bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of clay and organic matter on calcareous nannofossil ooze erodibility
Authors: Buls Toms , Anderskouv Kresten , Friend Patrick L. , Thompson Charlotte E. L. , Stemmerik Lars 
Published: October 2023

AbstractBottom current activity has been responsible for the formation of a multitude of erosional and depositional features recorded in chalk. Advanced knowledge on the mobility and transport of unlithified calcareous nannofossil ooze by bottom currents is increasingly important not only for understanding the deposition of ancient chalk, but also for modelling the behaviour of modern pelagic carbonate sediments. Whereas the erosional behaviour of very pure calcareous nannofossil ooze has recently been investigated, the effect of organic matter and clay minerals on the erosional behaviour of calcareous nannofossil ooze is as yet unquantified. The results of the present study are based on laboratory flume studies utilizing chalk ooze with varying concentrations of smectite clay (1 to 30 wt.%), two types of organic matter and bed porosity. Phytoplankton (Pavlova lutheri) was used as a proxy for particulate marine organic matter, and xanthan gum as a proxy for extracellular polymeric substances. The results show a significant decrease in nannofossil ooze mobility with increasing content of clay or marine organic matter. Organic matter is found to reduce erodibility at much lower concentrations than clay minerals at porosities equivalent to those of the seafloor. At lower porosities, corresponding to some depth below the seafloor, organic matter and clay minerals are less effective in bed stabilization. This suggests that clay minerals and especially organic matter will affect the likelihood of initiation of severe erosion on the seafloor, whereas their inhibiting effect will decrease as erosion scours progressively deeper into the sediment column. The effect of extracellular polymeric substances is more complex than marine organic matter, probably due to detachment of large aggregates from the bed and resulting increase in bed roughness. The choice of organic matter in sedimentological experiments may lead to significant differences in sediment behaviour and should therefore involve careful consideration.
A large single‐center cohort of bare lymphocyte syndrome: Immunological and genetic features in Turkey
Authors: Ünsal Hilal , Caka Canan , Bildik Hacer Neslihan , Esenboğa Saliha , Kupesiz Alphan , Kuşkonmaz Barış , Cetinkaya Duygu Uçkan , van der Burg Mirjam , Tezcan İlhan , Çağdaş Deniz 
Published: October 2023

AbstractMajor histocompatibility complex class II (MHC‐II) deficiency or bare lymphocyte syndrome (BLS) is a rare, early‐onset, autosomal recessive, and life‐threatening inborn error of immunity. We aimed to assess the demographic, clinical, laboratory, follow‐up, and treatment characteristics of patients with MHC‐II deficiency, together with their survival. We retrospectively investigated 21 patients with MHC‐II deficiency. Female/male ratio was 1.63. The median age at diagnosis was 16.3 months (5 months–9.7 years). Nineteen patients (90.5%) had parental consanguinity. Pulmonary diseases (pneumonia, chronic lung disease) (81%), diarrhoea (47.6%), and candidiasis (28.6%) were common. Four (19%) had autoimmunity, two developed septic arthritis, and three (14%) developed bronchiectasis in the follow‐up. Three patients (14%) had CMV viraemia, one with bilateral CMV retinitis. Eight (38.1%) had lymphocytopenia, and four (19%) had neutropenia. Serum IgM, IgA, and IgG levels were low in 18 (85.7%), 15 (71.4%), and 11 (52.4%) patients, respectively. CD4+ lymphocytopenia, a reversed CD4+/CD8+ ratio, and absent/low HLA‐DR expressions were detected in 93.3%, 86.7%, and 100% of the patients, respectively. Haematopoietic stem cell transplantation (HSCT) was performed on nine patients, and four died of septicaemia and ARDS after HSCT. The present median age of patients survived is 14 years (1–31 years). Genetic analysis was performed in 10 patients. RFX5 homozygous gene defect was found in three patients (P1, P4 and P8), and RFXANK (P2 and P14) and RFXAP (P18 and P19) heterozygous gene defects were found in each two patients, respectively. This large cohort showed that BLS patients have severe combined immunodeficiency (SCID)‐like clinical findings. Flow cytometric MHC‐II expression study is crucial for the diagnosis, differential diagnosis with SCID, early haematopoietic stem cell transplantation (HSCT), and post‐HSCT follow‐up. Genetic studies are required first for matched family donor evaluation before HSCT and then for genetic counselling.
The impact of sexual harassment on women's health and well‐being: A case for studying the casino gaming industry
Authors: Hoffman Shekinah 
Published: October 2023

