bluuebunny/crossref_metadata_2025 huggingface dataset:
Peripheral Perfusion Index in Ugandan Children With Plasmodium falciparum Severe Malaria: Secondary Analysis of Outcomes in a 2014–2017 Cohort Study
Authors: Boland Wesley , Datta Dibyadyuti , Namazzi Ruth , Bond Caitlin , Conroy Andrea L. , Mellencamp Kagan A. , Opoka Robert O. , John Chandy C. , Rivera Michael Lintner
Published: September 2024

OBJECTIVES:

Continuous, noninvasive tools to monitor peripheral perfusion, such as perfusion index (PI), can detect hemodynamic abnormalities and assist in the management of critically ill children hospitalized with severe malaria. In this study of hospitalized children with severe malaria, we aimed to assess whether PI correlates with clinical markers of perfusion and to determine whether combining PI with these clinical measures improves identification of children with greater odds of mortality.

DESIGN:

Post hoc analysis of a prospective, multicenter, cohort study conducted between 2014 and 2017.

SETTING:

Two referral hospitals in Central and Eastern Uganda.

PATIENTS:

Six hundred children younger than 5 years old with severe malaria and 120 asymptomatic community children.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

PI was measured at 6-hour intervals for the first 24 hours of hospitalization. We compared PI to standard clinical perfusion measures such as capillary refill time, presence of cold peripheral limbs, or temperature gradient. Admission PI was highly correlated with clinical measures of perfusion. Admission PI was lower in children with severe malaria compared with asymptomatic community children; and, among the children with severe malaria, PI was lower in those with clinical features of poor perfusion or complications of severe malaria, such as shock and hyperlactatemia (all p < 0.02). Among children with severe malaria, lower admission PI was associated with greater odds of mortality after adjustment for age, sex, and severe malaria criteria (adjusted odds ratio, 2.4 for each log decrease in PI [95% CI, 1.0–5.9]; p = 0.045). Diagnostically, the presence of two consecutive low PI measures (< 1%) predicted mortality, with a sensitivity of 50% and a specificity of 76%.

CONCLUSIONS:

In severe malaria, PI correlates with clinical complications (including shock and elevated serum lactate) and may be useful as an objective, continuous explanatory variable associated with greater odds of later in-hospital mortality.
Long-Term Three-Dimensional Morphometric Outcome Study of Nasal Bone in Cleft Patients
Authors: Enomoto Kei , Sakamoto Yoshiaki , Miyamoto Junpei
Published: September 2024

Cleft lip nose deformities are characterized by underlying features in the bony skeleton as well as the soft tissues; however, no previous study has focused on the evaluation of the nasal bone. The aim of this study was to compare nasal bone features among adult patients with unilateral cleft lip with or without cleft palate, those with bilateral cleft lip and palate, and controls. Included in this retrospective study were patients aged ≥16 years with nonsyndromic cleft who underwent long-term orthodontic treatment and controls aged 18–45 years who underwent surgery for jaw deformities at Keio University Hospital. Piriform width, nasal width, and nasomaxillary angle values measured on CT were compared among the groups using the Wilcoxon rank sum test. Nine patients had unilateral cleft lip and alveolar cleft, 19 had unilateral cleft lip and cleft palate, and 14 had bilateral cleft lip and palate (BCLCP). There were 18 controls. Mean piriform width and mean nasomaxillary angle were significantly greater in the BCLCP group than the control group (20.1±2.54 mm versus 18.8±1.35 mm, P<0.05; and 105.8±8.13 degrees versus 100.4±7.95 degrees, P<0.05, respectively). There was no significant difference in mean nasal width among the groups. Nasal bone morphology was not affected by initial cleft lip alone or by the presence or absence of cleft palate. Patients with bilateral cleft lip and palate have a wider and lower nose than those without cleft deformity and might benefit more from reduction of the bony nasal width than from treatment of the soft tissues.
Three-Part Analysis for Designing Nasal Alar Reduction Surgery in Asian Patients
Authors: Yang Jie , Dai Chuan-Chang , Yu Bao-Fu
Published: September 2024

Background:

The external nasal alar reduction can be associated with many complications, such as nostril malformation and significant scarring. The authors proposed a 3-part analysis method for the design of nasal alar reduction surgery with the aim of improving nasal alar morphology more precisely.

Methods:

The 3-part analysis was based on the patient’s flared nose, wide nasal base, and drooping ala, respectively. We included 20 patients who underwent this surgery between January 2021 and January 2022. The visual analog scale (VAS) and the Stony Brook Scar Evaluation Scale (SBSES) were used to assess postoperative scar outcomes. The preoperative and postoperative ratios of the interalar distance to intercanthal distance and nostril shape were analyzed. Patient-reported satisfaction with the esthetic outcome was also assessed.

Results:

All operations were successfully completed. There were no postoperative complications, such as wound infection or skin necrosis. Both VAS and SBSES assessment of postoperative scarring suggested keloid hyperplasia at 3 months postoperatively. At 12 months postoperatively, the scarring was insignificant and improved significantly over 3 months postoperatively. The mean ratio of the interalar distance to intercanthal distance decreased significantly from 1.15 preoperatively to 1.01 postoperatively (P<0.05). The shape of the patient’s nostrils was also significantly improved after surgery compared with the preoperative period. Patient-reported satisfaction after surgery was high at long-term follow-up.

