bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold Storage and Cryopreservation Methods For Spermatozoa of the sea urchinLytechinus pictus
Authors: Vacquier Victor D. , Hamdoun Amro 
Published: September 2023

AbstractSea urchins have contributed greatly to knowledge of fertilization, embryogenesis and cell biology. However, until now, they have not been a genetic model organism because of the long generation times of commonly used species, and lack of tools for husbandry and genetic manipulation. We recently establishedLytechinus pictus, as a multigenerational sea urchin model, because of its relatively short generation time of 4-6 months and ease of laboratory culture. To take full advantage of this new multigenerational species, methods are needed to biobank and share mutantL. pictussperm. Here, we describe a new extender based on sperm ion physiology before spawning of sperm into seawater. This extender maintains sperm capable of fertilization for at least 5-10 weeks when stored at 0 °C. We use the extender, and the cryoprotectant dimethyl sulfoxide (DMSO), to cryopreserve sperm of bothL. pictus, and the widely used sea urchin,Strongylocentrotus purpuratus. The simple methods we describe work well for both species, achieving > 90% development and producing larvae that successfully undergo metamorphosis to juvenile sea urchins. Sperm of these two species can be frozen and thawed at least twice and still give rise to larvae that undergo metamorphosis.Main PointsSperm can maintain fertilizing capacityex vivofor 5-10 weeks when stored at 0°C.When freezing in liquid nitrogen no stepwise addition of cryoprotectant, or stepwise drop in temperature are required.A standard fertilization assay is presented to score cleavage stage sea urchin embryos produced by cryopreserved sperm.Sperm frozen and thawed more than once can produce larvae.
Prediction of body weight from body volume of Savanna goats in Limpopo province, South Africa
Authors: Mathapo Madumetja Cyril , Tyasi Thobela Louis , Mugwabana Thinawanga Joseph 
Published: September 2023

AbstractSavanna goats is one of the South African commercial meat breeds. This study was conducted to predict body weight from body volume (BV), heart girth (HG) and body length (BL). A total of 139 savanna goats of the age between 1 and 5 years old of different sex (male and female) were used in the study for collection of body weight, body length and heart girth. The animals were kept under semi-intensive production system, where they were supplemented in the afternoon. Body volume was derived using cylinder volume formula from body length and heart girth as the components of model. R-studio software was employed for Pearson correlation matrix to assess the association between body weight, body length, heart girth and body volume. Simple linear regression was used to establish model to predict body weight. Pearson correlation results indicated that BW had a highly statistical significant (p<0.01) correlation with HG (r = 0.90), BV (r = 0.84) and BL (r = 0.66), respectively. Regression model findings indicated that HG had highest coefficient of determination (R2= 0.81) and lowest mean square error (MSE = 24.85), and BV indicated highest coefficient of determination (R2= 0.76) and low mean square error of (MSE = 35.07) while BL indicated lowest coefficient determination of (R2= 0.45) and high mean square error (MSE = 70.80). In conclusion, correlation result suggests that by improving HG, BV and BL will result in improving BW of Savanna goats. Simple linear regression suggest that HG and BV can be used to estimate BW of Savanna goats.
Documented Goals of Care Conversations with Hospitalized Patients after Severe Stroke
Authors: Comer Amber R. , Bartlett Stephanie , Holloway Robert , Creutzfeldt Claire J. , Williams Linda S. , Slaven James E. , D’Cruz Lynn , Endris Katlyn , Marchand McKenzie , Zepeda Isabel , Toor Sumeet , Waite Carly , Jawed Areeba , Torke Alexia M. 
Published: September 2023

