bluuebunny/crossref_metadata_2025 huggingface dataset:
Deciphering gut microbiota in patients with severe sepsis and septic shock
Authors: Lee Se Ju , Kim Dajeong , Ann Hea Won , Han Min , Lee Jung Ah , Lee Yongseop , Ahn Sangmin , Seo Hwi Won , Kim Jung Ho , Ahn Jin Young , Jeong Su Jin , Ku Nam Su , Yeom Joon-Sup , Ryu Choong-Min , Choi Jun Yong
Published: October 2023

Introduction

Gut microbiota dysbiosis is associated with susceptibility to sepsis and poor outcomes. However, changes to the intestinal microbiota during sepsis and their value as biomarkers are unclear. In this study, we compared the intestinal microbiota of patients with sepsis and healthy controls.

Methods

Stool was collected from patients with sepsis (subdivided according to mortality) and controls. Microbiome diversity and composition were analyzed by 16S rRNA gene pyrosequencing. The α-diversity of the intestinal microbiome was determined using operational taxonomic unit (OTU) counts and the Chao1, Shannon, and ACE indices. Adjusted Cox regression analyses assessed 6-month mortality risk factors.

Results

Fifty-nine patients (14 in-hospital deaths) and 29 healthy controls were enrolled. OTU counts and Chao1 and ACE indices were lower in the non-survivor than in the other groups. The controls showed a higher Shannon and lower Simpson index than did the sepsis group. The genus Blautia was more abundant in controls than in the sepsis group, and Faecalibacterium less abundant in the non-survivor than in the other groups. Regression analysis associated low Shannon index with 6-month mortality.

Conclusions

Survivors of sepsis, non-survivors, and healthy controls have different gut microbiomes, and a low Shannon index is a risk factor for 6-month mortality.
ANALYSIS AND IDENTIFICATION OF FERROPTOSIS-RELATED GENE SIGNATURE FOR ACUTE LUNG INJURY
Authors: Wang Jing , Yue Xiao-Qi , Li Yu-Ting , Jiang Miao , Liu Jun-Chao , Zhao Zi-Gang , Niu Chun-Yu
Published: October 2023

Background:Recent studies have shown that ferroptosis is involved in the evolution of acute lung injury (ALI), a serious respiratory pathological process leading to death. However, the regulatory mechanisms underlying ferroptosis in ALI remain largely unknown. The current study analyzed and identified a ferroptosis-related gene signature for ALI.Methods:Key genes associated with ferroptosis in ALI were identified by bioinformatics analysis. GSE104214, GSE18341, and GSE17355 datasets were downloaded from the Gene Expression Omnibus database. The signature genes were screened by least absolute shrinkage and selection operator regression, and the key genes of ALI were screened by weighted correlation network analysis (WGCNA), followed by immune infiltration analysis and functional enrichment analysis. In addition, mRNA expression of key genes in the lungs of mice with hemorrhagic shock (HS) and sepsis was verified.Results:A total of 2,132 differential genes were identified by various analyses, and 9 characteristic genes were detected using Lasso regression. We intersected nine signature genes with WGCNA module genes and finally determined four key genes (PROK2,IL6,TNF,SLC7A11). All four key genes were closely correlated with immune cells and regulatory genes of ALI, and the expression of the four genes was significantly different in the lung tissues of HS and sepsis models. Besides, the ferroptosis-related molecules GPX4 and ACSL4 showed remarkable difference in these models.Conclusion:These results indicate thatPROK2,IL6,TNF, andSLC7A11may be key regulatory targets of ferroptosis during ALI. This study proved that ferroptosis is a common pathophysiological process in three ALI models.
Barriers to Alzheimer Disease Clinical Trial Participation in a Minority Population
Authors: Lee Anson Y. , Jahansooz Julia R. , Guittu Darrell , Suzuki Rexton , Pak Lauren , Ishikawa Kyle M. , Goo Connor , Chen John J. , Carrazana Enrique , Viereck Jason , Liow Kore K.
Published: October 2023

Background:

Alzheimer disease (AD), the most common neurodegenerative disorder in the United States, disproportionately burdens minority populations.

Objective:

To explore barriers to AD clinical trial participation by Asian and Native Hawaiian patients diagnosed with AD or mild cognitive impairment.

Method:

We surveyed 187 patients with a Mini-Mental State Examination score ≥14 between January 2022 and June 2022. The score cutoff for clinical trial eligibility was set by the institution. Individuals also completed a 15-question telephone survey that assessed demographics, barriers to clinical trial participation, and clinical trial improvement methods.

Results:

Forty-nine patients responded, with a response rate of 26%. Asian and Native Hawaiian patients were less likely than White patients to participate in AD trials. The main barrier to participation was a lack of information about AD trials. Providing additional information regarding AD trials to patients and family members were listed as the top two reasons patients would consider participating in a clinical trial.

