bluuebunny/crossref_metadata_2025 huggingface dataset:
Lelliottia amnigena recovered from the lung of a harbour porpoise, and comparative analyses with Lelliottia spp.
Authors: Negus David , Foster Geoffrey , Hoyles Lesley
Published: November 2023

Strain M1325/93/1 (herein referred to by our laboratory identifier, GFKo1) of

Lelliottia amnigena

was isolated from the lung of a harbour porpoise in 1993. The genome sequence and antimicrobial resistance profile (genomic, phenotypic) of the strain were generated, with the genomic data compared with those from closely related bacteria. We demonstrate that the recently described chromosomally encoded AmpC β-lactamase bla
LAQ is a core gene of

L. amnigena

, and suggest that new variants of this class of lactamase are encoded by other members of the genus

Lelliottia

. Although presence of bla
LAQ is ubiquitous across the currently sequenced members of

L. amnigena

, we highlight that strain GFKo1 is sensitive to ampicillin and cephalosporins. These data suggest that bla
LAQ may act as a useful genetic marker for identification of

L. amnigena

strains, but its presence may not correlate with expected phenotypic resistances. Further studies are required to determine the regulatory mechanisms of bla
LAQ in

L. amnigena

.
Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov., isolated from coastal sediment
Authors: Zhou Zi-Yang , An Jing , Jia Ya-Wei , Xuan Xiao-Qi , Du Zong-Jun
Published: November 2023

Two novel rod-shaped, Gram-stain-negative, aerobic and non-motile bacterial strains, designated M39T and C2-7T, were isolated from the coastal sediment of Xiaoshi Island, Weihai, PR China. Growth of strain M39T occurred at 15–37 °C, at pH 6.0–9.0 and in the presence of 1.0–9.0 % (w/v) NaCl. Strain C2-7T grew at 15–40 °C, at pH 6.0–8.0 and in the presence of 0.5–8.0 % (w/v) NaCl. Phylogenetic analysis based 16S rRNA gene sequences revealed that strains M39T and C2-7T belong to the phylum

Bacteroidota

. Based on the results of 16S rRNA gene sequence analysis, the closest relative of strain M39T was Robiginitalea marina KCTC 92035T (95.4 %), and the closest relative of strain C2-7T was

Algoriphagus namhaensis

DPG-3T (97.0 %). The percentage of conserved protein and average nucleotide identity values between strain M39T and some species of the genus

Robiginitalea

were 66.9–77.6% and 69.3–71.0 %, respectively, while those between strain C2-7T and some species of the genus

Algoriphagus

were 68.0–70.1% and 56.1–72.6 %, respectively. The major cellular fatty acids (>10 %) of strain M39T consisted of iso-C15 : 1 F, iso-C15 : 0 and iso-C17 : 0 3-OH, while those of strain C2-7T were iso-C15 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. MK-6 was the only respiratory quinone that was compatible with the genus of strain M39T. The predominant menaquinone of strain C2-7T was MK-7. The major polar lipids of strain M39T were phosphatidylethanolamine and glycolipids, and those of strain C2-7T were phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. The DNA G+C contents of strains M39T and C2-7T were 46.9 and 40.8 mol%, respectively. Based upon the results presented in this study, strains M39T and C2-7T represent novel species of the genera

Robiginitalea

and

Algoriphagus

, respectively, for which the names Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov. are proposed with the type strains M39T (=MCCC 1H00498T=KCTC 92014T) and C2-7T (=MCCC 1H00414T=KCTC 92027T).
Sample-efficient Antibody Design through Protein Language Model for Risk-aware Batch Bayesian Optimization
Authors: Wang Yanzheng , Wang Boyue , Shi Tianyu , Fu Jie , Zhou Yi , Zhang Zhizhuo
Published: November 2023

Antibody design is a time-consuming and expensive process that often requires extensive experimentation to identify the best candidates. To address this challenge, we propose an efficient and risk-aware antibody design framework that leverages protein language models (PLMs) and batch Bayesian optimization (BO). Our framework utilizes the generative power of protein language models to predict candidate sequences with higher naturalness and a Bayesian optimization algorithm to iteratively explore the sequence space and identify the most promising candidates. To further improve the efficiency of the search process, we introduce a risk-aware approach that balances exploration and exploitation by incorporating uncertainty estimates into the acquisition function of the Bayesian optimization algorithm. We demonstrate the effectiveness of our approach through experiments on several benchmark datasets, showing that our framework outperforms state-of-the-art methods in terms of both efficiency and quality of the designed sequences. Our framework has the potential to accelerate the discovery of new antibodies and reduce the cost and time required for antibody design.
Poisoning scientific knowledge using large language models
Authors: Yang Junwei , Xu Hanwen , Mirzoyan Srbuhi , Chen Tong , Liu Zixuan , Ju Wei , Liu Luchen , Zhang Ming , Wang Sheng
Published: November 2023