Documented Goals of Care Conversations with Hospitalized Patients after Severe StrokeBackgroundIdentifying goals of care is important for patients suffering severe ischemic stroke (SIS) and their caregivers to ensure patient- and family-centered treatment decisions. This study sought to determine the prevalence and patient predictors associated with having a documented goals-of-care conversation (dGOCC) after SIS.MethodsWe reviewed the medical charts of all patients with National Institutes of Health Stroke Scale (NIHSS) ≥10 admitted to four hospitals in the Midwestern US. In addition to sociodemographic and clinical characteristics, we searched for dGOCC during the acute stroke hospitalization, defined as any documented conversation or meeting that addressed one or more of the following domains: prognostic information, treatment plan, patient preferences and values, quality of life, or establishing goals. We determined prevalence, frequency, timing, and content of dGOCC’s. Additionally, we obtained information on treatment utilization and outcomes.ResultsAmong 1297 patients, 26.5% (n=344) had at least one dGOCC. Treatment plan was the most discussed domain (n=264, 20% of all patients) and was the most common first dGOCC (n=207, 60% of first conversations). Median day for first dGOCC was on hospital day zero. Patient preferences, values, and goals were documented in 112 (8.6%) of all patients’ charts and quality of life conversations were documented in only 61 (4.7%) charts. In multivariate analysis, having a NIHSS ≥21 (OR 1.46, p-value.01) was associated with having a dGOCC.ConclusionAfter severe stroke, most patients do not have a dGOCC, despite the important decisions that often arise about treatment and rehabilitation. Documentation of patient preferences, values and goals are even rarer. This suggests missed opportunities for high quality decision making informed by patient goals to improve person centered care.
The paradox of plant preference: the malaria vectorsAnopheles gambiaeandAnopheles coluzziiselect suboptimal food sources for their survival and reproduction
Authors: Paré Prisca S. L. , Hien Domonbabele F. D. S. , Youba Mariam , Yerbanga Rakiswendé S. , Cohuet Anna , Gouagna Louis-Clément , Diabaté Abdoulaye , Ignell Rickard , Dabiré Roch K. , Gnankiné Olivier , Lefèvre Thierry 
Published: September 2023

AbstractAnopheles gambiae s.l.mosquitoes, the primary malaria vectors in sub-Saharan Africa, exhibit selectivity among plant species as potential food sources. However, it remains unclear if their preference aligns with optimal nutrient intake and survival. Following an extensive screening of the effects of 31 plant species onAn. coluzziiin Burkina Faso, we selected three species for their contrasting effects on mosquito survival, namelyIxora coccinea, Caesalpinia pulcherrima and Combretum indicum. We assessed the sugar content of these plants and their impact on mosquito fructose-positivity, survival, and insemination rate, usingAnopheles coluzziiandAnopheles gambiae, and with glucose 5% and water as controls. Plants displayed varying sugar content and differentially affected the survival, sugar intake and insemination rate of mosquitoes. All three plants were more attractive to mosquitoes than controls, withAn. gambiaebeing more responsive thanAn. coluzzii. Notably,C. indicumwas the most attractive but had the lowest sugar content and offered the lowest survival, insemination rate, and fructose positivity. Our findings unveil a performance-preference mismatch inAn. coluzziiandAn. gambiaeregarding plant food sources. Several possible reasons for this negative correlation between performance and preference are discussed.
Cohesin organizes 3D DNA contacts surrounding active enhancers inC. elegans
Authors: Kim Jun , Wang Haoyu , Ercan Sevinç 
Published: September 2023

AbstractIn mammals, cohesin and CTCF organize the 3D genome into topologically associated domains (TADs) to regulate communication betweencis-regulatory elements. Many organisms, includingS. cerevisiae,C. elegans, andA. thalianacontain cohesin but lack CTCF. Here, we usedC. elegansto investigate the function of cohesin in 3D genome organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features called “fountains”, which are also reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20-40 kb inC. elegans. Hi-C analysis upon cohesin and WAPL depletion support the idea that cohesin is preferentially loaded at NIPBL occupied sites and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains suggest that cohesin processivity is unequal on each side, possibly due to collision with cohesin loaded from surrounding sites. The putative cohesin loading sites are closest to active enhancers and fountain strength is associated with transcription. Compared to mammals, average processivity ofC. eleganscohesin is ∼10-fold shorter and NIPBL binding does not depend on cohesin. We propose that preferential loading and loop extrusion by cohesin is an evolutionarily conserved mechanism that regulates the 3D interactions of enhancers in animal genomes.
RATTACA: Genetic predictions in Heterogeneous Stock rats offer a new tool for genetic correlation and experimental design
Authors: Johnson Benjamin B. , Sanches Thiago M. , Okamoto Mika H. , Nguyen Khai-Min , Ortez Clara A. , Polesskaya Oksana , Palmer Abraham A. 
Published: September 2023

