bluuebunny/crossref_metadata_2025 huggingface dataset:
Written language preservation in glioma patients undergoing awake surgery: The value of tailored intra‐operative assessment
Authors: van Ierschot Fleur Céline , Veenstra Wencke , Miozzo Antonio , Santini Barbara , Jeltema Hanne‐Rinck , Spena Giannantonio , Miceli Gabriele
Published: October 2023

Written language is increasingly important, as contemporary society strongly relies on text‐based communication. Nonetheless, in neurosurgical practice, language preservation has classically focused on spoken language. The current study aimed to evaluate the potential role of intra‐operative assessments in the preservation of written language skills in glioma patients undergoing awake surgery. It is the first feasibility study to use a standardized and detailed Written language battery in glioma patients undergoing awakening surgery. Reading and spelling were assessed pre‐ and post‐operatively in eleven patients. Intra‐operatively, 7 cases underwent written language assessment in addition to spoken object naming. Results show that reading and spelling deficits may arise before and after glioma surgery and that written language may be differently affected than spoken language. In our case series, task‐specific preservation of function was obtained in all cases when a specific written language skill was monitored intra‐operatively. However, the benefits of intra‐operative testing did not always generalize, and non‐monitored written language tasks may not be preserved. Hence, when a specific written language skill needs to be preserved, to facilitate return to work and maintain quality of life, results indicate that intra‐operative assessment of that skill is advised. An illustrative case report demonstrates how profile analyses can be used pre‐operatively to identify cognitive components at risk and intra‐operatively to preserve written language abilities in clinical practice.
Fetal mosaicism, should conventional karyotype always be performed?
Authors: Su Linjuan , Wu Xiaoqing , Liang Bin , Lin Na , Xie Xiaorui , Cai Meiying , Zheng Lin , Wang Meiying , Xu Liangpu
Published: October 2023

Background and Purpose

The application of classical cytogenetic and DNA‐based molecular techniques to detect cell lineages of mosaicism derived from cultured or noncultured fetal cells may result in discordant results. This retrospective study aimed to assess the inconsistent diagnostic outcomes, technical availability, and limitations of chromosomal microarray analysis (CMA) and karyotyping for mosaicism.

Methodology

A total of 75 fetuses diagnosed with mosaicism by karyotype analysis or CMA were selected, and the results from both the methods were compared and further analyzed.

Results

A total of 42 (56%, 42/75) CMA results were consistent with karyotypes, consisting of 22 cases of mosaic sex chromosomal abnormalities, 8 routine autosomal aneuploidy cases, 8 other autosome aneuploidy cases, 3 large cryptic genomic rearrangements, and 1 small supernumerary marker chromosome. Discrepancy between karyotype analysis and CMA was observed in 33 (44%, 33/75) mosaicisms involving 15 sex chromosomal abnormalities, 1 routine autosomal aneuploidies, 5 other autosome aneuploidy cases, 8 large cryptic genomic rearrangements, and 4 small supernumerary marker chromosomes.

Conclusion

Considering the disparities between methods as well as the cell populations analyzed, both CMA and karyotype analysis have their own advantages and disadvantages. Therefore, CMA should ideally be used in combination with karyotyping to detect more cases of mosaicism than using either test alone.
Information Generation in Vertically Differentiated Markets*
Authors: Canidio Andrea , Gall Thomas
Published: October 2023

In a model of vertical competition two firms draw costly public signals that are informative about the quality of their products and then competitively set prices. When each firm generates information independently from the other, there will be overinvestment (underinvestment) in information generation if the market share of the quality follower in the subsequent market equilibrium is high (low). Moreover, information generation by one firm has a positive externality on the other firm. Hence, coordination (e.g., via industry associations) increases information generation. When product qualities are endogenous, information generation may prevent quality degradation and thus have an additional social benefit.
Undoing raciolinguistics
Authors: Flores Nelson , Rosa Jonathan
Published: October 2023

