bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns and drivers of abundance and diversity of reptiles and amphibians in the protected area of Mount Chelmos
Authors: Kypraios-Skrekas Vassilis , Lazaris Alexis , Koutrouditsou Lydia K. , Sotiropoulos Konstantinos , Giokas Sinos 
Published: September 2024

Abstract
The primary objective of this study was to investigate patterns of abundance and diversity among reptiles and amphibians within the protected area of Mount Chelmos, located in Peloponnese, Greece. Our aim was to examine the drivers influencing abundance (for lizards, snakes, chelonians, anurans, urodels) and diversity (for reptiles and amphibians) within the finely-scaled study area and identify biodiversity hotspots. Land cover significantly impacted the abundance and diversity of all studied groups. Elevation had a significant impact on the abundance of snakes, chelonians, and anurans, as well as on reptile and amphibian diversity. Climate influenced all groups except chelonians. Slope significantly impacted anuran abundance and amphibian diversity. Aspect primarily influenced the abundance of lizards, anurans, and urodels, as well as reptile diversity. We have also identified abundance and diversity hotspots, emphasizing the importance of conservation and management efforts. In reptiles, abundance hotspots were predicted in the west, east, and south of the mountainous massif, whereas amphibian abundance hotspots were mapped to the west and east-southeast of the massif. Regarding diversity, the patterns were similar for both reptiles and amphibians, with hotspots emerging in the west, south, and southeast boundaries of the study area, and a few spots north of the mountainous region. Notably, many of these hotspots coincided with areas susceptible to human exploitation and vehicular transit.
The impact of board composition and internationalisation on strategic change: Longitudinal empirical evidence
Authors: Samara Ihssan , Nandakumar MK , Sahadev Sunil , Pereira Vijay 
Published: September 2024

This study looks at the effect of board composition on a firm’s propensity for strategic change. We hypothesise that board composition influences strategic change and internationalisation moderates this relationship. We do a longitudinal study of 433 listed firms in the United States. The findings indicate that the board composition represented by two variables, namely board size and CEO duality, leads to less strategic change. In contrast, the third variable, interlocking directorships, leads to more strategic change. Our results also suggest that internationalisation mitigates the negative impact of board size and CEO duality on strategic change and strengthens the positive impact of interlocking directorships. JEL Classification: C12, L20, L21, M10
Neonatal Hyperekplexia: Is It Still a Diagnostic Challenge? Evidence From a Systematic Review
Authors: Falsaperla Raffaele , Sortino Vincenzo , Giacchi Valentina , Saporito Marco Andrea Nicola , Marino Silvia , Tardino Lucia Giovanna , Marino Lidia , Gennaro Alessia , Ruggieri Martino , Barberi Chiara , Polizzi Agata 
Published: September 2024

Hyperekplexia is a neurologic disorder characterized by an exaggerated startle reflex in response to different types of stimuli. Hyperekplexia is defined by the triad of neonatal hypertonia, excessive startle reflexes, and generalized stiffness following the startle. Although uncommon, hyperekplexia can lead to serious consequences such as falls, brain injury, or sudden infant death syndrome. Aim of this study was to identify cases of neonatal hyperekplexia with a confirmed genetic diagnosis and to establish the genotype-phenotype correlation at onset. Articles were selected from 1993 to 2024 and PRISMA Statement was applied including newborns within 28 days of life. So, we retrieved from literature 14 cases of genetically confirmed neonatal hyperekplexia. The onset of clinical manifestations occurred in the first day of life in 8 of 14 patients (57.14%). Clinical findings were muscle stiffness (100%), startle reflex (66.66%), apnea/cyanosis (41.66%), positive nose-tapping test (33.33%), jerks (33.33%), jitteriness (25%), and ictal blinking (25%). Genes involved were GLRA1 in 9 of 14 (64.28%), SLC6A5 in 2 of 14 (14.28%), GPHN in 1 of 14 (7.14%), and GLRB in 2 of 14 (14.28%). Patients showed heterozygous (66.66%) or homozygous (33.33%) status. In 7 of 14 cases (50%), the condition occurred in other family members. A genotype-phenotype correlation was not achievable. Timely diagnosis is crucial to improve the natural history of hyperekplexia avoiding/reducing possible major complications such as sudden infant death syndrome, brain injury, and serious falls. Early differentiation from epilepsy minimizes treatment cost and improves the quality of life of patients.
Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning
Authors: Lin Tzu-Chieh , Tsai Cheng-Hung , Shiau Cheng-Kai , Huang Jia-Hsin , Tsai Huai-Kuang 
Published: September 2024

