bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental investigation on de-icing by an array of impact rod-type plasma synthetic jets
Authors: LIU Xuecheng , LIANG Hua , ZONG Haohua , XIE Like , SU Zhi 
Published: September 2022

Abstract
Since flight accidents due to aircraft icing occur from time to time, this paper proposes an array of impact rod-type plasma synthetic jet de-icing methods for aircraft icing problems. The impact rod-type plasma synthetic jet actuator (PSJA) is based on the traditional PSJA with an additional impact rod structure for better de-icing in the flight environment. In this work, we first optimize the ice-breaking performance of a single-impact rod-type PSJA, and then conduct an array of impact rod-type plasma synthetic jet ice-breaking experiments to investigate the relationship between crack expansion and discharge energy, ice thickness and group spacing. The results show that the impact force and impulse of a single-impact rod-type PSJA are proportional to the discharge energy, and there exists a threshold energy Q
min for a single actuator to break the ice, which is proportional to the ice thickness. Only when the discharge energy reaches above Q
min can the ice layer produce cracks, and at the same time, the maximum radial crack length produced during the ice-breaking process is proportional to the discharge energy. When the ice is broken by an array of impact rod PSJAs, the discharge energy and group spacing together determine whether the crack can be extended to the middle region of the actuator. When the group spacing is certain, increasing the energy can increase the intersection of cracks in the middle region, and the ice-fragmentation degree is increased and the ice-breaking effect is better. At the same time, the energy estimation method of ice breaking by an array of impact rod-type PSJAs is proposed according to the law when a single actuator is breaking ice.
Gastric Histopathologic Findings Are Similar in Portal Hypertension Patients With and Without Endoscopic Portal Hypertensive Gastropathy
Authors: Morrow Matthew K , Gonzalez Raul S 
Published: September 2022

Abstract

Objectives
Portal hypertensive gastropathy (PHG) is a diagnosis made based on endoscopic findings in the appropriate clinical setting. Biopsy may be taken during endoscopy for correlation, but the pathologist may encounter a myriad of nonspecific histologic findings. We undertook this study to evaluate contexts where a histologic diagnosis of PHG might be rendered on biopsy.

Methods
Two cohorts were established: stomach biopsy specimens from patients with cirrhosis or undergoing varices screening (n = 188) and stomach biopsy specimens with findings interpreted as PHG in the pathology report (n = 29).

Results
In the first cohort, cases with endoscopic varices more frequently displayed foveolar hyperplasia and acute inflammation, with no other histologic differences between cases with and without endoscopic PHG, clinical varices, and clinical cirrhosis. Cases from the second cohort showed no histologic differences when stratified for endoscopic PHG, endoscopic varices, and clinical cirrhosis. Our second cohort displayed the majority of charted histologic findings more frequently than the first. Our results indicate that neither an endoscopic appearance of PHG nor particular clinical diagnoses associated with PHG translate into specific histologic findings.

Conclusions
Although the histologic findings charted displayed increased frequency in pathology reports with an interpretation of PHG, histology should not be used reliably in the diagnosis of PHG.
EXPERT: transfer learning-enabled context-aware microbial community classification
Authors: Chong Hui , Zha Yuguo , Yu Qingyang , Cheng Mingyue , Xiong Guangzhou , Wang Nan , Huang Xinhe , Huang Shijuan , Sun Chuqing , Wu Sicheng , Chen Wei-Hua , Coelho Luis Pedro , Ning Kang 
Published: September 2022

Abstract
Microbial community classification enables identification of putative type and source of the microbial community, thus facilitating a better understanding of how the taxonomic and functional structure were developed and maintained. However, previous classification models required a trade-off between speed and accuracy, and faced difficulties to be customized for a variety of contexts, especially less studied contexts. Here, we introduced EXPERT based on transfer learning that enabled the classification model to be adaptable in multiple contexts, with both high efficiency and accuracy. More importantly, we demonstrated that transfer learning can facilitate microbial community classification in diverse contexts, such as classification of microbial communities for multiple diseases with limited number of samples, as well as prediction of the changes in gut microbiome across successive stages of colorectal cancer. Broadly, EXPERT enables accurate and context-aware customized microbial community classification, and potentiates novel microbial knowledge discovery.
FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction
Authors: Cai Hanxuan , Zhang Huimin , Zhao Duancheng , Wu Jingxing , Wang Ling 
Published: September 2022

