bluuebunny/crossref_metadata_2025 huggingface dataset:
Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov., isolated from soil and faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau
Authors: Zhou Huimin , Cao Linglin , Yang Caixin , Zhang Sihui , Pu Ji , Yang Jing , Ning Shuo , Liu Xiaorui , Liu Chunmei , Liu Liyun , Xu Jianguo
Published: July 2024

Two novel strain pairs (HM61T/HM23 and S-34T/S-58) were isolated from soil and the faeces of Tibetan antelope (Pantholops hodgsonii) collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus Nocardioides. Strains HM61T and HM23 were most closely related to Nocardioides pelophilus THG T63T (98.58 and 98.65 % 16S rRNA gene sequence similarity). Strains S-34T and S-58 were most closely related to Nocardioides okcheonensis MMS20-HV4-12T (98.89 and 98.89 % 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61T and S-34T were 70.6 and 72.5 mol%, respectively. Strains HM61T, S-34T and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4–90.5 % as well as digital DNA–DNA hybridization values between 20.1 and 40.8 %, which clearly indicated that the four isolates represent two novel species within the genus Nocardioides. The chemotaxonomic characteristics of strains HM61T and S-34T were consistent with the genus Nocardioides. The major fatty acids of all four strains were iso-C16 : 0, C17 : 1
 ω8c or C18 : 1
 ω9c. For strains HM61T and S-34T, MK-8(H4) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61T and S-34T represent two novel species of the genus Nocardioides, respectively, with the names Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov. The type strains are HM61T (=GDMCC 4.343T=JCM 36399T) and S-34T (=CGMCC 4.7664T=JCM 33792T).
Encoding of T=1 virus capsid structures through the interfaces of oligomer subcomponents
Authors: Jeppesen Mads , André Ingemar
Published: July 2024

Virus capsid formation is one the most complex self-assembly processes in nature, involving the association of a large number of protein subunits into well-defined structural states. The ability of protein subunits to efficiently self-assembly is encoded in the protein sequence, and ultimately in the protein-protein interfaces within the growing capsid. The relative strengths of interfaces can be important in directing the self-assembly process, and determine which intermediates are formed early in the self-assembly process. In this study we characterize the interfaces in homomeric T=1 virus capsids to investigate to what extent interfaces within the assemblies are different from other protein-protein interfaces, and which interfaces are most critical for self-assembly. Interfaces were divided into dimers, trimers, and pentamers and compared to interfaces of non-viral homomeric dimers, trimers, and pentamers. The analysis suggests that viral interfaces are larger than non-viral counterparts, and differ in amino acid content, but are energetically similar in terms of the quality of intermolecular interactions. Trimers are predicted to be the most stable oligomers, which may imply that they form early in the self-assembly process. However, dimeric and pentameric interfaces are typically similar in terms of predicted stability suggesting that assembly formation in T=1 capsids may progress through many different routes, rather than progressing through a single dominant intermediate species. With symmetric docking calculations, the energy landscape of the assembled capsid was characterized, and the results highlight that the assemblies exhibit deeply funneled energy landscapes encoded by protein-protein interfaces that have a high degree of specificity.
Uncovering differential tolerance to deletions versus substitutions with a protein language model
Authors: Goldman Grant , Chati Prathamesh , Ntranos Vasilis
Published: July 2024

Deep mutational scanning (DMS) experiments have been successfully leveraged to understand genotype to phenotype mapping, with broad implications for protein engineering, human genetics, drug development, and beyond. To date, however, the overwhelming majority of DMS have focused on amino acid substitutions, excluding other classes of variation such as deletions or insertions. As a consequence, it remains unclear how indels differentially shape the fitness landscape relative to substitutions. In order to further our understanding of the relationship between substitutions and deletions, we leveraged a protein language model to analyze every single amino acid deletion in the human proteome. We discovered hundreds of thousands of sites that display opposing behavior for deletions versus substitutions, i.e. sites that can tolerate being substituted but not deleted, and vice versa. We identified secondary structural elements and sequence context to be important mediators of differential tolerability at these sites. Our results underscore the value of deletion-substitution comparisons at the genome-wide scale, provide novel insights into how substitutions could systematically differ from deletions, and showcase the power of protein language models to generate biological hypothesesin-silico. All deletion-substitution comparisons can be explored and downloaded athttps://huggingface.co/spaces/ntranoslab/diff-tol.
An applicable and efficient retrograde monosynaptic circuit mapping tool for larval zebrafish
Authors: Chen Tianlun , Deng Qiusui , Lin Kunzhang , Zheng Xiudan , Wang Xin , Zhong Yongwei , Ning Xinyu , Li Ying , Xu Fuqiang , Du Jiulin , Du Xufei
Published: July 2024

