bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat
Authors: Liu Ziao , Li Haobang , Luo Yang , Li Jianbo , Sun Ao , Ahmed Zulfiqar , Zhang Baizhong , Lei Chuzhao , Yi Kangle
Published: March 2024

Xiangdong black goats, indigenous to Hunan Province, China, exhibit remarkable adaptation to challenging environments and possess distinct black coat coloration alongside exceptional meat quality attributes. Despite their significance, comprehensive genomic investigations of this breed have been notably lacking. This study involved a comprehensive examination of population structure, genomic diversity, and regions of selection in Xiangdong black goats utilizing whole-genome sequencing data from 20 samples of this breed and 139 published samples from six other Chinese goat breeds. Our genomic analysis revealed a total of 19,133,125 biallelic single nucleotide polymorphisms (SNPs) within the Xiangdong black goat genome, primarily located in intergenic and intronic regions. Population structure analysis indicated that, compared with Jintang, Guizhou and Chengdu goats, Xiangdong black goats exhibit a reduced level of genetic differentiation but exhibit relatively greater divergence from Jining goats. An examination of genetic diversity within Xiangdong black goats revealed a moderate level of diversity, minimal inbreeding, and a substantial effective population size, which are more reflective of random mating patterns than other Chinese goat breeds. Additionally, we applied four distinct selective sweep methods, namely, the composite likelihood ratio (CLR), fixation index (FST), θπ ratio and cross-population extended haplotype homozygosity (XP-EHH), to identify genomic regions under positive selection and genes associated with fundamental biological processes. The most prominent candidate genes identified in this study are involved in crucial aspects of goat life, including reproduction (CCSER1, PDGFRB, IFT88, LRP1B, STAG1, and SDCCAG8), immunity (DOCK8, IL1R1, and IL7), lactation and milk production (SPP1, TLL1, and ERBB4), hair growth (CHRM2, SDC1, ITCH, and FGF12), and thermoregulation (PDE10A). In summary, our research contributes valuable insights into the genomic characteristics of the Xiangdong black goat, underscoring its importance and utility in future breeding programs and conservation initiatives within the field of animal breeding and genetics.
Characterization of atypical T cells generated during ex vivo expansion process for T cell-based adoptive immunotherapy
Authors: Mercier-Letondal Patricia , Kumar Abhishek , Marton Chrystel , Bonnefoy Francis , Fredon Maxime , Boullerot Laura , Dehecq Barbara , Adotévi Olivier , Godet Yann , Galaine Jeanne
Published: March 2024

Engineered T cell-based adoptive immunotherapies met promising success for the treatment of hematological malignancies. Nevertheless, major hurdles remain to be overcome regarding the management of relapses and the translation to solid tumor settings. Properties of T cell-based final product should be appropriately controlled to fine-tune the analysis of clinical trial results, to draw relevant conclusions, and finally to improve the efficacy of these immunotherapies. For this purpose, we addressed the existence of atypical T cell subsets and deciphered their phenotypic and functional features in an HPV16-E7 specific and MHC II-restricted transgenic-TCR-engineered T cell setting. To note, atypical T cell subsets include mismatched MHC/co-receptor CD8 or CD4 and miscommitted CD8+ or CD4+ T cells. We generated both mismatched and appropriately matched MHC II-restricted transgenic TCR on CD8 and CD4-expressing T cells, respectively. We established that CD4+ cultured T cells exhibited miscommitted phenotypic cytotoxic pattern and that both interleukin (IL)-2 or IL-7/IL-15 supplementation allowed for the development of this cytotoxic phenotype. Both CD4+ and CD8+ T cell subsets, transduced with HPV16-E7 specific transgenic TCR, demonstrated cytotoxic features after exposure to HPV-16 E7-derived antigen. Ultimately, the presence of such atypical T cells, either mismatched MHC II-restricted TCR/CD8+ T cells or cytotoxic CD4+ T cells, is likely to influence the fate of patient-infused T cell product and would need further investigation.
Real-world experience of teriflunomide in relapsing multiple sclerosis: paramagnetic rim lesions may play a role
Authors: Tan Hongmei , Li Xiang , Li Yuxin , He Fanru , ZhangBao Jingzi , Zhou Lei , Yang Liqin , Zhao Chongbo , Lu Chuanzhen , Dong Qiang , Li Haiqing , Quan Chao
Published: March 2024

Objectives

The aims of this study were to report the effectiveness and safety of teriflunomide in Chinese patients with relapsing–remitting multiple sclerosis (RRMS) and to explore the association of paramagnetic rim lesion (PRL) burden with patient outcome in the context of teriflunomide treatment and the impact of teriflunomide on PRL burden.

Methods

This is a prospective observational study. A total of 100 RRMS patients treated with teriflunomide ≥3 months were included in analyzing drug persistence and safety. Among them, 96 patients treated ≥6 months were included in assessing drug effectiveness in aspects of no evidence of disease activity (NEDA) 3. The number and total volume of PRL were calculated in 76 patients with baseline susceptibility-weighted imaging (SWI), and their association with NEDA3 failure during teriflunomide treatment was investigated.