In this commentary, we discuss common pitfalls associated with the study of race and language, focusing specifically on the recent emergence of raciolinguistics as a frame for these efforts. We examine how raciolinguistics can be taken up in ways that silo discussions of race from the rest of linguistics—as something that the “raciolinguists” do—such that careful study of issues including colonialism, power, and societal hierarchies is perpetually pushed to the margins of the field. We also consider how the nominalization of raciolinguistics can suggest that race and language are agreed upon objects in ways that reproduce troublesome essentializations. We show how a raciolinguistic perspective can resist such tendencies by continually interrogating the colonial reproduction and transformation of modern knowledge projects and lifeways across societal contexts, as well as by continually examining the fundamental nature of language, race, and power. We end with what we see as the implications of a raciolinguistic perspective for all of linguistics.
Quality of life between the hammer and the anvil: Challenges of living with a disability in areas of protracted political conflict
Authors: Karni‐Visel Yael , Roth Dana , Ali‐Saleh Darawshy Neveen , Schertz Mitchell
Published: October 2023

Article 11 of the United Nations' Convention for the Rights of Persons with Disabilities and various relevant humanitarian actors recognize the obligation to ensure the protection and safety of persons with disabilities in various situations of risk, including armed and political conflict. Nonetheless, protracted crises exacerbate the existing inequalities and vulnerabilities of individuals with disabilities. This article suggests that, in addition to recognized subcultural issues, the political context should be considered in the policies and practices concerning those with disabilities. To assist individuals with disabilities and their families who are living in situations of protracted political conflict and the professionals who serve them, research should further explore these issues and their effects in terms of quality‐of‐life measures. A better understanding of the individual, organizational, and social contextual factors of political conflict in the conceptualization and measurement of the quality of life of individuals with disabilities and their families will promote improved and more sensitive services, support, and interventions.
Association between Mediterranean diet and periodontitis among US adults: The mediating roles of obesity indicators
Authors: Wu Yuying , He Baochang , Chen Qiansi , Yu Rong , Wu Yuxuan , Yang Han , Yu Yiming , Yan Fuhua , Li Yanfen , Chen Fa
Published: October 2023

Objective

This study aimed to assess the association between the Mediterranean diet (MedDiet) and periodontitis in US adults and to further explore the mediating roles of obesity indicators in this association.

Background Data

The relationship between MedDiet and periodontitis is controversial. And it is unclear whether obesity indicators are potential mediators of this relationship.

Methods

Using data derived from the National Health and Nutrition Examination Survey (2009–2014). Weighted binary logistic regression and restricted cubic spline were used to assess the association between MedDiet and periodontitis. Weighted ordinal logistic regression was performed to evaluate the relationship between MedDiet and periodontitis severity. The mediating roles of body mass index (BMI) and waist circumference in the relationship between the MedDiet and periodontitis were explored. Association analyses were further performed using mean clinical attachment loss (CAL) or mean periodontal probing depth (PPD) as dependent variables. The false discovery rate method was used to correct the p‐values in the regression analyses.

Results

A total of 8290 eligible participants (4159 participants with periodontitis and 4131 without periodontitis) were included. A negative association between the MedDiet adherence score and periodontitis was observed in the binary logistic regression model (adjusted odds ratio = 0.94, 95% confidence interval: 0.90–0.97, p = .001). Restricted cubic spline regression revealed a dose–response relationship between the MedDiet adherence score and periodontitis. BMI and waist circumference significantly mediate this association, with mediation proportions of 9.7% (p = .032) and 9.3% (p = .012), respectively. Multivariable ordinal logistic regression showed that the MedDiet adherence score was negatively associated with the severity of periodontitis (all p < .05). Additionally, the MedDiet adherence score was negatively associated with mean PPD or mean CAL (all p < .05).