The larval zebrafish is a vertebrate model for in vivo monitoring and manipulation of whole-brain neuronal activities. Tracing its neural circuits still remains challenging. Here we report an applicable methodology tailored for larval zebrafish to achieve efficient retrograde trans-monosynaptic tracing from genetically defined neurons via EnvA-pseudotyped glycoprotein-deleted rabies viruses. By combinatorially optimizing multiple factors involved, we identified the CVS strain trans-complemented with advanced expression of N2cG at 36 degrees C as the optimal combination. It yielded a tracing efficiency of up to 20 inputs per starter cell. Its low cytotoxicity enabled the viable labeling and calcium imaging of infected neurons 10 days post-infection, spanning larval ages commonly used for functional examination. Cre-dependent labeling was further developed to enable input cell-type-specific tracing and circuit reconstruction. We mapped cerebellar circuits and uncovered the ipsilateral preference and subtype specificity of granule cell-to-Purkinje cell connections. Our method offers an efficient way for tracing neural circuits in larval zebrafish
A central steering circuit inDrosophila
Authors: Feng Kai , Khan Mariam , Minegishi Ryo , Müller Annika , Van De Poll Matthew N. , Swinderen Bruno van , Dickson Barry J.
Published: July 2024

Locomotion steering control enables animals to pursue targets, evade threats, avoid obstacles, and explore their environment. Steering commands are generated in the brain and communicated via descending neurons to leg or wing motor circuits. The diversity of ways in which turns are triggered and executed has led to the view that steering might rely on distributed neural processing across multiple control circuits. Here, however, we present evidence for a central steering circuit inDrosophilathat is used for both goal-directed and exploratory turns and is capable of eliciting turns ranging from subtle course corrections to rapid saccades. The circuit is organized in a hierarchy, the top layer of which comprises the reciprocally connected DNa03 and LAL013 neurons. Our data suggest that turns are initiated by DNa03 neurons and reinforced and stabilized through a winner-take-all mechanism involving LAL013. The descending DNa11 neurons form an intermediate layer. They receive input from both DNa03 and LAL013 and target leg motor circuits directly as well as indirectly through subordinate descending neurons. DNa11 activation coordinately changes the stepping directions of all six legs to generate rapid saccadic turns. Together, these data define a central steering control circuit inDrosophilathat is flexibly used to generate turns as the fly exploits or explores its environment.
Quantitative T1 and Effective Proton Density (PD*) mapping in children and adults at 7T from an MP2RAGE sequence optimised for uniform T1-weighted (UNI) and FLuid And White matter Suppression (FLAWS) contrasts
Authors: Sıla Dokumacı Ayşe , Vecchiato Katy , Tomi-Tricot Raphael , Eyre Michael , Bridgen Philippa , Di Cio Pierluigi , Casella Chiara , Wood Tobias C. , Sedlacik Jan , Wilkinson Tom , Giles Sharon L. , Hajnal Joseph V. , O’Muircheartaigh Jonathan , Malik Shaihan J. , Carmichael David W.
Published: July 2024

Introduction

Quantitative MRI is important for non-invasive tissue characterisation. In previous work we developed a clinically feasible multi-contrast protocol for T1-weighted imaging based on the MP2RAGE sequence that was optimised for both children and adults. It was demonstrated that a range of Fluid And White Matter Suppression (FLAWS) related contrasts could be produced while maintaining T1-weighted uniform image (UNI) quality, a challenge at higher field strengths. Here we introduce an approach to use these images to calculate effective proton density (PD*) and quantitative T1relaxation maps especially for shorter repetition times (TRMP2RAGE) than those typically used previously.

Methods

T1and PD* were estimated from the analytical equations of the MP2RAGE signal derived for partial Fourier acquisitions. The sensitivity of the fitting results was evaluated with respect to the TRMP2RAGEand B1+effects on both excitation flip angles and inversion efficiency and compared to vendor T1maps which do not use B1+information. Data acquired for a range of individuals (aged 10-54 years) at the shortest TRMP2RAGE(4000ms) were compared across white matter (WM), cortical grey matter, and deep grey matter regions.

Results

The T1values were insensitive to the choice of different TRMP2RAGE. The results were similar to the vendor T1maps if the B1+effects on the excitation flip angle and inversion efficiency were not included in the fits. T1values varied over development into adulthood, especially for the deep grey matter regions whereas only a very small difference was observed for WM T1. Effective PD maps were produced which did not show a significant difference between children and adults for the age range included.

Conclusion

We produced PD* maps and improved the accuracy of T1maps from an MP2RAGE protocol that is optimised for UNI and FLAWS-related contrasts in a single scan at 7T by incorporating the excitation flip angle and inversion efficiency related effects of B1+in the fitting. This multi-parametric protocol made it possible to acquire high resolution images (0.65mm iso) in children and adults within a clinically feasible duration (7:18 min:s). The combination of analytical equations utilizing B1+maps led to T1fits that were consistent at different TRMP2RAGEvalues. Average WM T1values of adults and children were very similar (1092ms vs 1117ms) while expected reductions in T1with age were found for GM especially for deep GM.
Transpirational water loss from flowers is low but unregulated
Authors: Roddy Adam B. , Schreel Jeroen D. M. , Paiva Dario Caminha , Qin Ni , Jiang Guo-Feng , Brodersen Craig R. , Simonin Kevin A.
Published: July 2024