Biomedical knowledge graphs constructed from scientific literature have been widely used to validate biological discoveries and generate new hypotheses. Recently, large language models (LLMs) have demonstrated a strong ability to generate human-like text data. While most of these text data have been useful, LLM might also be used to generate malicious content. Here, we investigate whether it is possible that a malicious actor can use LLM to generate a malicious paper that poisons scientific knowledge graphs and further affects downstream biological applications. As a proof-of-concept, we develop Scorpius, a conditional text generation model that generates a malicious paper abstract conditioned on a promoting drug and a target disease. The goal is to fool the knowledge graph constructed from a mixture of this malicious abstract and millions of real papers so that knowledge graph consumers will misidentify this promoting drug as relevant to the target disease. We evaluated Scorpius on a knowledge graph constructed from 3,818,528 papers and found that Scorpius can increase the relevance of 71.3% drug disease pairs from the top 1000 to the top 10 by only adding one malicious abstract. Moreover, the generation of Scorpius achieves better perplexity than ChatGPT, suggesting that such malicious abstracts cannot be efficiently detected by humans. Collectively, Scorpius demonstrates the possibility of poisoning scientific knowledge graphs and manipulating downstream applications using LLMs, indicating the importance of accountable and trustworthy scientific knowledge discovery in the era of LLM.
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling
Authors: Matchado Monica Steffi , Rühlemann Malte , Reimeiter Sandra , Kacprowski Tim , Frost Fabian , Haller Dirk , Baumbach Jan , List Markus
Published: November 2023

Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type 2 diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.
The saccadic repertoire of larval zebrafish reveals kinematically distinct saccades that are used in specific behavioural contexts
Authors: Dowell Charles K. , Lau Joanna Y. N. , Bianco Isaac H.
Published: November 2023

Saccades are rapid eye movements that are used by all species with good vision. They have been extensively studied, especially in vertebrates, and are understood to be controlled by a conserved brainstem circuit. However, despite the fact that saccades play important roles during diverse visually guided behaviours, little is known about whether their properties, including the manner in which they are coordinated with head/body movements, vary in the context of different visuomotor tasks. Here, we characterise the saccadic repertoire of larval zebrafish and identify five saccade types, defined by systematic differences in kinematics and binocular coordination. Each type was differentially expressed during visually guided behaviours. Conjugate saccades form a large group that are used in at least four contexts: Fast phases of the optokinetic nystagmus, visual scanning in stationary animals, and to shift or maintain gaze during locomotion. Convergent saccades play a specialised role during hunting and are coordinated with body movements to foveate prey. Furthermore, conjugate and convergent saccades follow distinct velocity main sequence relationships and show differences in the millisecond coordination of the eyes and body, pointing to differences in underlying neurophysiology. In summary, this study reveals unexpected diversity in horizontal saccades and predicts saccade type-specific neural activity patterns.

Highlights

Kinematic analysis of thousands of rapid eye movements reveals five saccade types.

Conjugate saccades have at least four identifiable visual functions.

Convergent saccades are coordinated with body movements to foveate prey.

Timing, kinematics and main sequence relationships indicate saccade type-specific neural control.
Self Fourier shell correlation: properties and application to cryo-ET
Authors: Verbeke Eric J. , Aurèle Gilles Marc , Bendory Tamir , Singer Amit
Published: November 2023

The Fourier shell correlation (FSC) is a measure of the similarity between two signals computed over corresponding shells in the frequency domain and has broad applications in microscopy. In structural biology, the FSC is ubiquitous in methods for validation, resolution determination, and signal enhancement. Computing the FSC usually requires two independent measurements of the same underlying signal, which can be limiting for some applications. Here, we analyze and extend on an approach proposed by Koho et al. [1] to estimate the FSC from a single measurement. In particular, we derive the necessary conditions required to estimate the FSC from downsampled versions of a single noisy measurement. These conditions reveal additional corrections which we implement to increase the applicability of the method. We then illustrate two applications of our approach, first as an estimate of the global resolution from a single 3-D structure and second as a data-driven method for denoising tomographic reconstructions in electron cryo-tomography. These results provide general guidelines for computing the FSC from a single measurement and suggest new applications of the FSC in microscopy.
Selection of experience for memory by hippocampal sharp wave ripples
Authors: Yang Wannan , Sun Chen , Huszár Roman , Hainmueller Thomas , Buzsáki György
Published: November 2023

A general wisdom is that experiences need to be tagged during learning for further consolidation. However, brain mechanisms that select experiences for lasting memory are not known. Combining large-scale neural recordings with a novel application of dimensionality reduction techniques, we observed that successive traversals in the maze were tracked by continuously drifting populations of neurons, providing neuronal signatures of both places visited and events encountered (trial number). When the brain state changed during reward consumption, sharp wave ripples (SPW-Rs) occurred on some trials and their unique spike content most often decoded the trial in which they occurred. In turn, during post-experience sleep, SPW-Rs continued to replay those trials that were reactivated most frequently during awake SPW-Rs. These findings suggest that replay content of awake SPW-Rs provides a tagging mechanism to select aspects of experience that are preserved and consolidated for future use.
Does winterkill explain contrasting demographics of winter-breeding freshwater mussel populations in Ishikari River floodplain?
Authors: Negishi Junjiro , Izumi Hokuto , Wu Junyi , Fukui Sho , Koizumi Itsuro
Published: November 2023