Conclusions:

The 3-part analysis to design an external nasal alar reduction procedure can accurately improve the morphology of nasal flaring, excessively wide nasal alar base, and nasal ptosis in Asian patients.

Level of Evidence:

IV.
Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus
Authors: Ishaq Nabila , Zhang Mimi , Gao Luyao , Ilan Micha , Li Zhiyong
Published: September 2024

A novel bacterium, designated as MI-GT, was isolated from marine sponge Diacarnus erythraeanus. Cells of strain MI-GT are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-GT is able to grow at 10–40 °C (optimum, 28 °C), with 1.0–8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5–9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-GT shows 98.35, 97.32 and 97.25% similarity to those of Microbulbifer variabilis Ni-2088T, Microbulbifer maritimus TF-17T and Microbulbifer echini AM134T, respectively. Phylogenetic analysis also exhibits that strain MI-GT falls within a clade comprising members of the genus Microbulbifer (class Gammaproteobacteria). The genome size of strain MI-GT is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MI-GT and other type strains are 71.61–76.44% (ANIb), 83.27–84.36% (ANIm) and 13.4–18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-GT and other closely related species are 52.04–59.13% and 67.47–77.21%, respectively. The major cellular fatty acids of MI-GT are composed of summed feature 8 (C18 : 1
ω7c or C18 : 1
ω6c), iso-C11 : 0 3-OH, iso-C15 : 0, C16 : 0, and summed feature 9 (C17 : 1 iso ω9c or C16 : 0 10-methyl). The polar lipids of MI-GT mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-GT is considered to represent a novel species of genus Microbulbifer, for which the name Microbulbifer spongiae sp. nov. is proposed. The type strain is MI-GT (=MCCC 1K07826T=KCTC 8081T).
Assessing antimicrobial resistance profiles of Salmonella enterica in the pork production system
Authors: Prasertsee Teerarat , Prachantasena Sakaoporn , Tantitaveewattana Phakawat , Chuaythammakit Podjanakorn , Pascoe Ben , Patchanee Prapas
Published: September 2024

Introduction.
Salmonella enterica is a significant enteric pathogen affecting human and livestock health. Pork production is a common source of Salmonella contamination, with emerging multidrug resistance (MDR) posing a global health threat.

Gap statement.
Salmonella contamination and antimicrobial resistance (AMR) profiles in the pig production chain are underreported.

Aim. To investigate the prevalence of S. enterica in the pig production chain and characterise their AMR profiles.

Methodology. We collected 485 samples from pig farms, a standard pig abattoir and retail markets in Patthalung and Songkhla provinces in southern Thailand. Antimicrobial susceptibility testing was performed on these samples, and AMR profiles were determined.

Results.
S. enterica was detected in 68.67% of farm samples, 45.95% of abattoir samples and 50.67% of retail market samples. Analysis of 264 isolates, representing 18 serotypes, identified S. enterica serotype Rissen as the most prevalent. The predominant resistance phenotypes included ampicillin (AMP, 91.29%), tetracycline (TET, 88.26%) and streptomycin (STR, 84.47%). Over 80% of isolates showed resistance to three or more antimicrobial classes, indicating MDR. The AMP–STR–TET resistance pattern was found in nearly 70% of all MDR isolates across the production chain.

Conclusions. The high prevalence of MDR is consistent with extensive antimicrobial use in the livestock sector. The presence of extensively resistant S. enterica highlights the urgent need for antimicrobial stewardship. Strengthening preventive strategies and control measures is crucial to mitigate the risk of MDR Salmonella spreading from farm to fork.
Current status of clinical trials for phage therapy
Authors: Uchechukwu Chidiebere F. , Shonekan Adedayo
Published: September 2024

Recently, bacteriophages have been considered alternatives to antibacterial treatments. Infectious diseases continue to plague the world because bacteria can adapt and develop defence mechanisms against antibiotics. The growing incidence of antibiotic-resistant bacterial infections necessitated the development of new techniques for treating bacterial infections worldwide. Clinical trials have shown efficiency against antibiotic-resistant bacteria. However, scientists in future clinical trials should scrutinize phage resistance implications, assess combination strategies with antimicrobial agents and address challenges in phage therapy delivery for effective implementation.
Genomic study substantiates the intensive care unit as a reservoir for carbapenem-resistant Klebsiella pneumoniae in a teaching hospital in China
Authors: Jiang Shuo , Ma Zheng , Cao Huiluo , Mo Li , Jin Jinlan , Yu Bohai , Chu Kankan , Hu Jihua
Published: September 2024