Conclusion:

Insufficient information about AD clinical trials is the primary barrier to participation among Asian and Native Hawaiian patients, followed by difficulty coordinating transportation and, in the case of Asians, the time required for clinical trials. Increased outreach, education, and assistance with logistics in these populations should be pursued to improve rates of participation in clinical trials.
Alishewanella maricola sp. nov., isolated from seawater of the Yellow Sea
Authors: Kim Kyung Hyun , Kim Jeong Min , Jin Hyun Mi , Hao Lujiang , Jeon Che Ok
Published: October 2023

A Gram-stain-negative and facultative aerobic bacterium, strain 16-MAT, was isolated from seawater of Yellow Sea in South Korea. Cells were catalase- and oxidase-positive and non-motile rods. Growth occurred at 4–37 °C (optimum, 30 °C) and pH 6.0–11.0 (optimum, 8.0), and in the presence of 0–7.0% NaCl (optimum, 3 %). Strain 16-MAT contained ubiquinone-8 as the sole isoprenoid quinone, C16 : 0 and summed feature three as the major fatty acids (>10 %), and phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid, and an unidentified polar lipid as the major polar lipids. The genome size and DNA G+C content of strain 16-MAT were 3.69 Mb and 46.0 mol%, respectively. Strain 16-MAT was most closely related to

Alishewanella alkalitolerans

LNK-7.1T with a 97.9 % 16S rRNA gene sequence similarity. A phylogenomic tree based on whole genome sequences showed that strain 16-MAT formed a phylogenetic lineage within the genus

Alishewanella

. Based on the phenotypic, chemotaxonomic, and molecular analyses, strain 16-MAT represents a novel species of the genus

Alishewanella

, for which the name Alishewanella maricola is proposed. The type strain is 16-MAT (=KACC 22238T =JCM 34596T).
Campylobacter magnus sp. nov., isolated from caecal contents of domestic pigs (Sus scrofa domesticus)
Authors: Gruntar Igor , Kostanjšek Rok , Pirš Tina , Papić Bojan
Published: October 2023

During the 2021 European Food Safety Authority coordinated harmonized monitoring of antimicrobial resistance in

Campylobacter

species in Slovenia, five

Campylobacter

-like strains were cultured from caeca of a total of 104 domestic pigs that could not be identified using the standard-prescribed biochemical tests or MALDI-TOF MS. The isolates were obtained using the standard ISO 10272 procedure for the isolation of thermotolerant

Campylobacter

with prolonged cultivation time. Small

Campylobacter

-like colonies were observed on mCCDA and CASA agar plates after 2–4 days of incubation; dark-field microscopy revealed relatively big spirilli-shaped bacteria exhibiting characteristic

Campylobacter

-like motility. The cells were 1.5–3 µm long and 0.5–0.7 µm wide, Gram-negative, oxidase-positive and catalase-positive. MALDI-TOF mass spectra were distinctive and consistent, but with low MALDI-TOF MS log scores and the closest matches being those of

Campylobacter hyointestinalis

and

Campylobacter fetus

. All five strains underwent whole-genome sequencing. Analysis of 16S rRNA gene sequences revealed that the isolates were most similar (98.3–98.4 % identity) to

Campylobacter lanienae

. Pairwise average nucleotide identity (ANI) values revealed that the five studied strains shared pairwise ANI of 96.2–96.5 % but were clearly distinct from the previously described

Campylobacter

species (ANI ≤72.8 %). The core genome-based phylogeny confirmed that the new strains form a distinct and well-supported clade within the genus

Campylobacter

. The conducted polyphasic taxonomic analysis confirmed that the five strains represent a novel

Campylobacter

species for which the name Campylobacter magnus sp. nov. is suggested, with strain 46386T (=DSM 115534T=CCUG 76865T) as the type strain.
Winogradskyella bathintestinalis sp. nov., isolated from the intestine of the deep-sea loosejaw dragonfish, Malacosteus niger
Authors: Uniacke-Lowe Shona , Johnson Crystal N. , Stanton Catherine , Hill Colin , Ross Paul
Published: October 2023

A novel bacterial strain, APC 3343T, was isolated from the intestine of a deep-sea loosejaw dragon fish, Malacosteus niger, caught at a depth of 1000 m in the Northwest Atlantic Ocean. Cells were aerobic, rod-shaped, yellow/orange-pigmented, non-motile and Gram-negative. Growth of strain APC 3343T was observed at 4–30 °C (optimum, 21–25 °C), pH 5.5–10 (optimum, pH 7–8) and 0.5–8 % (w/v) NaCl (optimum, 2–4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain APC 3343T was most closely related to members of the genus

Winogradskyella

, with the most closely related type strains being

Winogradskyella algae

Kr9-9T (98.46 % identity),

Winogradskyella damuponensis

F081-2T (98.07 %),

Winogradskyella eximia

CECT 7946T (97.93 %),

Winogradskyella litoriviva

KMM 6491T (97.79 %) and

Winogradskyella endarachnes

HL2-2T (97.79 %). Major fatty acids (>10 % of total) were iso-C16 : 0 3-OH, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). Polar lipids were phosphatidylethanolamine, three unknown aminolipids and eight unknown lipids. The draft genome sequence was 3.8 Mb in length with a G+C content of 33.43 mol%. Based on the phenotypic characteristics and phylogenetic analysis, strain APC 3343T is deemed to be a novel species of the genus

Winogradskyella

, and for which the name Winogradskyella bathintestinalis sp. nov. is proposed. The type strain of this species is APC 3343T (=DSM 115832T=NCIMB 15464T).
Substrate profiling of human Transglutaminase 1 using cDNA display and next-generation sequencing
Authors: Munaweera T.I.K. , Damnjanović Jasmina , Camagna Maurizio , Nezu Moeri , Jia Beixi , Hitomi Kiyotaka , Nemoto Naoto , Nakano Hideo
Published: October 2023

