bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic, enzymatic and structural characterization ofTrichuris suishexosaminidase HEX-2
Authors: Dutkiewicz Zuzanna , Varrot Annabelle , Breese Karen J. , Stubbs Keith A. , Nuschy Lena , Adduci Isabella , Paschinger Katharina , Wilson Iain B. H. 
Published: November 2023

AbstractHexosaminidases are key enzymes in glycoconjugate metabolism and occur in all kingdoms of life. Here, we have investigated the phylogeny of the GH20 glycosyl hydrolase family in nematodes and identified a β-hexosaminidase subclade only present in the Dorylaimia. We have expressed one of these, HEX-2 fromTrichuris suis, a porcine parasite, and shown that it prefers an aryl β-N-acetylgalactosaminidein vitro. HEX-2 has an almost neutral pH optimum and is best inhibited by GalNAc-isofagomine. Towards N-glycan substrates, it displays a preference for the removal of GalNAc residues from LacdiNAc motifs as well as the GlcNAc attached to the α1,3-linked core mannose. Thereby, it has a broader specificity than insect fused lobes (FDL) hexosaminidases, but one narrower than distant homologues from plants. Its X-ray crystal structure, the first of any subfamily 1 GH20 hexosaminidase to be determined, is closest toStreptococcus pneumoniaeGH20C and the active site is predicted to be compatible with accommodating both GalNAc and GlcNAc. The new structure extends our knowledge about this large enzyme family, particularly asT. suisHEX-2 also possesses the key glutamate residue found in human hexosaminidases of either GH20 subfamily, including HEXD whose biological function remains elusive.
Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images
Authors: Nirmal Ajit J. , Yapp Clarence , Santagata Sandro , Sorger Peter K. 
Published: November 2023

ABSTRACTHighly multiplexed tissue imaging and in situ spatial profiling aim to extract single-cell data from specimens containing closely packed cells of diverse morphology. This is challenging due to the difficulty of accurately assigning boundaries between cells (segmentation) and then generating per-cell staining intensities. Existing methods use gating to convert per-cell intensity data to positive and negative scores; this is a common approach in flow cytometry, but one that is problematic in imaging. In contrast, human experts identify cells in crowded environments using morphological, neighborhood, and intensity information. Here we describe a computational approach (Cell Spotter or CSPOT) that uses supervised machine learning in combination with classical segmentation to perform automated cell type calling. CSPOT is robust to artifacts that commonly afflict tissue imaging and can replace conventional gating. The end-to-end Python implementation of CSPOT can be integrated into cloud-based image processing pipelines to substantially improve the speed, accuracy, and reproducibility of single-cell spatial data.
Age-related fornix decline predicts conservative response strategy-based slowing in perceptual decision-making
Authors: Revie Lauren , Metzler-Baddeley Claudia 
Published: November 2023

AbstractAging leads to increased response latencies but the underpinning cognitive and neural mechanisms remain elusive. We modelled older and younger adults’ response time (RT) data from a 2-choice flanker task with a diffusion drift model (DDM) and employed multi-shell diffusion weighted magnetic resonance imaging and spectroscopy to study neurobiological predictors of DDM components thought to govern RTs: drift rate, boundary separation and non-decision time. Microstructural indices of fractional anisotropy (FA), diffusivities and the restricted signal fraction (FR) from the Composite Hindered and Restricted Model of Diffusion (CHARMED) were derived from white matter pathways of visuo-perceptual and attention networks (optic radiation, inferior and superior longitudinal fasciculi, fornix) and estimates of metabolite concentrations [N-acetyl aspartate (NAA), glutamate (Glx), γ-aminobutyric acid (GABA), creatine (Cr), choline (Cho) and myoinositol (mI)] were measured from occipital (OCC), anteri- or and posterior cingulate cortices (ACC, PPC). Ageing was associated with increased RT, boundary separation, and non-decision time. Differences in boundary separation but not non-decision time mediated age-related response slowing. Regression analyses revealed a network of brain regions involved in top-down (fornix FA, diffusivities in right SLF) and bottom-up processing (mI in OCC, AD in left optic radiation) and verbal intelligence as significant predictors of RTs and non-decision time (NAA in ACC, AD in the right ILF, creatine in the OCC) while fornix FA was the only predictor for boundary separation. Fornix FA mediated the effects of age on RTs but notvice versa. These results provide novel insights into the cognitive and neural underpinnings of age-related slowing.
A long-read draft assembly of the Chinese mantis (Mantodea: Mantidae:Tenodera sinensis) genome reveals patterns of ion channel gain and loss across Arthropoda
Authors: Goldberg JK , Godfrey RK , Barrett M 
Published: November 2023