AbstractThe sexual harassment of women in the casino gaming industry is pervasive and normative, yet the study of harassment and women's employment in this industry remains critically understudied. In this article, I argue the casino gaming industry is an opportune research setting in which to observe the adverse health outcomes and health disparities of workplace sexual harassment. Gaming demonstrates two salient organizational characteristics: (1) a historically male‐dominated, overtly‐sexualized culture that is primed for sexual harassment; and (2) a highly diverse, predominantly immigrant and minority workforce. As such, studying sexual harassment in the gaming industry may help in gaining key theoretical insights into who is more likely to a be target of sexual harassment; the forms in which harassment manifests (gendered, racialized, and class‐based); and who is more likely to experience its adverse health and job‐related outcomes. As more studies are warranted to disentangle the complexity of gender, race, class, citizenship status, and power in sexual harassment, and these factors intersecting and multiplying impacts on women's health and well‐being, I recommend linking the literature on sexual harassment and health with the gaming‐hospitality literature.
How do I manage a blood product shortage?
Authors: Gammon Richard , Becker Joanne , Cameron Tracy , Eichbaum Quentin , Jindal Aikaj , Lamba Divjot Singh , Nalezinski Shaughn , Rios Jorge , Shaikh Salima , Shepherd Janine , Tanhehco Yvette C. 
Published: October 2023

AbstractBackgroundThe demand for blood products sometimes exceeds the available inventory. Blood product inventories are dependent upon the availability of donors, supplies and reagents, and collection staff. During prolonged extreme shortages, blood centers and transfusion services must alter practices to meet the needs of patients.Study Design and MethodsThe Association for the Advancement of Blood and Biotherapies Donor and Blood Component Management Subsection compiled some strategies from its blood center and hospital transfusion service members that could be implemented during blood product shortages.ResultsSome strategies that blood centers could use to increase their available inventories include increasing donor recruitment efforts, using alternate types of collection kits, manufacturing low‐yield apheresis‐derived platelets and/or whole blood‐derived platelets, using cold−stored platelets, transferring inventory internally among centers of the same enterprise, using frozen inventory, decreasing standing order quantities, prioritizing allocation to certain patient populations, filling partial orders, and educating customers and blood center staff. Transfusion service strategies that could be implemented to maximize the use of the limited available inventory include increasing patient blood management efforts, using split units, finding alternate blood suppliers, trading blood products with other hospital transfusion services, developing a patient priority list, assembling a hospital committee to decide on triaging priorities, using expired products in extreme situations, and accepting nonconforming products after performing safety checks.DiscussionBlood centers and transfusion services must choose the appropriate strategies to implement based on their needs.
The infected diabetes‐related foot: Comparison of erythrocyte sedementation rate/albumin and C‐reactive protein/albumin ratios with erythrocyte sedimentation rate and C‐reactive protein to differentiate bone and soft tissue infections
Authors: Coye Tyler L. , Suludere Mehmet A. , Kang Gu Eon , Crisologo P. Andrew , Malone Matthew , Rogers Lee C. , Lavery Lawrence A. 
Published: October 2023