Results

Over a treatment period of 19.7 (3.1–51.7) months, teriflunomide reduced annualized relapse rate (ARR) from 1.1 ± 0.8 to 0.3 ± 0.5, and Expanded Disability Status Scale (EDSS) scores remained stable. At month 24, the NEDA3% and drug persistence rate were 43.8% and 65.1%, respectively. In patients with a baseline SWI, 81.6% had at least 1 PRL, and 42.1% had ≥4 PRLs. The total volume of PRL per patient was 0.3 (0.0–11.5) mL, accounting for 2.3% (0.0%–49.0%) of the total T2 lesion volume. Baseline PRL number ≥ 4 (OR = 4.24, p = 0.009), younger onset age (OR = 0.94, p = 0.039), and frequent relapses in initial 2 years of disease (OR = 13.40, p = 0.026) were associated with NEDA3 failure. The PRL number and volume were not reduced (p = 0.343 and 0.051) after teriflunomide treatment for more than 24 months. No new safety concerns were identified in this study.

Conclusion

Teriflunomide is effective in reducing ARR in Chinese patients with RRMS. Patients with less PRL burden, less frequent relapses, and relatively older age are likely to benefit more from teriflunomide, indicating that PRL might be a valuable measurement to inform clinical treatment decision.
Transcription termination and readthrough in African swine fever virus
Authors: Cackett Gwenny , Sýkora Michal , Portugal Raquel , Dulson Christopher , Dixon Linda , Werner Finn
Published: March 2024

Introduction

African swine fever virus (ASFV) is a nucleocytoplasmic large DNA virus (NCLDV) that encodes its own host-like RNA polymerase (RNAP) and factors required to produce mature mRNA. The formation of accurate mRNA 3′ ends by ASFV RNAP depends on transcription termination, likely enabled by a combination of sequence motifs and transcription factors, although these are poorly understood. The termination of any RNAP is rarely 100% efficient, and the transcriptional “readthrough” at terminators can generate long mRNAs which may interfere with the expression of downstream genes. ASFV transcriptome analyses reveal a landscape of heterogeneous mRNA 3′ termini, likely a combination of bona fide termination sites and the result of mRNA degradation and processing. While short-read sequencing (SRS) like 3′ RNA-seq indicates an accumulation of mRNA 3′ ends at specific sites, it cannot inform about which promoters and transcription start sites (TSSs) directed their synthesis, i.e., information about the complete and unprocessed mRNAs at nucleotide resolution.

Methods

Here, we report a rigorous analysis of full-length ASFV transcripts using long-read sequencing (LRS). We systematically compared transcription termination sites predicted from SRS 3′ RNA-seq with 3′ ends mapped by LRS during early and late infection.

Results

Using in-vitro transcription assays, we show that recombinant ASFV RNAP terminates transcription at polyT stretches in the non-template strand, similar to the archaeal RNAP or eukaryotic RNAPIII, unaided by secondary RNA structures or predicted viral termination factors. Our results cement this T-rich motif (U-rich in the RNA) as a universal transcription termination signal in ASFV. Many genes share the usage of the same terminators, while genes can also use a range of terminators to generate transcript isoforms varying enormously in length. A key factor in the latter phenomenon is the highly abundant terminator readthrough we observed, which is more prevalent during late compared with early infection.

Discussion

This indicates that ASFV mRNAs under the control of late gene promoters utilize different termination mechanisms and factors to early promoters and/or that cellular factors influence the viral transcriptome landscape differently during the late stages of infection.
Effect of carbide slag and steel slag as alkali activators on the key properties of carbide slag-steel slag-slag-phosphogypsum composite cementitious materials
Authors: Yang Guihong , Li Chao , Xie Wangshan , Yue Yao , Kong Chuiyuan , Li Xiaolong
Published: March 2024

In order to enhance the utilization of alkaline carbide slag (CS) and steel slag (SS) in solid waste-based cementitious materials (SWBCM). In this study, slag (GGBS) was utilized as the primary material, phosphogypsum (PG) as the sulfat activator, and carbide slag (CS) and steel slag (SS) as the alkali activators to prepare carbide slag-steel slag-slag-phosphogypsum composite cementitious material (CS-SS-GGBS-PG). The impact of partial SS (mass fraction) substitution by CS on the flowability, mechanical properties, softening coefficient, pore solution pH value, hydration heat, and microstructure of CS-SS-GGBS-PG was studied. The hydration products, microstructure, and pore structure of CS-SS-GGBS-PG were studied via XRD, FTIR, TG-DTG, SEM, and MIP. The results show that CS replacement with SS decreases the flowability of CS-SS-GGBS-PG compared to the specimen without CS doping (A0). The addition of CS provides an abundance of Ca2+ and OH− to facilitate the hydration reaction in the system, prompting CS-SS-GGBS-PG to form more C-(A)-S-H gels and ettringite (AFt) in the early stages. This significantly enhances the 3 and 7 days strength of CS-SS-GGBS-PG. Compared to A0, the sample group with 5% CS substitution for SS showed a respective increase of 400% and 1,150% in flexural strength at 3 and 7 days, and an increase of 800% and 1,633% in compressive strength. However, if CS is substituted for SS in excess, the system’s late hydration process will be inhibited, increasing the volume of harmful pores in the specimen’s microstructure and lowering its degree of compactness. This leads to a decrease of 28 days of strength and a deterioration of the water resistance of CS-SS-GGBS-PG. It is advised that the blending ratio of SS to CS be 3:1 in order to maintain equilibrium between the early strength enhancement of CS-SS-GGBS-PG and the stability of strength and water resistance in the latter stage. This study has a positive impact on improving the utilization of CS and SS in SWBCM, reducing the dependence of SWBCM on traditional high-angstrom chemical alkali activators, and promoting the development of SWBCM.
The effectiveness and safety of lifestyle medicine and integrative therapies in inflammatory arthritis: an umbrella review using a hierarchical evidence gathering approach
Authors: Lin Joshua , Liu Jing , O’Fee Allana , Pandey Chhiti , Benna-Doyle Sarah , Maunder Alison , Rao Vibhuti , Alesi Simon , Ng Beverly , Ee Carolyn
Published: March 2024

Objective

An umbrella review was conducted to provide a comprehensive evaluation of the evidence on lifestyle medicine and integrative therapies for inflammatory arthritis.