Human transglutaminase 1 regulates skin development and is linked with several disease conditions with yet fully unknown mechanisms. To uncover all of its roles in health and disease, the understanding of protein substrates and their reactivity with transglutaminase 1 is necessary. To gain insight into the substrate profile of human transglutaminase 1, this study uses anin vitroselection system based on the cDNA display technology to screen two displayed peptide libraries differing in the number and position of mutated sites relative to the reactive glutamine, in terms of their reactivity to transglutaminase 1. Analysis of the selected DNA pools of by next-generation sequencing and in-house bioinformatics methods revealed a detailed transglutaminase 1 substrate profile indicating preferred and non-preferred amino acid sequences. We have identified a peptide with sequence AEQHKLPSKWPF showing high reactivity to human transglutaminase 1 and low reactivity to transglutaminase 2 and transglutaminase 3. The position weight matrix consisting of per residue amino acid enrichment factors of all selected peptides was used to search human proteins by our in-house search algorithm and identify highly scoring sequence motifs in their primary structure. The search identified six already known transglutaminase 1 substrate proteins as highly scored hits as well as a list of candidate substrates that are under investigation.
Visual and pharmacotherapy outcomes after transverse sinus stenting for idiopathic intracranial hypertension
Authors: Handzic Armin , Xie Jim Shenchu , Hendriks Eef , Mosimann Pascal , Nicholson Patrick , Micieli Jonathan , Margolin Edward
Published: October 2023

Background

Transverse sinus stenting (TSS) is an increasingly commonly used treatment for patients with idiopathic intracranial hypertension (IIH). However, detailed neuro-ophthalmic evidence on visual and pharmacotherapy outcomes after TSS is scarce and heterogeneous. This study aimed to describe the visual outcomes of patients undergoing TSS for IIH and to ascertain the proportion of patients who could be weaned off intracranial pressure (ICP)-lowering medication after this procedure.

Methods

A retrospective chart review of all patients with IIH from two tertiary academic neuro-ophthalmology practices who underwent TSS between 2016 and 2022 was performed. Indications for stenting included failure of pharmacotherapy, intolerance of pharmacotherapy, and acute vision loss from severe papilledema. Data on demographics, symptoms, visual function, and TSS were collected. The paired Wilcoxon rank sum test was used to compare changes in visual acuity (VA) and visual field mean deviation (VFMD) between the baseline and most recent visits.

Results

Of 435 patients with IIH, 15 (13 women) met inclusion criteria. After TSS, ICP-lowering pharmacotherapy was discontinued in 10 patients and decreased in 4; one patient was not on ICP-lowering medication before TSS. All patients experienced resolution or improvement of symptoms (10 resolution, 4 improved, 1 asymptomatic before TSS) and papilledema (11 resolution, 4 improved) after stenting. Papilledema resolution was confirmed with optical coherence tomography-measured peripapillary nerve fibre layer thickness (median decrease 147 μm, interquartile range 41.8 – 242.8, p<0.001). Change in VA between the baseline and most recent visit was not significant, but VFMD improved significantly after stenting (median increase 3.0, IQR 2.0 – 4.2, p<0.001). No patient developed transverse sinus restenosis nor in-stent thrombosis postoperatively across a median venogram follow-up of 20.8 weeks (11.3 – 49.8) and no patient required subsequent surgical intervention for IIH.

Conclusion

In this cohort of patients with IIH and fulminant presentation, medication resistance, or medication intolerance, TSS was an effective and safe treatment modality. Most patients were able to stop ICP-lowering medications while demonstrating striking improvement in symptomatology and visual function.
A possible mechanistic insight on how Compromised Hydrolysis of Triacylglycerol 7 (CHT7) restrains the involvement of it’s DNA binding CXC domain from quiescence repression
Authors: Chauhan Manisha , Arshi Syeda Amna , Narayanan Naveen , Arfin Haseeb Ul , Sharma Amit
Published: October 2023

CHT7 is a regulator of quiescence repression and TAG degradation between the nitrogen deprived and the nitrogen replenished states inChlamydomonas reinhardtii. Initially it was thought that the CHT7’s repression activity is managed by its DNA binding CXC domain which is a tandem repeat of two cysteine rich subdomains. Later, it was found that the CXC (CHT7_CXC) domain is effectively dispensable for CHT7’s activities. Rather, CHT7’s predicted protein binding domains are proposed to be involved in gene regulation activities by binding through other repressors in the cell. Yet, it remains unclear why and how CHT7 manages to refrain its own CXC domain from participating in any transcriptional activities. The question becomes more intriguing, because CXC binding regions are available in promoter regions of some of the misregulated genes in the CHT7 mutant (cht7). Through the combination of biophysical experiments and molecular dynamics approaches, we have studied the DNA recognition behavior of CHT7_CXC. The results show that CHT7_CXC domain is highly selective towards DNA sequences and this selectivity is imparted due to the differential binding abilities of the CXC subdomains. Further, to understand if the case is - that CXC looses it’s DNA binding capabilities in the vicinity of other repressor molecules, we carried out CHT7_CXC’s DNA binding stability test by simulating the spatial constraint conditions using the AsLOV2- CXC fusion. Our test results show limited ability of CHT7_CXC to withstand steric forces and provide insights to why and how algal cells may hold back CHT7_CXC’s indulgence in quiescence repression.