Flowers play a critical role in reproduction for most of the flowering plants, and maintaining flowers throughout their lifespan can require substantial resources, such as carbon and water. Increases in temperature and aridity due to climate change are shifting the atmospheric conditions experienced by flowers, potentially altering the costs of floral maintenance. However, little is known about floral physiology and the capacity of flowers to regulate water loss. Because many flowers have few, if any, stomata, flowers may not be able to curtail water loss when the atmospheric demand for water vapor is high. Here, we tested whether the surface conductance of of flower petals, tepals, and showy bracts responds dynamically to changes in the vapor pressure gradient driving water loss. We measure the responses of flower surface conductance (gs) to step changes in the vapor pressure gradient on nine species. Across species, gs was low among all species, and there was little, if any, response in gs to step changes in humidity. The lack of response in gs resulted in linear responses of transpirational water loss to variation in vapor pressure deficit. These results suggest that unusually hot, dry conditions could elevate water loss from flowers, leading to premature wilting and senescence, thereby shortening floral longevity.
Target of rapamycin (TOR) regulatesCURLY LEAF(CLF) translation in response to environmental stimuli
Authors: Dong Yihan , Oubassou Ez-Zahra , Hoffmann Elise , Zhang Wenna , Uslu Veli , Berr Alexandre
Published: July 2024

The target of rapamycin (TOR)-Polycomb repressive complex 2 (PRC2) pathway is a crucial link that translates environmental and developmental cues into chromatin, thus reprogramming transcription. While the PRC2 methyltransferase Curly leaf (CLF) is known to be specifically involved, the underlying mechanism remains unclear. This study sheds light on how TOR fine-tunes CLF protein levels by promoting translation re-initiation mediated by eIF3h. We found that the second upstream open reading frame (uORF) located in the 5’ leader region of theCLFtranscript significantly represses its translation (by 50%). Plants lacking this uORF leader displayed reduced sensitivity to TOR inhibition and impaired induction of stress-responsive genes. Interestingly, this uORF sequence exhibits partial conservation across diverse plant species, suggesting a potential role in adaptation to various environmental conditions. Our findings reveal a dynamic mechanism within the TOR-PRC2 pathway, highlighting its responsiveness to environmental stimuli.
Despotic long-tailed macaques benefit others in a group service paradigm
Authors: de Laat E.J.A.M. , Waasdorp S. , Roth T.S. , Massen J.J.M. , Sterck E.H.M.
Published: July 2024

For animals living in social groups, cooperation is a key factor to success. It has been postulated that in social systems with cooperative breeding or a tolerant dominance style, individuals will benefit each other. Cooperation is, therefore, not expected in long-tailed macaques, since they do not breed together and experience a steep unidirectional hierarchy. However, previous studies have shown that they can be prosocial in a dyadic setting. This would comply with the more recently postulated dyadic interdependence hypothesis. To be able to compare their cooperative performances with other species, we set up a group service paradigm similar to that, which has been tested in a number of other species. We presented a swing set apparatus, which an actor could pull in the middle to provide a reward to another individual but without access to the reward for the actor, to three groups of socially housed long-tailed macaques. The macaques showed prosocial behaviour in the test significantly more often than in two control condition. They preferably provided to kin. The prosocial behaviour of the despotic, individual breeding long-tailed macaques counters the cooperative breeding and self-domestication hypotheses, yet supports the dyadic interdependence hypothesis, although future studies on other macaque species with more tolerant dominance styles should elucidate the effect of dominance styles on prosociality.
Sponges of the Lower Greensand Group (Lower Cretaceous) of England; a revision
Authors: Sendino Consuelo , Kershaw Stephen
Published: July 2024

Sponges of the Lower Greensand Group (LGS) are well preserved, and occur in sediments of a sandy matrix. Abundant in the Faringdon Sponge Gravel Member (FSG), these sponges, mostly Calcareans are found in Oxfordshire, with notable preservation at Little Coxwell quarries. Classical researchers described sponges and spicules from the LGS, including Lhuyd (considered to have been the first to publish illustrations of LGS sponges), Sharpe, Sowerby and Parkinson. In addition to the FSG, the Folkestone, Hythe, and Atherfield Clay formations within the LGS also contain sponge remains, including spicules as well as whole sponge fossils. These sponges include mostly samples from traditional sponge class Calcarea and a taxon of Hexactinellida; Altogether, the sponge assemblage developed in warm seas of the Lower Cretaceous, and display diverse shapes of sponge bodies and robust spicules. This study provides descriptions of common species following updated Porifera classification and recent sponge taxonomy research, illustrated with specimens from the Natural History Museum, London (NHM) and British Geological Survey (BGS) collections. The following taxa are recorded and described: 1) Calcareans:Barroisia anastomosans(Parkinson, 1811),Barroisia clavata(Keeping, 1883),Barroisia irregularis(Hinde, 1884),Dehukia crassa(de Fromentel, 1861),[Elasmoierea] faringdonensis(Mantell, 1854),[Elasmoierea] mantelli(Hinde, 1884),Peronidella gillieroni(Loriol, 1869),Peronidella prolifera(Hinde, 1884),Peronidella ramose(Roemer, 1839),Oculospongia dilatate(Roemer, 1864),Tremospongia pulvinaria(Goldfuss, 1826),Raphidonema contortum(Hinde, 1884),Raphidonema porcatum(Sharpe, 1854),Raphidonema farringdonensis(Sharpe, 1854),Raphidonema macropora(Sharpe, 1854),Raphidonema pustulatumHinde, 1884,Endostoma foraminosa(Goldfuss, 1829); 2) Hexactinellids:Lonsda contortuplicataLonsdale, 1849.
Differential Toxicity of Perfluorooctane Sulfonate (PFOS) in Wild-Type and Oatp1d1 Mutant Zebrafish Embryos
Authors: Mihaljevic Ivan , Vujica Lana , Dragojević Jelena , Lončar Jovica , Smital Tvrtko
Published: July 2024