1. Environmental conditions bottlenecking species population demographics are less known in cold regions with harsh winters despite of global concerns of declining freshwater mussels (Unionidae). Few studies examined both cold and summer environments in attempts to promote habitat conservation of Unionidae species. 2. We identified the taxonomically confused Unionidae species using phylogenetic analysis with mtDNA (COI region) and tested the hypothesis that winter mortality is the main cause of contrasting population demographics and structures in floodplain lakes in northern Japan. Demographic surveys were conducted in two lakes, which contrasted in recruitment rates, over one year including 4-month ice-covered periods 3. Although previous studies have identified freshwater mussels as introduced Anemina arcaeformis (Heude 1877) based on morphology, this study confirmed the focal species as potentially native Buldowskia iwakawai (Suzuki, 1939). High winter mortality (30-40%) of adult mussels was found, although the mortality did not significantly differ between the populations with contrasting recruitment. 4. Surprisingly, the annual mortality was much lower in juveniles (10%) than in gravid and nongravid adult individuals (40-75%). The main inter-population difference was attributed to the higher summer mortality of gravid females, but not juveniles and non-gravid individuals, in the population with low recruitment. 5. These results collectively suggest that summer hypoxia combined with physiological stresses on females in winter is a likely population growth-limiting mechanism. To prevent a chain of adult abundance decreases in winter and high mortality of gravid mussels and newly born juveniles in summer, improvements in summer habitat conditions are necessary, while winter conditions need to be considered simultaneously. Increases in water circulation rates and alleviations of hypoxic conditions is an option for short-term habitat improvement approach. The current study sheds light on the winter-mediated mortality of freshwater mussels in shallow eutrophic floodplain lakes and contributes to improved management strategies for degraded floodplain waterbodies.
Multi-modal microvascular cerebral blood flow velocity mapping with 14T single-vessel MRI and optical microscopy in the mouse brain
Authors: Miller D. R. , Zhou X. A. , Liang S. , Xie Z. , Fu B. , Shin P. , Pian Q. , Jiang Y. , Liu A. , Tang J. , Devor A. , Yu X. , Sakadzic S.
Published: November 2023

In this study, we imaged the same penetrating cortical vessels in a mouse using ultrahigh field single-vessel MRI at 14 T and high-resolution optical microscopy imaging. The optical imaging was performed through a chronic sealed cranial window, while the single-vessel MRI was facilitated by a custom-designed, chronically implanted radiofrequency coil surrounding the window. The MRI and optical imaging were performed sequentially focused on the same penetrating cortical arterioles and surfacing venules within the whisker barrel cortex. With MRI, we obtained high-resolution multi-gradient echo (MGE) images and single-vessel phase contrast (PC) velocity maps. With optical imaging, we acquired microvascular angiograms using 2-Photon Microscopy (2PM) and Optical Coherence Tomography (OCT) and measured the blood flow velocity using Dynamic Light Scattering OCT (DLS-OCT). The MGE images, PC-based MRI velocity maps, OCT angiograms, and DLS-OCT velocity maps were coregistered with the 2PM microvascular angiograms. Using these tools, we cross-validated blood flow velocity in the penetrating cortical arterioles and surfacing venules measured by single-vessel MRI and OCT at rest. Our novel method demonstrates the possibility of combining ultrahigh field single-vessel MRI and high-resolution optical methods (e.g., 2PM and OCT) for studying brain structure and function with single microvessel precision.
NLRP3 Cys126 palmitoylation by ZDHHC7 Promotes Inflammasome Activation
Authors: Yu Tao , Hou Dan , Zhao Jiaqi , Lu Xuan , Greentree Wendy K. , Zhao Qian , Yang Min , Conde Don-Gerard , Linder Maurine E. , Lin Hening
Published: November 2023

NACHT-, leucine-rich-repeat- (LRR), and pyrin domain-containing protein 3 (NLRP3) mediates inflammasome activation in response to multiple pathogen and damage-associated molecular patterns in macrophages. Hyperactivation of NLRP3 inflammasome contributes to many human chronic inflammatory diseases. Understanding how NLRP3 inflammasome is regulated can potentially provide new strategies to treat inflammatory diseases. Here, we demonstrated that NLRP3 is palmitoylated on Cys126 by palmitoyl-acyltransferase ZDHHC7 in macrophages, which is critical for NLRP3-mediated inflammasome activation. Perturbating NLRP3 Cys126 palmitoylation by ZDHHC7 knockout, pharmacological inhibition, or modification site mutation, diminishes NLRP3 activation and the consequential Caspase-1 and Gasdermin D (GSDMD) cleavage, and IL-1β and IL-18 secretion in mouse primary macrophages and human macrophages. Furthermore, NLRP3 Cys126 palmitoylation is vital for inflammasome activationin vivo, asZdhhc7knockout, pharmacological inhibition, or NLRP3 C126A mutation protects mice from LPS-induced endotoxic shock and monosodium urate (MSU)-induced peritonitis. Mechanistically, ZDHHC7-mediated NLRP3 Cys126 palmitoylation promotes resting NLRP3 localizing on thetrans-Golgi network (TGN) and activated NLRP3 on the dispersed TGN (dTGN), which is indispensable for the recruitment and oligomerization of adaptor protein ASC after inflammasome activation. The activation of NLRP3 by ZDHHC7-mediated Cys126 palmitoylation is different from the previously reported inhibitory effect by ZDHHC12-mediated Cys841 palmitoylation, highlighting the versatile regulatory roles ofS-palmitoylation. Therefore, our study identifies a new regulatory mechanism of NLRP3 activation and suggests targeting ZDHHC7 or NLRP3 Cys126 residue as a potential therapeutic strategy to treat NLRP3-related human disorders.