AbstractGenetic correlations between traits are a common first step in studies identifying causal genetic pathways and mechanisms. Using this framework with inbred or selected lines, however, requires intensive labor investment through breeding and phenotyping, and is prone to confounding, as observed trait correlations do not necessarily reflect a causative genetic architecture shared between distinct populations. When drawn from a single outbred population, genetic trait predictions offer a viable alternative to experimental phenotyping and can be used to identify putative genetic correlations when samples with divergent trait predictions also diverge in a second measured trait. Here, we present a novel research paradigm and service called RATTACA, in which genotypes from Heterogenous Stock (HS) rats are used to predict trait values using linear mixed models. These predictions are used to select samples of individuals with high and low extreme trait values, facilitating (1)a priorisampling of desired trait values without oversampling across phenotypic space and (2) easy identification of putative genetic correlations between predicted and newly measured traits. We validated prediction models using four example phenotypes with measured trait values and found sufficient accuracy to distinguish extreme trait samples, even when using a small number of genome-wide variants (n = 50,000) for traits with modest heritability (h2= 0.13). Given genotypes and trait measurements available through previous research in HS rats, we propose RATTACA as a service to reliably predict more than 80 behavioral and physiological traits.
Plant-based production of diverse human milk oligosaccharides
Authors: Barnum Collin R. , Paviani Bruna , Couture Garret , Masarweh Chad , Chen Ye , Huang Yu-Ping , Mills David A. , Lebrilla Carlito B. , Barile Daniela , Yang Minliang , Shih Patrick M. 
Published: September 2023

AbstractHuman milk oligosaccharides (HMOs) are a diverse class of carbohydrates that aid in the health and development of infants. The vast health benefits of HMOs have made them a commercial target for microbial production; however, producing the ∼130 structurally diverse HMOs at scale has proven difficult. Here, we produce a vast diversity of HMOs by leveraging the robust carbohydrate anabolism of plants. This diversity includes high value HMOs, such as lacto-N-fucopentaose I, that have not yet been commercially produced using state-of-the-art microbial fermentative processes. HMOs produced in transgenic plants provided strong bifidogenic properties, indicating their ability to serve as a prebiotic supplement. Technoeconomic analyses demonstrate that producing HMOs in plants provides a path to the large-scale production of specific HMOs at lower prices than microbial production platforms. Our work demonstrates the promise in leveraging plants for the cheap and sustainable production of HMOs.
Expanding the toolbox for phycobiliprotein assembly: phycoerythrobilin biosynthesis inSynechocystis
Authors: Heck Steffen , Sommer Frederik , Zehner Susanne , Schroda Michael , Gehringer Michelle M. , Frankenberg-Dinkel Nicole 
Published: September 2023

AbstractPhycobiliproteins (PBPs) play a vital role in light harvesting by cyanobacteria, which enables efficient utilization of photon energy for oxygenic photosynthesis. The PBPs carry phycobilins, open-chain tetrapyrrole chromophores derived from heme. The structure and chromophore composition of PBPs is dependent on the organism’s ecological niche. In cyanobacteria, these holo-proteins typically form large, macromolecular antenna complexes called phycobilisomes (PBSs). The PBS ofSynechocystissp. PCC 6803 (hereafterSynechocystis) consists of allophycocyanin (APC) and phycocyanin (PC), which exclusively harbor phycocyanobilin (PCB) as a chromophore. Investigations into heterologous PBP biosynthesis inE. colihave proven limiting with respect to PBP assembly and their functional characterization. Consequently, we wanted to engineer a platform for the investigation of heterologously produced PBPs, focusing on unusual, phycoerythrobilin (PEB)-containing light-harvesting proteins called phycoerythrins (PEs) inSynechocystis. As a first step, a gene encoding for the synthesis of the natural cyanobacterial chromophore, PEB, was introduced intoSynechocystis. We provide spectroscopic evidence for heterologous PEB formation and show covalent attachment of PEB to the α-subunit of PC, CpcA, by HPLC and LC-MS/MS analyses. Fluorescence microscopy and PBS isolation demonstrate a cellular dispersal of PBPs with modified phycobilin content. However, these modifications have minor effects on physiological responses, as demonstrated by growth rates, oxygen evolution, nutrient accumulation, and PBP content analyses. As a result,Synechocystisdemonstrates the capacity to efficiently manage PEB biosynthesis and therefore reflects a promising platform for both biochemical and physiological investigations of foreign and unusual PEs.
Optimal Decoding of Neural Dynamics Occurs at Mesoscale Spatial and Temporal Resolutions
Authors: Samiei Toktam , Zou Zhuowen , Imani Mohsen , Nozari Erfan 
Published: September 2023