AbstractThe objective of this study was to evaluate the effectiveness of C‐reactive protein (CRP)/albumin, erythrocyte sedimentation rate (ESR)/albumin ratio, ESR, CRP and albumin to differentiate bone and soft tissue infection in persons with diabetes. We retrospectively evaluated 242 individuals admitted to hospital with diabetes‐related foot infections (DFI). We categorised DFI cases as either bone (OM) or soft tissue infection based on bone culture and/or histology. We evaluated the diagnostic accuracy of CRP, ESR, albumin, CRP/albumin and ESR/albumin as biomarkers to diagnose OM in persons with diabetes. The median age was 53 years (74% male). There were 224 diabetes‐related patients of which 125 had been diagnosed with osteomyelitis. The ESR/albumin and CRP/albumin ratios cut‐points were >17.84 and >1.83, respectively. ESR/albumin and CRP/albumin ratios had similar diagnostic parameters: AUC (0.71, 0.71), sensitivity (70.0%, 57.0%), specificity (62.0%, 75.0%), positive predictive value (67.0%, 71.0%) and negative predictive value (66.0% and 71.0%). In contrast diagnostic efficiency of CRP and ESR were AUC 0.71 and 0.71, sensitivity (45.6%, 71.2%), specificity (85.5%, 60.7%), positive predictive value (70.0%, 65.9%) and negative predictive value (59.5%, 66.4%), respectively. When comparing area under the curves, the results showed that ESR/albumin was not significantly different to ESR alone (Delong test pvs ESR >0.1). Similarly, CRP/albumin was not significantly different to CRP alone (Delong test pvs CRP >0.1). In conclusion, ESR/albumin and CRP/albumin ratios provided comparable results as using ESR and CRP alone.
From stability to chaos in last‐passage percolation
Authors: Ahlberg Daniel , Deijfen Maria , Sfragara Matteo 
Published: October 2023

AbstractWe study the transition from stability to chaos in a dynamic last passage percolation model on with random weights at the vertices. Given an initial weight configuration at time 0, we perturb the model over time in such a way that the weight configuration at time is obtained by resampling each weight independently with probability . On the cube , we study geodesics, that is, weight‐maximizing up‐right paths from to , and their passage time . Under mild conditions on the weight distribution, we prove a phase transition between stability and chaos at . Indeed, as grows large, for small values of , the passage times at time 0 and time are highly correlated, while for large values of , the geodesics become almost disjoint.
On Waring's problem: Beyond Freĭman's theorem
Authors: Brüdern Jörg , Wooley Trevor D. 
Published: October 2023

AbstractLet satisfy . Freĭman's theorem shows that when , there exists such that all large integers are represented in the form , with , if and only if diverges. We make this theorem effective by showing that, for each fixed , it suffices to impose the condition
More is established when the sequence of exponents forms an arithmetic progression. Thus, for example, when and , all large integers are represented in the form , with .
Regulation of water flow in the ocular lens: new roles for aquaporins
Authors: Donaldson Paul J. , Petrova Rosica S. , Nair Nikhil , Chen Yadi , Schey Kevin L. 
Published: October 2023

AbstractThe ocular lens is an important determinant of overall vision quality whose refractive and transparent properties change throughout life. The lens operates an internal microcirculation system that generates circulating fluxes of ions, water and nutrients that maintain the transparency and refractive properties of the lens. This flow of water generates a substantial hydrostatic pressure gradient which is regulated by a dual feedback system that uses the mechanosensitive channels TRPV1 and TRPV4 to sense decreases and increases, respectively, in the pressure gradient. This regulation of water flow (pressure) and hence overall lens water content, sets the two key parameters, lens geometry and the gradient of refractive index, which determine the refractive properties of the lens. Here we focus on the roles played by the aquaporin family of water channels in mediating lens water fluxes, with a specific focus on AQP5 as a regulated water channel in the lens. We show that in addition to regulating the activity of ion transporters, which generate local osmotic gradients that drive lens water flow, the TRPV1/4‐mediated dual feedback system also modulates the membrane trafficking of AQP5 in the anterior influx pathway and equatorial efflux zone of the lens. Since both lens pressure and AQP5‐mediated water permeability () can be altered by changes in the tension applied to the lens surface via modulating ciliary muscle contraction we propose extrinsic modulation of lens water flow as a potential mechanism to alter the refractive properties of the lens to ensure light remains focused on the retina throughout life.
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Modeling Flame Transfer Functions of an Industrial Premixed Burner
Authors: John Tony , Magina Nicholas , Han Fei , Kaufmann Jan , Vogel Manuel , Sattelmayer Thomas 
Published: October 2023