AbstractPraying mantids (Mantodea: Mantidae) are iconic insects that have captivated biologists for decades, especially the species with cannibalistic copulatory behavior. This behavior has been cited as evidence that insects lack nociceptive capacities and cannot feel pain; however, this behaviorally-driven hypothesis has never been rigorously tested at the genetic or functional level. To enable future studies of nociceptive capabilities in mantids, we sequenced and assembled a draft genome of the Chinese praying mantis (Tenodera sinensis) and identified multiple classes of nociceptive ion channels by comparison to orthologous gene families in Arthropoda. Our assembly - produced using PacBio HiFi reads - is not chromosome-scale (Total size = 3.03Gb; N50 = 1.8Mb; 4966 contigs), but is highly complete with respect to gene content (BUSCO complete = 98.7% [odb10_insecta]). The size of our assembly is substantially larger than that of most other insects, but is consistent with the size of other mantid genomes. We found that most families of nociceptive ion channels are present in theT. sinensisgenome; that they are most closely related to those found in the damp-wood termite (Zootermopsis nevadensis); and that some families have expanded inT. sinensiswhile others have contracted relative to nearby lineages. Our findings suggest that mantids are likely to possess nociceptive capabilities and provide a foundation for future experimentation regarding ion channel functions and their consequences for insect behavior.
Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis
Authors: Kosmopoulos James C. , Batstone-Doyle Rebecca T. , Heath Katy D. 
Published: November 2023

ABSTRACTThe ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legumeMedicago truncatulaalongsideSinorhizobium melilotiin native soils. Our objectives were to (1) examine the direct and indirect effects of NREs onM. truncatulaandS. melilotifitness, and (2), determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novelPaenibacillusspecies, another strain (717A) as a novelBacillusspecies, and the other two (702A and 733B) as novelPseudomonasspecies. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongsideS. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.
Cross-talk between tissues is critical for intergenerational acclimation to environmental change
Authors: Suresh Sneha , Welch Megan J , Munday Philip L , Ravasi Timothy , Schunter Celia 
Published: November 2023

AbstractAn organism’s reaction to environmental changes is mediated by coordinated responses of multiple tissues. Additionally, parental priming may increase offsprings’ acclimation potential to changing environmental conditions. As the effects of human-induced climate change, such as ocean acidification (OA), continue to intensify it is critical to assess the acclimation potential of species at the whole organismal scale. For this we need to understand the cross-talk between tissues in regulating and responding to pH changes. Here by using a multi-tissue approach we determine the influence of 1) variation in parental behavioural tolerance and 2) parental environment, on molecular responses of their offspring in a coral reef fish. The gills and liver showed the highest transcriptional response to OA conditions in juvenile fish regardless of the parental environment, while the brain and liver showed the greatest signal of intergenerational acclimation. Key functional pathways that were altered in the brain upon within-generational CO2exposure were restored to control levels when parents were exposed to OA conditions. Furthermore, the expression of a new complement of genes involved in key functions was altered in the offspring only when parents were previously exposed to OA conditions. Therefore, previous parental conditioning to OA can reprogram tissue transcriptomic profiles of the offspring enabling them to better cope in an environment with elevated CO2levels. Overall, our results reveal tissue-specific transcriptional changes underlying intergenerational plastic responses to elevated CO2exposure and highlight the integration of these changes in promoting organismal acclimation to OA.
Reduction of coastal lighting decreases seabird strandings
Authors: Burt Tori V. , Collins Sydney M. , Green Sherry , Doiron Parker B. , Wilhelm Sabina I. , Montevecchi William A. 
Published: November 2023