Methods

Five electronic databases were searched for umbrella reviews, meta-analyses, and systematic reviews of randomised controlled trials on acupuncture, diet, exercise, herbal medicine, nutrient supplements, and mind–body therapies for rheumatoid arthritis, spondyloarthritis, and gout published from January 2012 to December 2022. The primary outcomes were functional status and quality of life. Quality assessment was performed using the A MeaSurement Tool to Assess systematic Reviews (AMSTAR-2) tool, and the certainty of evidence for our primary outcomes was assessed using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach where possible.

Results

We included 52 reviews. Exercise was beneficial for functional status in both rheumatoid arthritis and spondyloarthritis, with moderate certainty of evidence. Chinese herbal medicine in combination with disease-modifying anti-rheumatic drugs may improve functional status in rheumatoid arthritis (very low certainty evidence). Acupuncture may improve functional status in rheumatoid arthritis and pain in both rheumatoid arthritis and gout; however, the evidence is of very low certainty. Evidence for other therapies was not clinically significant; however, it suggests possible benefits from quercetin and polyunsaturated fatty acids. Yoga may result in a moderate improvement in functional status when used as an adjunct to medication; however, the certainty of evidence is very low. Diet interventions offered inconsistent improvements to functional status in rheumatoid arthritis, spondyloarthritis, and gout with low to very low certainty.

Conclusion

Exercise should be prescribed for people with rheumatoid arthritis and spondyloarthritis. More research is needed to confirm or refute evidence for Chinese herbal medicine, acupuncture, yoga, and anti-inflammatory diets.
The alternative coproporphyrinogen III oxidase (CgoN) catalyzes the oxygen-independent conversion of coproporphyrinogen III into coproporphyrin III
Authors: Mingers Toni , Barthels Stefan , Mass Violetta , Acuña José Manuel Borrero-de , Biedendieck Rebekka , Cooke Ana , Dailey Tamara A. , Gerdes Svetlana , Blankenfeldt Wulf , Dailey Harry A. , Warren Martin J. , Jahn Martina , Jahn Dieter
Published: March 2024

Nature utilizes three distinct pathways to synthesize the essential enzyme cofactor heme. The coproporphyrin III-dependent pathway, predominantly present in Bacillaceae, employs an oxygen-dependent coproporphyrinogen III oxidase (CgoX) that converts coproporphyrinogen III into coproporphyrin III. In this study, we report the bioinformatic-based identification of a gene called ytpQ, encoding a putative oxygen-independent counterpart, which we propose to term CgoN, from Priestia (Bacillus) megaterium. The recombinantly produced, purified, and monomeric YtpQ (CgoN) protein is shown to catalyze the oxygen-independent conversion of coproporphyrinogen III into coproporphyrin III. Minimal non-enzymatic conversion of coproporphyrinogen III was observed under the anaerobic test conditions employed in this study. FAD was identified as a cofactor, and menadione served as an artificial acceptor for the six abstracted electrons, with a KM value of 3.95 μmol/L and a kcat of 0.63 per min for the substrate. The resulting coproporphyrin III, in turn, acts as an effective substrate for the subsequent enzyme of the pathway, the coproporphyrin III ferrochelatase (CpfC). Under aerobic conditions, oxygen directly serves as an electron acceptor, but is replaced by the more efficient action of menadione. An AlphaFold2 model of the enzyme suggests that YtpQ adopts a compact triangular shape consisting of three domains. The N-terminal domain appears to be flexible with respect to the rest of the structure, potentially creating a ligand binding site that opens and closes during the catalytic cycle. A catalytic mechanism similar to the oxygen-independent protoporphyrinogen IX oxidase PgoH1 (HemG), based on the flavin-dependent abstraction of six electrons from coproporphyrinogen III and their potential quinone-dependent transfer to a membrane-localized electron transport chain, is proposed.
BRCA1/2 alterations and reversion mutations in the area of PARP inhibitors in high grade ovarian cancer: state of the art and forthcoming challenges
Authors: Collet Laetitia , Hanvic Brunhilde , Turinetto Margherita , Treilleux Isabelle , Chopin Nicolas , Le Saux Olivia , Ray-Coquard Isabelle
Published: March 2024