Conclusions

This study suggests a significant negative association between adherence to the MedDiet and periodontitis and a possible mediating role of obesity indicators in this association. Furthermore, studies are still warranted to confirm our findings.
Experience, Subjectivity, Selfhood: Beyond a Meadian Sociology of the Self
Authors: Zahavi Dan , Zelinsky Dominik
Published: October 2023

Sociologists tend to see G. H. Mead's conceptualization of self as fundamentally correct. In this paper, we develop a critique of Mead's notion of the self as constituted through social interactions. Our focus will be on Mead's categorial distinction between the socially constructed self and subjective experience, as well as on the tendency of post‐Meadian sociologists to push Mead's position in ever more radical directions. Drawing inspiration from a multifaceted understanding of selfhood that can be found in Husserlian phenomenology, we then propose that the most basic level of selfhood is anchored in irreducible subjective experience.
‘I'm rewriting the law’ when children bring literacy into nursery school
Authors: Holm Lars , Laursen Helle Pia , Ahrenkiel Annegrethe
Published: October 2023

Based on an analysis of three literacy events in nursery schools, this article focuses on how literacy forms part of children's social practices and co‐creates the language environment in the nursery and how place, affect and materiality play a key role in children's multimodal and embodied meaning‐making around literacy. The analysis is based on ethnographic fieldwork in two nursery schools, in which we followed different children through their days in order to explore how they used language in different contexts, what characterised their language practices and what appeared to encourage and constrain their desire to express themselves. It shows how the written word means much more to children than knowledge about the structure of books and identification of letters and how children draw on their own experience and include the place and the available materials in their joint meaning‐making processes. Against this background, we argue for the need for a reconceptualisation of what literacy is and can be in a nursery school context and for a discussion of the implications of this for teaching literacy.
Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)
Authors: Reeve James , Butlin Roger K. , Koch Eva L. , Stankowski Sean , Faria Rui
Published: October 2023

Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.
Origins of lineage‐specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa
Authors: Wang Zheng , Wang Yen‐Wen , Kasuga Takao , Hassler Hayley , Lopez‐Giraldez Francesc , Dong Caihong , Yarden Oded , Townsend Jeffrey P.
Published: October 2023

The origin of new genes has long been a central interest of evolutionary biologists. However, their novelty means that they evade reconstruction by the classical tools of evolutionary modelling. This evasion of deep ancestral investigation necessitates intensive study of model species within well‐sampled, recently diversified, clades. One such clade is the model genus Neurospora, members of which lack recent gene duplications. Several Neurospora species are comprehensively characterized organisms apt for studying the evolution of lineage‐specific genes (LSGs). Using gene synteny, we documented that 78% of Neurospora LSG clusters are located adjacent to the telomeres featuring extensive tracts of non‐coding DNA and duplicated genes. Here, we report several instances of LSGs that are likely from regional rearrangements and potentially from gene rebirth. To broadly investigate the functions of LSGs, we assembled transcriptomics data from 68 experimental data points and identified co‐regulatory modules using Weighted Gene Correlation Network Analysis, revealing that LSGs are widely but peripherally involved in known regulatory machinery for diverse functions. The ancestral status of the LSG mas‐1, a gene with roles in cell‐wall integrity and cellular sensitivity to antifungal toxins, was investigated in detail alongside its genomic neighbours, indicating that it arose from an ancient lysophospholipase precursor that is ubiquitous in lineages of the Sordariomycetes. Our discoveries illuminate a “rummage region” in the N. crassa genome that enables the formation of new genes and functions to arise via gene duplication and relocation, followed by fast mutation and recombination facilitated by sequence repeats and unconstrained non‐coding sequences.
Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon exchange in the marine cyanolichen Lichina pygmaea
Authors: Chrismas Nathan , Tindall‐Jones Beth , Jenkins Helen , Harley Joanna , Bird Kimberley , Cunliffe Michael
Published: October 2023

Lichens are exemplar symbioses based upon carbon exchange between photobionts and their mycobiont hosts. Historically considered a two‐way relationship, some lichen symbioses have been shown to contain multiple photobiont partners; however, the way in which these photobiont communities react to environmental change is poorly understood.

Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores where it is submerged in seawater during every tidal cycle. Recent work has indicated that L. pygmaea has a complex photobiont community including the cyanobionts Rivularia and Pleurocapsa. We performed rRNA‐based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont at high and low tide to investigate community response to immersion in seawater.