Abstract
Background
Alternative splicing is a pivotal mechanism of post-transcriptional modification that contributes to the transcriptome plasticity and proteome diversity in metazoan cells. Although many splicing regulations around the exon/intron regions are known, the relationship between promoter-bound transcription factors and the downstream alternative splicing largely remains unexplored.

Results
In this study, we present computational approaches to unravel the regulatory relationship between promoter-bound transcription factor binding sites (TFBSs) and the splicing patterns. We curated a fine dataset that includes DNase I hypersensitive site sequencing and transcriptomes across fifteen human tissues from ENCODE. Specifically, we proposed different representations of TF binding context and splicing patterns to examine the associations between the promoter and downstream splicing events. While machine learning models demonstrated potential in predicting splicing patterns based on TFBS occupancies, the limitations in the generalization of predicting the splicing forms of singleton genes across diverse tissues was observed with carefully examination using different cross-validation methods. We further investigated the association between alterations in individual TFBS at promoters and shifts in exon splicing efficiency. Our results demonstrate that the convolutional neural network (CNN) models, trained on TF binding changes in the promoters, can predict the changes in splicing patterns. Furthermore, a systemic in silico substitutions analysis on the CNN models highlighted several potential splicing regulators. Notably, using empirical validation using K562 CTCFL shRNA knock-down data, we showed the significant role of CTCFL in splicing regulation.

Conclusion
In conclusion, our finding highlights the potential role of promoter-bound TFBSs in influencing the regulation of downstream splicing patterns and provides insights for discovering alternative splicing regulations.
Sickness absence after work accidents and post-traumatic stress among white-collar workers in the retail and wholesale industry; a longitudinal Swedish cohort study
Authors: Farrants Kristin , Alexanderson Kristina 
Published: September 2024

Abstract
Background
Most studies about accidents and about PTSD, respectively, have been conducted either on blue-collar workers, or on the entire working population. There are very few such studies on white-collar workers.

Aim
To examine diagnosis-specific sickness absence (SA) and disability pension (DP) after a work accident or PTSD, respectively, among white-collar workers in the private retail and wholesale industry.

Methods
A prospective population-based cohort study of all 192,077 such workers aged 18–67 (44% women) in Sweden in 2012, using linked microdata from nationwide registers. We identified individuals who had secondary healthcare due to work-related accidents (n = 1114; 31% women) or to PTSD (n = 216; 79% women) in 2012–2016. Their average number of net days of diagnosis-specific SA (in SA spells > 14 days) and DP were calculated for 365 days before and 365 days after the healthcare visit.

Results
35% of the women and 24% of the men had at least one new SA spell during the 365 days after healthcare due to work accidents. Among women, the average number of SA/DP days increased from 14 in the year before the visit to 31 days the year after; among men from 9 to 21 days. SA days due to fractures and other injuries increased most, while SA days due to mental diagnoses increased somewhat. 73% of women and 64% of men who had healthcare due to PTSD had at least one new SA spell in the next year. Women increased from 121 to 157 SA/DP days and men from 112 to 174. SA due to stress-related disorders and other mental diagnoses increased the most, while DP due to stress-related diagnoses and SA due to musculoskeletal diagnoses increased slightly.

Conclusions
About a quarter of those who had secondary healthcare due to work accidents, and the majority of those with such healthcare due PTSD, had new SA in the following year. SA due to injury and mental diagnoses, respectively, increased most, however, SA/DP due to other diagnoses also increased slightly. More knowledge is needed on factors associated with having or not having SA/DP in different diagnoses after work accidents and among people with PTSD.
Integrating nutrition and culinary medicine into preclinical medical training
Authors: Johnston Emily A. , Torres Maria , Goldgraben Sara , Burns Christopher M. 
Published: September 2024

Abstract
Background
Poor nutrition is a leading cause of preventable death, but is inconsistently taught in medical education and inadequately discussed in medical care. To overcome this problem, we developed a hybrid nutrition team-based learning/culinary medicine approach to integrate practical nutrition knowledge and basic cooking skills into the training of future health professionals.

