bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of a recombinant Saffold Virus expressing UnaG as a marker for the visualization of viral infection
Authors: Okuwa Takako , Himeda Toshiki , Utani Koichi , Higuchi Masaya 
Published: August 2023

Abstract
Background
Saffold virus (SAFV), which belongs to the genus Cardiovirus of the family Picornaviridae, is associated with acute respiratory or gastrointestinal illnesses in children; it is also suspected to cause severe diseases, such as acute flaccid paralysis and aseptic meningitis. However, the understanding of the mechanism of its pathogenicity is still limited due to the many unknowns about its lifecycle; for example, the cellular receptor for its infection remains to be determined. A system to monitor SAFV infection in vitro and in vivo is required in order to accelerate research on SAFV.

Results
We generated a recombinant SAFV expressing green fluorescent protein (GFP) or UnaG, a novel fluorescent protein derived from Japanese eel. HeLa cells infected by either GFP or UnaG-expressing SAFV showed a bright green fluorescent signal, enabling convenient monitoring of SAFV infection. However, the expression of GFP but not UnaG was quickly lost during virus passaging due to the difference in genetic stability in the SAFV virus genome; the UnaG gene was stably maintained in the virus genome after at least five passages.

Conclusions
SAFV infection of cultured cells can easily be monitored using UnaG-expressing SAFV, which is superior to GFP in terms of genetic stability in the virus genome. This virus could be a useful tool for SAFV research, such as comparing the susceptibility of various cells to SAFV infection and evaluating the effects of antivirals on SAFV infection in high-throughput screening.
Collision tumor of a papillary and follicular thyroid carcinoma: a case report
Authors: Kawasaki Kanako , Kai Keita , Tanaka Nariyuki , Kido Shinichi , Ibi Arisa , Minesaki Akimichi , Yamauchi Moriyasu , Kuratomi Yuichiro , Aishima Shinichi , Nakashima Masahiro , Ito Masahiro 
Published: August 2023

Abstract
Background
Papillary thyroid carcinoma (PTC) and follicular thyroid carcinoma (FTC) are common differentiated thyroid cancers, but the detection of a collision tumor is an extremely rare event.

Case presentation
The patient was a 69-year-old Japanese female with multiple cervical lymph node swellings and a thyroid tumor. Preoperative fine needle aspiration cytology of the enlarged lymph node revealed a cytological diagnosis of papillary thyroid carcinoma (PTC). A total thyroidectomy, right cervical dissection and paratracheal dissection were performed. Histopathological and immunohistochemical analyses of resected specimens revealed a collision tumor of PTC and FTC. Multiple metastases of papillary carcinoma were found in the dissected lymph nodes. In the PTC lesion, IHC for BRAF (V600E) was positive but negative for the FTC lesion. Genetic analyses further revealed a TERT promoter C228T mutation in PTC and a NRAS codon 61 mutation in FTC. The patient died of recurrent cancer 8 months after surgery.

Conclusions
A case of a collision tumor of PTC and FTC is very rare, and even fewer cases have been subjected to genetic scrutiny. The present case was successfully diagnosed by pathological examination using immunohistochemical and genetic analyses. The TERT promoter mutation in the PTC lesion was consistent with the aggressive behavior of the cancer.
The forgotten cohort-lessons learned from prehospital trauma death: a retrospective cohort study
Authors: Jakob Dominik A. , Müller Martin , Jud Sebastian , Albrecht Roland , Hautz Wolf , Pietsch Urs 
Published: August 2023