Highlights

NLRP3 Cys126 is palmitoylated by ZDHHC7.

ZDHHC7 promotes NLRP3 activation in macrophages, which can be inhibited by ZDHHCs inhibitors, 2-bromopalmitate and MY-D4.

Cys126 palmitoylation of NLRP3 is critical for NLRP3 activation.

NLRP3 TGN/dTGN localization depends on ZDHHC7-mediated Cys126 palmitoylation, which is crucial for ASC recruitment and inflammasome assembly.

NLRP3 inflammasome activation by ZDHHC7 differs from ZDHHC12-mediated NLRP3 inhibition.
Feasibility assessment of LI-RADS based ultrasonic screening and CT diagnosis for hepatocellular carcinoma in low middle income setting: observation from a small study
Authors: Malindi Ephranzia Chao , Mutala Timothy Musila , Ayo Stephen Onyango , Ogaro Roseline Kerubo
Published: November 2023

In our cross-sectional study, we assessed the feasibility of using the ACR LI-RADS screening and diagnostic pathway for Hepatocellular Carcinoma (HCC) in a low-middle-income setting. HCC develops in a well-defined high-risk population, but many countries in this income category lack HCC screening and surveillance guidelines. The ACR’s practical approach through LI-RADS provides a valuable solution. Our study showed that 5.66% of patients had positive ultrasound findings, and significant lesions were detected on multiphasic CT scans. Out of these, 1.89% were diagnosed with definite HCC (LR-5 lesions). We conclude that HCC screening and diagnosis using ACR LI-RADS algorithms are feasible in such settings. However, success hinges on knowledge, skills, and technical capacity building, and it is vital to consider the downstream effects of the screening and surveillance program during the design process.

HCC screening and diagnosis using the ACR LI-RADS algorithms are feasible in low-middle-income settings, making it applicable and recommendable for even lower-income countries. However, successful implementation requires a focus on knowledge, skills, and technical capacity building.

Key points

Eligible patients for hepatocellular carcinoma screening and surveillance programs are easily identifiable in low middle income countries.

American College of Radiology’s Liver Imaging Reporting and Data Systems algorithm provides a practical approach to hepatocellular carcinoma screening and surveillance.

With proper knowledge, skills, and technical capacity, this algorithm is feasible in a low middle income setting, factoring tiered levels of care and referral systems.
A systematic review and meta-analysis of the risk of hepatitis B virus (HBV) genotypic resistance in people treated with entecavir or tenofovir
Authors: Lumley Sheila F , Delphin Marion , Mokaya Jolynne F , Tan Cedric CS , Martyn Emily , Anderson Motswedi , Li Ka Chun , Waddilove Elizabeth , Sukali Gloria , Downs Louise O , Said Khadija , Okanda Dorcas , Campbell Cori , Harriss Eli , Shimakawa Yusuke , Matthews Philippa C
Published: November 2023

Background

As nucleos/tide analogue (NA) therapy for chronic Hepatitis B virus (HBV) infection becomes more widely indicated and available, understanding drug resistance is essential. We performed a systematic review and meta-analysis to estimate the risk of genotypic resistance to tenofovir and entecavir.

Methods

We searched nine databases up to 29-Aug-23. We included studies of HBV infection featuring >10 individuals, written in English, reporting tenofovir or entecavir treatment ≥48 weeks, with assessment of HBV genotypic resistance. Data were analysed according to prior exposure history to NA, and treatment with tenofovir or entecavir. Analyses were performed in R.

Results

62 studies involving a total of 12,358 participants were included. For tenofovir, pooled resistance risk was 0.0% at all time points, whether previously NA naive (11 studies; 3778 individuals) or experienced (19 studies; 2059 individuals). For entecavir, in treatment-naive individuals (22 studies; 4326 individuals), risk of resistance increased over time to 0.9% at ≥5 years (95%CI 0.1-2.3%). Entecavir resistance was increased in NA-experienced individuals (18 studies;1112 individuals), to 20.1% (95%CI 1.6-50.1%) at ≥5 years. There was a lack of consistent definitions, poor global representation and insufficient metadata to support subgroup analysis.