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has recently emerged as a notable public health concern, while the underlying drivers of CRKP transmission among patients across different healthcare facilities have not been fully elucidated. To explore the transmission dynamics of CRKP, 45 isolates were collected from both the intensive care unit (ICU) and non-ICU facilities in a teaching hospital in Guangdong, China, from March 2020 to August 2023. The collection of clinical data and antimicrobial resistance phenotypes was conducted, followed by genomic data analysis for these isolates. The mean age of the patients was 75.2 years, with 18 patients (40.0%) admitted to the ICU. The predominant strain in hospital-acquired CRKP was sequence type 11 (ST11), with k-locus type 64 and serotype O1/O2v1 (KL64:O1/O2v1), accounting for 95.6% (43/45) of the cases. The CRKP ST11 isolates from the ICU exhibited a low single nucleotide polymorphism (SNP) distance when compared to isolates from other departments. Genome-wide association studies identified 17 genes strongly associated with SNPs that distinguish CRKP ST11 isolates from those in the ICU and other departments. Temporal transmission analysis revealed that all CRKP isolates from other departments were genetically very close to those from the ICU, with fewer than 16 SNP differences. To further elucidate the transmission routes among departments within the hospital, we reconstructed detailed patient-to-patient transmission pathways using hybrid methods that combine TransPhylo with an SNP-based algorithm. A clear transmission route, along with mutations in potential key genes, was deduced from genomic data coupled with clinical information in this study, providing insights into CRKP transmission dynamics in healthcare settings.
Brain tumor MRI classification and identification using an image classification model via Convolutional Neural Networks
Authors: Mohanty Naitik , Sarmadi Morteza
Published: September 2024

Malignant brain tumors are generally classified to be extremely aggressive and often can be fatal when not met with immediate action. Glioblastoma Multiforme is the most common type of malignant tumor found in the brain and is extremely aggressive. For this reason, advanced detection of malignant brain tumors is necessary for optimal mitigation. Conversely, the classification of tumors during Medical Resonance Imaging can be difficult due to bodily movements resulting in the movement of the tumor. The movement of the tumor can disrupt targeted radiotherapy and can also, at times, result in treatments about radiotherapy damaging healthy areas of the brain rather than areas of the tumor. This study proposes a novel deep learning system that can identify tumors from MRI images; which can be helpful for the case of early detection, as well as being able to track tumors during active imaging; resulting in higher efficiency with targeted radiotherapy. This is done utilizing Convolutional Neural Networks (CNNs) created via deep learning frameworks. With the image classification of tumors; 97% accuracy was achieved with optimization. The tumor-classification deep learning system achieved an accuracy of 98%. Further testing is required for optimization; with this optimization, higher accuracy can be reached.
Social determinants of injection drug use-associated bacterial infections and treatment outcomes: systematic review and meta-analysis
Authors: Brothers Thomas D. , Lewer Dan , Bonn Matthew , Kim Inhwa , Comeau Emilie , Figgatt Mary , Eger William , Webster Duncan , Hayward Andrew , Harris Magdalena
Published: September 2024

Background

Individual injecting practices (e.g., intramuscular injecting, lack of skin cleaning) are known risk factors for injection drug use-associated bacterial and fungal infections; however, social contexts shape individual behaviours and health outcomes. We sought to synthesize studies assessing potential social determinants of injecting-related infections and treatment outcomes.

Methods

We searched five databases for studies published between 1 January 2000 and 18 February 18 2021 (PROSPERO CRD42021231411). We included studies of association (aetiology), assessing social determinants, substance use, and health services exposures influencing development of injecting-related infections and treatment outcomes. We pooled effect estimates via random effects meta-analyses.

Results

We screened 4,841 abstracts and included 107 studies. Several factors were associated with incident or prevalent injecting-related infections: woman/female gender/sex (adjusted odds ratio [aOR] 1.57, 95% confidence interval [CI] 1.36-1.83; n=20 studies), homelessness (aOR 1.29, 95%CI 1.16-1.45; n=13 studies), cocaine use (aOR 1.31, 95%CI 1.02–1.69; n=10 studies), amphetamine use (aOR 1.74, 95%CI 1.39-2.23; n=2 studies), public injecting (aOR 1.40, 95%CI 1.05–1.88; n=2 studies), requiring injecting assistance (aOR 1.78, 95%CI 1.40–2.27; n=8 studies), and use of opioid agonist treatment (aOR 0.92, 95%CI 0.89–0.95; n=9 studies). Studies assessing outcomes during treatment (e.g., premature hospital discharge) or afterward (e.g., rehospitalization; all-cause mortality) typically had smaller sample sizes and imprecise effect estimates.

Conclusions

Injecting-related infections and treatment outcomes may be shaped by multiple social contextual factors. Approaches to prevention and treatment should look beyond individual injecting practices towards addressing the social and material conditions within which people live, acquire and consume drugs, and access health care.
Evaluation of Sex-Related Differences in Cerebrovascular Bypass Patency: An Institutional Review of 357 Direct Cerebral Bypasses
Authors: McGuire Laura Stone , Abou-Mrad Tatiana , Du Xinjian , Alaraj Ali , Amin-Hanjani Sepideh , Atwal Gursant , Charbel Fady T.
Published: September 2024

Introduction

Demographics and comorbid conditions play a role in vascular health, yet their specific impact on cerebrovascular bypass patency remains unclear.