Carbon exchange in L. pygmaea is a dynamic process, influenced by both tidal cycle and the biology of the individual symbiotic components. The mycobiont and two cyanobiont partners exhibit distinct transcriptional responses to seawater hydration.

Sugar‐based compatible solutes produced by Rivularia and Pleurocapsa in response to seawater are a potential source of carbon to the mycobiont. We propose that extracellular processing of photobiont‐derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea and is analogous to uptake of plant‐derived carbon in ectomycorrhizal symbioses.
Dynamic nitrogen reallocation in rice plants upon insect herbivory by a generalist lepidopteran pest Spodoptera litura (Fabricius)
Authors: Liu Jian , Tong Lu , Zhang Xiyong , Zhang Huiying , Tao Baoxiang , Gong Qiangbin , Zeng Rensen , Song Yuanyuan
Published: October 2023

Nitrogen (N) is a limited nutrient for both plants and herbivores. How plants reallocate N upon herbivore attack is vital for plant tolerance to herbivores. Here we investigated N reallocation in rice during a 2‐day herbivore attack by a generalist herbivore Spodoptera litura and 2 days after herbivore removal. Labeled 15N was translocated during insect attack from feeding‐damaged leaves to roots, particularly to young roots. The amounts of chlorophyll and Rubisco were significantly reduced in the attacked leaves. Both free amino acids and nitrate accumulated in the damaged leaves and young roots, while ammonium content was decreased. Activities of nitrate reductase and glutamine synthetase were enhanced in feeding‐damaged leaves but inhibited in young roots. The expression of amino acid transporters OsAAP6, OsAAT15, and jasmonate‐responsive genes OsAOS, OsMAPK3, OsMAPK6 was induced in the damaged leaves. However, 2 days after herbivore removal, N uptake was increased and herbivory‐induced 15N transfer to roots was partially reverted back to the damaged leaves, resulting in N levels in the previously damaged leaves were even higher than that in control leaves. Collectively, our results indicate a dynamic N reallocation in rice responses to insect herbivory.
“Keeping Things under the Rug”: Racial Dynamics in the Context of Large Immigration Raids in Rural Mississippi☆
Authors: Thompson Diego
Published: October 2023

A large body of literature has evidenced racism and other challenges experienced by Latinx immigrants working in the food system and rural communities in the U.S. Despite a large number of studies showing complex and difficult realities experienced by Latinx immigrants, little has been studied about how immigration law enforcement operations impact Latinx communities and racial dynamics in rural communities. Analyzing 26 interviews with Latinx organizers and allies involved in community responses in the aftermath of large immigration raids, this study examines how the raids shaped racial dynamics and local actions to address Latinxs' problems. Findings show the immigration raids were seen as an “invasion” that created fear, distrust, and racial stigmatization among Latinx immigrants. After the raids, Latinx groups and allies mobilized resources for the affected families, contesting the binary racial order. However, community responses were challenged by white supremacy and racism that aimed to keep “things under the rug” by ignoring Latinxs' problems created and exacerbated by the immigration raids. These findings highlight unique characteristics of ongoing racialization processes in U.S. rural settings and illustrate how white supremacy and racism continue to shape what goes on within and outside rural communities.
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

Bottom 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

Major 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

The 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

Background

The 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 Methods

The 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.

Results

Some 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.

Discussion

Blood 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

The 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

We 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

Let 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

The 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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CO-INFECTION WITH COVID-19 AND GENETIC DIVERSITY OF SARS-COV-2 IN CHILDREN
Authors: Kamalova D. , Makibayeva M. , Amirgazin A. , Abdrakhmanova S. , Sytnik I. , Tuleubaeva A. , Ramankulov E , Shevtsov A.
Published: October 2023