This study presents a comprehensive analysis of the effects of perfluorooctane sulfonate (PFOS) exposure on zebrafish embryos, focusing on the differential responses between wild-type (WT) and oatp1d1 mutant embryos. The findings improve our understanding of the toxicokinetic and toxicodynamic mechanisms of PFOS, a persistent and bioaccumulative member of the per- and polyfluoroalkyl substances (PFAS) family. The study revealed significant differences in mortality rates with calculated LC50 values of 23.57 µM for WT and 16.71 µM for oatp1d1 mutants, indicating a higher susceptibility of the mutants to PFOS toxicity. This indicates the crucial role of the Oatp1d1 transporter in mediating the toxic effects of PFOS, possibly related to detoxification processes or regulation of bioavailability. Developmental abnormalities, particularly in the swim bladder, were more pronounced in mutant embryos, indicating the role of the transporter in mitigating PFOS-induced developmental toxicity. Gene expression analysis showed differential modulation of biotransformation genes, including cytochrome P450 (cyp) and glutathione S-transferase (gst) genes, underscoring the complexity of PFOS toxicity. The study also highlighted disruptions in lipid metabolism with altered expression of genes involved in lipid synthesis and oxidation, leading to abnormal lipid accumulation. These findings have significant implications for aquatic ecosystems and human health, as PFOS is persistent and bioaccumulative in the environment. The study emphasizes the need for stringent regulatory measures and effective remediation strategies to address PFOS contamination and protect both aquatic life and human populations.
Synthesis of alkyl glucosides catalyzed by immobilized α-amylase fromThermotoga maritima
Authors: Xolalpa-Villanueva Wendy , Ramírez-Amador Fidel O. , Olvera Leticia , Miranda-Molina Alfonso , López-Munguía Agustín , Saab-Rincón Gloria
Published: July 2024

The enzymatic production of alkyl glucosides is limited by the stability of the enzymes in the presence of alcohols. In the present study, we investigated three different supports: Sepharose 4B, crosslinked Sepharose (Fast Flow), and Eupergit C for the immobilization of α-amylase fromThermotoga maritima, AmyA, to increase its stability during the alcoholysis reaction. The enzyme immobilized on crosslinked Sepharose showed the best results, allowing its reutilization for at least five cycles while maintaining more than 50% residual activity. In addition, the immobilization of a previously reported H222Q variant resulted in a superior transglycosidic activity (> 50%) when compared to that of the wild-type (WT) AmyA. Moreover, both versions of the enzyme increased their residual activity after 24 h of incubation at 85°C upon immobilization. The alcoholysis withn-butanol,n-hexanol, andn-octanol was investigated to optimize the reaction conditions. Here, the addition of DMSO had a positive effect on the alcoholysis reactions with AmyA WT, achieving a total octyl glucoside title 1.75-fold higher than that obtained in the absence of DMSO.

Importance

Alkyl glucosides are valuable, non-toxic surfactants primarily synthesized chemically. The development of biocatalysts for their production has become a significant goal in the field of biocatalysis to avoid the disposal of toxic waste and environmentally harmful processes. To make these processes competitive, the use of low-cost raw materials and the recycling of biocatalysts are essential. The immobilization ofThermotoga maritimaα-amylase has enabled its use in the presence of long-chain alcohols, achieving octyl glucoside production of 0.7 mg/mL—an unprecedented feat for an amylase. This study represents a breakthrough in the use of α-amylases for alkyl glucoside production.
Multidimensional and Longitudinal Impact of a Genetic Diagnosis for Critically Ill Infants
Authors: Wojcik Monica H , del Rosario Maya C , Feldman Henry A , Smith Hadley Stevens , Holm Ingrid A
Published: July 2024

Background and Objectives

Many genetic conditions present in the neonatal intensive care unit (NICU), where a diagnostic evaluation is pursued. However, understanding of the impact of a genetic diagnosis on clinical outcomes and health-related quality of life for these infants remains incomplete. We therefore evaluated parent-reported outcomes complemented by clinical outcomes measures over one year for a cohort of infants in the NICU undergoing genetic evaluation.