Methods

An institutional database of 357 patients with intracranial bypass procedures between 08/2001-05/2022 was retrospectively reviewed. Patients with bypass for all causes (e.g., aneurysm, atherosclerotic disease, Moyamoya disease) were included. Medical history, surgical technique, and flow-related measurements (intraoperatively and on quantitative MRA at follow-up) were compared across biological sex and in relation to bypass patency.

Results

Of 357 patients, 141 were male (39.5%) and 216 were female (60.5%) with average age 49.0+/-16.7. Bypass patency at last follow-up was 84.4% for men vs. 69.2% for women (p=0.001). Significant differences were seen in underlying diagnoses, with more aneurysm and Moyamoya cases represented in female sex (p<0.001); irrespective of diagnosis, lower patency rates were seen in women when considering bypass for aneurysm (p=0.032), Moyamoya disease (p=0.035), and for atherosclerotic disease (p=0.159). Medical comorbidities were seen at higher rates in men, with comorbidity score 2.7 vs. 2.1 (p<0.001). Cut flow was higher in men 59.2 vs. 51.1 (p=0.028), but no significant differences were seen in intraoperative bypass flow, cut flow index (CFI), or follow-up QMRA. After removing cases using interposition grafts, similar differences were redemonstrated. Propensity score matched analysis found females have a 2.71 higher chance of bypass occlusion after adjusting for CFI (p=0.017, 95% CI: 1.19-6.18).

Conclusion

Biological sex appears to play a significant role in bypass patency, across diagnoses. Women were significantly less likely to have patent bypasses at last follow-up, despite having less medical comorbidities than men and despite having similar intraoperative and perioperative flows. Further study is required to better elucidate the influence of sex on long-term bypass patency.
Prevalence and Determinants of E-Cigarette Use Among Diploma Students in a Vocational College: A Cross-Sectional Study
Authors: Mohd Shoaib Siti Munisah , Ahmad Norliza , Mahmud Aidalina
Published: September 2024

Introduction

The prevalence of e-cigarette use is increasing globally, particularly among young adults which can predispose them to various health risks. This study aimed to determine the prevalence and factors associated with e-cigarette use among diploma students in a vocational college in a state in Malaysia.

Methodology

A cross-sectional study using probability proportionate to size sampling was conducted among 700 diploma students at a vocational college in Malaysia. A validated, self- administered questionnaire was distributed through the online method from April to May 2024. Bivariate analysis was done using Pearson’s chi-square test or Fisher’s exact and simple logistic regression. Multivariable analysis was performed using multiple logistic regression for variables with a p<0.25 in the bivariate analysis. A value of p<0.05 was considered statistically significant, with a 95% confidence interval.

Results

The response rate was 87.7% with the prevalence of e-cigarette use was 29.0%. Factors significantly associated with e-cigarette use included male (aOR = 5.2, 95% CI: 2.7- 10.1), other races (aOR = 83.1, 95% CI: 2.2-3146.3), perceived e-cigarette aids in quit smoking (aOR = 1.6, 95% CI: 1.2-2.1), perceived e-cigarette does not contain the toxic chemicals found in conventional cigarette (aOR = 1.4, 95% CI: 1.0-2.0), having close friends who use conventional cigarette (aOR = 2.1, 95% CI: 1.0-4.1) or e-cigarette (aOR = 8.0, 95% CI: 2.3- 28.1), e-cigarette exposure on television (aOR = 2.1, 95% CI: 1.0-4.2), positive attitude towards e-cigarette (aOR = 1.2, 95% CI: 1.1-1.2), higher willingness to use (aOR = 1.2, 95% CI: 1.0-1.3), and higher intention to use (aOR = 1.4, 95% CI: 1.2-1.5).

Conclusion

Factors associated with e-cigarette use among diploma students included being male, other races (Bumiputera Sabah and Sarawak), positive health risks perceptions, peer influence, and exposure to e-cigarettes on television. Targeted interventions addressing these factors may be more effective in changing social norms and reducing e-cigarette use among this population.
Macrophages redeploy functional cancer cell surface proteins following phagocytosis
Authors: Volk Regan F. , Casebeer Sara W. , Condon Andrew C. , Zirak Bahar , Manon Nayelis , Irkliyenko Iryna , Liao Huajun , Tao Shao , Pollini Tommaso , Ramani Vijay , Maker Ajay V. , Fidler Trevor , Goodarzi Hani , Zaro Balyn W.
Published: September 2024