AbstractLeach’s Storm-Petrels (Hydrobates leucorhous) are small, threatened seabirds with an extensive breeding range in the North Atlantic and North Pacific Oceans. The Atlantic population, which represents approximately 40 - 48% of the global population, is declining sharply. Positive phototaxis, the movement towards artificial light at night (ALAN), is considered to be a key contributing factor. Many seabirds exhibit positive phototaxis, which can result in stranding on land. The Leach’s Storm-Petrel is the seabird most often found stranded around ALAN in the North Atlantic, though there is little experimental evidence showing that reducing ALAN will decrease the occurrence of stranded storm-petrels. During a two-year study at a large, brightly illuminated seafood processing plant adjacent to the Leach’s Storm-Petrel’s largest colony, we compared the number of birds that stranded when the lights at the plant were turned on versus off. We recorded survival, performed carcass counts of both adults and juveniles, and released any rescued individuals. Turning the lights off reduced strandings by 39.15% (CI: 11.45% - 58.19%). The peak stranding period occurred from 25 September to 28 October, and most of the stranded birds were fledglings. These results provide evidence to support the widespread reduction and modification of coastal artificial light, especially during avian fledging and migration periods.
Corythauma ayyari(Insecta, Heteroptera, Tingidae) depends on its host plant to invade Europe
Authors: Durand Manon , Guilbert Eric 
Published: November 2023

AbstractBiological invasions increase with the intensity of globalization, human activities, and climate change. Insects represent a high potential of invasive species due to their adaptability to new environment. We analysed here the invasiveness of an Asian phytophagous bug,Corythauma ayyari(Heteroptera, Tingidae), recently recorded in Europe, and that depends onJasminumspp., an ornamental plant widespread in Europe. We modelled its current distribution, projected it into the future and tested its niche overlap between native and invaded areas. When considering the host plant as environmental variable, the analysis shows thatC. ayyarishifted to a new ecological niche but its distribution is restricted by its host plant distribution. Including or excluding the host plant as environmental variable has an impact on species distribution and should be considered when dealing with phytophagous species.
Point mutations in Arf1 reveal cooperative effects of the N-terminal region and myristate for GTPase-activating protein catalytic activity
Authors: Rosenberg Eric M. , Jian Xiaoying , Soubias Olivier , Jackson Rebekah A. , Gladu Erin , Andersen Emily , Esser Lothar , Sodt Alexander J. , Xia Di , Byrd R. Andrew , Randazzo Paul A. 
Published: November 2023

AbstractThe ADP-ribosylation factors (Arfs) constitute a family of small GTPases within the Ras superfamily, with a distinguishing structural feature of a hypervariable N-terminal extension of the G domain modified with myristate. Arf proteins, including Arf1, have roles in membrane trafficking and cytoskeletal dynamics. While screening for Arf1:small molecule co-crystals, we serendipitously solved the crystal structure of the non-myristoylated engineered mutation [L8K]Arf1 in complex with a GDP analogue. Like wild-type (WT) non-myristoylated Arf1•GDP, we observed that [L8K]Arf1 exhibited an N-terminal helix that occludes the hydrophobic cavity that is occupied by the myristoyl group in the GDP-bound state of the native protein. However, the helices were offset from one another due to the L8K mutation, with a significant change in position of the hinge region connecting the N-terminus to the G domain. Hypothesizing that the observed effects on behavior of the N-terminus affects interaction with regulatory proteins, we mutated two hydrophobic residues to examine the role of the N-terminal extension for interaction with guanine nucleotide exchange factors (GEFs) and GTPase Activating Proteins (GAPs). Different than previous studies, all mutations were examined in the context of myristoylated Arf. Mutations had little or no effect on spontaneous or GEF-catalyzed guanine nucleotide exchange but did affect interaction with GAPs. [F13A]myrArf1 was less than 1/2500, 1/1500, and 1/200 efficient as substrate for the GAPs ASAP1, ARAP1 and AGAP1; however, [L8A/F13A]myrArf1 was similar to WT myrArf1. We hypothesized that the myristate moiety associates with the N-terminal extension to alter its structure, thereby affecting its function. Using molecular dynamics simulations, the effect of the mutations on forming alpha helices was examined, yet no differences were detected. The results indicate that lipid modifications of GTPases and consequent anchoring to a membrane influences protein function beyond simple membrane localization. Hypothetical mechanisms are discussed.
Baseline resting EEG measures differentiate rTMS treatment responders and non-responders
Authors: Kaewpijit Pakin , Fitzgerald Paul B , Hoy Kate , Bailey Neil W 
Published: November 2023