Significance

Microalgae, under nutrient rich conditions, provide biomass. Whereas, nutrient deprivation leads to accumulation of biofuel feedstock, but cells enter quiescence. Net enhancement in feedstock, therefore relies on the precision of the quiescence regulator. InChlamydomonas reinhardtii, CHT7 is a central regulator of quiescence. Surprisingly, rather than using its own DNA binding domain (DBD) for the regulatory activities, CHT7 recruits external transcriptional regulators using its non DBDs. To ensure smooth functioning, CHT7’s DBD must rapidly switch to inactive form. Modifications in DNA binding profiles of DBDs due to non DBDs are seen in transcription factors of many organisms. The switching mechanism discussed could therefore be a generic approach of timely regulation of individual components of the complex transcriptional machineries.
Bioinformatics analysis of Uncyclotides: a potential antimicrobial peptide to protect against heart failure diseases
Authors: Maya-Ramírez Carlos Eliel , Sufyan Muhammad , Alanzi Abdullah R
Published: October 2023

Heart failure (also known as HF) is a clinical disorder triggered by functional and structural defects in cardiac muscles causing blood ejection or damage of ventricular filling. Even though the progression in the field of medicine, HF control, which generally presents as a syndrome, has been a task to healthcare sources. This is reproduced by the comparatively higher ration of readmissions with enhanced disease and death linked with HF. Congestive heart failure is also linked with expressional changes of human uncoupling protein proteins. So, we need to tackle the heart failure problem with the help of bioinformatics analysis. In this study, we retrieved three antimicrobial peptides (Cathelicidins, CRAMP and Uncyclotides) and four human uncoupling proteins (UCP 1, UCP 2, UCP 3 & UCP 4) from DRAMP and NCBI web server. Physiochemical properties and domains analysis of UCPs and antimicrobial peptides was performed by using Protparam, DRAMP and InterPro databases correspondingly. To predict the UCPs structure, homology modelling was performed by SWISS-MODEL server and structural assessment was done by Ramachandran plots. We detected the best antimicrobial peptide (Uncyclotides) against heart failure diseases after HPEPDOCK analysis. We also confirmed stability of UCP 1-Uncyclotides complex, and shown the slight distortion of the deformability plot supported by highest eigenvalues after Molecular Dynamics analysis. Therefore, this in silico approach identifies potential antimicrobial peptides “Uncyclotides” (acts as inhibitors) of heart failure diseases, which have to be confirmed further after experimental and clinical trials.
Mechanism for controlled assembly of transcriptional condensates by Aire
Authors: Huoh Yu-San , Zhang Qianxia , Torner Ricarda , Baca Sylvan C. , Arthanari Haribabu , Hur Sun
Published: October 2023

Transcriptional condensates play a crucial role in gene expression and regulation1–4, yet the mechanisms governing their assembly at the correct location and time remain poorly understood2,5–7. We here report a multi-layered mechanism for condensate assembly by the Autoimmune regulator (Aire), an essential transcriptional regulator (TR) that orchestrates gene expression reprogramming for central T-cell tolerance8,9. Previous studies demonstrated that Aire utilizes its polymerizing domain CARD to form nuclear condensates critical for its transcriptional activity10,11. Our current data show that Aire condensates assemble on enhancers, stimulating local transcriptional activities, while also connecting disparate inter-chromosomal genomic loci. This process of functional condensate formation hinges upon the coordination between three Aire domains: the CARD, the histone binding domain PHD1 and the activation domain C-terminal tail (CTT). Specifically, CTT directly binds CBP/p300 coactivators, recruiting Aire to CBP/p300-rich enhancers and promoting CARD-mediated condensate assembly. Conversely, PHD1 restrains spontaneous Aire polymerization by binding to the ubiquitous unmethylated H3K4, ensuring Aire remains dispersed throughout the genome until it nucleates on enhancers. Accordingly, deletion of CTT or PHD1 leads to a complete loss of Aire’s functions through distinct mechanisms––deletion of CTT abrogates Aire condensate formation, whereas deletion of PHD1 leads to dysfunctional Aire condensates detached from chromatin. Thus, our findings highlight the balance between PHD1-mediated suppression and CTT-mediated stimulation of Aire polymerization to form transcriptionally active condensates at appropriate target sites, providing new insights into controlled polymerization of TRs.
Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics
Authors: Thurimella Kumar , Mohamed Ahmed M. T. , Graham Daniel B. , Owens Róisín M. , La Rosa Sabina Leanti , Plichta Damian R. , Bacallado Sergio , Xavier Ramnik J.
Published: October 2023

In metagenomics, the pool of uncharacterized microbial enzymes presents a challenge for functional annotation. Among these, carbohydrate-active enzymes (CAZymes) stand out due to their pivotal roles in various biological processes related to host health and nutrition. Here, we present CAZyLingua, the first tool that harnesses protein language model embeddings to build a deep learning framework that facilitates the annotation of CAZymes in metagenomic datasets. Our benchmarking results showed on average a higher F1 score (reflecting an average of precision and recall) on the annotated genomes ofBacteroides thetaiotaomicron,Eggerthella lentaandRuminococcus gnavuscompared to the traditional sequence homology-based method in dbCAN2. We applied our tool to a paired mother/infant longitudinal dataset and revealed unannotated CAZymes linked to microbial development during infancy. When applied to metagenomic datasets derived from patients affected by fibrosis-prone diseases such as Crohn’s disease and IgG4-related disease, CAZyLingua uncovered CAZymes associated with disease and healthy states. In each of these metagenomic catalogs, CAZyLingua discovered new annotations that were previously overlooked by traditional sequence homology tools. Overall, the deep learning model CAZyLingua can be applied in combination with existing tools to unravel intricate CAZyme evolutionary profiles and patterns, contributing to a more comprehensive understanding of microbial metabolic dynamics.
Application of Transfer Learning for Rapid Calibration of Spatially-resolved Diffuse Reflectance Probes for Extraction of Tissue Optical Properties
Authors: Hannan Md Nafiz , Baran Timothy M.
Published: October 2023