AbstractBackgroundTrauma related deaths remain a relevant public health problem, in particular in the younger male population. A significant number of these deaths occur prehospitally without transfer to a hospital. These patients, sometimes termed “the forgotten cohort”, are usually not included in clinical registries, resulting in a lack of information about prehospitally trauma deaths. The aim of the present study was to compare patients who died prehospital with those who sustained life-threatening injuries in order to analyze and potentially improve prehospital strategies.MethodsThis cohort study included all primary operations carried out by Switzerland's largest helicopter emergency medical service (HEMS) between January 1, 2011, and December 31, 2021. We included all adult trauma patients with life-threatening or fatal conditions. The outcome of this study is the vital status of the patient at the end of mission, i.e. fatal or life-threatening. Injury, rescue characteristics, and interventions of the forgotten trauma cohort, defined as patients with a fatal injury (NACA score of VII), were compared with life-threatening injuries (NACA score V and VI).ResultsOf 110,331 HEMS missions, 5534 primary operations were finally analyzed, including 5191 (93.8%) life-threatening and 343 (6.2%) fatal injuries. More than two-thirds of patients (n = 3772, 68.2%) had a traumatic brain injury without a significant difference between the two groups (p > 0.05). Thoracic trauma (44.6% vs. 28.7%,p < 0.001) and abdominal trauma (22.2% vs. 16.1%,p = 0.004) were more frequent in fatal missions whereas pelvic trauma was similar between the two groups (13.4% vs. 12.9%,p = 0.788). Pneumothorax decompression rate (17.2% vs. 3.7%,p < 0.001) was higher in the forgotten cohort group and measures for bleeding control (15.2% vs. 42.7%,p < 0.001) and pelvic belt application (2.9% vs. 13.1%p < 0.001) were more common in the life-threating injury group.ConclusionChest decompression rates and measures for early hemorrhage control are areas for potential improvement in prehospital care.
Synthesis, DFT and molecular docking of novel (Z)-4-bromo-N-(4-butyl-3 (quinolin-3-yl)thiazol-2(3H)-ylidene)benzamide as elastase inhibitor
Authors: Mustafa Muhammad Naeem , Channar Pervaiz Ali , Ejaz Syeda Abida , Afzal Saira , Aziz Mubashir , Shamim Tahira , Saeed Aamer , Alsfouk Aisha A. , Ujan Rabail , Abbas Qamar , Hökelek Tuncer 
Published: August 2023

AbstractA new compound, C23H20BrN3OS, containing a quinoline-based iminothiazoline with a thiazoline ring, was synthesized and its crystal and molecular structures were analyzed through single crystal X-ray analysis. The compound belongs to the triclinic systemP − 1 space group, with dimensions of a = 9.2304 (6) Å, b = 11.1780 (8) Å, c = 11.3006 (6) Å, α = 107.146 (5)°, β = 93.701 (5)°, γ = 110.435 (6)°, Z = 2 and V = 1025.61 (12) Å3. The crystal structure showed that C–H···N and C–H···O hydrogen bond linkages, forming infinite double chains along the b-axis direction, and enclosing R22(14) and R22(16) ring motifs. The Hirshfeld surface analysis revealed that H…H (44.1%) and H…C/C…H (15.3%) interactions made the most significant contribution. The newly synthesized (Z)-4-bromo-N-(4-butyl-3 (quinolin-3-yl)thiazol-2(3H)-ylidene)benzamide, in comparison to oleanolic acid, exhibited more strong potential against elastase with an inhibition value of 1.21 µM. Additionally, the derivative was evaluated using molecular docking and molecular dynamics simulation studies, which showed that the quinoline based iminothiazoline derivative has the potential to be a novel inhibitor of elastase enzyme. Both theoretical and experimental findings suggested that this compound could have a number of biological activities.
Expression of hes, iha, and tpsA codified in locus of adhesion and autoaggregation and their involvement in the capability of shiga toxin-producing Escherichia coli strains to adhere to epithelial cells
Authors: Colello Rocío , Vélez M. Victoria , Farias M. Victoria Nieto , Rodríguez Marcelo , Montero David , Vidal Roberto , Etcheverría Analía I. , Padola Nora Lía 
Published: August 2023

Abstract
Objectives
Shiga toxin-producing Escherichia coli strains LAA-positive are important cause of human infection. The capability to adhere to epithelial cells is a key virulence trait, and genes codified in LAA pathogenicity island could be involved in the adhesion during the pathogenesis of LAA-positive STEC strains. Thus, our objectives were to compare hes-negative and hes-positive STEC strains in their adherence capability to epithelial cells (HEp-2) and to evaluate the expression levels of the hes, iha, and tpsA in the bacteria adhered and non-adhered to HEp-2 cells. These genes are encoded in LAA, and are virulence factors that participate in adhesion and autoaggregation.