ABSTRACTIntroductionUnderstanding the neural code has been one of the central aims of neuroscience research for decades. Spikes are commonly referred to as the units of information transfer, but multi-unit activity (MUA) recordings are routinely analyzed in aggregate forms such as binned spike counts, peri-stimulus time histograms, firing rates, or population codes. Various forms of averaging also occur in the brain, from the spatial averaging of spikes within dendritic trees to their temporal averaging through synaptic dynamics. However, how these forms of averaging are related to each other or to the spatial and temporal units of information representation within the neural code has remained poorly understood.Materials and MethodsIn this work we developed NeuroPixelHD, a symbolic hyperdimensional model of MUA, and used it to decode the spatial location and identity of static images shown ton= 9 mice in the Allen Institute Visual Coding - NeuroPixels dataset from large-scale MUA recordings. We parametrically varied the spatial and temporal resolutions of the MUA data provided to the model, and compared its resulting decoding accuracy.ResultsFor almost all subjects, we found 125ms temporal resolution to maximize decoding accuracy for both the spatial location of Gabor patches (81 classes for patches presented over a 9x9 grid) as well as the identity of natural images (118 classes corresponding to 118 images). The optimal spatial resolution was more heterogeneous among subjects, but was still found at either of two mesoscale levels in nearly all cases: the area level, where the spiking activity of neurons within each brain area are combined, and the population level, where the former are aggregated into two variables corresponding to fast spiking (putatively inhibitory) and regular spiking (putatively excitatory) neurons, respectively.DiscussionOur findings corroborate existing empirical practices of spatiotemporal binning and averaging in MUA data analysis, and provide a rigorous computational framework for optimizing the level of such aggregations. Our findings can also synthesize these empirical practices with existing knowledge of the various sources of biological averaging in the brain into a new theory of neural information processing in which theunit of informationvaries dynamically based on neuronal signal and noise correlations across space and time.
Glutamylation of Npm2 and Nap1 acidic disordered regions increases DNA charge mimicry to enhance chaperone efficiency
Authors: Lorton Benjamin M. , Warren Christopher , Ilyas Humaira , Nandigrami Prithviraj , Hegde Subray , Cahill Sean , Lehman Stephanie M , Shabanowitz Jeffrey , Hunt Donald F. , Fiser Andras , Cowburn David , Shechter David 
Published: September 2023

AbstractHistone chaperones–structurally diverse, non-catalytic proteins enriched with acidic intrinsically disordered regions (IDRs)–protect histones from spurious nucleic acid interactions and guide their deposition into and out of nucleosomes. Despite their conservation and ubiquity, the function of the chaperone acidic IDRs remains unclear. Here, we show that theXenopus laevisNpm2 and Nap1 acidic IDRs are substrates for TTLL4 (Tubulin Tyrosine Ligase Like 4)-catalyzed post-translational glutamate-glutamylation. We demonstrate that, to bind, stabilize, and deposit histones into nucleosomes, chaperone acidic IDRs function as DNA mimetics. Our biochemical, computational, and biophysical studies reveal that glutamylation of these chaperone polyelectrolyte acidic stretches functions to enhance DNA electrostatic mimicry, promoting the binding and stabilization of H2A/H2B heterodimers and facilitating nucleosome assembly. This discovery provides insights into both the previously unclear function of the acidic IDRs and the regulatory role of post-translational modifications in chromatin dynamics.
Bone marrow-derived CCR5-expressing macrophages promote venous thrombus resolution by up-regulating plasminogen activators and VEGF
Authors: Nosaka Mizuho , Ishida Yuko , Kuninaka Yumi , Ishigami Akiko , Kimura Akihiko , Taruya Akira , Tanaka Atsushi , Mukaida Naofumi , Kondo Toshikazu 
Published: September 2023