Methods

Prospective cohort study evaluating outcomes after genetics consultation in a level IV NICU via parent-report and electronic medical records (EMR) review. Eligible infants were genetically undiagnosed at enrollment. Parent surveys were administered at baseline and three, six-, and 12-months following enrollment and assessed genetic testing utility as well as parent-reported infant health-related quality of life using the Infant Toddler Quality of Life Questionnaire.

Results

110 infant-parent pairs were enrolled. Infants had a median age at enrollment of 15 days (interquartile range 8-37.75). At baseline, 74% (81/110) of parents endorsed high importance of finding a genetic diagnosis, but perceived importance significantly decreased over time. Over the study period, 38 infants received a molecular diagnosis per parent report, though this was discordant with EMR review. Identification of a diagnosis did not significantly impact health-related quality of life across most domains, which was lower overall than population norms.

Conclusions

A genetic diagnosis is highly desired by parents in the NICU, though waning interest over time for undiagnosed families may reflect parental emotional adaptation and acceptance. Additional supports are needed to improve perceived quality of life.
Prevalence of catheter associated Urinary Tract Infection (UTI) in hospitalized patient in Karachi
Authors: Ali Syed Rohan , Raqib Moosa Abdur , Kashif Shahida , Shafique Muhammad Ashir , Haseeb Abdul , Anis Aisha
Published: July 2024

Background

Catheter-associated urinary tract infections (CAUTIs) are a prevalent healthcare-associated infection, accounting for significant morbidity, mortality, and increased healthcare costs.

Method

This is a cross-sectional study of patients diagnosed with UTI associated with catheter use. The sample was collected from November 2023 to June 2024, consisting of 200 patients admitted to the surgical, medical, and trauma wards of tertiary hospitals in Karachi, namely Jinnah Postgraduate Medical Centre Karachi and Dr. Ruth K. M. Pfau Civil Hospital Karachi. Data is analyzed using SPSS Version 22 and P-value of 0.05 considered significant.

Result

The majority of respondents (59.5%) had their catheters changed since insertion, predominantly by trained nurses (93.0%). There were notable associations with underlying conditions such as hypertension (56.5%) and diabetes (44.5%). Gender differences were significant, with females leading in medical cases and males in surgical and trauma cases (p-value 0.017). Age-related trends showed the 55+ age group dominated medical cases, while surgical and trauma cases varied by age group. There was a significant relationship between bleeding during catheterization and UTI (p-value: 0.000).

Conclusion

The study revealed a minimal incidence of CAUTI in Karachi’s tertiary care hospitals, indicating effective practices. However, further research is needed to explore the potential risk factors identified, such as female gender and comorbidities, to develop targeted interventions for reducing CAUTI incidence and improving patient outcomes.
Research Letter: Characterizing spin in psychiatric clinical research literature using large language models
Authors: Perlis Roy H.
Published: July 2024

Importance

Spin is a common form of biased reporting that misrepresents study results in publications as more positive than an objective assessment would indicate, but its prevalence in psychiatric journals is unknown.

Objective

To apply a large language model to characterize the extent to which original reports of pharmacologic and non-pharmacologic interventions in psychiatric journals reflect spin.

Design

We identified abstracts from studies published between 2013 and 2023 in 3 high-impact psychiatric journals describing randomized trials or meta-analyses of interventions.

Main Outcome and Measure

Presence or absence of spin estimated by a large language model (GPT4-turbo, turbo-2024-04-09), validated using gold standard abstracts with and without spin.

Results

Among a total of 663 abstracts, 296 (44.6%) exhibited possible or probable spin – 230/529 (43.5%) randomized trials, 66/134 (49.3%) meta-analyses; 148/310 (47.7%) for medication, 107/238 (45.0%) for psychotherapy, and 41/115 (35.7%) for other interventions. In a multivariable logistic regression model, reports of randomized trials, and non-pharmacologic/non-psychotherapy interventions, were less likely to exhibit spin, as were more recent publications

Conclusions and Relevance

A substantial subset of psychiatric intervention abstracts in high-impact journals may contain results presented in a potentially misleading way, with the potential to impact clinical practice. The success in automating spin detection via large language models may facilitate identification and revision to minimize spin in future publications.
Aging and Diabetes: Insights from American Seniors on Self-Care Practices, A Systematic Review & Meta-Synthesis
Authors: Lo David F. , Gawash Ahmed , Shah Kunal P. , Emanuel Jasmine , Goodwin Brandon , Shamilov Don D. , Kumar Gaurav , Jean Nathan , White Christian P.
Published: July 2024