Discussion

Based on existing data, tenofovir has an excellent resistance profile. More resistance is seen with entecavir, particularly in treatment-experienced groups. Due to data gaps, we may have under-estimated the true risk of resistance. Robust prospective data collection is crucial as treatment is rolled out more widely.
Skeletal muscle energetics explain the sex disparity in mobility impairment in the Study of Muscle, Mobility and Aging (SOMMA)
Authors: Kramer Philip A. , Coen Paul M. , Cawthon Peggy M. , Distefano Giovanna , Cummings Steven R. , Goodpaster Bret H. , Hepple Russell T. , Kritchevsky Stephen B. , Shankland Eric G. , Marcinek David J. , Toledo Frederico G. S. , Duchowny Kate A. , Ramos Sofhia V. , Harrison Stephanie , Newman Anne B. , Molina Anthony J. A.
Published: November 2023

The age-related decline in muscle mitochondrial energetics contributes to the loss of mobility in older adults. Women experience a higher prevalence of mobility impairment compared to men, but it is unknown whether sex-specific differences in muscle energetics underlie this disparity. In the Study of Muscle, Mobility and Aging (SOMMA), muscle energetics were characterized using in vivo phosphorus-31 magnetic resonance spectroscopy and high-resolution respirometry of vastus lateralis biopsies in 773 participants (56.4% women, age 70-94 years). A Short Physical Performance Battery score ≤ 8 was used to define lower-extremity mobility impairment. Muscle mitochondrial energetics were lower in women compared to men (e.g. Maximal Complex I&II OXPHOS: Women=55.06 +/− 15.95; Men=65.80 +/− 19.74; p<0.001) and in individuals with mobility impairment compared to those without (e.g., Maximal Complex I&II OXPHOS in women: SPPB≥9=56.59 +/− 16.22; SPPB≤8=47.37 +/− 11.85; p<0.001). Muscle energetics were negatively associated with age only in men (e.g., Maximal ETS capacity: R=-0.15, p=0.02; age/sex interaction, p=0.04), resulting in muscle energetics measures that were significantly lower in women than men in the 70-79 age group but not the 80+ age group. Similarly, the odds of mobility impairment were greater in women than men only in the 70-79 age group (70-79 age group, ORage-adjusted=1.78, 95% CI=1.03, 3.08, p=0.038; 80+ age group, ORage-adjusted=1.05, 95% CI=0.52, 2.15, p=0.89). Accounting for muscle energetics attenuated up to 75% of the greater odds of mobility impairment in women. Women had lower muscle mitochondrial energetics compared to men, which largely explain their greater odds of lower-extremity mobility impairment.
Bioprocess optimization enables enhanced protopanaxadiol production in yeast
Authors: Qiu Shangkun , Gilani Mariam Dianat Sabet , Müller Conrad , Liebal Ulf , Blank Lars M.
Published: November 2023

Ginsenosides are the primary active metabolites of ginseng and have been used in traditional herbal medicine in Asia for more than 4,000 years. Protopanaxadiol (PPD) is the precursor of dammarane-type ginsenosides, exhibiting different pharmacological activities. However, extraction of PPD from plant material is cumbersome because of its low concentration. Precision fermentation using recombinant yeast is a promising alternative strategy to produce PPD. For increasing PPD production, the medium and fermentation conditions were optimized by a Design of Experiment (DoE) approach. PPD production increased by 7.5-fold in the final cultivation condition compared to the reference condition. The PPD titer reached 1.2 g/L during simple 500 mL shake flask cultivations, the highest PPD production in shake flasks to date. The protocol presented facilitates parallel evaluation of recombinant yeast, thereby contributing to the much-needed sustainable synthesis of the versatile molecule class of triterpenoids.
ChatGPT usage in the Reactome curation process
Authors: Tiwari Krishna , Matthews Lisa , May Bruce , Shamovsky Veronica , Orlic-Milacic Marija , Rothfels Karen , Ragueneau Eliot , Gong Chuqiao , Stephan Ralf , Li Nancy , Wu Guanming , Stein Lincoln , D’Eustachio Peter , Hermjakob Henning
Published: November 2023

Appreciating the rapid advancement and ubiquity of generative AI, particularly ChatGPT, a chatbot using large language models like GPT, we endeavour to explore the potential application of ChatGPT in the data collection and annotation stages within the Reactome curation process. This exploration aimed to create an automated or semi-automated framework to mitigate the extensive manual effort traditionally required for gathering and annotating information pertaining to biological pathways, adopting a Reactome “reaction-centric” approach. In this pilot study, we used ChatGPT/GPT4 to address gaps in the pathway annotation and enrichment in parallel with the conventional manual curation process. This approach facilitated a comparative analysis, where we assessed the outputs generated by ChatGPT against manually extracted information. The primary objective of this comparison was to ascertain the efficiency of integrating ChatGPT or other large language models into the Reactome curation workflow and helping plan our annotation pipeline, ultimately improving our protein-to-pathway association in a reliable and automated or semi-automated way. In the process, we identified some promising capabilities and inherent challenges associated with the utilisation of ChatGPT/GPT4 in general and also specifically in the context of Reactome curation processes. We describe approaches and tools for refining the output given by ChatGPT/GPT4 that aid in generating more accurate and detailed output.
Spatial organization of bacterial sphingolipid synthesis enzymes
Authors: Uchendu Chioma G. , Klein Eric A.
Published: November 2023