BRCA1/2 genes are part of homologous recombination (HR) DNA repair pathways in charge of error-free double-strand break (DSB) repair. Loss-of-function mutations of BRCA1/2 genes have been associated for a long time with breast and ovarian cancer hereditary syndrome. Recently, polyadenosine diphosphate–ribose polymerase inhibitors (PARPi) have revolutionized the therapeutic landscape of BRCA1/2-mutated tumors, especially of BRCA1/2 high-grade serous ovarian cancer (HGSC), taking advantage of HR deficiency through the synthetic lethality concept. However, PARPi efficiency differs among patients, and most of them will develop resistance, particularly in the relapse setting. In the current proposal, we aim to review primary and secondary resistance to PARPi in HGSC owing to BRCA1/2 alterations. Of note, as several mechanisms of primary or secondary resistance to PARPi have been described, BRCA1/2 reversion mutations that restore HR pathways are by far the most reported. First, the type and location of the BRCA1/2 primary mutation have been associated with PARPi and platinum-salt sensitivity and impact the probability of the occurrence and the type of secondary reversion mutation. Furthermore, the presence of multiple reversion mutations and the variation of allelic frequency under treatment underline the role of intratumor heterogeneity (ITH) in treatment resistance. Of note, circulating tumor DNA might help us to detect and characterize reversion mutations and ITH to finally refine the treatment strategy. Importantly, forthcoming therapeutic strategies, including combination with antiangiogenics or with targeted therapies, may help us delay and overcome PARPi resistance secondary to BRCA1/2 reversion mutations. Also, progression despite PARPi therapy does not preclude PARPi rechallenge in selected patients.
Unraveling trajectories from aplastic anemia to hematologic malignancies: genetic and molecular insights
Authors: Kim Namsoo , Choi Yu Jeong , Lee Seung-Tae , Choi Jong Rak , Lyu Chuhl Joo , Shin Saeam , Cheong June-Won
Published: March 2024

Background

Aplastic anemia (AA), characterized by hematopoietic stem cell deficiency, can evolve into different hematologic malignancies. Our understanding of the genetic basis and mechanisms of this progression remains limited.

Methods

We retrospectively studied 9 acquired AA patients who later developed hematologic malignancies. Data encompassed clinical, laboratory, karyotype, and next-generation sequencing (NGS) information. We explored chromosomal alterations and mutation profiles to uncover genetic changes underlying the transition.

Results

Nine AA patients developed myelodysplastic syndrome (seven patients), acute myeloid leukemia (one patient), or chronic myelomonocytic leukemia (one patient). Among eight patients with karyotype results at secondary malignancy diagnosis, monosomy 7 was detected in three. Trisomy 1, der(1;7), del(6q), trisomy 8, and del(12p) were detected in one patient each. Among three patients with NGS results at secondary malignancy diagnosis, KMT2C mutation was detected in two patients. Acquisition of a PTPN11 mutation was observed in one patient who underwent follow-up NGS testing during progression from chronic myelomonocytic leukemia to acute myeloid leukemia.

Conclusion

This study highlights the genetic dynamics in the progression from AA to hematologic malignancy. Monosomy 7’s prevalence and the occurrence of PTPN11 mutations suggest predictive and prognostic significance. Clonal evolution underscores the complexity of disease progression.
Development of a prognostic model based on different disulfidptosis related genes typing for kidney renal clear cell carcinoma
Authors: Feng Yuanyuan , Wang Wenkai , Jiang Shasha , Liu Yongming , Wang Yan , Zhan Xiangyang , Zhu Huirong , Du Guoqing
Published: March 2024

Background: Kidney renal clear cell carcinoma (KIRC) is a common and clinically significant subtype of kidney cancer. A potential therapeutic target in KIRC is disulfidptosis, a novel mode of cell death induced by disulfide stress. The aim of this study was to develop a prognostic model to explore the clinical significance of different disulfidptosis gene typings from KIRC.

Methods: A comprehensive analysis of the chromosomal localization, expression patterns, mutational landscape, copy number variations, and prognostic significance of 10 disulfide death genes was conducted. Patients were categorized into distinct subtypes using the Non-negative Matrix Factorization (NMF) typing method based on disulfidptosis gene expression patterns. Weighted Gene Co-expression Network Analysis (WGCNA) was used on the KIRC dataset to identify differentially expressed genes between subtype clusters. A risk signature was created using LASSO-Cox regression and validated by survival analysis. An interaction between risk score and immune cell infiltration, tumor microenvironment characteristics and pathway enrichment analysis were investigated.

Results: Initial findings highlight the differential expression of specific DRGs in KIRC, with genomic instability and somatic mutation analysis revealing key insights into their role in cancer progression. NMF clustering differentiates KIRC patients into subgroups with distinct survival outcomes and immune profiles, and hierarchical clustering identifies gene modules associated with key biological and clinical parameters, leading to the development of a risk stratification model (LRP8, RNASE2, CLIP4, HAS2, SLC22A11, and KCTD12) validated by survival analysis and predictive of immune infiltration and drug sensitivity. Pathway enrichment analysis further delineates the differential molecular pathways between high-risk and low-risk patients, offering potential targets for personalized treatment. Lastly, differential expression analysis of model genes between normal and KIRC cells provides insights into the molecular mechanisms underlying KIRC, highlighting potential biomarkers and therapeutic targets.