Abstract

Significance

Treatment planning for light-based therapies including photodynamic therapy requires tissue optical property knowledge. These are recoverable with spatially-resolved diffuse reflectance spectroscopy (DRS), but requires precise source-detector separation (SDS) determination and time-consuming simulations.

Aim

An artificial neural network (ANN) to map from DRS at short SDS to optical properties was created. This trained ANN was adapted to fiber-optic probes with varying SDS using transfer learning.

Approach

An ANN mapping from measurements to Monte Carlo simulation to optical properties was created with one fiber-optic probe. A second probe with different SDS was used for transfer learning algorithm creation. Data from a third were used to test this algorithm.

Results

The initial ANN recovered absorber concentration with RMSE=0.29 µM (7.5% mean error) and µs’at 665 nm (µs,665’) with RMSE=0.77 cm-1(2.5% mean error). For probe-2, transfer learning significantly improved absorber concentration (0.38 vs. 1.67 µM, p=0.0005) and µs,665’(0.71 vs. 1.8 cm-1, p=0.0005) recovery. A third probe also showed improved absorber (0.7 vs. 4.1 µM, p<0.0001) and µs,665’(1.68 vs. 2.08 cm-1, p=0.2) recovery.

Conclusions

A data-driven approach to optical property extraction can be used to rapidly calibrate new fiber-optic probes with varying SDS, with as few as three calibration spectra.
Rewiring of cortical glucose metabolism fuels human brain cancer growth
Authors: Scott Andrew J. , Mittal Anjali , Meghdadi Baharan , Palavalasa Sravya , Achreja Abhinav , O’Brien Alexandra , Kothari Ayesha U. , Zhou Weihua , Xu Jie , Lin Angelica , Wilder-Romans Kari , Edwards Donna M. , Wu Zhe , Feng Jiane , Andren Anthony C. , Zhang Li , Tarnal Vijay , Redic Kimberly A. , Qi Nathan , Fischer Joshua , Yang Ethan , Regan Michael S. , Stopka Sylwia A , Baquer Gerard , Lawrence Theodore S. , Venneti Sriram , Agar Nathalie Y. R. , Lyssiotis Costas A. , Al-Holou Wajd N. , Nagrath Deepak , Wahl Daniel R.
Published: October 2023

The brain avidly consumes glucose to fuel neurophysiology. Cancers of the brain, such as glioblastoma (GBM), lose aspects of normal biology and gain the ability to proliferate and invade healthy tissue. How brain cancers rewire glucose utilization to fuel these processes is poorly understood. Here we perform infusions of13C-labeled glucose into patients and mice with brain cancer to define the metabolic fates of glucose-derived carbon in tumor and cortex. By combining these measurements with quantitative metabolic flux analysis, we find that human cortex funnels glucose-derived carbons towards physiologic processes including TCA cycle oxidation and neurotransmitter synthesis. In contrast, brain cancers downregulate these physiologic processes, scavenge alternative carbon sources from the environment, and instead use glucose-derived carbons to produce molecules needed for proliferation and invasion. Targeting this metabolic rewiring in mice through dietary modulation selectively alters GBM metabolism and slows tumor growth.

Significance

This study is the first to directly measure biosynthetic flux in both glioma and cortical tissue in human brain cancer patients. Brain tumors rewire glucose carbon utilization away from oxidation and neurotransmitter production towards biosynthesis to fuel growth. Blocking these metabolic adaptations with dietary interventions slows brain cancer growth with minimal effects on cortical metabolism.
Identification of proteotoxic and proteoprotective bacteria that non-specifically affect proteins associated with neurodegenerative diseases
Authors: Walker Alyssa C , Bhargava Rohan , Bucher Michael , Brust Amanda S , Czyż Daniel M
Published: October 2023

Neurodegenerative protein conformational diseases (PCDs), such as Alzheimer’s, Parkinson’s, and Huntington’s, are a leading cause of death and disability worldwide and have no known cures or effective treatments. Emerging evidence suggests a role for the gut microbiota in the pathogenesis of neurodegenerative PCDs; however, the influence of specific bacteria on the culprit proteins associated with each of these diseases remains elusive, primarily due to the complexity of the microbiota. In the present study, we employed a single-strain screening approach to identify human bacterial isolates that enhance or suppress the aggregation of culprit proteins and the associated toxicity inCaenorhabditis elegansexpressing Aβ1-42, α-synuclein, and polyglutamine tracts. Here, we reveal the first comprehensive analysis of the human microbiome for its effect on proteins associated with neurodegenerative diseases. Our results suggest that bacteria affect the aggregation of metastable proteins by modulating host proteostasis rather than selectively targeting specific disease-associated proteins. These results reveal bacteria that potentially influence the pathogenesis of PCDs and open new promising prevention and treatment opportunities by altering the abundance of beneficial and detrimental microbes.
A quantitative genetics framework for understanding the selection response of microbial communities
Authors: Xie Li , Yuan Alex E , Shou Wenying
Published: October 2023