Macrophage-mediated phagocytosis is a vital innate immune process altered in cancer. We show here that tumor-associated macrophages (TAMs) redeploy intact cell surface proteins from cancer cells to their own cell surface. We initially observed the canonical epithelial cancer surface marker EpCAM on the surface of TAMs in primary human solid tumors but not paired peripheral blood macrophages. In a murine model of metastatic breast cancer, we also observed EpCAM on the surface of primary TAMs that have phagocytosed breast cancer cells. In a model of a myeloproliferative neoplasm, we again found engulfed cell-derived surface proteins on the surface of macrophages following phagocytosis. A co-culture system and proteomics assay that tags proteins based on their cell-of-origin revealed hundreds of cell surface proteins synthesized in cancer cells are present and fully intact on the surface of macrophages following phagocytosis. Using a biotin transfer assay, we determined that these proteins were on the surface of the cancer cell prior to redeployment by the macrophage following phagocytosis. Furthermore, macrophages that redeploy a neutral amino acid transporter correspondingly show increased transport of an unnatural amino acid substrate. Widespread acquisition of proteins from engulfed cells may contribute to two critical TAM phenotypes: the inability to phagocytose and reprogrammed metabolism.
Independent evolution of ipecac alkaloid biosynthesis
Authors: Colinas Maite , Morweiser Clara , Dittberner Olivia , Chioca Bianca , Alam Ryan , Leucke Helena , Nakamura Yoko , Guerrero Delia Ayled Serna , Heinicke Sarah , Kunert Maritta , Wurlitzer Jens , Ploss Kerstin , Hong Benke , Grabe Veit , Lopes Adriana A. , O’Connor Sarah E.
Published: September 2024

Ipecac alkaloids are medicinal monoterpenoid-derived tetrahydroisoquinoline alkaloids found in two distantly related plants:Carapichea ipecacuanha(Gentianales) andAlangium salviifolium(Cornales). We have elucidated ipecac alkaloid biosynthesis in both species, conclusively demonstrating that biosynthesis of the structurally complex ipecac alkaloid protoemetine has evolved independently. We show that although protoemetine biosynthesis proceeds via the same chemical logic in both species, each plant uses a distinct monoterpene precursor. Moreover, we provide evidence that both plants initiate ipecac biosynthesis by a non-enzymatic Pictet-Spengler reaction, and we elucidate the biosynthetic fate of both the 1Rand 1Sstereoisomers that are produced in this non-stereoselective reaction. Phylogenetic analyses clearly show independent pathway evolution through parallel and convergently evolved enzymes. This work provides insight into how nature can capitalize on highly reactive starting substrates, the manner in which multi-step pathways can arise, and also lays the foundation for metabolic engineering of these important medicinal compounds.
Molecular changes in agroinfiltrated leaves ofNicotiana benthamianaexpressing suppressor of silencing P19 and coronavirus-like particles
Authors: Hamel Louis-Philippe , Poirier-Gravel Francis , Paré Marie-Ève , Tardif Rachel , Comeau Marc-André , Lavoie Pierre-Olivier , Langlois Andréane , Goulet Marie-Claire , Michaud Dominique , D’Aoust Marc-André
Published: September 2024

The production of coronavirus disease 2019 vaccines can be achieved by transient expression of the Spike (S) protein of Severe Acute Respiratory Syndrome Coronavirus 2 in agroinfiltrated leaves ofNicotiana benthamiana. Relying on bacterial vectorAgrobacterium tumefaciens, this process is favored by the co-expression of viral silencing suppressor P19. Upon expression, the S protein enters the cell secretory pathway, before being trafficked to the plasma membrane where formation of coronavirus-like particles (CoVLPs) occurs. We previously characterized effects of influenza virus hemagglutinin forming VLPs through similar processes. However, leaf samples were only collected after six days of expression and it remains unknown whether influenza VLPs and CoVLPs induce similar responses. Here, time course sampling was used to profile responses ofN. benthamianaleaf cells expressing P19 only, or P19 along with the S protein. The latter triggered early, but transient activation of the unfolded protein response and waves of transcription factor genes involved in immunity. Accordingly, defense genes were induced with different expression kinetics, including those promoting lignification, terpene biosynthesis, and oxidative stress. Crosstalk between stress hormone pathways also occurred, notably leading to the repression of jasmonic acid biosynthesis genes after agroinfiltration, and dampening of salicylic acid-inducible responses upon S protein accumulation. Overall, influenza VLP- and CoVLP-induced responses broadly overlapped, suggesting nanoparticle production to have the most effects on plant immunity, regardless of the virus surface proteins expressed. Taking advantage of RNAseq inferences, we finally show the co-expression of Kunitz trypsin inhibitors to reduce CoVLP-induced defense and leaf symptoms, with no adverse effect on plant productivity.
Do Protein Language Models Learn Phylogeny?
Authors: Tule Sanjana , Foley Gabriel , Bodén Mikael
Published: September 2024

Deep machine learning demonstrates a capacity to uncover evolutionary relationships directly from protein sequences, in effect internalising notions inherent to classical phylogenetic tree inference. We connect these two paradigms by assessing the capacity of protein-based language models (pLMs) to discern phylogenetic relationships without being explicitly trained to do so. We evaluate ESM2, ProtTrans and MSA-Transformer relative to classical phylogenetic methods, while also considering sequence insertions and deletions (indels) across 114 Pfam datasets. The largest ESM2 model tends to outperform other pLMs (including the multimodal ESM3) by recovering phylogenetic relationships among homologous protein sequences in both low- and high-gap settings. pLMs agree with conventional phylogenetic methods in general, but more so for protein families with fewer implied indels, highlighting indels as a key factor differentiating classical phylogenetics from pLMs. We find that pLMs preferentially capture broader as opposed to finer evolutionary relationships within a specific protein family, where ESM2 has a sweet spot for highly divergent sequences, at remote distance. Less than 10% of neurons are sufficient to broadly recapitulate classical phylogenetic distances; when used in isolation the difference between the paradigms is further diminished. We show these neurons are polysemantic, shared among different homologous families but never fully overlapping. We highlight the potential of ESM2 as a complementary tool for phylogenetic analysis, especially when extending to remote homologs that are difficult to align and imply complex histories of insertions and deletions.
Epitranscriptome Mapping of m6A RNA Modifications in Glioma Tumor Tissue
Authors: Batool Syeda Maheen , Khan Saad Murtaza , Muralidharan Koushik , Escobedo Ana K. , Lee Hanna , Ekanyake Emil , Hsia Tiffaney , Carter Bob S. , Balaj Leonora
Published: September 2024