Methods
Nutrition was integrated into the systems-based courses at a college of osteopathic medicine, complemented by culinary medicine sessions based on the Health meets Food curriculum (HmF; culinarymedicine.org). Students participated in the program for one year and two cohorts of students were included in this analysis. Outcomes were measured via online food frequency questionnaire (FFQ, Vioscreen, Viocare, Inc) and surveys administered via Qualtrics online survey software. Diet quality was measured using the Healthy Eating Index (HEI)-2015. Data were analyzed using SAS 9.4.

Results
One hundred and ninety-five first year students completed a baseline FFQ (97.5% response rate). Mean age of students was 26 years, 47% were female (n = 92/195). The average BMI of participants was 24.8 kg/m2 (range 17-45.4) and the majority of participants reported being active. Seventy-five students (38%) completed an end of year FFQ. Diet quality was poor among students at baseline (n = 195; 67.59 (SD 10.54)) and improved slightly but significantly at the end of year 1 (n = 75, 69.63 (SD: 12.42), p = 0.04). The survey was administered to the second cohort only; 63 students responded (53% response rate). Talking to patients about nutrition was seen as more relevant to future practice among respondents than talking to patients about safe sex, weight, tobacco, alcohol, other substance abuse and domestic violence.

Conclusions
This study evaluated the nutrition and culinary medicine curriculum at a new college of osteopathic medicine. Students rated the program highly and attendance was excellent, even though not required. Student diet quality did not decline over the first year of medical school. Students rated talking to patients about nutrition as highly relevant, providing encouragement that they will do so in future practice. We believe our work shows that nutrition can be integrated into the training of future physicians and that it may pay dividends, particularly with the increasing awareness of the importance of preventive care.
Data set for Gambung green tea aroma using on electronic nose
Authors: Wijaya Dedy Rahman , Handayani Rini , Badri Muhammad Dzakyyuddin , Shabri Shabri , Rahadi Vitria Puspitasari 
Published: September 2024

Abstract
Objectives
In recent years, there has been much discussion and research on electronic nose (e-nose). This topic has developed mainly in the medical and food fields. Typically, e-nose is combined with machine learning algorithms to predict or detect multiple sensory classes in each tea sample. Therefore, in e-nose systems, e-nose signal processing is an important part. In many situations, a comprehensive set of experiments is required to ensure the prediction model can be generalized well. This data set specifically focuses on two main goals such as classification of green tea quality and prediction of organoleptic score. In this experiment, Gambung dry green tea samples were used. The challenge is that dry tea does not emit as strong an aroma as tea infusions, making it more difficult for the e-nose system to detect and identify the aromas. This data set offers a valuable resource for researchers and developers to conduct investigations and experiments by classifying and detecting organoleptic scores that aim to categorize and identify organoleptic ratings. This enables a deeper understanding of the quality of dry green tea and encourages further integration of e-nose technology in the tea industry.

Data description
This experiment focused on analyzing green tea aroma using six gas sensors. Seventy-eight green tea samples were tested, each observed three times, using a tea chamber connected to a sensor chamber via a hose and an intake micro air pump. Air flowed from the tea chamber to the sensor chamber for 60 s, followed by 60 s of aroma data recording. This data was saved into CSV files and labeled according to the Indonesian National Standard (SNI) 3945:2016, which includes special and general requirements for green tea quality. An organoleptic test by a tea tester further labeled the data set into “good” or “quality defect” for classification and provided organoleptic scores based on dry appearance, brew color, taste, aroma, and dregs of brewing for continuous label.
Enhanced motor noise in an autism subtype with poor motor skills
Authors: Mandelli Veronica , Landi Isotta , Ceccarelli Silvia Busti , Molteni Massimo , Nobile Maria , D’Ausilio Alessandro , Fadiga Luciano , Crippa Alessandro , Lombardo Michael V. 
Published: September 2024

Abstract
Background
Motor difficulties are common in many, but not all, autistic individuals. These difficulties can co-occur with other problems, such as delays in language, intellectual, and adaptive functioning. Biological mechanisms underpinning such difficulties are less well understood. Poor motor skills tend to be more common in individuals carrying highly penetrant rare genetic mutations. Such mechanisms may have downstream consequences of altering neurophysiological excitation-inhibition balance and lead to enhanced behavioral motor noise.