Results
We could not observe differences between the adhesion of strains but also in the expression level of of hes, iha, and tpsA. Genes encoded in LAA contribute to the adhesion phenotype though the expression of STEC adhesins is a coordinated event that depends not only the strain but also on the environment as well as its genetic background. Therefore, the results of this study suggest that LAA ,the most prevalent PAI among LEE-negative STEC strains, plays a role in pathogenesis.
Global effects of identity and aging on the human sperm methylome
Authors: de Sena Brandine Guilherme , Aston Kenneth I. , Jenkins Timothy G. , Smith Andrew D. 
Published: August 2023

AbstractBackgroundAs the average age of fatherhood increases worldwide, so too does the need for understanding effects of aging in male germline cells. Molecular change, including epigenomic alterations, may impact offspring. Age-associated change to DNA cytosine methylation in the cytosine–guanine (CpG) context is a hallmark of aging tissues, including sperm. Prior studies have led to accurate models that predict a man’s age based on specific methylation features in the DNA of sperm, but the relationship between aging and global DNA methylation in sperm remains opaque. Further clarification requires a more complete survey of the methylome with assessment of variability within and between individuals.ResultsWe collected sperm methylome data in a longitudinal study of ten healthy fertile men. We used whole-genome bisulfite sequencing of samples collected 10 to 18 years apart from each donor. We found that, overall, variability between donors far exceeds age-associated variation. After controlling for donor identity, we see significant age-dependent genome-wide change to the methylome. Notably, trends of change with age depend on genomic location or annotation, with contrasting signatures that correlate with gene density and proximity to centromeres and promoter regions.ConclusionsWe uncovered epigenetic signatures that reflect a stable process which begins in early adulthood, progressing steadily through most of the male lifespan, and warrants consideration in any future study of the aging sperm epigenome.
Improving the classification of cardinality phenotypes using collections
Authors: Alghamdi Sarah M. , Hoehndorf Robert 
Published: August 2023

Abstract
Motivation
Phenotypes are observable characteristics of an organism and they can be highly variable. Information about phenotypes is collected in a clinical context to characterize disease, and is also collected in model organisms and stored in model organism databases where they are used to understand gene functions. Phenotype data is also used in computational data analysis and machine learning methods to provide novel insights into disease mechanisms and support personalized diagnosis of disease. For mammalian organisms and in a clinical context, ontologies such as the Human Phenotype Ontology and the Mammalian Phenotype Ontology are widely used to formally and precisely describe phenotypes. We specifically analyze axioms pertaining to phenotypes of collections of entities within a body, and we find that some of the axioms in phenotype ontologies lead to inferences that may not accurately reflect the underlying biological phenomena.

Results
We reformulate the phenotypes of collections of entities using an ontological theory of collections. By reformulating phenotypes of collections in phenotypes ontologies, we avoid potentially incorrect inferences pertaining to the cardinality of these collections. We apply our method to two phenotype ontologies and show that the reformulation not only removes some problematic inferences but also quantitatively improves biological data analysis.
Intention to use maternal waiting home and its predictors among pregnant women in Ethiopia: systematic review and meta-analysis
Authors: Gebeyehu Natnael Atnafu , Assefa Yibeltal , Abebe Kelemu 
Published: August 2023