Conclusion: This study contributes to the understanding of KIRC and provides a potential prognostic model using disulfidptosis gene for personalized management in KIRC patients. The risk signature shows clinical applicability and sheds light on the biological mechanisms associated with disulfide-induced cell death.
Genome-wide association study for yield-related traits in faba bean (Vicia faba L.)
Authors: Gutierrez Natalia , Pégard Marie , Solis Ignacio , Sokolovic Dejan , Lloyd David , Howarth Catherine , Torres Ana M.
Published: March 2024

Yield is the most complex trait to improve crop production, and identifying the genetic determinants for high yield is a major issue in breeding new varieties. In faba bean (Vicia faba L.), quantitative trait loci (QTLs) have previously been detected in studies of biparental mapping populations, but the genes controlling the main trait components remain largely unknown. In this study, we investigated for the first time the genetic control of six faba bean yield-related traits: shattering (SH), pods per plant (PP), seeds per pod (SP), seeds per plant (SPL), 100-seed weight (HSW), and plot yield (PY), using a genome-wide association study (GWAS) on a worldwide collection of 352 homozygous faba bean accessions with the aim of identifying markers associated with them. Phenotyping was carried out in field trials at three locations (Spain, United Kingdom, and Serbia) over 2 years. The faba bean panel was genotyped with the Affymetrix faba bean SNP-chip yielding 22,867 SNP markers. The GWAS analysis identified 112 marker–trait associations (MTAs) in 97 candidate genes, distributed over the six faba bean chromosomes. Eight MTAs were detected in at least two environments, and five were associated with multiple traits. The next step will be to validate these candidates in different genetic backgrounds to provide resources for marker-assisted breeding of faba bean yield.
Attitudes towards women in the military and their relation to both quantity and quality contact with female leaders
Authors: Nicol Adelheid A. M. , Mayrand Nicol Amélie
Published: March 2024

Contact experiences with women in senior leadership roles are important for creating acceptance of women in organizations dominated by men, such as the military, as leadership roles are considered demanding, requiring numerous agentic qualities that are often ascribed to men. The military lacks women in leadership levels within its organization. We wished to determine whether quality and quantity contact with women in leadership positions reduces intergroup anxiety, increases empathy and perspective-taking, and subsequently creates more favorable attitudes toward women in the military. This was examined in three studies, one with a military sample consisting of men (n = 95), another with a civilian sample of men (n = 367), and a third study with a civilian sample of women (n = 374). Our findings revealed that quality contact was related to attitudes toward women in the military for all three samples. Results from the indirect effects tests conducted for the civilian male and female samples revealed that for civilian men, intergroup anxiety demonstrated a significant indirect effect between quantity contact and attitudes toward women in the military, while both intergroup anxiety and perspective-taking demonstrated significant indirect effects between quality contact and attitudes toward women in the military. Furthermore, both quantity and quality contact demonstrated significant direct effects. On the other hand, results revealed that for civilian women the only significant relation was the direct effect between quality contact and attitudes toward women in the military. Intergroup anxiety, perspective-taking, and empathy did not demonstrate any indirect effects for the civilian women sample. Thus, given that interactions with women in leadership positions are related to views of women in the military, research should further explore the role of contact for women in non-traditional work roles.
Temporal patterns of sleep latency in central hypersomnia and attention deficit hyperactivity disorder: a cluster analysis exploration using Multiple Sleep Latency Test
Authors: Maruo Takashi , Takagi Shunsuke , Uchida Sunao , Takahashi Hidehiko , Sugihara Genichi
Published: March 2024

Introduction

Excessive daytime sleepiness (EDS) is a crucial symptom that diminishes the quality of life. The primary causes of EDS are central hypersomnia, including narcolepsy type 1 (NT1), type 2 (NT2), and idiopathic hypersomnia (IH). EDS is often associated with other psychiatric disorders, particularly attention deficit hyperactivity disorder (ADHD). The Multiple Sleep Latency Test (MSLT) is the standard assessment tool for EDS. Although the MSLT yields numerous parameters, most are not employed in clinical practice. In this study, we leveraged novel MSLT parameters to discern central hypersomnia and ADHD presence. Our analysis focused on sleep latency variability and employed cluster analysis to identify unique temporal patterns.

Methods

We examined the MSLT data from 333 patients; of these, 200 (aged 14–54, mean: 24.9 ± 8.1, years; 114 females) met the inclusion criteria comprising comprehensive data an Apnea-Hypopnea Index (AHI) below 5, and no prior diagnosis of sleep apnea syndrome. We employed a time-course cluster approach that specifically targeted sleep latency variability during the MSLT.

Results

Considering both multiple clustering quality evaluations and the study’s objectives, we identified 9 distinct clusters. Clusters 1 and 3 predominantly had MSLT-positive results; Cluster 2 was entirely MSLT-positive; Clusters 4, 5, 6, 8, and 9 were mainly MSLT-negative; and Cluster 7 had mixed results. The diagnosis of hypersomnia varied notably among Clusters 1, 2, 3, and 7, with Cluster 2 demonstrating a pronounced tendency towards NT1 and NT2 diagnoses (p < 0.005). However, no significant correlation was observed between ADHD diagnoses and specific sleep latency patterns in any cluster.