Glioma represents the most common primary central nervous system (CNS) neoplasm in adults. IDH1 mutation is recognized as a hallmark alteration with important diagnostic and prognostic implications. There is considerable evidence for global DNA hypermethylation induced secondary to IDH mutation. However, there is limited understanding of the RNA methylation patterns and its role in glioma biology. In this study, we performed transcriptome wide profiling of N6-methyladenosine (m6A) modifications across IDH mutant (n = 8) and wild-type (n = 7) gliomas using Oxford Nanopore Technologies’ direct RNA sequencing platform. Our approach enabled high-depth coverage of native transcripts, revealing nearly twice as many full-length transcripts in IDH mutant gliomas compared to wild-type. Notable differences in alternative splicing were observed across glioma subtypes, with truncated and non-coding isoforms more prevalent in glioblastoma (GBM). We further identified significant changes in isoform usage within key metabolic (NAMPT, PKM) and immune (CD63, CD151, CD81) pathways. Chromosomal distribution of m6A sites showed a higher prevalence of m6A modifications in IDH mutant gliomas, with the most pronounced differences on chromosomes 19 and 16. Further stratification by TERT, MGMT, and TP53 mutations revealed similar patterns of increased m6A site numbers in mutant groups, highlighting the importance of integrating epigenomic and epitranscriptomic data in glioma research. These findings highlight the role of m6A modifications in the metabolic reprogramming unique to IDH mutant gliomas, providing insights into potential mechanisms of tumorigenesis and therapeutic resistance.
Perceptions of students on artificial intelligence-generated content avatar utilization in learning management system
Authors: Tan Saw Fen
Published: September 2024

Purpose

This study aims to explore students’ perceptions of the use of an artificial intelligence-generated content avatar (AIGC avatar) within a learning management system (LMS).

Design/methodology/approach

This qualitative research involved seven postgraduate students. Data were collected through individual, in-depth interviews. The videos of the AIGC avatar, created using Leonardo, ChatGPT and Heygen, were uploaded to the LMS to communicate with students for the purposes of a welcome note, assignment guide, assignment feedback, tutorial reminders and preparation as well as to provide encouragement and study tips. Students were interviewed at the end of the semester.

Findings

The findings of this study indicated that the majority of participating students held positive perceptions regarding the use of the AIGC avatar in the LMS. They reported that it enhanced their perceived instructor’s social presence and motivation to learn. The assignment guide and feedback were particularly valued by the participants. While some students noted the AIGC avatar’s lack of naturalness, others appreciated the clear and professional speech it delivered.

Research limitations/implications

The study was confined to seven students from a single course at one institution, which may limit the generalizability of the findings. Future research could involve a larger and more diverse group of participants.

Practical implications

The findings may offer education providers an alternative solution for engaging students in an LMS.

Originality/value

This study highlights the potential of AIGC avatars to replace text-based communication in LMS and enhance students’ perceived instructor social presence.
The role of HR practices, big data analytics capabilities and supply chain resilience in achieving firm disaster immunity: the moderating effect of data-driven culture
Authors: Yamin Mohammad Ali Yousef
Published: September 2024

Purpose

The rising global competition and uncertainty in business environment has led logistics firms to redesign supply chain strategies which boost disaster immunity. Therefore, the current study develops an integrated research framework that combines big data analytics capability, HR practices, resilience and resource reconfiguration to investigate logistic firm disaster immunity. In addition to that, the moderating effect of data-driven culture is tested between disaster immunity and supply chain performance.

Design/methodology/approach

The research design of this study is based on quantitative techniques and followed by positivist research paradigm. Data are collected through structured questionnaires. Overall, 219 managers have participated in this logistics research survey. Data are computed with structural equation modeling approach.

Findings

Statistical findings have revealed that collectively HR practices, innovation capability, proactive capability, reactive capability, resource configuration and supply chain resilience explained R2 71.5% variance in disaster immunity. Therefore, in the extended model, disaster immunity and data-driven culture have depicted R2 49.2% variance in manufacturing firm supply chain performance.

Practical implications

The integration of big data analytics capability factors with HR practices, supply chain resilience and resource configuration has enriched logistic literature in the disaster immunity setting. Practically, this study has concluded that factors such as data analytics capabilities, resource reconfiguration, supply chain resilience and HR practices need policymakers’ attention to boost disaster immunity and supply chain performance.