Abstract
Accurate prediction of molecular properties, such as physicochemical and bioactive properties, as well as ADME/T (absorption, distribution, metabolism, excretion and toxicity) properties, remains a fundamental challenge for molecular design, especially for drug design and discovery. In this study, we advanced a novel deep learning architecture, termed FP-GNN (fingerprints and graph neural networks), which combined and simultaneously learned information from molecular graphs and fingerprints for molecular property prediction. To evaluate the FP-GNN model, we conducted experiments on 13 public datasets, an unbiased LIT-PCBA dataset and 14 phenotypic screening datasets for breast cell lines. Extensive evaluation results showed that compared to advanced deep learning and conventional machine learning algorithms, the FP-GNN algorithm achieved state-of-the-art performance on these datasets. In addition, we analyzed the influence of different molecular fingerprints, and the effects of molecular graphs and molecular fingerprints on the performance of the FP-GNN model. Analysis of the anti-noise ability and interpretation ability also indicated that FP-GNN was competitive in real-world situations. Collectively, FP-GNN algorithm can assist chemists, biologists and pharmacists in predicting and discovering better molecules with desired functions or properties.
DistilProtBert: a distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts
Authors: Geffen Yaron , Ofran Yanay , Unger Ron 
Published: September 2022

Abstract

Summary
Recently, deep learning models, initially developed in the field of natural language processing (NLP), were applied successfully to analyze protein sequences. A major drawback of these models is their size in terms of the number of parameters needed to be fitted and the amount of computational resources they require. Recently, ‘distilled’ models using the concept of student and teacher networks have been widely used in NLP. Here, we adapted this concept to the problem of protein sequence analysis, by developing DistilProtBert, a distilled version of the successful ProtBert model. Implementing this approach, we reduced the size of the network and the running time by 50%, and the computational resources needed for pretraining by 98% relative to ProtBert model. Using two published tasks, we showed that the performance of the distilled model approaches that of the full model. We next tested the ability of DistilProtBert to distinguish between real and random protein sequences. The task is highly challenging if the composition is maintained on the level of singlet, doublet and triplet amino acids. Indeed, traditional machine-learning algorithms have difficulties with this task. Here, we show that DistilProtBert preforms very well on singlet, doublet and even triplet-shuffled versions of the human proteome, with AUC of 0.92, 0.91 and 0.87, respectively. Finally, we suggest that by examining the small number of false-positive classifications (i.e. shuffled sequences classified as proteins by DistilProtBert), we may be able to identify de novo potential natural-like proteins based on random shuffling of amino acid sequences.

Availability and implementation
https://github.com/yarongef/DistilProtBert.
A unique glimpse into the crosstalk between different epigenetic mechanisms in porcine embryonic development
Authors: Gan Jianyu , Zhang Xin , Lu Yongchang , Wu Zhenfang , Cai Gengyuan , Hong Linjun 
Published: September 2022

Abstract
The pig is an excellent animal model for simulating human physiology and a major animal for meat production and xenotransplantation. Therefore, researching porcine embryonic development is crucial for studying human reproductive diseases and improving litter size in commercial pigs. Embryonic development in pigs occurs under a complex regulatory mechanism, in which epigenetic regulatory mechanisms play an essential role. Recently, studies on the effects of epigenetic modifications on embryonic development have been conducted at different developmental stages and in different cell lines. Increasing evidence suggests that a certain amount of crosstalk exists between different epigenetic modifications. This review describes four regulatory mechanisms of epigenetics involved in porcine embryonic development: DNA methylation, histone modification, non-coding RNA function, and chromatin accessibility, and explores the possible crosstalk between them.
Efficacy of surgical skin preparation with chlorhexidine in alcohol according to the concentration required to prevent surgical site infection: meta-analysis
Authors: Hasegawa Tatsuki , Tashiro Sho , Mihara Takayuki , Kon Junya , Sakurai Kazuki , Tanaka Yoko , Morita Takumi , Enoki Yuki , Taguchi Kazuaki , Matsumoto Kazuaki , Nakajima Kazuhiko , Takesue Yoshio 
Published: September 2022