Sphingolipids are produced by nearly all eukaryotes where they play significant roles in cellular processes such as cell growth, division, programmed cell death, angiogenesis, and inflammation. While it was previously believed that sphingolipids were quite rare among bacteria, bioinformatic analysis of the recently identified bacterial sphingolipid synthesis genes suggests that these lipids are likely to be produced by a wide range of microbial species. The sphingolipid synthesis pathway consists of three critical enzymes. Serine palmitoyltransferase catalyzes the condensation of serine with palmitoyl-CoA (or palmitoyl-acyl carrier protein), ceramide synthase adds the second acyl chain, and a reductase reduces the ketone present on the long-chain base. While there is general agreement regarding the identity of these bacterial enzymes, the precise mechanism and order of chemical reactions for microbial sphingolipid synthesis is more ambiguous. Two mechanisms have been proposed. First, the synthesis pathway may follow the well characterized eukaryotic pathway in which the long-chain base is reduced prior to the addition of the second acyl chain. Alternatively, our previous work suggests that addition of the second acyl chain precedes the reduction of the long-chain base. To distinguish between these two models, we investigated the subcellular localization of these three key enzymes. We found that serine palmitoyltransferase and ceramide synthase are localized to the cytoplasm whereas the ceramide reductase is in the periplasmic space. This is consistent with our previously proposed model wherein the second acyl chain is added in the cytoplasm prior to export to the periplasm where the lipid molecule is reduced.
Founder Mutation Effect Seen ByCERKLGene Mutation Causing Retinal Dystrophy in North Indian Population
Authors: Bansal Mayank , Chakraborty Debojyoti
Published: November 2023

Purpose

This paper describes the clinical features, genotype phenotype correlation ofCERKLgene mutation, one of the most common genetic mutations of Inherited Retinal Dystrophy (IRD) patients seen in our cohort in North India.

Materials and Methods

Patients clinically diagnosed with an IRD were included in the study. Patients underwent ultra widefield (UWF) fundus photographs, fundus autofluorescence (FAF), optical coherence tomography (OCT). A pedigree charting was done. Genetic testing by next generation sequencing (NGS) was done, clinical exome was analyzed.

Results

We report ophthalmic and genetic findings of seven patients withCERKLgene mutation of the thirty five patients that chose to undergo genetic sequencing (amongst our cohort of sixty two patients with IRD). The age ranged from 17 to 45 (median 25) years. Vision ranged from LogMAR 0.18 to 1.8. OCT showed central macular thickness (CMT) ranging from 103 to 268 microns. Majority patients’ fundus exhibited macular pigmentary changes with atrophy, paucipigmentary or limited peripheral retinal pigmentary changes; mild optic disc pallor, and minimal vascular attenuation. Stippled hypo autofluorescence at the macula was the most common finding, with minimal hypoautoflorescence in the retinal periphery.. The genetic sequencing of all patients showed the same mutation, a 2 base pair deletion in exon 7 of theCERKLgene (chr2:g.181548785_181548786del). Coincidentally, all patients withCERKLgene mutation were found to be from a single ethnic community suggesting a founder mutation effect.

Conclusions

Mutation in theCERKLgene results are among the most common causes of IRD in North India. Affected patients showed a definitive early macular involvement. This study reports the presence of a founder mutation effect in theCERKLgene in a large ethnic community in North India.
HIV prevalence in transgender populations and cisgender men who have sex with men in sub-Saharan Africa 2010-2022: a meta-analysis
Authors: Stevens Oliver , Anderson Rebecca L. , Sabin Keith , Arias Garcia Sonia , Fearon Elizabeth , Manda Kingsley , Dikobe Wame , Crowell Trevor A. , Tally Leigh , Mulenga Lloyd , Philip Neena M. , Maheu-Giroux Mathieu , McIntyre Anne , Hladik Wolfgang , Zhao Jinkou , Mahy Mary , Eaton Jeffrey W.
Published: November 2023

Introduction

The Global AIDS Strategy 2021-2026 calls for equitable and equal access to HIV prevention and treatment programmes for all populations to reduce HIV incidence and end HIV/AIDS as a public health threat by 2030. Transgender populations (TGP), including transmen (TGM) and transwomen (TGW) are populations that have been marginalised and are at high risk of HIV infection in sub-Saharan Africa (SSA). Limited surveillance data on HIV among TGP are available in the region to guide programmatic responses and policymaking. Surveillance data on cisgender men who have sex with men (cis-MSM) are comparatively abundant and may be used to infer TGP HIV prevalence.

Methods

Data from key population surveys conducted in SSA between 2010-2022 were identified from existing databases and survey reports. Studies that collected HIV prevalence on both TGP and cis-MSM populations were analysed in a random effect meta-analysis to estimate the ratio of cis-MSM:TGW HIV prevalence.

Results

Eighteen studies were identified encompassing 8,052 TGW and 19,492 cis-MSM. TGW HIV prevalence ranged from 0-71.6% and cis-MSM HIV prevalence from 0.14-55.7%. HIV prevalence in TGW was 50% higher than in cis-MSM (prevalence ratio (PR) 1.50 95% CI 1.26-1.79). TGW HIV prevalence was highly correlated with year/province-matched cis-MSM HIV prevalence (R2= 0.62), but poorly correlated with year/province-matched total population HIV prevalence (R2= 0.1). Five TGM HIV prevalence estimates were identified ranging from 1-24%. Insufficient TGM data were available to estimate cis-MSM:TGM HIV prevalence ratios.