Heritability, a quantity that reflects the degree of resemblance between parent and offspring traits, is measured during plant and animal breeding because it predicts selection success during artificial selection of individuals. However, when whole microbial communities are under artificial selection to improve their traits, high heritability of the community trait does not necessarily predict selection success. To better understand the relationship between heritability and success during community selection, we establish a quantitative genetics framework, and in doing so, we obtain practical recommendations. Specifically, we decompose a community trait into “trait determinants”: genotype compositions and species compositions that impact the community trait and that vary among communities. This allows us to interpret heritability of a community trait in terms of the heritability of its determinants. We then use the Price equation to partition the selection response of a community trait into three phenomena: inter-community selection (heritability multiplied by selection intensity), transmission infidelity (the change in community trait from parent to offspring), and nonlinearity (due to a nonlinear relationship between parent and offspring traits). We illustrate that evolution within a community can cause the three terms to covary: in addition to the known effect of worsening transmission infidelity, intra-community evolution can lead to inflated heritability values greater than one (through an effect whereby “the poor get poorer”), and simultaneously magnify nonlinearity. As a consequence of these effects, heritability no longer predicts the selection response of a community trait. We propose effective selection strategies that improve heritability without accelerating intra-community evolution.
Cocrystallization of ubiquitin–deubiquitinase complexes through disulfide linkage
Authors: Negron Teron Kristos I. , Das Chittaranjan
Published: October 2023

Structural characterization of the recognition of ubiquitin (Ub) by deubiquitinases (DUBs) has largely relied on covalent complexation of the DUB through its catalytic cysteine with a Ub C-terminal electrophile. The Ub electrophiles are accessed through intein chemistry in conjunction with chemical synthesis. Here, it was asked whether DUB–Ub covalent complexes could instead be accessed by simpler disulfide chemistry using a Ub cysteine mutant in which the last glycine has been replaced with a cysteine. The Ub cysteine mutant displayed a wide variability in disulfide formation across a panel of eukaryotic and prokaryotic DUBs, with some showing no detectable reaction while others robustly produced a disulfide complex. Using this approach, two disulfide-linked ubiquitin-bound complexes were crystallized, one involving the Legionella pneumophila effector SdeA DUB and the other involving the Orientia effector OtDUB. These DUBs had previously been crystallized in Ub-bound forms using the C-terminal electrophile strategy and noncovalent complexation, respectively. While the disulfide-linked SdeA DUB–Ub complex crystallized as expected, in the OtDUB complex the disulfide bond to the Ub mutant involved a cysteine that differed from the catalytic cysteine. Disulfide formation with the SdeA DUB catalytic cysteine was accompanied by local distortion of the helix carrying the active-site cysteine, whereas OtDUB reacted with the Ub mutant using a surface-exposed cysteine.
Unfolding the potential of the ARIMA model in forecasting maize production in Tanzania
Authors: Lwaho Joseph , Ilembo Bahati
Published: October 2023

Purpose

This paper was set to develop a model for forecasting maize production in Tanzania using the autoregressive integrated moving average (ARIMA) approach. The aim is to forecast future production of maize for the next 10 years to help identify the population at risk of food insecurity and quantify the anticipated maize shortage.

Design/methodology/approach

Annual historical data on maize production (hg/ha) from 1961 to 2021 obtained from the FAOSTAT database were used. The ARIMA method is a robust framework for forecasting time-series data with non-seasonal components. The model was selected based on the Akaike Information Criteria corrected (AICc) minimum values and maximum log-likelihood. Model adequacy was checked using plots of residuals and the Ljung-Box test.

Findings

The results suggest that ARIMA (1,1,1) is the most suitable model to forecast maize production in Tanzania. The selected model proved efficient in forecasting maize production in the coming years and is recommended for application.

Originality/value

The study used partially processed secondary data to fit for Time series analysis using ARIMA (1,1,1) and hence reliable and conclusive results.
From lagging behind to going beyond: windows of opportunity and latecomers' catch-up strategies
Authors: Li Yicun , Teng Yuanyang , Wu Dong , Wu Xiaobo
Published: October 2023

Purpose

To answer the questions: what roles windows of opportunity act in the catchup process of latecomers, what strategies latecomer enterprises should adopt to size windows of opportunity to catch-up with incumbents even going beyond?

Design/methodology/approach

This paper studies the catch-up history of the Chinese mobile phone industry and proposes a sectoral innovation system under scenario of technology paradigm shifts. Then a history-friendly simulation model and counterfactual analysis are conducted to learn how different windows of opportunity and catch-up strategies influence the catch-up performance of latecomers.

Findings

Results show latecomers can catch up with technology ability by utilizing technology window and path-creating strategy. However, catching up with the market is not guaranteed. Demand window can help latecomers to catch up with market as it increases their survival rates, different sized windows benefit different strategies. However, it also enlarges incumbents' scale effect. Without technology window technology catch up is not guaranteed. Two windows have combination effects. Demand window affects the “degree” of change in survival rates, while the technology window affects the “speed” of change. Demand window provides security; technology window provides the possibility of a breakthrough for technology ability.