Abstract

Background
A combination of chlorhexidine gluconate and alcohol (CHG–alcohol) is recommended for surgical skin preparation to prevent surgical site infection (SSI). Although more than 1 per cent CHG–alcohol is recommended to prevent catheter-related bloodstream infections, there is no consensus regarding the concentration of the CHG compound for the prevention of SSI.

Methods
A systematic review and meta-analysis was performed. Four electronic databases were searched on 5 November 2020. SSI rates were compared between CHG–alcohol and povidone-iodine (PVP-I) according to the concentration of CHG (0.5 per cent, 2.0 per cent, 2.5 per cent, and 4.0 per cent).

Results
In total, 106 of 2716 screened articles were retrieved for full-text review. The risk ratios (RRs) of SSI for 0.5 per cent (6 studies) and 2.0 per cent (4 studies) CHG–alcohol were significantly lower than those for PVP-I (RR = 0.71, 95 per cent confidence interval (c.i.) 0.52 to 0.97; RR = 0.52, 95 per cent c.i 0.31 to 0.86 respectively); however, no significant difference was observed in the compounds with a CHG concentration of more than 2.0 per cent.

Conclusions
This meta-analysis is the first study that clarifies the usefulness of an alcohol-based CHG solution with a 0.5 per cent or higher CHG concentration for surgical skin preparation to prevent SSI.
Supplementary motor area driving changes of structural brain network in blepharospasm
Authors: Xu Jinping , Luo Yuhan , Peng Kangqiang , Guo Yaomin , Zhong Linchang , Liu Ying , Weng Ai , Ou Zilin , Yan Zhicong , Wang Ying , Zeng Jinsheng , Zhang Weixi , Hu Qingmao , Liu Gang 
Published: September 2022

Abstract
Blepharospasm is traditionally thought to be a movement disorder that results from basal ganglia dysfunction. Recently, accumulating morphometric studies have revealed structural alterations outside the basal ganglia, such as in the brainstem, cerebellum and sensorimotor cortex, suggesting that blepharospasm may result from network disorders. However, the temporal and causal relationships between structural alterations and whether there are disease duration-related hierarchical structural changes in these patients remain largely unknown. Structural MRI was performed in 62 patients with blepharospasm, 62 patients with hemifacial spasm and 62 healthy controls to assess the structural alterations using voxel-based morphology and structural covariance networks. The use of the causal structural covariance network, modularity analysis and functional decoding were subsequently performed to map the causal effect of grey matter change pattern, hierarchical topography and functional characterizations of the structural network throughout the disease duration of blepharospasm. Greater grey matter volume in the left and right supplementary motor areas was identified in patients with blepharospasm compared to that in patients with hemifacial spasm and healthy controls, whereas no significant difference was identified between patients with hemifacial spasm and healthy controls. In addition, increased grey matter volume covariance between the right supplementary motor area and right brainstem, left superior frontal gyrus, left supplementary motor area and left paracentral gyrus was found in patients with blepharospasm compared to healthy controls. Further causal structural covariance network, modularity analysis and functional decoding showed that the right supplementary motor area served as a driving core in patients with blepharospasm, extending greater grey matter volume to areas in the cortico-basal ganglia–brainstem motor pathway and cortical regions in the vision–motor integration pathway. Taken together, our results suggest that the right supplementary motor area is an early and important pathologically impaired region in patients with blepharospasm. With a longer duration of blepharospasm, increased grey matter volume extends from the right supplementary motor area to the cortico-basal ganglia motor and visual–motor integration pathways, showing a hierarchy of structural abnormalities in the disease progression of blepharospasm, which provides novel evidence to support the notion that blepharospasm may arise from network disorders and is associated with a wide range of grey matter abnormalities.
Personal insult disrupts regulatory brain networks in violent offenders
Authors: Hofhansel Lena , Weidler Carmen , Clemens Benjamin , Habel Ute , Votinov Mikhail 
Published: September 2022