Conclusion

Transgender women experience a significantly greater HIV burden than cis-MSM in SSA. Bio-behavioural surveys designed and powered to measure determinants of HIV infection, treatment coverage, and risk behaviours among transgender populations, distinct from cis-MSM, will improve understanding of HIV risk and vulnerabilities among TGP and support improved programmes.
Predicting default risk bancassurance using GMDH and dce-GMDH neural network models
Authors: Jaber Jamil , Alkhawaldeh Rami S. , Khatatbeh Ibrahim N.
Published: November 2023

Purpose

This study aims to develop a novel approach for predicting default risk in bancassurance, which plays a crucial role in the relationship between interest rates in banks and premium rates in insurance companies. The proposed method aims to improve default risk predictions and assist with client segmentation in the banking system.

Design/methodology/approach

This research introduces the group method of data handling (GMDH) technique and a diversified classifier ensemble based on GMDH (dce-GMDH) for predicting default risk. The data set comprises information from 30,000 credit card clients of a large bank in Taiwan, with the output variable being a dummy variable distinguishing between default risk (0) and non-default risk (1), whereas the input variables comprise 23 distinct features characterizing each customer.

Findings

The results of this study show promising outcomes, highlighting the usefulness of the proposed technique for bancassurance and client segmentation. Remarkably, the dce-GMDH model consistently outperforms the conventional GMDH model, demonstrating its superiority in predicting default risk based on various error criteria.

Originality/value

This study presents a unique approach to predicting default risk in bancassurance by using the GMDH and dce-GMDH neural network models. The proposed method offers a valuable contribution to the field by showcasing improved accuracy and enhanced applicability within the banking sector, offering valuable insights and potential avenues for further exploration.
Integrated artificial and deep neural networks with time series to predict the ratio of the low bid to owner estimate
Authors: Almohsen Abdulmohsen S. , Alsanabani Naif M. , Alsugair Abdullah M. , Al-Gahtani Khalid S.
Published: November 2023

Purpose

The variance between the winning bid and the owner's estimated cost (OEC) is one of the construction management risks in the pre-tendering phase. The study aims to enhance the quality of the owner's estimation for predicting precisely the contract cost at the pre-tendering phase and avoiding future issues that arise through the construction phase.

Design/methodology/approach

This paper integrated artificial neural networks (ANN), deep neural networks (DNN) and time series (TS) techniques to estimate the ratio of a low bid to the OEC (R) for different size contracts and three types of contracts (building, electric and mechanic) accurately based on 94 contracts from King Saud University. The ANN and DNN models were evaluated using mean absolute percentage error (MAPE), mean sum square error (MSSE) and root mean sums square error (RMSSE).

Findings

The main finding is that the ANN provides high accuracy with MAPE, MSSE and RMSSE a 2.94%, 0.0015 and 0.039, respectively. The DNN's precision was high, with an RMSSE of 0.15 on average.

Practical implications

The owner and consultant are expected to use the study's findings to create more accuracy of the owner's estimate and decrease the difference between the owner's estimate and the lowest submitted offer for better decision-making.

Originality/value

This study fills the knowledge gap by developing an ANN model to handle missing TS data and forecasting the difference between a low bid and an OEC at the pre-tendering phase.
Aggregating distributed KOSs: enriching with meta information and linking to the multilingual KOS registry
Authors: Park Ziyoung
Published: November 2023

Purpose

This study aims to collect distributed knowledge organization systems (KOSs) from various domains, enrich each with meta information and link them to the multilingual KOS registry, facilitating integrated search alongside KOSs from various languages and regions.

Design/methodology/approach

This research involved collecting and organizing KOS information through three primary steps. The initial phase involved finding KOSs from Web search results, supplemented by the Korea ON-line E-Procurement System (KONEPS) and the National R&D Integrated Notification Service. After obtaining these KOSs, they were enriched by structuring contextual meta information using Basic Register of Thesauri, Ontologies and Classification (BARTOC) metadata elements and established dedicated media wiki pages for each. Finally, the KOSs were linked to the multilingual KOS registry, BARTOC, ensuring seamless integration with KOSs from various languages and regions and creating connections between each registry entry and its associated KOS wiki page.

Findings

The research findings revealed several insights, as follows: (1) importance of a stable source for collecting KOS: no national body currently oversees KOS registration, underscoring the need for a systematic approach to collect dispersed KOSs. For Korean KOSs (K-KOSs), KONEPS and National R&D Integrated Notification Service are effective data sources. (2) Importance of enhanced metadata: merely collecting KOSs were not enough. Enhanced metadata bridges access gaps and dedicated wiki pages aid user identification and understanding. (3) Observations from multilingual registry uploads: When adding KOSs to a multilingual registry, similarities were observed across languages and regions. Recognizing this, the K-KOSs were linked with their international counterparts, fostering potential global collaboration.

Research limitations/implications

Due to the absence of a dedicated KOS registry agency, the study might have missed KOSs from certain fields or potentially over-collected from others. Furthermore, this study primarily focused on K-KOSs and their integration into the BARTOC registry, which might influence the methods and perspectives on collecting and establishing links among analogous KOSs in the registry.