Originality/value

This research is original as it unveils three core factors of big data analytics capability, namely proactive, reactive and innovative capability, and examines firm disaster immunity. Similarly, research is unique as it combines capability factors with resilience, HR practices and resource reconfiguration and investigates logistic firm disaster immunity.
Identifying high-growth firms in five European countries: micro firms vs. larger firms
Authors: Rico-Belda Paz , Cabrer-Borrás Bernardí
Published: September 2024

Purpose

This study uses an extensive sample of firms from Germany, France, UK, Portugal and Spain with the aim of obtaining conclusive results on the determinants that drive a firm to be high-growth firm (HGF). This sample includes micro firms, which are not generally considered in the literature. There are several reasons to take them into account: not excluding an important part of the business fabric, the results can be extrapolated, the study can show if micro firms also present high growth and if there are differences in the factors that determine the probability of being an HGF between both segments of firms.

Design/methodology/approach

A multivariate dynamic model of binary choice is used to analyse the probability of a company being classified as high growth. Then, with the Blinder and Oaxaca decomposition, the differences in the probability of being an HGF between micro firms and non-micro firms are studied.

Findings

The results show that HGFs demonstrate persistence, and younger firms are more likely to be HGFs. Micro firms also register high growth, although they are less dynamic and show a negative differential with respect to larger firms as highlighted by the characteristic component.

Originality/value

In some countries, such as Spain and Portugal, micro firms predominate, and these tend to be less dynamic, so to identify how to improve business dynamics, the factors that limit the growth of this type of company must first be determined. In this paper, in line with Acs and Mueller (2008), we therefore include firms with less than ten employees so as not to exclude an important part of the business fabric and to ascertain whether this type of firm also shows high growth.
The impact of digital transformation on achieving outstanding performance in educational administration
Authors: Khatir Nadjet , Madani Hassiba
Published: September 2024

Purpose

The present study aims to analyze the impact of digital transformation on achieving outstanding performance in educational administration, improving and developing electronic services and facilitating beneficiaries’ access to services.

Design/methodology/approach

This study applied descriptive/analytical quantitative and qualitative methodologies to a sample of 206 employees from an educational administration. Confirmatory inferential analysis was conducted to investigate the relationship and mutual impact between the variables under examination by Structural Equation Modeling requirements.

Findings

The study found that the model effectively explained the phenomenon being studied with digital transformation efforts in infrastructure, human resources and culture, as hypothesized. However, an unexpected negative relationship was found between the transformation strategy and outstanding performance. Interviews with the participants confirmed gradual improvements in various aspects of the digital transformation.

Practical implications

This study underscores the immediate and tangible benefits of transitioning from traditional to advanced electronic governments. This transformation is necessary and highly advantageous, as it bolsters the administration’s ability to meet technical, professional and human requirements, elevating the educational system’s overall performance.

Originality/value

This study stands out for its unique focus on digital transformation as an independent variable, a perspective evaluated using four indicators. The study’s exploration of how these factors influence the performance of the directorate of education is a significant contribution to the field. The study’s approach saves time, effort and money and enhances employee performance and task completion speed with good quality and efficiency, thereby improving services for the educational system’s beneficiaries.
Way to achieve sustainable benefits of ISO 9001 practices
Authors: Sherwani Karwan H. , Demir Ahmet , Maroof Lubna
Published: September 2024

Purpose

The primary aim of the current study is to validate the theoretical model presented by Demir (2021a, b, c) via empirical evidence. In this respect, the study intends to offer a holistic pathway for obtaining both external and internal advantages from the implementation of ISO 9001, with a particular emphasis on developing countries.

Design/methodology/approach

The research utilized an empirical methodology to investigate the research objective. Data were collected from various sources, including employees and managers of the various companies. In this context, a model was developed, and 170 data points were collected from businesses in the Kurdistan region of Iraq in order to test the hypotheses in this model.

Findings

After the collected data passed the reliability and validity test, the hypotheses designed were tested by applying the partial least squares method. When the results were examined, it was observed that organizational culture and organizational learning variables were the two key antecedents that these factors would emerge after applying ISO 9001 practices with discipline for a certain period of time and that organizational benefits could be obtained only as a result of them. Detailed results and suggestions were given to managers and theorists as a result of the analysis.

Originality/value

This study contributes to the literature as an empirical application of the theoretical work written by Demir in 2021. Demir's work, which produced a theoretical concept based on many empirical and theoretical studies done before, still needs much more empirical work in developing countries.
Impact of ESG ratings on Chinese market performance during the COVID-19 crisis
Authors: Zhou Chensong , Wang Kuo , Liu Ruixin , Shu Ao , Wang Dailing
Published: September 2024

Purpose

This study investigates the role of environmental, social and governance (ESG) policies in enhancing the resilience of Chinese firms during the COVID-19 crisis. By analyzing data from over 3,069 publicly listed companies, the research aims to elucidate the impact of robust ESG practices on stock market performance and operational outcomes during economic disruptions.