Practical implications

The findings of this paper provide theoretical guidance for latecomer enterprises to choose appropriate catch-up strategies to seize different opportunity windows.

Originality/value

This paper emphasizes the abrupt change of industrial innovation system caused by technology paradigm shifts, which makes up for the shortcomings of previous researches on industrial innovation system which either studied the influence of static factors or based on the influence of continuous changes.
Understanding women's performance of entrepreneurship in the Sri Lankan context
Authors: Peiris Pathiranage Padmali Manesha , Tatli Ahu , Ozturk Mustafa Bilgehan
Published: October 2023

Purpose

The aim of this study is to explore how women in Sri Lanka cultivate entrepreneurial personae to navigate the various gendered roles they situationally enact, as they attempt to secure legitimacy and acceptance and overcome their otherness. Drawing on Goffman's theorisation of symbolic interaction, this study investigates how gender informs the performance of entrepreneurship in Sri Lanka. In this way, the study engages with the challenges women in the Global South navigate while undertaking entrepreneurship, and it contributes to the critical entrepreneurship literature on the intertwined nature of gender and entrepreneurship.

Design/methodology/approach

Following feminist standpoint epistemology (FSE), this qualitative study focuses on women entrepreneurs in Sri Lanka by examining the performance of entrepreneurship through 44 life history interviews (LHIs) and 40 Field Observations conducted over a seven-month period.

Findings

The findings reveal that women carefully cultivate entrepreneurial personae by striking a balance between entrepreneurial ideals and patriarchal social expectations around womanhood. The findings of the study present how the entrepreneurial personae are constructed by way of appearance, mannerism and setting, which presents opportunities for future research to explore the dramaturgical aspect of gender and entrepreneurship.

Originality/value

This study contributes to the growing body of feminist research surrounding women entrepreneurs, by drawing on insights from the lived experiences of women entrepreneurs in the Global South. This study also expands Goffman's theorisation of audience segregation and shows that a subject's understanding of the audience shapes their personae. A further contribution of this research is how space becomes an extension of the personae at play.
The more, the merrier? The role of an auditor's certification in loan pricing
Authors: Enkhtaivan Bolortuya , Davaadorj Zagdbazar
Published: October 2023

Purpose

The purpose of this paper is to explore the role of three different audit characteristics in loan pricing—the most significant credit term for borrowers. Three characteristics include audit reputation, audit tenure and audit specialization.

Design/methodology/approach

To examine audit characteristics simultaneously to measure their effect on loan pricing, this study uses a full-rank, three-way interaction model and conducts slope difference tests. It also includes the joint effects of these variables to estimate any incremental benefits of possessing multiple qualifications.

Findings

When studying the three qualifications together, none of them alone is strong enough to affect the loan interest. But, a Big 4 auditor with tenure can benefit the client by reducing the interest by about 1.98%. The more expertise the auditor has, the better value it brings to borrowers. A highly qualified auditor with additional expertise can significantly reduce loan pricing further by about 2.96 percent.

Originality/value

Examining the costs and benefits of hiring certified auditors is crucial for borrowers. While the variables are not exhaustive, an understanding of the added value of hiring high-quality auditors with more than one or two qualifications to their potential premium fees helps borrowers in managers' audit selection decisions. At the same time, the results shed some light on which of the auditor's qualifications lenders might prioritize when pricing a borrower's loan.
Unpacking the influence of anthropomorphism and stereotypes on consumer attitude towards luxury brand
Authors: Malhotra Gunjan , Dandotiya Gunjan
Published: October 2023

Purpose

This study aims to understand consumers' attitudes towards luxury products based on the stereotype content model, brand anthropomorphism and the psychological ownership theory.

Design/methodology/approach

The authors collected data from Indian consumers using the online questionnaire survey method. Data analysis was conducted using SPSS AMOS version 24 and PROCESS SPSS macro, using both mediation and moderated mediation models.

Findings

The findings suggest that increasing brand anthropomorphism and stereotypes enhance consumers' attitudes through a significant mediating role of brand credibility. The results also show that consumers' psychological ownership positively moderates the mediating path via brand credibility from low to high levels.

Originality/value

In doing so, this study contributes to the literature on luxury retail by examining how brand stereotypes and brand anthropomorphism impact consumers' attitudes towards luxury brands through the mediating role of brand credibility and the moderating role of psychological ownership. In the process, the study provides an understanding of Indian consumers' attitudes in the context of the Indian luxury retail sector.
What do individuals know, feel and do from a financial perspective? An empirical study on financial satisfaction
Authors: Kumar Jitender , Rani Manju , Rani Garima , Rani Vinki
Published: October 2023

Purpose

Financial satisfaction is a potential ambition of individuals' lives that requires well-strategized economic behaviors. The authors examine the impact of various factors on the financial behavior (FB) and financial satisfaction (FIS) of individuals in India's National Capital Region (NCR).

Design/methodology/approach

Through a literature review, a survey questionnaire was formulated using existing scales on FIS. For more in-depth insights, data are obtained from 427 respondents in the NCR region using self-administered questionnaires. This article used “partial least square structural equation modeling (PLS-SEM)” to inspect the hypothesized model of individuals' FIS.