Originality/value

This research pursued a stable method to detect KOS development and revisions across various fields. To facilitate this, we used the integrated e-procurement and R&D notification system and added meta information to aid in the identification and understanding of KOSs, which includes media wiki pages. Furthermore, link information was provided between the BARTOC registry and the Korean KOS websites and media wiki pages.
Comprehending women beliefs towards sustainable menstrual products – a fundamental step in healthcare
Authors: Ahuja Prerna , Singh Navjit
Published: November 2023

Purpose

Access to good menstrual products is a human rights issue. Yet, there are rising health concerns of women regarding traditional–plastic sanitary napkins. The usage of these products has raised apprehensions towards the environmental pollution due to the plastic content. The solution for both these issues lies in the sustainable menstrual products. As menstruation is a public health issue, this study aims to identify the role of health beliefs on attitude of women towards sustainable menstrual products.

Design/methodology/approach

A survey was conducted for the purpose of data collection. The study uses questionnaire as a research instrument to gain an insight on women health beliefs towards sustainable menstrual products. Data was collected from 527 women respondents through convenience sampling. SPSS and Smart-PLS 4 were used for analysing the data.

Findings

Results of the study indicate that all the health belief perceptions had a significant impact on attitude. Women with more positive health belief and less negative health beliefs are the potential consumers for sustainable menstrual products.

Originality/value

To the best of the authors’ knowledge, this the first study that uses health belief model to explore and add to the menstruation literature especially sustainable menstrual hygiene.
Understanding the impact of fashion app emotional attachment on consumer responses: the role of e-servicescape, customer experience and perceived value of online shopping
Authors: Patel Vipul V. , Pandit Richa , Sama Ramzan
Published: November 2023

Purpose

The primary purpose of this study is to examine the relationship between conumers' emotional attachment towards fashion apps and positive behavioral outcomes, such as e-WoM and repurchase intention. The study also aims to explore how e-servicescape, customer experience and perceived value of online shopping influence this relationships.

Design/methodology/approach

The study has used quantitative research methods to collect data from a sample of 484 consumers who had previous experience of purchasing using fashion apps. Data were collected from university students enrolled in university in Gujarat, India using an online self-administered questionnaire. The data are analyzed using structure equation modeling to determine the relationships between the variables under investigation.

Findings

The results demonstrate relationships between e-servicescape, customer experience and perceived value of online shopping, emotional attachment and the two consumer outcomes: repurchase intention and e-WoM. The study found support for hypotheses 1, 2 and 3, highlighting the influence of e-servicescape, customer experience and perceived value of online shopping in developing emotional attachment with fashion apps. The study also confirmed hypotheses 5 and 6, which suggest that consumers who have a stronger emotional attachment to fashion apps are more likely to intend to repurchase fashion products and engage in positive electronic word-of-mouth behavior for fashion brands.

Originality/value

In today's digital age, fashion apps are vital for fashion retailers to remain competitive and offer their customers a smooth and immersive shopping experience . Given the potential impact of fashion apps on the customer behavior, it is essential to investigate the relationship relationships between e-servicescape, customer experience and perceived value of online shopping, emotional attachment and the two consumer outcomes: repurchase intention and e-WoM in the context of fashion apps. The findings of the study are expected to contribute to the understanding of consumer behavior in the context of fashion apps and e-commerce more broadly. The results may also provide insights into how fashion retailers can improve their online presence and customer experiences to increase emotional attachment and positive behavioral outcomes.

Practical implications

The results of this study have several implications for online retail managers and fashion app developers. The study provides strong support for the idea that the extent to which online customers feel emotionally attached to fashion apps is strongly related to their e-WoM and repurchase intention. Moreover, the results of the study suggest that online retailers who are looking to cultivate emotional connections with consumers through fashion apps should prioritize three key areas: e-servicescape, customer experience and perceived value of online shopping.
Purchase intention of fashion brand retailers: a journey through consumer engagement and happiness
Authors: Gutiérrez-Rodríguez Pablo , Cuesta-Valiño Pedro , Ravina-Ripoll Rafael , García-Henche Blanca
Published: November 2023

Purpose

The objective of this paper is to define a structural equation model (SEM) that examines how fashion consumers' expectations of consumer brand engagement (CBE) influence purchase intention, both directly and through consumer happiness as a mediator. For this purpose, the authors will develop the components of CBE and consumer happiness variables, whose relevance in the literature has increased considerably.

Design/methodology/approach

For this purpose, a cross-sectional descriptive study was carried out by means of a survey developed on the basis of the scales found in the literature, with a sample of 1,296 consumers representative of the Spanish population. The method used to test the hypotheses was partial least squares SEM.

Findings

The results of this research indicate that both CBE and consumer happiness positively influence the purchase intention of fashion brands. In turn, the importance of the dimensions of the antecedent variables can be established.

Research limitations/implications

The current research does not allow a longitudinal analysis of the consumption of fashion retailers. The findings of this scientific study provide a wealth of theoretical and practical information for managers to develop management models based on the sensory enjoyment of their consumers.

Originality/value

One of the novelties of this study is that it considers the consumer happiness variable and its dimensions in a consumer behavior model together with CBE.