Conclusions

Our study highlights the value of time-course clustering in understanding sleep latency patterns of patients with central hypersomnia.
Efficient Estimation of Generative Models Using Tukey Depth
Authors: Vo Minh-Quan , Nguyen Thu , Riegler Michael A. , Hammer Hugo L.
Published: March 2024

Generative models have recently received a lot of attention. However, a challenge with such models is that it is usually not possible to compute the likelihood function, which makes parameter estimation or training of the models challenging. The most commonly used alternative strategy is called likelihood-free estimation, based on finding values of the model parameters such that a set of selected statistics have similar values in the dataset and in samples generated from the model. However, a challenge is how to select statistics that are efficient in estimating unknown parameters. The most commonly used statistics are the mean vector, variances, and correlations between variables, but they may be less relevant in estimating the unknown parameters. We suggest utilizing Tukey depth contours (TDCs) as statistics in likelihood-free estimation. TDCs are highly flexible and can capture almost any property of multivariate data, in addition, they seem to be as of yet unexplored for likelihood-free estimation. We demonstrate that TDC statistics are able to estimate the unknown parameters more efficiently than mean, variance, and correlation in likelihood-free estimation. We further apply the TDC statistics to estimate the properties of requests to a computer system, demonstrating their real-life applicability. The suggested method is able to efficiently find the unknown parameters of the request distribution and quantify the estimation uncertainty.
Equine Headshaking Syndrome: Triggers, Seasonality, and Treatment Efficacy in Australia
Authors: Bell Teagan , Kyriazopoulou Panoraia , Mowbray Camilla , Murphy Barbara A.
Published: March 2024

Equine headshaking syndrome is a poorly understood neuropathic pain condition presenting as uncontrollable shaking, flicking, or striking of the head. Therapeutic options are limited, and treatments are only partially successful. Currently, epidemiological information on headshaking in the Southern Hemisphere is lacking. An online survey was circulated to Australian owners of headshaking horses to collect information on triggers, symptoms, seasonality, treatments, and perceived treatment efficacy. The responses (n = 216) showed the mean age at symptom onset as 9.6 (±4.7) years. More geldings were affected than mares (76% vs. 24%), and symptom onset occurred later in geldings compared to mares (10.1 ± 4.7 vs. 7.9 ± 4.0 years; p < 0.01). Bright sunlight, wind, and high pollen were the most commonly reported triggers (61%, 46% and 40%, respectively), and seasonal onset of symptoms was reported by 54% of respondents. In total, 71% of respondents reported using two or more treatments. The most common treatments were supplements (68%), nose nets (63%), light-blocking masks (48%), bodywork (48%) and pharmaceutical compounds (38%). Overall, treatments were considered ineffective by 33% of respondents. The findings were in agreement with surveys from the Northern Hemisphere. Of note was the perception of bright light as a primary trigger, alongside the reported low treatment efficacy of light-blocking masks. Seasonal intensification of symptoms and its relationship to day length merits further exploration.
Infrared Thermography of Teat in French Dairy Alpine Goats: A Promising Tool to Study Animal–Machine Interaction during Milking but Not to Detect Mastitis
Authors: Marnet Pierre-Guy , Velasquez Alejandro B. , Dzidic Alen
Published: March 2024

There is a need to develop tools for mastitis management in goats and to measure the effects of milking machines on teats. Infrared thermography (IRT), as shown in cows, was a good candidate for early mastitis detection and focusing on milking equipment and settings implicated in potential problems. The aim of this study was to test IRT to detect udder inflammation and the effects of mechanical milking on teats in relation to inflammation status, udder balance, and teat shape in Alpine goats. IRT spectra were compared before and after milking in 551 goats from three commercial herds compared to their individual SCC (somatic cell count). We found no regression or trend between logSCC and IRT measurement or response to milking, even in highly inflamed goat udders. The effect of milking was significant (p < 0.05) with global temperature reduction after milking, but differences were seen between teat parts and unbalanced half udders. The highest reduction in skin temperature was observed at the teat orifice (−1.06 ± 0.05) and the lowest at the teat barrel (−0.37 ± 0.05). The teats with long barrels showed more IRT reactions, which clearly indicates poor adaptation to the liners used. In conclusion, the IRT was not able to detect mastitis, but it is a good tool to diagnose the effects of the milking machine in order to adapt milking equipment and settings to the goats and improve their welfare.
Preliminary Study on Microplastic Contamination in Black Sea Cetaceans: Gastrointestinal Analysis of Phocoena phocoena relicta and Tursiops truncatus ponticus
Authors: Filimon Adrian , Ciucă Andreea-Mădălina , Harcotă George-Emanuel , Stoica Elena
Published: March 2024

Plastic pollution is a global concern that has a significant impact on marine life. Plastic is widely used and has become a pervasive pollutant in marine environments. Plastic contamination has been documented both in marine environments and biota. Plastic contamination in cetacean gastro-intestinal tract (GIT) content has received limited attention, especially in the Black Sea. This study aims to investigate plastic contamination in the GITs of bottlenose dolphins and harbour porpoises, introducing a novel methodology. Given the limited exploration of this issue in the Black Sea, the research predominantly focuses on microplastic contamination. The GITs were sampled through necropsy from stranded and by-caught cetaceans, and content was washed through a multi-sieves tool. The material retained on each sieve was analysed following specific protocols. All (100%) of the GITs contained plastics (meso- and microplastics). In total, 1059 items (fibres, fragments, and beads) ranging from 22.86 µm to 5776 µm were found, suggesting a high contamination level in the Black Sea cetaceans. Future efforts should concentrate on increasing the number of samples and using the results for the implementation of the Marine Strategy Framework Directive (MSFD).
Comparison of Exposure to Pb and Mn Levels by Using Environmental Personal Monitors and Biomarkers in Relation to Cognitive and Motor Function
Authors: Santibáñez Miguel , Ruiz-Azcona Laura , Expósito Andrea , Markiv Bohdana , Fernández-Olmo Ignacio
Published: March 2024