AbstractBackgroundRepetitive transcranial magnetic stimulation (rTMS) has been increasingly used worldwide in the treatment of depression, however, we currently lack the means to reliably predict whether patients will respond to the treatment. Recent research suggests that the neurophysiological measures of beta power and correlation dimension may have predictive potential, however, studies of beta power and correlation dimension to differentiate rTMS group response in individuals with major depression are limited.MethodsFifty treatment-resistant patients with major depressive disorder were recruited. Forty-two participants underwent baseline resting EEG sessions and 5-8 weeks of rTMS treatments and 12 participants were responders to the treatment. Beta power and correlation dimension from baseline resting EEG were compared between responders and non-responders.ResultsResponders demonstrated significantly lower beta power in baseline resting EEG, however, correlation dimension did not show a significant difference between groups.LimitationsThere were a small number of responders in this study.ConclusionBaseline resting beta power may help to differentiate responders from non-responders to rTMS treatment. However, further studies are needed with larger sample sizes.
Clinical Characteristics and Laboratory Biomarkers in ICU-admitted Septic Patients with and without Bacteremia: A Predictive Analysis
Authors: Baek Sangwon , Lee Seung Jun 
Published: November 2023

AbstractBackgroundFew studies have investigated the diagnostic utilities of biomarkers for predicting bacteremia among septic patients admitted to intensive care units (ICU). Therefore, this study evaluated the prediction power of laboratory biomarkers to utilize those markers with high performance to optimize the predictive model for bacteremia.MethodsA retrospective cross-sectional study was conducted at the ICU department of Gyeongsang National University Changwon Hospital in 2019. Adult patients qualifying SEPSIS-3 (increase in sequential organ failure score ≥ 2) criteria with at least two sets of blood culture were selected. Collected data was initially analyzed independently to identify the significant predictors, which was then used to build the multivariable logistic regression (MLR) model.ResultsA total of 218 patients with 48 cases of true bacteremia were analyzed in this research. Both CRP and PCT showed a substantial area under the curve (AUC) value for discriminating bacteremia among septic patients (0.757 and 0.845, respectively). To further enhance the predictive accuracy, we combined PCT, bilirubin, neutrophil-lymphocyte ratio (NLR), platelets, lactic acid, erythrocyte sedimentation rate (ESR), and Glasgow Coma Scale (GCS) score to build the predictive model with an AUC of 0.907 [0.843–0.956]. In addition, a high association between bacteremia and mortality rate was discovered through the survival analysis (P=0.004).ConclusionsWhile PCT is certainly a useful index for distinguishing patients with and without bacteremia by itself, our MLR model indicates that the accuracy of bacteremia prediction substantially improves by the combined use of PCT, bilirubin, NLR, platelets, lactic acid, ESR, and GCS score.
Characterization of sleep apnea among a sample of adults from Samoa
Authors: Heinsberg Lacey W. , Pomer Alysa , Cade Brian E. , Carlson Jenna C. , Naseri Take , Reupena Muagututia Sefuiva , Viali Satupa’itea , Weeks Daniel E. , McGarvey Stephen T. , Redline Susan , Hawley Nicola L. 
Published: November 2023