AbstractBackgroundA high maternal death rate is a result of maternal delays in seeking emergency obstetric care, particularly in countries with limited resources like Ethiopia. Utilizing maternity waiting homes is a strategy to overcome geographical barriers and improve maternal and neonatal health outcomes. Pregnant women must intend to use this service in addition to it being available. Therefore, the goal of this study was to assess pregnant women's intentions to use maternity waiting homes and associated characteristics.MethodsPubMed, Google Scholar, Scopus, Science Direct, and online institutional repository homes were searched. Data were extracted using Microsoft Excel and analyzed using STATA statistical software (v. 14). Publication bias was checked by forest plot, Begg's, and Egger's tests. To look for heterogeneity,I2was computed, and an overall estimated analysis was carried out. Subgroup analysis was done by study region, sample size, and publication. The pooled odds ratio for associated factors was also computed.ResultsOut of 258 articles assessed, 8 studies with 4111 study participants met the criteria and were included in this study. The pooled prevalence of intention to use maternity waiting home was 52.25% (95% CI 45.88–58.66),I2 = 93.8%). Amhara region had a higher intention to use maternal waiting for home prevalence (63.5%), per subgroup analysis. In studies with sample sizes higher than 5000, the usage of maternity waiting homes was less prevalent (45.2%). Between published research (52.9%) and unpublished studies (51.3%), there was no appreciable difference in the intention to use a maternity waiting home. Experience of maternity waiting home (AOR = 3.337; 95% CI 2.038–5.463), direct subjective norm (AOR = 2.763; 95% CI 1.395–5.471), and direct perceived behavioral control (AOR = 23.147; 95% CI 2.341–4.231).ConclusionIn Ethiopia, the intention to use maternity waiting was low. There was an intentional variation in to use of maternity waiting homes across regions of Ethiopia. Improving behavioral perception through intervention programs such as antenatal education should have been strengthened.
Linking fine-scale behaviour to the hydraulic environment shows behavioural responses in riverine fish
Authors: Elings J. , Mawer R. , Bruneel S. , Pauwels I. S. , Pickholtz E. , Pickholtz R. , Coeck J. , Schneider M. , Goethals P. 
Published: August 2023

AbstractBackgroundFish migration has severely been impacted by dam construction. Through the disruption of fish migration routes, freshwater fish communities have seen an incredible decline. Fishways, which have been constructed to mitigate the problem, have been shown to underperform. This is in part due to fish navigation still being largely misunderstood. Recent developments in tracking technology and modelling make it possible today to track (aquatic) animals at very fine spatial (down to one meter) and temporal (down to every second) scales. Hidden Markov models are appropriate models to analyse behavioural states at these fine scales. In this study we link fine-scale tracking data of barbel (Barbus barbus) and grayling (Thymallus thymallus) to a fine-scale hydrodynamic model. With a HMM we analyse the fish’s behavioural switches to understand their movement and navigation behaviour near a barrier and fishway outflow in the Iller river in Southern Germany.MethodsFish were tracked with acoustic telemetry as they approached a hydropower facility and were presented with a fishway. Tracking resulted in fish tracks with variable intervals between subsequent fish positions. This variability stems from both a variable interval between tag emissions and missing detections within a track. After track regularisation hidden Markov models were fitted using different parameters. The tested parameters are step length, straightness index calculated over a 3-min moving window, and straightness index calculated over a 10-min window. The best performing model (based on a selection by AIC) was then expanded by allowing flow velocity and spatial velocity gradient to affect the transition matrix between behavioural states.ResultsIn this study it was found that using step length to identify behavioural states with hidden Markov models underperformed when compared to models constructed using straightness index. Of the two different straightness indices assessed, the index calculated over a 10-min moving window performed better. Linking behavioural states to the ecohydraulic environment showed an effect of the spatial velocity gradient on behavioural switches. On the contrary, flow velocity did not show an effect on the behavioural transition matrix.ConclusionsWe found that behavioural switches were affected by the spatial velocity gradient caused by the attraction flow coming from the fishway. Insight into fish navigation and fish reactions to the ecohydraulic environment can aid in the construction of fishways and improve overall fishway efficiencies, thereby helping to mitigate the effects migration barriers have on the aquatic ecosystem.
A detection method for the ridge beast based on improved YOLOv3 algorithm
Authors: Hou Miaole , Hao Wuchen , Dong Youqiang , Ji Yuhang 
Published: August 2023