This review aims to unravel the intricacies of diabetic self-management among geriatric people, drawing on current insights and understanding the complex paths geriatric people navigate. A wide search was conducted in health-oriented databases, including CINAHL, Embase, PsycINFO, MEDLINE, PubMed, Web of Science, and Cochrane Library while gray literature was excluded. The search combined keywords and subject headings, focusing on the geriatric population, diabetes, self-management, and qualitative research. A three-tiered screening process was employed, with titles and then abstracts initially reviewed. Full-text analysis followed, with disagreements resolved among reviewers. In total, there were 248 participants included across these eight studies. Positive attitudes and perceptions were found to play a significant role in optimizing diabetes self-care outcomes. Support from family and friends was identified as crucial for self-care, while healthcare professionals often lacked adequate support and encouragement. Participants emphasized the importance of listening to their bodies and acknowledging hidden issues. These themes collectively highlight the multifaceted aspects of diabetes self-care and the impact of various factors on the self-management experiences of geriatric individuals with diabetes. The goal of this review is not to objectify self-management as a treatment strategy but to emphasize the importance of cultivating positive attitudes, respecting individual values, and addressing cultural and ethnic differences in healthcare practices to enhance self-management in this population. By embracing cultural diversity, understanding barriers, and respecting individual values, healthcare professionals and policymakers can improve the quality of life for the geriatric population living with diabetes.
Plasma glycosaminoglycans and cell-free DNA to discriminate benign and malignant lung diseases
Authors: Qvick Alvida , Bratulic Sinisa , Carlsson Jessica , Stenmark Bianca , Karlsson Christina , Nielsen Jens , Gatto Francesco , Helenius Gisela
Published: July 2024

We aimed to investigate the use of free glycosaminoglycan profiles (GAGomes) and cfDNA in plasma to differentiate between lung cancer and benign lung disease. GAGs were analyzed using the MIRAM® Free Glycosaminoglycan Kit with ultra-high-performance liquid chromatography and electrospray ionization triple-quadrupole mass spectrometry. We detected two GAGome features, 0S chondroitin sulfate (CS) and 4S CS, with cancer-specific changes. Based on the observed GAGome changes, we devised a model to predict lung cancer. The model, named the GAGome score, could detect lung cancer with 41.2% sensitivity (95% CI: 9.2-54.2%) at 96.4% specificity (CI: 95.2-100.0%, n=113). Furthermore, we found that the GAGome score, when combined with a cfDNA test, could increase the sensitivity for lung cancer from 42.6% (95% CI: 31.7-60.6%, cfDNA alone) to 70.5% (CI: 57.4 - 81.5%) at 95% specificity (CI: 75.1-100%, n=74). Notably, the combined GAGome and cfDNA testing improved the sensitivity, especially in early stages, relative to the cfDNA alone. Our findings show that plasma GAGome profiles can enhance cfDNA testing performance, highlighting the applicability of a multiomics approach in lung cancer diagnostics.
Self-growing protocell models in aqueous two-phase system induced by internal DNA replication reaction
Authors: Minagawa Yoshihiro , Yabuta Moe , Su’etsugu Masayuki , Noji Hiroyuki
Published: July 2024

The bottom-up reconstitution of self-growing artificial cells is a critical milestone toward realizing autonomy and evolvability. However, building artificial cells that exhibit self-growth coupled with internal replication of gene-encoding DNA has not been achieved yet. Here, we report self-growing artificial cell models based on dextran-rich droplets in an aqueous two-phase system of poly(ethylene glycol) (PEG) and dextran (DEX). Motivated by the finding that DNA induces the generation of DEX-rich droplets, we integrated DNA amplification system with DEX-rich droplets, which exhibited active self-growth. We implemented the protocells with cell-free transcription-translation (TXTL) systems coupled with DNA amplification/replication, which also showed active self-growth. We also observed self-growth activity of protocells carrying a single copy of DNA. Considering the simplicities in terms of the chemical composition and the mechanism, these results underscore the potential of DEX droplets as a foundational platform for engineering protocells, giving implications for the emergence of protocells under prebiotic conditions.
Multi-sample non-negative spatial factorization
Authors: Wang Yi , Woyshner Kyla , Sriworarat Chaichontat , Stein-O’Brien Genevieve , Goff Loyal A , Hansen Kasper D.
Published: July 2024

Analyzing multi-sample spatial transcriptomics data requires accounting for biological variation. We present multi-sample non-negative spatial factorization (mNSF), an alignment-free framework extending single-sample spatial factorization (NSF) to multi-sample datasets. mNSF incorporates sample-specific spatial correlation modeling and extracts low-dimensional data representations. Through simulations and real data analysis, we demonstrate mNSF’s efficacy in identifying true factors, shared anatomical regions, and region-specific biological functions. mNSF’s performance is comparable to alignment-based methods when alignment is feasible, while enabling analysis in scenarios where spatial alignment is unfeasible. mNSF shows promise as a robust method for analyzing spatially resolved transcriptomics data across multiple samples.
Deep genetic substructure within bonobos
Authors: Han Sojung , de Filippo Cesare , Parra Genís , Meneu Juan Ramon , Laurent Romain , Frandsen Peter , Hvilsom Christina , Gronau Ilan , Marques-Bonet Tomas , Kuhlwilm Martin , Andrés Aida M
Published: July 2024

Establishing the genetic and geographic structure of populations is fundamental both to understand their evolutionary past and preserve their future, especially for endangered species. Nevertheless, the patterns of genetic population structure are unknown for most endangered species, including some of our closest living relatives. This is the case of bonobos (Pan paniscus) which together with chimpanzees (Pan troglodytes) are humans’ closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies (Groves, 2001), with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity (Fischer et al. 2011) despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Placing bonobos’ genetics in space is however challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyse the exomes and mtDNA from 20 wild-born bonobos, the whole-genomes of 10 captive bonobos and the mtDNA of 61 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to ∼145,000 years ago, and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. We identify putative signatures of differential genetic adaptation among populations for genes associated with homeostasis, metabolism and the nervous system. Furthermore, our estimated long-termNefor Far-West (∼3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need of attention to bonobo substructure, both in terms of research and conservation.