We conducted a cross-sectional study of 130 participants living near a ferromanganese alloy plant, analyzing Pb and Mn exposure by biomarkers (blood, hair, and fingernails) and particulate matter personal environmental monitors (PEMs). Cognitive and motor function were assessed by five and three tests, respectively. Mean differences (MDs) adjusted for age, sex, and study level were determined. In addition, MDs for Pb were adjusted for Mn levels and vice versa. Medians of 9.14 µg/L, 149.04 ng/g, and 96.04 ng/g were obtained for blood, scalp hair, and fingernails Pb levels, respectively. Regarding PEMs, median Pb levels were 6.56 ng/m3 for the fine fraction and, for the coarse fraction, they were below the limit of detection in 97% of participants. Exposure to Pb at low levels was not associated with worse cognitive function. In comparison, exposure to high levels of Mn was associated with worse cognitive function at least in the domains evaluated through Stroop, Digit Span, and Verbal Fluency tests. In terms of motor function, our results suggest that even the currently low Pb levels may have negative health effects on dynamometer-determined strength—adjusted MD on dominant hand = −2.68; 95%CI (−4.85 to −0.51), p = 0.016. Further studies should investigate this association.
Cancer and Non-Cancer Effects Following Ionizing Irradiation
Authors: Hamada Nobuyuki
Published: March 2024

On the one hand, ionizing radiation has been used to treat not only cancer, but also non-cancer diseases. On the other hand, associations with radiation exposure have increasingly been reported not only for cancer, but also non-cancer diseases, both at doses or dose rates much lower than previously suggested or considered. This underscores the need for considering both cancer and non-cancer effects of medical (diagnostic or therapeutic), occupational or environmental exposure to radiation. As such, this Special Issue aims to serve as a forum to gather the latest developments and discuss future prospects in the field of normal tissue responses to radiation exposure. The Special Issue is composed of 18 articles outlining the radiation effects arising in various tissues (e.g., those in the circulatory, sensory, nervous, respiratory, and reproductive systems).
Patterns in Temporal Networks with Higher-Order Egocentric Structures
Authors: Arregui-García Beatriz , Longa Antonio , Lotito Quintino Francesco , Meloni Sandro , Cencetti Giulia
Published: March 2024

The analysis of complex and time-evolving interactions, such as those within social dynamics, represents a current challenge in the science of complex systems. Temporal networks stand as a suitable tool for schematizing such systems, encoding all the interactions appearing between pairs of individuals in discrete time. Over the years, network science has developed many measures to analyze and compare temporal networks. Some of them imply a decomposition of the network into small pieces of interactions; i.e., only involving a few nodes for a short time range. Along this line, a possible way to decompose a network is to assume an egocentric perspective; i.e., to consider for each node the time evolution of its neighborhood. This was proposed by Longa et al. by defining the “egocentric temporal neighborhood”, which has proven to be a useful tool for characterizing temporal networks relative to social interactions. However, this definition neglects group interactions (quite common in social domains), as they are always decomposed into pairwise connections. A more general framework that also allows considering larger interactions is represented by higher-order networks. Here, we generalize the description of social interactions to hypergraphs. Consequently, we generalize their decomposition into “hyper egocentric temporal neighborhoods”. This enables the analysis of social interactions, facilitating comparisons between different datasets or nodes within a dataset, while considering the intrinsic complexity presented by higher-order interactions. Even if we limit the order of interactions to the second order (triplets of nodes), our results reveal the importance of a higher-order representation.In fact, our analyses show that second-order structures are responsible for the majority of the variability at all scales: between datasets, amongst nodes, and over time.
Multi-Step Approach for Fast Calculation of Magnetic Field in Transformer Tank Shields
Authors: Jurković Zvonimir , Jurišić Bruno , Župan Tomislav
Published: March 2024

A multi-step approach for the fast calculation of the magnetic field inside transformer tank shields, based on the 2D FEM, is presented in the paper. Due to the limitations of the 2D FEM, the proposed approach utilizes several 2D FEM models and calculates the magnetic field in multiple steps to account for the 3D geometry of the problem. In the first step, a distribution of the magnetic flux density that enters the tank shields is calculated using the quasi-3D model of the transformer. This quasi-3D model is obtained by superimposing the solution of multiple axisymmetric 2D FEM models, and assumes a considerably simplified transformer geometry. To account for the tank shield geometry that is neglected in the quasi-3D FEM model, an additional 2D FEM model with tank shields is introduced. After the distribution of the magnetic flux density that enters the tank shields is calculated, it is imposed in the final 2D FEM model with a non-linear tank shield which is used to calculate the magnetic flux density distribution inside the tank shields. The proposed approach enables a fast calculation of magnetic field distributions, both in the vertical and horizontal directions. The results of the proposed approach are compared against the 3D FEM. The relative error of the maximum magnetic flux density is under 2%, while the NRMSE of the magnetic flux density distribution within the tank shields is under 10%. The key contribution of the proposed approach is a low computation time. In the presented case study, the total computation time of the proposed approach is ~30 s, while the computation time of the 3D FEM is ~1 h. As the computation time is significantly reduced, while the accuracy is acceptable, the proposed approach can be a good alternative to the 3D FEM for design purposes. Therefore, it has industrial value.
Conversion of Sewage Sludge into Biofuels via Different Pathways and Their Use in Agriculture: A Comprehensive Review
Authors: Kowalski Zygmunt , Makara Agnieszka , Kulczycka Joanna , Generowicz Agnieszka , Kwaśnicki Paweł , Ciuła Józef , Gronba-Chyła Anna
Published: March 2024