Methods
This study combined publicly available and in-house datasets of autistic (n = 156), typically-developing (TD, n = 149), and developmental coordination disorder (DCD, n = 23) children (age 3–16 years). Autism motor subtypes were identified based on patterns of motor abilities measured from the Movement Assessment Battery for Children 2nd edition. Stability-based relative clustering validation was used to identify autism motor subtypes and evaluate generalization accuracy in held-out data. Autism motor subtypes were tested for differences in motor noise, operationalized as the degree of dissimilarity between repeated motor kinematic trajectories recorded during a simple reach-to-drop task.

Results
Relatively ‘high’ (n = 87) versus ‘low’ (n = 69) autism motor subtypes could be detected and which generalize with 89% accuracy in held-out data. The relatively ‘low’ subtype was lower in general intellectual ability and older at age of independent walking, but did not differ in age at first words or autistic traits or symptomatology. Motor noise was considerably higher in the ‘low’ subtype compared to ‘high’ (Cohen’s d = 0.77) or TD children (Cohen’s d = 0.85), but similar between autism ‘high’ and TD children (Cohen’s d = 0.08). Enhanced motor noise in the ‘low’ subtype was also most pronounced during the feedforward phase of reaching actions.

Limitations
The sample size of this work is limited. Future work in larger samples along with independent replication is important. Motor noise was measured only on one specific motor task. Thus, a more comprehensive assessment of motor noise on many other motor tasks is needed.

Conclusions
Autism can be split into at least two discrete motor subtypes that are characterized by differing levels of motor noise. This suggests that autism motor subtypes may be underpinned by different biological mechanisms.
RAIChU: automating the visualisation of natural product biosynthesis
Authors: Terlouw Barbara R. , Biermann Friederike , Vromans Sophie P. J. M. , Zamani Elham , Helfrich Eric J. N. , Medema Marnix H. 
Published: September 2024

AbstractNatural products are molecules that fulfil a range of important ecological functions. Many natural products have been exploited for pharmaceutical and agricultural applications. In contrast to many other specialised metabolites, the products of modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) systems can often (partially) be predicted from the DNA sequence of the biosynthetic gene clusters. This is because the biosynthetic pathways of NRPS and PKS systems adhere to consistent rulesets. These universal biosynthetic rules can be leveraged to generate biosynthetic models of biosynthetic pathways. While these principles have been largely deciphered, software that leverages these rules to automatically generate visualisations of biosynthetic models has not yet been developed. To enable high-quality automated visualisations of natural product biosynthetic pathways, we developed RAIChU (Reaction Analysis through Illustrating Chemical Units), which produces depictions of biosynthetic transformations of PKS, NRPS, and hybrid PKS/NRPS systems from predicted or experimentally verified module architectures and domain substrate specificities. RAIChU also boasts a library of functions to perform and visualise reactions and pathways whose specifics (e.g., regioselectivity, stereoselectivity) are still difficult to predict, including terpenes, ribosomally synthesised and posttranslationally modified peptides and alkaloids. Additionally, RAIChU includes 34 prevalent tailoring reactions to enable the visualisation of biosynthetic pathways of fully maturated natural products. RAIChU can be integrated into Python pipelines, allowing users to upload and edit results from antiSMASH, a widely used BGC detection and annotation tool, or to build biosynthetic PKS/NRPS systems from scratch. RAIChU’s cluster drawing correctness (100%) and drawing readability (97.66%) were validated on 5000 randomly generated PKS/NRPS systems, and on the MIBiG database. The automated visualisation of these pathways accelerates the generation of biosynthetic models, facilitates the analysis of large (meta-) genomic datasets and reduces human error. RAIChU is available at https://github.com/BTheDragonMaster/RAIChU and https://pypi.org/project/raichu.Scientific contributionRAIChU is the first software package capable of automating high-quality visualisations of natural product biosynthetic pathways. By leveraging universal biosynthetic rules, RAIChU enables the depiction of complex biosynthetic transformations for PKS, NRPS, ribosomally synthesised and posttranslationally modified peptide (RiPP), terpene and alkaloid systems, enhancing predictive and analytical capabilities. This innovation not only streamlines the creation of biosynthetic models, making the analysis of large genomic datasets more efficient and accurate, but also bridges a crucial gap in predicting and visualising the complexities of natural product biosynthesis.
Characterization of a GDS(L)-like hydrolase from Pleurotus sapidus with an unusual SGNH motif
Authors: Fingerhut Miriam A. , Henrich Lea , Lauber Christiane , Broel Niklas , Ghezellou Parviz , Karrer Dominik , Spengler Bernhard , Langfelder Kim , Stressler Timo , Zorn Holger , Gand Martin 
Published: September 2024