ABSTRACTSleep apnea is a public health concern around the world, but little research has been dedicated to examining this issue in low- and middle-income countries, including Samoa. Using data collected through theSoifua Manuia(“Good Health”) study, which aimed to investigate the impact of the body mass index (BMI)-associated genetic variant rs373863828 in CREB3 Regulatory Factor (CREBRF) on metabolic traits in Samoan adults, we examined the sample prevalence and characteristics of sleep apnea using data collected with a validated home sleep apnea device (WatchPAT, Itamar). A total of 330 participants (sampled to overrepresent the obesity-risk allele of interest) had sleep data available. Participants (53.3% female) had a mean (SD) age of 52.0 (9.9) years and BMI of 35.5 (7.5) kg/m2and 36.3% of the sample had type 2 diabetes. Based on the 3% and 4% apnea hypopnea indices (AHI) and the 4% oxygen desaturation index (ODI), descriptive analyses revealed that many participants had potentially actionable sleep apnea defined as >5 events/hr (87.9%, 68.5%, and 71.2%, respectively) or clinically actionable sleep apnea defined as ≥15 events/hr (54.9%, 31.5%, and 34.5%, respectively). Sleep apnea was more severe in men; for example, clinically actionable sleep apnea (≥15) based on the AHI 3% definition was observed in 61.7% of men and 48.9% of women. Correction for non-representational sampling related to theCREBRFobesity-risk allele resulted in only slightly lower estimates. Across the AHI 3%, AHI 4%, and ODI 4%, multiple linear regression revealed associations between a greater number of events/hr and higher age, male sex, higher body mass index, higher abdominal-hip circumference ratio, and geographic region of residence. Our study identified a much higher frequency of sleep apnea in Samoa compared with published data from other studies, but similar predictors. Continued research addressing generalizability of these findings, as well as a specific focus on diagnosis and affordable and equitable access to treatment, is needed to alleviate the burden of sleep apnea in Samoa and around the world.
Anatomical, Functional, and Hemodynamic Determinants of Increased Pulmonary Capillary Wedge Pressure V-Wave Amplitude
Authors: Torosoff Mikhail , Khorolsky Ciril , Banerjee Riju , Yager Neil 
Published: November 2023

AbstractIntroductionIncreased pulmonary capillary wedge pressure (PCWP) V-wave amplitude has been traditionally associated with significant mitral regurgitation (MR). However, increased PCWP V-waves may also occur in patients with elevated left ventricular end-diastolic pressure (LVEDP) or with dilated left atrium (LA). Interactions between MR, increased LVEDP, and LA dilatation in the genesis of increased PCWP V-waves were not well investigated.Material and MethodsIt was a single-center cohort study of 153 consecutive hemodynamically stable patients referred for invasive hemodynamic evaluation of dyspnea. Patients with significant valvular disease other than MR, acute coronary syndromes (ACS), hemodynamic instability, pericardial disease, and mechanical ventilation or mechanical LV support were excluded.ResultsStudy cohort included 41% males, 68.4+/-11.9 years old, 60% were on beta-adrenergic antagonists and 69.3% were on afterload reduction therapy. PCWP V-wave amplitude was significantly increased in patients with moderate or more severe MR (p<0.001), dilated LA (p=0.002), with a trend towards increased V-wave amplitude in elevated >12 mmHg LVEDP (p=0.117). There were no significant differences in age, gender, prevalence of LV dysfunction, other co-morbidities, and/or E/e’ ratio according to the MR degree, LA volume, and LVEDP. In patients categorized according to moderate or more severe MR, dilated LA, and increased >12 mmHg LVEDP - the presence of any two of these abnormal parameters was associated with 50-65% prevalence of elevated V-waves and reached 100% when all three were parameters were abnormal (p<0.002).ConclusionsIn euvolemic patients undergoing elective invasive hemodynamic evaluation of dyspnea, elevated PCWP V-waves are determined by three major pathophysiological parameters: moderate or more severe MV regurgitation, LA dilatation, and elevated LVEDP.