Highlights

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We identified three genetically distinct populations of bonobos, inferred as having Central, Western and Far-Western geographic origin within the species range. The estimated split time is ∼145,000 years ago for the Central and Western populations, and ∼60,000 years ago for the two Western populations.

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The genetic differentiation between the Central and Far-Western bonobo populations is in the order of that between Central and Eastern chimpanzee subspecies, while the genetic differentiation among Western bonobo populations is similar to that among human groups.

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Once substructure is accounted for, we infer a long-term effective population size (Ne) of only ∼3,000 for Far-Western bonobos, genetic isolation and inbreeding.
Charge-breaking domain walls separating neutral vacua in multi-Higgs models
Authors: Yang Yucheng , Ivanov Igor P.
Published: July 2024

The scalar potential of a multi-Higgs model can possess a rich structure of minima and saddle points, which evolves in an intricate way as the parameters change. In the hot early Universe, it could trigger multistep phase transitions, with exotic intermediate phases and peculiar domain wall configurations. Here, we provide a glimpse into this richness with the example of the three-Higgs-doublet model with the symmetry group Σ(36), either exact or softly broken. We present its phase diagram tracking not only the global minimum but all of its extrema. In particular, we reveal parameter space regions in which the deepest saddle point is charge breaking. This naturally leads to phase transitions between neutral vacua which involve expanding and colliding charge-breaking bubble walls. We also comment on opportunities of multistep phase transitions, on charge-breaking intermediate phases, and on phase transitions between different charge-breaking vacua. We illustrate the general discussion with two benchmark models, one of which possesses competing saddle points and allows for emergence of bubbles of the same true vacuum but with bubble walls of different nature. The intriguing cosmological implications of all these possibilities deserve dedicated study.

Published by the American Physical Society
2024
Impact of weak lensing on bright standard siren analyses
Authors: Mpetha Charlie T. , Congedo Giuseppe , Taylor Andy , Hendry Martin A.
Published: July 2024

Gravitational waves from binary mergers at cosmological distances will experience weak lensing by large scale structure. This causes a (de)magnification, μ, of the wave amplitude, and a completely degenerate modification to the inferred luminosity distance dL. The customary method to address this is to increase the uncertainty on dL according to the dispersion of the magnification distribution at the source redshift, σμ(z). But this term is dependent on the cosmological parameters that are being constrained by gravitational wave “standard sirens,” such as the Hubble parameter H0, and the matter density fraction Ωm. The dispersion σμ(z) is also sensitive to the resolution of the simulation used for its calculation. Tension in the measured value of H0 from independent datasets, and the present use of weak-lensing fitting functions calibrated using outdated cosmological simulations, suggest σμ(z) could be underestimated. This motivates an investigation into the consequences of mischaracterizing σμ(z). We consider two classes of standard siren, supermassive black hole binary and binary neutron star mergers. Underestimating H0 and Ωm when calculating σμ(z) increases the probability of finding a residual lensing bias on these parameters greater than 1σ by 1.5–3 times. Underestimating σμ(z) by using low resolution/small sky-area simulations can also significantly increase the probability of biased results; the probability of a 1σ(2σ) bias in H0 and Ωm found from binary neutron star mergers is 54% (19%) in this case. For neutron star mergers, the mean bias on H0 caused by magnification selection effects is ΔH0=−0.1  km s−1 Mpc−1. The spread around this mean bias—determined by assumptions on σμ(z)—is ΔH0=±0.25  km s−1 Mpc−1, comparable to the forecasted uncertainty. These effects do not impact merging neutron stars’ utility for addressing the H0 tension, but left uncorrected they limit their use for precision cosmology. For supermassive black hole binaries, the spread of possible biases on H0 is significant, ΔH0=±5  km s−1 Mpc−1, but O(200) observations are needed to reduce the variance below the bias. To achieve accurate subpercent level precision on cosmological parameters using standard sirens, first much improved knowledge on the form of the magnification distribution and its dependence on cosmology is needed.

Published by the American Physical Society
2024
Understanding the dynamics of English-speaking challenges for students in Kazakhstan
Authors: Yessenbekova Kymbat
Published: July 2024

Purpose

The purpose of this paper is to explore the English-speaking challenges confronted by English as Foreign Language (EFL) students in the context of Kazakhstan, a Central Asian, post-Soviet nation, particularly focusing on the interrelation of English language fluency issues, psychological conditions and the influence of environmental factors.