Findings

According to the study results, financial attitude (FA), financial self-efficacy (FSE), financial knowledge (FK) and demographic characteristics (DC) significantly influence FB. Conversely, financial stress (FS) negatively impacts FB. It also highlights that FA, FSE, FK and FB all significantly impact FIS. Nevertheless, FS and DC insignificantly influence FIS.

Originality/value

To the best knowledge of the authors, this article is an initial attempt to offer a novel perspective of individuals' FB and FIS in India. It would help the government and stakeholders by providing various pioneering economic schemes and making policies that help increase individuals' FIS.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-03-2023-0239
Market reactions to drugs price reduction during COVID-19 distress in an emerging economy: value creation through CSR
Authors: Kumar Gopal , Chan Felix T.S. , Goswami Mohit
Published: October 2023

Purpose

The coronavirus (COVID-19) is the worst pandemic in recent memory in terms of its economic and social impacts. Deadly second wave of COVID-19 in India shook the country and reshaped the ways organizations functions and societies behave. Medical infrastructure was unaffordable and unsupportive which created high distress in the Indian society, especially for poor. At this juncture, some pharmaceutical firms made a unique social investment when they reduced price of drugs used to treat COVID-19 patients. This study aims to examine how the market and the society respond to the price reduction announcement during the psychological distress of COVID-19.

Design/methodology/approach

Market reactions have been analyzed by conducting an event study on stock market data and visual analytics-based sentiment analysis on Twitter data.

Findings

Overall, this study finds positive abnormal returns on the day and around the day of event. Interestingly, this study finds that returns during the time of high distress are significantly higher. Sentiment analysis conveys that net sentiment is favorable to the pharmaceutical firms around the day of event and it sustains more during the time of high distress.

Originality/value

This study is unique in contributing to the business and industrial management literature by highlighting market reactions to social responsibility of business during the time of psychological distress in emerging economies.
How did the outcome of international cooperation in school-based management help schools respond to the COVID-19 pandemic in Nepal?
Authors: Ishida Yoko , Shrestha Bhim Kumar , Thapa Uma , Subba Khagendra
Published: October 2023

Purpose

This study aims to determine how school-based management (SBM) capacity developed through international cooperation functioned to overcome challenges during the coronavirus disease 2019 (COVID-19) pandemic in Nepal.

Design/methodology/approach

The research structure was designed based on the success case method. The researchers conducted a questionnaire survey of head teachers to understand schools’ responses during the COVID-19 pandemic period, identified likely success-case schools, held workshops at the likely success-case schools and conducted in-depth interviews with head teachers and school management committee (SMC) members to understand how SBM functioned and contributed to the success cases.

Findings

Storytelling from the success-case schools provided reliable evidence that the localised approaches of SBM are effective for planning and implementing suitable responses at school. The reviews of the head teachers showed that both head teachers and teachers had strong leadership and understood the importance of collaboration with teachers, SMC members, Parent Teacher Association (PTA), guardians and students. Although the research could not show clear evidence of a causal relationship between their achievement and Japan’s project input, the success-case schools clearly benefited from the head teachers’ appropriate execution of SBM with their strong leadership as well as the collaborative efforts of the stakeholders.

Originality/value

The research tries to clarify the influence of the effects of SBM capacity development projects by analysing the changes of head teachers and teachers through the storytelling aspect of the success case method with in-depth consideration of actual school responses during the emergency period of the COVID-19 pandemic.
A stakeholder analysis for sustainable development of Maritime Village in Semarang coastal community, Indonesia
Authors: Kismartini Kismartini , Roziqin Ali , Authori Naila
Published: October 2023

Purpose

This paper aims to examine the role of stakeholders and their interconnected relationships based on power and interests in realising sustainable development in coastal areas using the Maritime Village program in Tambaklorok, Semarang City, Indonesia as a case study.

Design/methodology/approach

Data were collected from in-depth interviews and focus group discussions (FGD) with stakeholders, observations, as well as online news, and official government reports, followed by taxonomic analysis.

Findings

The results showed the four categories of stakeholders, namely players, context setters, subjects, and crowd. The Ministry of Public Works and Housing (PUPR), Regional Development Planning Agency (BAPPEDA) of Semarang City, Spatial Planning Agency (DISTARU) of Semarang City, and the Fisheries Office of Semarang City were found to be key players with a role in the success of the program. PT Pelindo (Indonesia Port Corporations) was identified as a context setter with low interests but high power, acting as an accelerator in the development program.

Originality/value

The originality of this study lied in its examination of the power and interests of stakeholders involved in government projects. It was recommended to strengthen coordination among the stakeholders to ensure the success of the program.
Investing in social responsibility to achieve full sustainability
Authors: Moura Carlos
Published: October 2023

Purpose

This article aims to analyze sustainability in tourism as the unavoidable path for the sector and the planet.

Design/methodology/approach

Argues that through sustainability, it will be possible to develop companies in full harmony with the already evident needs of the planet and that it is urgent that they continue to evolve, without further erosion by creating a firm and sustainable basis for the future.

Findings

Proposes that it is necessary to think about social responsibility to achieve full sustainability but that above all, each of us—individually and collectively, has a role to play. In fact, for this path of sustainability to be followed, it is necessary to create a sustainable business environment that companies, in particular the smaller ones, can adopt.

Originality/value

The article presents the views and main initiatives of the Association of Hotels, Restaurants and Similar Establishments of Portugal as they interconnect social responsibility and full sustainability and illustrates these with several projects and a best practice case in energy management for restaurants.