AbstractThe failure to adequately regulate negative emotions represents a prominent characteristic of violent offenders. In this functional magnetic resonance imaging study, we used technical, nonsocial frustration to elicit anger in violent offenders (n = 19) and then increased the provocation by adding personal insults (social provocation). The aim was to investigate neural connectivity patterns involved in anger processing, to detect the effect of increasing provocation by personal insult, and to compare anger-related connectivity patterns between offenders and noncriminal controls (n = 12). During technical frustration, the offenders showed increased neural connectivity between the amygdala and prefrontal cortex compared to the controls. Conversely, personal insults, and thus increased levels of provocation, resulted in a significant reduction of neural connectivity between regions involved in cognitive control in the offenders but not controls. We conclude that, when (nonsocially) frustrated, offenders were able to employ regulatory brain networks by displaying stronger connectivity between regulatory prefrontal and limbic regions than noncriminal controls. In addition, offenders seemed particularly sensitive to personal insults, which led to increased implicit aggression (by means of motoric responses) and reduced connectivity in networks involved in cognitive control (including dorsomedial prefrontal cortex, precuneus, middle/superior temporal regions).
Risk of Psychiatric Disorders, Use of Psychiatric Hospitals, and Receipt of Psychiatric Medication in Patients With Brain Abscess in Denmark
Authors: Omland Lars Haukali , Bodilsen Jacob , Tetens Malte Mose , Helweg-Larsen Jannik , Jarløv Jens Otto , Ziebell Morten , Ellermann-Eriksen Svend , Justesen Ulrik Stenz , Frimodt-Møller Niels , Mortensen Preben Bo , Obel Niels 
Published: September 2022

Abstract

Background
It is unknown whether patients diagnosed with brain abscess have an increased risk of psychiatric disorders.

Methods
In this nationwide, population-based matched cohort study from Denmark, we compared the incidence of psychiatric disorders, use of psychiatric hospitals, and receipt of psychiatric medications between patients diagnosed with brain abscess and individuals from the general population, matched on date of birth, sex, and residential area.

Results
We included 435 patients diagnosed with brain abscess and 3909 individuals in the comparison cohort: 61% were male and median age was 54 years. Patients diagnosed with brain abscess were more likely to suffer from comorbidity. The risk of a hospital diagnosis of psychiatric disorders was increased the first 5 years of observation. In the subpopulation, who had never been in contact with psychiatric hospitals or received psychiatric medication before study inclusion, the risk of developing psychiatric disorders was close to that of the background population, especially when we excluded dementia from this outcome. There was a substantial increase in the receipt of anxiolytics and antidepressants. The difference in the proportion of individuals who received anxiolytics and antidepressants increased from 4% (95% confidence interval [CI], 0%–7%) and 2% (95% CI, −1% to 5%) 2 years before study inclusion to 17% (95% CI, 12%–21%) and 11% (95% CI, 7%–16%) in the year after study inclusion.

Conclusions
Patients with brain abscess without prior psychiatric disorders or receipt of psychiatric medicine are not at increased risk psychiatric disorders diagnosed in psychiatric hospitals, but they have an increased receipt of psychiatric medication.
Living With Inflammatory Bowel Disease: Online Surveys Evaluating Patient Perspectives on Treatment Satisfaction and Health-Related Quality of Life
Authors: Charabaty Aline , Schneider Beth , Zambrano Javier A , Keefer Laurie 
Published: September 2022

Abstract

Background
The quality of life of persons living with inflammatory bowel disease (IBD) is impacted by the physical and psychosocial burdens of disease, as well as by their satisfaction with the quality of care they receive. We sought to better understand (1) the drivers of satisfaction with treatment, including treatment goals, treatment selection, and attributes of patient/health care professional (HCP) interactions, and (2) how IBD symptoms affect aspects of daily life and overall quality of life.