Design/methodology/approach

This qualitative inquiry is firmly situated in Krashen’s second language acquisition theory. The research cohort comprises ten undergraduates from the esteemed Foreign Languages and Translation Studies Department, their narratives forming the basis for data analysis. The author conducted structured interviews with the participants.

Findings

The findings demonstrate that limited language proficiency not only hinders fluency but also initiates psychological challenges, forming a difficult cycle. Additionally, environmental elements, such as interactions with teachers and peers, have both beneficial and adverse impacts on speaking improvement. Acknowledging and tackling these complex dynamics is crucial for developing focused interventions that foster a supportive learning environment conducive to enhancing language acquisition and fluency.

Research limitations/implications

The limitation of this research is that the triangulation method in the form of additional semi-structured interviews and/or observation was not used to get more in-depth data.

Practical implications

The study might be helpful for stakeholders to reflect on the English difficulties they experience and to prepare effective teaching and learning strategies. In particular, EFL teachers may need to use more speaking activities in lessons to help students overcome language barriers in speaking. EFL teachers might also adopt strategies such as not judging learners’ mistakes in the first phase of their language practices until they get used to speaking without any psychological blocks and paying additional attention to vocabulary and grammar knowledge in communicative lessons. EFL students may use the strategies to consciously evaluate their skills and not learn the speaking material by heart beforehand. In addition, university administration may organize regular speaking clubs for students in order to create an immersive environment. Moreover, they might require teachers to show up with their speaking capabilities before hiring English teachers, especially in English-related specialization departments.

Originality/value

The research indicates a lack of support and a judgmental environment, passive involvement in communicative pursuits and memorization as instrumental strategies for augmenting oral proficiency. These reasons have created difficulties in speaking English for students studying in English-specialized departments in Kazakhstan.
Online faith-holder communities in crisis: proposing and testing a dual-challenge model
Authors: Ren Ruqin , Yan Bei
Published: July 2024

Purpose

Though current literature has started to recognize the significant role that online faith-holders play in the context of brand reputation crises, extant research lacks a theoretical framework to explain the process in which online faith-holders endure the harm in brand reputation while collectively rebuilding the reputation. We propose and test a dual-challenge model for a more systematic understanding of faith-holder communities in brand reputation crises.

Design/methodology/approach

Focusing on collective-level communication activities, we quantitatively compared the volume, valence and variance of a faith-holder community’s communication (441,611 posts by 3,228 fans over 14 days) before and after a brand reputation crisis.

Findings

Our longitudinal data demonstrated that the crisis was a significant threat to group sentiment and cohesion. Nevertheless, the community was highly resilient and adaptive. Their emotions quickly recovered, and they promptly restored group cohesion and coordinated crisis response efforts after the crisis.

Originality/value

This study challenges the traditional assumption that online users are independent, static and reactive during brand crises. Instead, it conceptualizes online faith-holder community as a connected, proactive and dynamically adaptive group in crisis situations. This dual-challenge model highlights the importance of internally fostering collective resilience while externally coordinating crisis responses in a faith-holder community.
Unmanned ground vehicle (UGV) based automated construction progress measurement of road using LSTM
Authors: Patel Tirth , Guo Brian H.W. , van der Walt Jacobus Daniel , Zou Yang
Published: July 2024

Purpose

Current solutions for monitoring the progress of pavement construction (such as collecting, processing and analysing data) are inefficient, labour-intensive, time-consuming, tedious and error-prone. In this study, an automated solution proposes sensors prototype mounted unmanned ground vehicle (UGV) for data collection, an LSTM classifier for road layer detection, the integrated algorithm for as-built progress calculation and web-based as-built reporting.

Design/methodology/approach

The crux of the proposed solution, the road layer detection model, is proposed to develop from the layer change detection model and rule-based reasoning. In the beginning, data were gathered using a UGV with a laser ToF (time-of-flight) distance sensor, accelerometer, gyroscope and GPS sensor in a controlled environment. The long short-term memory (LSTM) algorithm was utilised on acquired data to develop a classifier model for layer change detection, such as layer not changed, layer up and layer down.

Findings

In controlled environment experiments, the classification of road layer changes achieved 94.35% test accuracy with 14.05% loss. Subsequently, the proposed approach, including the layer detection model, as-built measurement algorithm and reporting, was successfully implemented with a real case study to test the robustness of the model and measure the as-built progress.

Research limitations/implications

The implementation of the proposed framework can allow continuous, real-time monitoring of road construction projects, eliminating the need for manual, time-consuming methods. This study will potentially help the construction industry in the real time decision-making process of construction progress monitoring and controlling action.

Originality/value

This first novel approach marks the first utilization of sensors mounted UGV for monitoring road construction progress, filling a crucial research gap in incremental and segment-wise construction monitoring and offering a solution that addresses challenges faced by Unmanned Aerial Vehicles (UAVs) and 3D reconstruction. Utilizing UGVs offers advantages like cost-effectiveness, safety and operational flexibility in no-fly zones.