In the pediatric population, coronavirus infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is more commonly observed in asymptomatic and moderately symptomatic cases. However, when COVID-19 coexists with other infections, it can result in a more severe disease progression. Various subtypes of the SARS-CoV-2 virus are associated with different clinical presentations, with certain subtypes exhibiting a predominance of specific symptoms or manifestations. Clinical manifestations of COVID-19 in children, both during the acute phase of the disease and in the post-COVID-19 period, are not fully understood and different compared to adults. This article presents four clinical cases in which PCR-confirmed COVID-19 was observed in combination with infections caused by viruses such as Ebstein-Barr, varicella, and rotavirus. The severity of the disease in these cases was attributed to symptoms related to intoxication, as well as skin and intestinal syndromes. To understand important genomic signatures of SARS-CoV-2 virus circulating in the area, the genome-wide sequencing was performed for the SARS-CoV-2 samples isolated from nasopharyngeal swabs collected from four patients. Based on the genotyping results, all four samples were found belonging to the SARS-CoV-2 virus Omicron lineage. Three months after the initial testing, follow-up evaluations of the children indicated a higher likelihood of complete recovery. However, some underlying disease manifestations, including anemia and atopic dermatitis, persisted despite the resolution of COVID-19 symptoms.
COMBINED EFFECT OF TBSV P19 MUTANTS AND HEAVY METALS ON ANTIOXIDANT ENZYME ACTIVITY
Authors: Akbassova A. , Beisekova M. , Tassanbiyeva A. , Zhamshitova D. , Kurmanbayeva A. , Zhangazin S. , Moldakimova N. , Shalabayeva A. , Masalimov Zh. , Akbassova A.
Published: October 2023

Crops of food value are often exposed to viral pathogens. Therefore, crops can noticeably decrease or die completely. For example, in 2021, the tomato brown wrinkle virus was detected in Kazakhstan, the main hosts of which are tomatoes and peppers. At the same time, in farms where the pathogen was detected, yield loss ranged from 30 to 70%. Therefore, it is important to develop methods aimed at increasing plant stress tolerance to viral infection. The scientific novelty of this manuscript is that previously the simultaneous effect of viral pathogens and heavy metals on plants has not been studied. Antioxidant enzymes play an important role in regulating the concentration of reactive oxygen species in plant cells. The enzyme catalase catalyzes the conversion of hydrogen peroxide into water and molecular oxygen, thereby neutralizing superoxide radicals. Thus, antioxidant enzymes prevent tissue damage and necrosis. Molybdenum enzymes can produce reactive oxygen species when exposed to adverse conditions, such as pathogen infestation or drought. Molybdenum is an integral part of the Moco cofactor within molybdoenzymes, but tungsten has the ability to substitute for molybdenum, resulting in a reversible loss of enzyme function. Consequently, tungsten acts as a stressor for plants. Inoculation of plants with tomato bush stunt virus of the wild type leads to their death. At the same time, when infected with TBSV 157, RMJ1 and RMJ2 mutants, the plants recovered after some time. Plants are expected to be more viable when the subject is exposed to heavy metal solutions and inoculated with viruses.
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

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

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

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

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

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.
Genome sequence of a symbiotic cyanobacterium from the flowering plant
Gunnera tinctoria
Authors: Ang Warren Shou Leong , Burleigh Olivia , Frail Sarah , Santos Yago V. S. , Tyagi Bhavyaa , Li Fay-Wei
Published: October 2023

Metagenomic analysis of the symbiotic cyanobacteria colonies within
Gunnera tinctoria
stems revealed a new strain of
Nostoc
. Here, we report its genome sequence.
GRB 221009A, Its Precursor, and Two Afterglows in the Fermi Data
Authors: Stern B. , Tkachev I.
Published: October 2023

We study GRB 221009A, the brightest gamma-ray burst in the history of observations, using Fermi data. To calibrate them for large inclination angles, we use the Vela X gamma-ray source. Light curves in different spectral ranges demonstrate a 300 s overlap of afterglow and delayed episodes of soft prompt emission. We demonstrate that a relatively weak burst precursor that occurs 3 min before the main episode has its own afterglow, i.e., presumably, its own external shock. This is the first observation of such phenomenon which rules out some theoretical models of GRB precursors. The main afterglow is the brightest one, includes a photon with an energy of 400 GeV 9 h after the burst, we show that it is visible in the LAT data for up to two days.