AbstractBackgroundDeep vein thrombosis (DVT) is a common peripheral vascular disease arising from endothelial damage and can frequently result in pulmonary embolism. C-C chemokine receptor 5 (CCR5) is essentially involved in skin wound healing and pulmonary fibrosis, but the role of CCR5 still remains elusive.MethodsDeep vein thrombus was induced by the ligation of the inferior vena cava (IVC) in wild-type (WT) mice andCcr5-/-mice, and thrombi were collected over time and various analyzes were performed.ResultsAfter ligation of the IVC in WT mice, a venous thrombus developed progressively until 5 days, and then resolved. Concomitantly, IVC ligation enhanced intrathrombotic gene and protein expression ofCcr5and its ligand,Ccl5, and both were expressed mainly by intrathrombotic macrophages. The same treatment ofCcr5-/-mice resulted in significantly greater thrombus mass than WT mice. Moreover, the administration of a specific CCR5 inhibitor to WT mice recapitulated similar phenotypes asCcr5-/-mice while that of CCL5 caused the opposite phenotypes. InCcr5-/-mice, the production of intrathrombotic vascular endothelial growth factor (VEGF), tissue plasminogen activator (tPA), and urokinase-type plasminogen activator (uPA) from macrophages was significantly reduced and intrathrombotic recanalization was also suppressed compared to WT mice. Moreover, CCL5 enhancedVegf, Plat,andPlaugene expression in WT-derived peritoneal macrophages by activating the ERK MAPK signaling pathway in vitro.ConclusionsCCR5-deficient mice exhibited reduced expression ofVegf, Plat,andPlau,with concomitant attenuated neovascularization and reduced thrombus resolution. the Thus, the augmentation of the CCL5-CCR5 axis may be effective for DVT treatment by enhancing thrombolysis.
Identifying patients at risk for myasthenic crisis with hemogram and inflammation-related laboratory parameters – a pilot study
Authors: Mehnert Anne , Bershan Sivan , Kollmus-Heege Jil , Gerischer Lea , Herdick Meret Luise , Hoffmann Sarah , Lehnerer Sophie , Scheibe Franziska , Stascheit Frauke , Stein Maike , Buchan Alastair M. , Meisel Andreas , Aigner Annette , Mergenthaler Philipp 
Published: September 2023

ABSTRACTBackgroundMyasthenia gravis (MG) is a rare autoimmune disease characterized by fatigable weakness of the voluntary muscles and can exacerbate to life-threatening myasthenic crisis (MC), requiring intensive care treatment. Routine laboratory parameters are a cost-effective and widely available method for estimating clinical outcomes of several diseases, but so far such parameters have not been established to detect disease progression in MG.MethodsWe conducted a retrospective analysis of selected laboratory parameters related to inflammation and hemogram for MG patients with MC matched to MG patients without MC. To identify potential risk factors for MC, we applied time-varying Cox regression for time to MC, and as a sensitivity analysis generalized estimating equations logistic regression for the occurrence of MC at the next patient visit.Results15 of the 58 examined MG patients suffered at least one MC. There was no notable difference in the occurrence of MC by antibody status or sex. Both regression models showed that higher counts of basophils (per 0.01 units increase: HRlJ=lJ1.32, 95% CIlJ=1.02-1.70), neutrophils (per 1 unit increase: HRlJ=lJ1.40, 95% CIlJ=lJ1.14-1.72), and potentially leukocytes (per 1 unit increase: HR = 1.15, 95% CI = 0.99-1.34), and platelets (per 100 units increase: HR = 1.54, 95% CI = 0.99-2.38) may indicate increased risk for a myasthenic crisis.ConclusionThis pilot study provides proof of concept that increased counts of basophils, neutrophils, leukocytes, and platelets may be associated with a higher risk for developing MC in patients with MG.