pathogens.
Spatial Transcriptomics Reveals the Requirement of ADGRG6 in Maintaining Chondrocyte Homeostasis in Mouse Growth Plates
Authors: Bian Fangzhou , Hansen Victoria , Feng Hong Colleen , Chen Yanshi , Gray Ryan S. , Wu Chia-Lung , Liu Zhaoyang 
Published: September 2023

ABSTRACTThe growth plate is essential for maintaining skeletal growth; however, the mechanisms governing postnatal growth plate homeostasis are poorly understood. Here we show that ADGRG6/GPR126, a cartilage-enriched G protein-coupled receptor (GPCR), is dispensable for embryonic limb development but is required for postnatal growth plate homeostasis.Adgrg6ablation in osteochondral progenitor cells or postnatal chondrocytes leads to reduced cellularity and impaired maintenance of the resting zone in the growth plate, coupled with increased cell death and reduced cell proliferation.Adgrg6mutant growth plates also exhibit disorganized extracellular matrix structures and dysregulated hypertrophic differentiation. Furthermore, using a novel spatial transcriptomics workflow that applies to FFPE tissue sections of mineralized mouse knee joints, we demonstrate thatAdgrg6ablation leads to reduced SOX9 expression, induced Indian hedgehog (IHH) signaling, and a precocious chondrogenic-to-osteogenic conversion of the growth plate chondrocytes that may be driven by increased POSTN/integrin receptor signaling. We further demonstrated that ADGRG6 regulates the proper formation of the resting zone growth plate by maintaining the PTHrP and SOX9-positive cell populations. Altogether, our findings elucidate the essential role of ADGRG6 in maintaining chondrocyte fate, survival, and homeostasis of the postnatal growth plates.
Tangled up in fibers: How a lytic polysaccharide monooxygenase binds its chitin substrate
Authors: Sørensen Henrik Vinther , Montserrat-Canals Mateu , Coder Ayla , Prévost Sylvain , Krueger Susan , Vaaje-Kolstad Gustav , Bjerregaard-Andersen Kaare , Lund Reidar , Krengel Ute 
Published: September 2023

AbstractLytic polysaccharide monooxygenases (LPMOs) are redox enzymes that bind to and oxidize insoluble carbohydrate substrates, such as chitin or cellulose. This class of enzymes has attracted considerable attention due to their ability to convert biomaterials of high abundance into oligosaccharides that can be useful for producing biofuels and bioplastics. However, processes at the interface between solution and insoluble substrates represent a major challenge to biochemical and structural characterization. Here, we investigated the four-domain LPMO fromVibrio cholerae,N-acetyl glucosamine binding protein A (GbpA), to elucidate how it docks onto its insoluble substrate with its two terminal domains. First, we developed a protocol that allowed GbpA and chitin to form a stable complex in suspension, overcoming incompatibilities of the two binding partners with respect to pH. Using contrast variation small-angle neutron scattering (SANS), we attempted to isolate the scattering signal from the individual components of the chitin-GbpA complex. After determining the neutron scattering contrast match point for chitin (47% D2O), we characterized the structure of GbpA in complex with chitin by SANS. We found that GbpA binds rapidly to chitin, where it spreads out on the chitin fibers, and smooths them. In some locations, GbpA binding induces the formation of protein-chitin clumps containing hundreds of GbpA molecules. These findings are supported by electron microscopy. Placing our findings into a biological context, we discussed the potential advantages of GbpA secretion and how chitin binding may prepare the ground for microcolony formation by the bacteria.
A paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies
Authors: Kellner Fabian L. , Moullec Mathilde Le , Ellegaard Martin R. , Rosvold Jørgen , Peeters Bart , Burnett Hamish A. , Pedersen Åshild Ønvik , Brealey Jaelle C. , Dussex Nicolas , Bieker Vanessa C. , Hansen Brage B. , Martin Michael D. 
Published: September 2023

AbstractOverharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-Arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20thcentury. Here we investigate changes in genetic diversity, population structure and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient nuclear (n= 11) and mitochondrial (n= 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n= 90), to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation and 400 years of genetic drift have altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long- term interplay of past, current, and future stressors in wildlife conservation.