The valorisation of sewage sludge for sustainable agricultural use and biofuel production proposes an effective and beneficial management of sewage sludge in a closed-loop cycle. The management of sewage sludge biowaste is a rising problem due to increasing waste storage expenses. In this sense, the use of circular economy principles in sewage sludge management creates opportunities to develop new technologies for processing. The biorefinery model allows the application of wasteless technologies via sewage sludge valorisation in terms of agricultural use and biofuel production, especially with the hydrothermal carbonisation method. Applying hydrothermal carbonisation in the treatment of biosolid sewage sludge has numerous benefits due to processing highly hydrated organic waste into carbon hydro char, a high-quality solid biofuel. The direct use of sewage sludge in the soil does not allow for full use of its functional properties. However, the hydrothermal carbonisation of sewage sludge results in biocarbon pellets, making it a viable approach. This work also discusses the barriers (legal, chemical, biological, and technical) and possibilities related to sewage sludge biorefining processes.
A Computational Methodology for Assessing Wind Potential
Authors: Christakis Nicholas , Evangelou Ioanna , Drikakis Dimitris , Kossioris George
Published: March 2024

This paper introduces an innovative and eco-friendly computational methodology to assess the wind potential of a location with the aid of high-resolution simulations with a mesoscale numerical weather prediction model (WRF), coupled with the statistical “10% sampling condition”. The proposed methodology is tested for a location with complex terrain on the Greek island of Crete, where moderate to strong winds prevail for most of the year. The results are promising, indicating that this method has great potential for studying and assessing areas of interest. Adverse effects and challenges associated with wind energy production may be mitigated with methods such as the proposed one. Mitigating such effects should constitute the main focus and priority in research concerning wind energy production.
Novel Space-Vector PWM Schemes for Enhancing Efficiency and Decoupled Control in Quasi-Z-Source Inverters
Authors: Grgić Ivan , Bašić Mateo , Vukadinović Dinko , Marinović Ivan
Published: March 2024

This paper investigates the development of pulse width modulation (PWM) schemes for three-phase quasi-Z-source inverters (qZSIs). These inverters are notable for their voltage boost capability, built-in short-circuit protection, and continuous input current, making them suitable for low-voltage-fed applications like photovoltaic or fuel cell-based systems. Despite their advantages, qZSIs confront challenges such as increased control complexity and a larger number of passive components compared to traditional voltage source inverters (VSIs). In addition, most existing PWM schemes for qZSIs lack the capability for independent control of the amplitude modulation index and duty cycle, which is essential in closed-loop applications. This study introduces innovative space-vector PWM (SVPWM) schemes, addressing issues of independent control, synchronization, and unintentional short-circuiting in qZSIs. It evaluates several established continuous and discontinuous PWM schemes, and proposes two novel decoupled SVPWM-based schemes that integrate dead time and in which the shoot-through occurrence is synchronized with the beginning of the zero switching state. These novel schemes are designed to reduce switching losses and improve qZSI controllability. Experimental validation is conducted using a custom-developed electronic circuit board that enables the implementation of a range of PWM schemes, including the newly proposed ones. The obtained results indicate that the proposed PWM schemes can offer up to 6.8% greater efficiency and up to 7.5% reduced voltage stress compared to the closest competing PWM scheme from the literature. In addition, they contribute to reducing the electromagnetic interference and thermal stress of the related semiconductor switches.
Barriers to Cardiac Rehabilitation among Patients Diagnosed with Cardiovascular Diseases—A Scoping Review
Authors: Iyngkaran Pupalan , Appuhamilage Pavithra Yapa , Patabandige Gayani , Sarathchandra Peru Kandage Prasadi Saubhagya , Usmani Wania , Hanna Fahad
Published: March 2024

Background: Cardiovascular diseases (CVDs) are a rising global burden. Preventative strategies such as cardiac rehabilitation (CR) have shown a marked reduction in disease burden. Despite this, CR is underutilized worldwide. This study aims to identify the barriers to CR among patients diagnosed with CVD. Methods: A scoping review of the literature was conducted following the Joanna Briggs Institute (JBI) guidelines. Four major databases, including CINAHL, PubMed, EBSCOhost, and Scopus, were used to obtain studies published between 2010 and 2023. Search terms such as “Cardiac rehab*”, “Barrier*”, “Cardiovascular”, “Disease”, and “diagnosis*” were utilized in order to obtain subject-specific studies relevant to the research question. Results: From the initial 2098 studies, only 14 were included in the final analysis, consisting of both qualitative and quantitative designs. The thematic analysis included “healthcare system-related factors”, “Socioeconomic factors”, and “individual characteristics”. Healthcare system-related factors were mostly related to the poor availability of CR programs, lack of proper referral strategies, inadequate knowledge of CR provider and inter-provider communication issues, and lack of alternative methods of CR delivery. The socioeconomic barriers were lack of education, longer distance to CR facilities, high cost of care, unemployment, and poor income status. The identified individual characteristics were female gender, older age, and comorbidities. Conclusions: Lack of resources, poor access, educational attainment, and high cost of care were some of the barriers to CR, particularly in low- and middle-income countries (LMICs). Health policymakers and healthcare providers should implement strategies incorporating the issues identified in this scoping review. Systematic reviews may be required to confirm these findings.