Design/methodology/approach

Using a dataset comprising ESG scores and financial performance metrics of Chinese firms, we conduct an empirical analysis to assess the correlation between ESG practices and corporate resilience during the COVID-19 pandemic. The study focuses on evaluating the individual contributions of the social and governance components to overall firm performance.

Findings

The analysis reveals that firms with higher ESG scores, especially in social and governance aspects, exhibit superior stock market performance and operational outcomes during the pandemic. Companies with strong governance mechanisms demonstrate more pronounced benefits, including better long-term sales growth and return on equity (ROE). The findings highlight the critical role of ESG policies in ensuring corporate stability and competitive advantage during crises.

Originality/value

This article provides a comprehensive overview of the impact of corporate ESG ratings on corporate trust and offers a detailed discussion on the protective role of ESG/CSR on firm value during crises, thus providing an original literature contribution.
Corporate reporting through social media: a comprehensive literature review
Authors: Hamade Malak , Hussainey Khaled , Albitar Khaldoon
Published: September 2024

Purpose

This systematic review aims to comprehensively explore the existing literature on the use of corporate communication within the realm of social media.

Design/methodology/approach

A total of 136 peer-reviewed journal articles are explored and analysed using both performance and bibliometric analysis.

Findings

This review identifies five main findings: (1) trends in corporate social media research that highlight the growth trajectory of research on social media use for corporate disclosure, (2) geographical coverage of studies indicating the concentration of research in certain regions, such as the USA, followed by China and the UK, with notable gaps in others, such as developing countries, (3) theoretical frameworks employed demonstrate that various theoretical frameworks are utilized, although a significant portion of the studies do not specify any theoretical underpinning, (4) social media platforms studied, confirming Twitter to be the most studied channel followed by Facebook and (5) thematic analysis of articles on disclosure type that categorized the articles using bibliometric analysis into five themes of disclosure: general disclosure, corporate social responsibility-related information, financial information, CEO announcements and strategic news communication. A subsequent cross-theme analysis classifies disclosure determinants and consequences of corporate social media usage.

Originality/value

Through a comprehensive and systematic analysis of existing research, this review offers novel insights into the current state of corporate communication on social media. It consolidates current knowledge, highlights under-explored areas in the existing literature and proposes new directions and potential avenues for future research.
“It’s that gut feeling isn’t it”: general practitioner experiences of safeguarding in care homes for older people
Authors: White Caroline , Alton Elisabeth
Published: September 2024

Purpose

General practitioners (GPs) play an important role in adult safeguarding. However, their experiences of this role have received scant attention in the UK and internationally. This study aimed to explore their experiences of safeguarding within care homes (CHs) for older adults where, as they are among the practitioner groups most frequently visiting, they are well-positioned to contribute to bringing abuse and neglect to light.

Design/methodology/approach

This study involved qualitative methods. Semi-structured interviews were undertaken with 12 GPs to explore their experiences of safeguarding in CHs. This included the issues that prompted their concerns, actions taken in response, difficulties and dilemmas experienced, CH safeguarding during the COVID-19 pandemic. Thematic analysis was undertaken, taking an inductive approach to the analysis.

Findings

GPs seldom witnessed what they considered clear signs of abuse/neglect, but instead more frequently observed “softer”, more ambiguous signs. They undertook a range of actions in response to these, in addition to formally reporting concerns. They experienced difficulties and dilemmas in respect of the hidden nature of abuse, uncertainty about the legitimacy of their concerns and thresholds for reporting, as well as dilemmas associated with the need to preserve essential working relationships with CHs, yet avoiding collusion with staff.

Originality/value

Although GPs play an important role in identifying signs of abuse/neglect, this role has been little explored to date. Their safeguarding role within CHs has been especially neglected, and the authors are aware of no other studies that have explored GPs’ roles and experiences in this context, within or outwith the UK.
Assessing the sovereign-bank interdependence in Eurozone core countries
Authors: Capasso Salvatore , D’Uva Marcella , Fiorelli Cristiana , Napolitano Oreste
Published: September 2024

Purpose

The aim of this study is to determine whether financial contagion is transmitted through macroeconomic fundamentals, not only in weaker countries but also in strong European Monetary Union (EMU) economies.

Design/methodology/approach

This study conducts, for the first time, an analysis of the spillover effects resulting from a shock to Italian sovereign risk on the banking systems and credit default swaps (CDS) of five EMU core countries during the period 2012–2018, employing a global vector autoregressive (GVAR) approach. Spatial interdependence is quantified through the cross-country distance in the deficit-to-gross domestic product (GDP) ratio.

Findings

The findings reveal the existence of both a “doom-loop” between banks and sovereign bonds and a “bad neighbours” effect. The susceptibility to spillovers is notably higher in economies displaying a larger deficit-to-GDP ratio. These results suggest that differences in fiscal fundamentals could drive financial contagion even within core countries, indicating a need for evaluating the stability of the entire EMU system.

Originality/value

Unlike previous studies, we utilize the cross-country distance in the deficit-to-GDP ratio as a measure of fiscal fundamentals distance for the countries under investigation. To the best of our knowledge, our study is the first to analyse this matter in EMU core countries using a GVAR methodology.