Abstract
The ridge beast is a beast placed on the ridge of the roof of ancient Chinese buildings, not only has a decorative function, and has a strict hierarchical meaning, the number and form of the ridge beast placed on different levels of buildings are strictly limited. The detection technology of ridge beast decorative parts has important application value in the fields of fine 3D reconstruction of ancient buildings, historical dating and cultural and tourism services. Aiming at the problem of poor detection performance of traditional detection algorithms due to high texture similarity and poor discrimination of ridge beast, this paper proposed an improved YOLOv3 based detection algorithm for ridge beast decorative pieces. In terms of basic network improvement, local features are aggregated to the deep separable convolution internal embedding summation layer, and point convolution is used to connect the channel information of original features and aggregated features, so as to expand the receptive field and learn more diverse features. The residual structure of the feature extraction network was constructed by using the convolution, and the extraction effect of the model on the fine-grained features of the ridge beast was optimized, so that the detection accuracy was improved. In the prediction head improvement of the model, the original linear structure was reconstructed, and the extrusion and excitation modules were introduced to model the channel relationship of multi-scale feature map, which suppressed the response of interference signals and made the feature more directivity. The parallel 1 × 1 and 3 × 3 convolution are used to construct a multi-size convolution structure, which enhances the semantic information extraction ability of the model and further improves the detection effect. Experiments were conducted on the constructed ridge-beast dataset, and the results showed that the mAP of the improved algorithm can reach 86.48%, which is 3.05% higher than YOLO-v3, and the model parameters are reduced by 70%, which has a better detection performance and can provide a reference for the automated detection of ancient building components.
Does different vertical position of maxillary central incisors in women with different facial vertical height affect smile esthetics perception?
Authors: Atik Ezgi , Turkoglu Hilal 
Published: August 2023

Abstract
Background
The aim of this study was to assess the esthetic perceptions of orthodontists, prosthodontists and laypersons with regard to different vertical positions of the maxillary central incisors related to lateral incisors for different facial vertical height cases.

Subject and methods
Frontal full-face photographs showing social smiles of three adult women aged between 18 and 25 years were used. Vertical position of the maxillary central incisor was changed (intruded or extruded) with 0.5 mm increments according to the reference gingival line resulting five images for each woman in a full-face view yielding a total of 15 images. A visual analog scale was placed below each smile to allow the raters to evaluate the attractiveness of each smile independently. One-way analysis of variance was used to determine whether there was a difference between more than two independent groups in terms of quantitative variables. Comparisons of more than two dependent groups were examined with repeated measures one-way ANOVA. The significance level was taken as 0.05 for all analyses.

Results
For increased facial vertical height, the highest scores for orthodontists were given to the 0.5 mm extruded (64.18 ± 26.36), for prosthodontists to the control (57.28 ± 19.80), and for layperson to the 1 mm extruded (61.27 ± 25.98) central incisor position. For decreased facial vertical height, the highest scores were obtained at the 0.5 mm intrusion with an increasing pattern from orthodontists to laypersons (63.95 ± 22.08 for orthodontists, 79.87 ± 21.43 for prosthodontists, and 79.88 ± 19.17 for laypersons). All three rater groups gave the highest scores to the 0 mm (control) smile design for normal facial vertical height. When these scores were compared among the groups, laypersons gave significantly higher scores compared to orthodontists (p < 0.001) and prosthodontists (p = 0.005).

Conclusions
The facial vertical height significantly affected the perception of smile esthetics. Keeping the distance between the central and lateral incisors longer than 1 mm in individuals with increased facial height may be important in terms of increasing patient satisfaction in terms of clinical aesthetics. On the contrary, keeping the distance between the central and lateral incisors shorter than 1 mm may create a more esthetically acceptable result in individuals with short facial height.
Uniaxial attitude control of uncrewed aerial vehicle with thrust vectoring under model variations by deep reinforcement learning and domain randomization
Authors: Osedo Atsushi , Wada Daichi , Hisada Shinsaku 
Published: August 2023

AbstractThe application of neural networks for nonlinear control has been actively studied in the field of aeronautics. Successful techniques have been demonstrated to achieve improved control performance in simulation using deep-reinforcement learning. To transfer the controller learnt in the simulation of real systems, domain randomization is an approach that encourages the adaptiveness of neural networks to changing environments through training with randomized parameters in environments. This approach applies to an extended context, with changing working environments, including model configurations. In previous studies, the adaptive performance of the domain-randomization-based controllers was studied in a comparative fashion over the model variations. To understand the practical applicability of this feature, further studies are necessary to quantitatively evaluate the learnt adaptiveness with respect to the training conditions. This study evaluates deep-reinforcement-learning and the domain-randomization-based controller, with a focus on its adaptive performance over the model variations. The model variations were designed to allow quantitative comparisons. The control performances were examined, with a specific highlight of whether the model variation ranges fell within or exceeded the randomization range in training.