Methods
Two online questionnaires were accessed via MyCrohnsAndColitsTeam.com. The Treatment Survey assessed desired treatment outcomes, past and present therapies, and experiences with the patient’s primary treating HCP. The Quality of Life survey assessed respondents’ most problematic IBD symptoms and their influence on family and social life, work, and education. Respondents had Crohn’s disease (CD) or ulcerative colitis (UC), were 19 years or older, and resided in the United States. All responses were anonymous.

Results
The Treatment Experience survey was completed by 502 people (296 CD, 206 UC), and the Quality of Life survey was completed by 302 people (177 CD, 125 UC). Reduced pain, diarrhea, disease progression, and fatigue were the most desired goals of treatment. Biologics and 5-aminosalicylates were reported as a current or past treatment by the greatest proportion of patients with CD and UC, respectively. A numerically lower proportion of respondents with UC than CD reported use of biologic or small molecule therapy; conversely, a numerically greater proportion of respondents with UC than CD reported these drugs to be very or extremely effective. The HCP was key in the decision to switch to, and in the selection of, biologic or small molecule therapy. Overall satisfaction with an HCP was greatly driven by the quality and quantity of the communication and of the time spent with the HCP. Troublesome abdominal symptoms most impacted aspects of social and family life. Emotional challenges associated with IBD were experienced by most respondents.

Conclusions
Treatment goals of respondents seem to align with HCPs overall treatment goals, including control of gastrointestinal symptoms and prevention of disease progression. Persons with UC might be offered biologic and small molecule therapies less often, despite reported high efficacy by users. Feeling heard and understood by the HCP are key drivers of treatment satisfaction. Quality communication in the patient/HCP relationship enables a better understanding of the patients’ goals, disease burden, and emotional needs, which are all key factors to consider when developing a personalized and comprehensive treatment plan and optimizing quality of life.
Thymosin β4 and prothymosin α promote cardiac regeneration post-ischaemic injury in mice
Authors: Gladka Monika M , Johansen Anne Katrine Z , van Kampen Sebastiaan J , Peters Marijn M C , Molenaar Bas , Versteeg Danielle , Kooijman Lieneke , Zentilin Lorena , Giacca Mauro , van Rooij Eva 
Published: September 2022

Abstract

Aims
The adult mammalian heart is a post-mitotic organ. Even in response to necrotic injuries, where regeneration would be essential to reinstate cardiac structure and function, only a minor percentage of cardiomyocytes undergo cytokinesis. The gene programme that promotes cell division within this population of cardiomyocytes is not fully understood. In this study, we aimed to determine the gene expression profile of proliferating adult cardiomyocytes in the mammalian heart after myocardial ischaemia, to identify factors to can promote cardiac regeneration.

Methods and results
Here, we demonstrate increased 5-ethynyl-2’deoxyuridine incorporation in cardiomyocytes 3 days post-myocardial infarction in mice. By applying multi-colour lineage tracing, we show that this is paralleled by clonal expansion of cardiomyocytes in the borderzone of the infarcted tissue. Bioinformatic analysis of single-cell RNA sequencing data from cardiomyocytes at 3 days post ischaemic injury revealed a distinct transcriptional profile in cardiomyocytes expressing cell cycle markers. Combinatorial overexpression of the enriched genes within this population in neonatal rat cardiomyocytes and mice at postnatal day 12 (P12) unveiled key genes that promoted increased cardiomyocyte proliferation. Therapeutic delivery of these gene cocktails into the myocardial wall after ischaemic injury demonstrated that a combination of thymosin beta 4 (TMSB4) and prothymosin alpha (PTMA) provide a permissive environment for cardiomyocyte proliferation and thereby attenuated cardiac dysfunction.

Conclusion
This study reveals the transcriptional profile of proliferating cardiomyocytes in the ischaemic heart and shows that overexpression of the two identified factors, TMSB4 and PTMA, can promote cardiac regeneration. This work indicates that in addition to activating cardiomyocyte proliferation, a supportive environment is a key for regeneration to occur.