AbstractThe GDS(L)-like lipase from the Basidiomycota Pleurotus sapidus (PSA_Lip) was heterologously expressed using Trichoderma reesei with an activity of 350 U L−1. The isoelectric point of 5.0 was determined by isoelectric focusing. The novel PSA_Lip showed only 23.8–25.1%, 25.5%, 26.6% and 28.4% identity to the previously characterized GDSL-like enzymes phospholipase, plant lipase, acetylcholinesterase and acetylxylan esterase, from the carbohydrate esterase family 16, respectively. Therefore, the enzyme was purified from the culture supernatant and the catalytic properties and the substrate specificity of the enzyme were investigated using different assays to reveal its potential function. While no phospholipase, acetylcholinesterase and acetylxylan esterase activities were detected, studies on the hydrolysis of ferulic acid methyl ester (~ 8.3%) and feruloylated carbohydrate 5-O-transferuloyl-arabino-furanose (~ 0.8%) showed low conversions of these substrates. By investigating the hydrolytic activity towards p-nitrophenyl-(pNP)-esters with various chain-lengths, the highest activity was determined for medium chain-length pNP-octanoate at 65 °C and a pH value of 8, while almost no activity was detected for pNP-hexanoate. The enzyme is highly stable when stored at pH 10 and 4 °C for at least 7 days. Moreover, using consensus sequence analysis and homology modeling, we could demonstrate that the PSA_Lip does not contain the usual SGNH residues in the actives site, which are usually present in GDS(L)-like enzymes.
Insights into the biodegradation process of 2,4,5-trichlorophenoxyacetic acid under anaerobic condition
Authors: Li Xiuying , Lv Yan , Wang Yuanzhi , Zhang Zhipeng , Wang Jingjing , Jin Huijuan , Zhou Tongyue , Cui Yiru , Yang Yi , Yan Jun 
Published: September 2024

Abstract
Background
Chlorophenoxy compounds represent a group of selective herbicides widely used around the world. Chlorophenoxy herbicides are toxic, chemically stable, and can migrate into groundwater through soil leaching, posing a significant threat to drinking water safety and human health. Chlorophenoxy herbicides in groundwater aquifers are subject to anaerobic processes; however, the pathway and microbiology involved in the attenuation of chlorophenoxy herbicides under anaerobic condition are largely unknown. Here, the anaerobic degradation process of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), a typical chlorophenoxy herbicide, was investigated.

Results
The initial 52.5 ± 2.3 μM 2,4,5-T was completely degraded by a sediment-derived microbial consortium, with 3,4-dichlorophenol, 2,5-dichlorophenol, 3-chlorophenol (3-CP) and phenol being identified as the intermediate products. Reductive dechlorination of 3-CP to phenol and the subsequent elimination of phenol were the key transformation steps in the overall degradation process of 2,4,5-T. Amplicon sequencing suggested that Dehalobacter, Sulfuricurvum, Bacteroides, Acetobacterium, and Clostridium sensu stricto 7 might contribute to the transformation of 2,4,5-T to phenol, and Smithella, Syntrophorhabdus, Methanofollis and Methanosaeta likely cooperated to accomplish the complete mineralization of phenol.

Conclusions
This study reported the anaerobic degradation of 2,4,5-T via reductive dechlorination and the subsequent syntrophic metabolization of phenol, an intermediate product transformed from 2,4,5-T. Dehalobacter was identified as the organohalide-respiring population catalyzing the reductive dechlorination reaction. Syntrophorhabdus and methanogenic populations were likely involved in anaerobic phenol oxidation and facilitated the complete mineralization of 2,4,5-T.