Abstract
This paper presents an analysis of the unsteady heat release rate response of industrially relevant axisymmetric premixed flames to harmonic velocity perturbations. The heat release rate response, quantified using the flame transfer function (FTF) definition, is measured from an acoustically forced swirl burner under perfectly premixed conditions. To understand the features of the measured FTF, a physics-based analytical model is developed in this study. To describe the heat release rate dynamics, a model for the flame spatiotemporal response is derived in the linear limit using the G-equation formulation. Inputs to the flame response model are selected to be consistent with values observed in the corresponding industrial burner, based on experimental and numerical studies. The relative contributions of acoustic and convecting vortical disturbances on specific features of the FTF are explored in this study. The results highlight the importance of capturing the appropriate disturbance velocity field as an input to the flame response model for accurate FTF predictions.
Unlocking the secrets of peptide transport in wine yeast: insights into oligopeptide transporter functions and nitrogen source preferences
Authors: Berg Hidde Yaël , Arju Georg , Becerra-Rodríguez Carmen , Galeote Virginie , Nisamedtinov Ildar 
Published: October 2023

ABSTRACT

Oligopeptides from grape must represent a secondary source of nitrogen for yeasts to grow and carry out fermentation.
Saccharomyces cerevisiae
takes up oligopeptides from the environment through multiple oligopeptide transporters with different peptide length specificities. However, due to difficulties associated with the qualitative and quantitative measurement of peptides in natural matrices, peptide transporter specificities have been mostly researched in single peptide environments. Using a peptide mapping method, we monitored the relative consumption of peptides derived from a protein hydrolysate by a set of CRISPR-Cas9-engineered
S. cerevisiae
wine strains to study oligopeptide transporters from the Opt and Fot families. Results show that Opt2 can import peptides containing three to at least seven amino acid residues, which is a broader peptide length specificity than previously reported, while Opt1 activity was not sufficient to support growth on peptides as nitrogen source. Fot1, Fot2, and Fot3, previously referred to as di-tripeptide transporters in
S. cerevisiae
wine strains, could also import tetrapeptides. The consumption order of peptides was determined by the peptide length as higher chain length peptides were taken up by Opt2 only after most di-tetrapeptides were depleted from the media. Altogether, Fot and Opt2 activity assured completion of the fermentation process without necessarily requiring ammonia or free amino acids. Analysis of peptide transporter gene expression during fermentation showed an effect of SO
4
2−
not only on
OPT1
but also on
FOT
and supported the assumption of a possible interplay between Fot and Opt2 activities.

IMPORTANCE

Limited nitrogen supply can prevent the completion of alcoholic fermentation. Supplementation through peptides as an alternative, natural source of nitrogen for yeast offers an interesting solution for this issue. In this work, the
S. cerevisiae
peptide transporters of the Opt and Fot families were studied. We demonstrated that Fot and Opt2 have a broader peptide length preference than previously reported, enabling yeasts to acquire sufficient nitrogen from peptides without requiring additional ammonia or amino acids to complete fermentation. On the contrary, Opt1 was unable to consume any peptide in the given conditions, whereas it has been described elsewhere as the main peptide transporter for peptides longer than three amino acid residues in experiments in laboratory conditions. This controversy signifies the need in applied sciences for approaching experimental conditions to those prevalent in the industry for its more accurate characterization. Altogether, this work provides further evidence of the importance of peptides as a nitrogen source for yeast and their consequent positive impact on fermentation kinetics.
HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women
Authors: Barton Kirston , Ferguson James M. , Deveson Ira W. , Falcinelli Shane D. , James Katherine S. , Kirchherr Jennifer , Ramirez Catalina , Gay Cynthia L. , Hammond Jillian M. , Bevear Brent , Carswell Shaun L. , Margolis David M. , Smith Martin A. , Adimora Adaora A. , Archin Nancie M. 
Published: October 2023

ABSTRACT

The persistence of replication-competent HIV-1 in people living with HIV (PLWH) is a barrier to a cure for HIV. Early-phase studies of clinical interventions to deplete the intact persistent HIV-1 reservoir are ongoing. However, the ability to distinguish intact proviruses is limited by sequence variation and the predominance of defective proviruses. In this study, we developed HIVepsilon-seq (HIVε-seq), a novel assay to analyze 33 samples consisting of unfractionated peripheral blood mononuclear cells and/or resting CD4
+
T cells from antiretroviral therapy (ART)-treated durably suppressed PLWH, including samples from 17 female participants. HIVε-seq combines simplified target enrichment and long-read sequencing methodology with advanced bioinformatic analysis to increase the depth, characterization, and detection of intact persistent HIV-1 provirus. HIVε-seq detected persistent sequence-intact HIV-1 proviruses in samples from both male and female participants and represents a robust, scalable assay to detect intact proviral sequences that could be applied to studies of HIV cure interventions.

IMPORTANCE
The lack of a reliable method to accurately detect when replication-competent HIV has been cleared is a major challenge in developing a cure. This study introduces a new approach called the HIVepsilon-seq (HIVε-seq) assay, which uses long-read sequencing technology and bioinformatics to scrutinize the HIV genome at the nucleotide level, distinguishing between defective and intact HIV. This study included 30 participants on antiretroviral therapy, including 17 women, and was able to discriminate between defective and genetically intact viruses at the single DNA strand level. The HIVε-seq assay is an improvement over previous methods, as it requires minimal sample, less specialized lab equipment, and offers a shorter turnaround time. The HIVε-seq assay offers a promising new tool for researchers to measure the intact HIV reservoir, advancing efforts towards finding a cure for this devastating disease.
Predicting cardiovascular disease risk from gut microbial genes
Authors: Claesen Jan , Brown J. Mark 
Published: October 2023

ABSTRACT

Gut bacteria-driven production of trimethylamine (TMA) is strongly associated with cardiovascular disease. Borton et al. (mBio 14:e01511-23, 2023,
https://doi.org/10.1128/mbio.01511-23
) introduce the Methylated Amine Gene Inventory of Catabolism database (MAGICdb), comprehensively cataloging pathways involved in TMA metabolism. By integrating transcriptomics, proteomics, and metagenomic data, this work identifies key bacterial players in the process and can link gut microbial gene content to fecal TMA concentrations. This work shows that methylated amine metabolism is a keystone microbiome process carried out by a small proportion of the community. Proatherogenic pathways are more widely distributed among the gut microbiota, and new TMA-reducing genera were identified that might offer new potential for probiotic strategies or targeted microbiome interventions. Remarkably, MAGICdb’s power to predict cardiovascular disease risk matches an approach using more traditional lipid risk factors. This open source will be a valuable tool for the community to link methylated amine metabolism to gut microbiome-related human health conditions.
The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in
Staphylococcus aureus
Authors: Sharkey Liam K. R. , Guerillot Romain , Walsh Calum J. , Turner Adrianna M. , Lee Jean Y. H. , Neville Stephanie L. , Klatt Stephan , Baines Sarah L. , Pidot Sacha J. , Rossello Fernando J. , Seemann Torsten , McWilliam Hamish E. G. , Cho Ellie , Carter Glen P. , Howden Benjamin P. , McDevitt Christopher A. , Hachani Abderrahman , Stinear Timothy P. , Monk Ian R. 
Published: October 2023

ABSTRACT

Among the 16 two-component systems in the opportunistic human pathogen
Staphylococcus aureus
, only WalKR is essential. Like the orthologous systems in other Bacillota,
S. aureus
WalKR controls autolysins involved in peptidoglycan remodeling and is therefore intimately involved in cell division. However, despite the importance of WalKR in
S. aureus
, the basis for its essentiality is not understood and the regulon is poorly defined. Here, we defined a consensus WalR DNA-binding motif and the direct WalKR regulon by using functional genomics, including chromatin immunoprecipitation sequencing, with a panel of isogenic
walKR
mutants that had a spectrum of altered activities. Consistent with prior findings, the direct regulon includes multiple autolysin genes. However, this work also revealed that WalR directly regulates at least five essential genes involved in lipoteichoic acid synthesis (
ltaS
): translation (
rplK
), DNA compaction (
hup
), initiation of DNA replication (
dnaA
,
hup
) and purine nucleotide metabolism (
prs
). Thus, WalKR in
S. aureus
serves as a polyfunctional regulator that contributes to fundamental control over critical cell processes by coordinately linking cell wall homeostasis with purine biosynthesis, protein biosynthesis, and DNA replication. Our findings further address the essentiality of this locus and highlight the importance of WalKR as a
bona fide
target for novel anti-staphylococcal therapeutics.

IMPORTANCE

The opportunistic human pathogen
Staphylococcus aureus
uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to
S. aureus
versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental
S. aureus
cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.