bluuebunny/crossref_metadata_2025_split huggingface dataset:
Passivation of perovskite layer surface states with pyridine in flexible and printed perovskite solar cells
Authors: Kakimov Alibek G , Yerlanuly Yerassyl , Akhanuly Assylan , Dossayev Iliyas T , Shalenov Erik O , Sadirkhanov Zhandos T , Dzhumagulova Karlygash N , Ng Annie , Jumabekov Askhat N 
Published: August 2022

Abstract
Perovskite solar cells (PSCs), prepared by using solution-processed printing techniques, gained much attention over the past few years and a considerable progress has been achieved in improving the power conversion efficiencies of these devices. Nevertheless, there are still some advancements that can be implemented, especially in terms of passivation of surface defects in the perovskite photoactive layer. Passivation can afford considerable reduction in surface recombination of charge carriers in the photoactive layer and help to obtain devices with better performance. In this work, poly(3-hexylthiophene-2,5-diyl)-based inks with small amount of pyridine as an additive are used to deposit the hole transport layer and simultaneously passivate the surface defects of the perovskite layer in flexible and printed PSCs. The devices are fabricated on flexible conductive plastic substrates using a slot-die coating method. It is found that 2.5 wt.% pyridine-containing inks for preparing hole transport layer have a positive effect on the performance of resulting PSCs. On average, around 13% improvement in the power conversion efficiency is observed for the devices with passivation as opposed to the reference devices without passivation. The effect of pyridine passivation on the structural and electronic properties of the perovskite layer on a flexible substrate is studied using experimental and analytical techniques, whereas the computer simulation methods are employed to rule out the possible mechanisms for the performance improvements in the devices with passivation. The approach presented here can be useful for developing simplified protocols for printing of flexible PSCs with the passivated perovskite layer and improved device efficiency.
Simulation and analysis of mechanical properties of cold-formed lock-seam of truss rods for on-orbit construction
Authors: Yang Xingwen , Han Jingtao , Liu Jing , Liang Jinchao 
Published: August 2022

Abstract
In this paper, a new process of spiral cold forming of truss rods for on-orbit construction is proposed. The influence of the width of the lock-seam overlapping region, stirp thickness and lock-seam buckle structure types on the mechanical properties of the rods’ lock-seam was investigated by using a method combining of single tensile experiment and numerical simulation. The results show that for the flat buckle samples with the stirp thickness of 0.3 mm, with the increase of the width of overlapping region of the lock-seam, the maximum occlusal force and maximum occlusal strength of the lock-seam are monotonically decreasing. Although the simulated maximum occlusal force is slightly higher than the actual maximum occlusal force, the simulation results show reasonable agreement with the experimental values. In the simulation, with the increase of the stirp thickness, the maximum occlusal force of the flat buckle has a linear increase, while the maximum occlusal strength increases slightly. Compared with the flat buckle type, when the lock-seam is designed as a pressed rib buckle type, the overall mechanical properties of the lock-seam are improved by 80%. It is more effective to improve the mechanical properties of the rods’ lock-seam by changing the buckle type.
Collisions and collisional transport—II. Fully-ionized plasmas—Unmagnetized
Authors: Bers Abraham 
Published: August 2022

Abstract
This chapter expands the discussion of collisional scattering of particles by examining collisional relaxation rates and some collisional transport characteristics in unmagnetized, fully-ionized plasmas. The material is presented here so that students can develop qualitative and quantitative knowledge about the effects of collisions and some important collisional transport phenomena in such plasmas. This is particularly relevant at this stage, since collective modes of waves and instabilities in high-temperature plasmas are conveniently studied, in first-approximation, from “collisionless” models of plasma dynamics. To gain some insight into the dynamics of elastic Coulomb collisional processes—the binary elastic collision between two charged particles interacting through their own electric field—the chapter considers the evolution of a tenuous beam of “test” particles at a given velocity, colliding with a Maxwellian distribution of “field” particles, of density and temperature, which is much more numerous and remains (at least initially) essentially unchanged.
Prediction of gene co-expression from chromatin contacts with graph attention network
Authors: Zhang Ke , Wang Chenxi , Sun Liping , Zheng Jie 
Published: August 2022

AbstractMotivationThe technology of high-throughput chromatin conformation capture (Hi-C) allows genome-wide measurement of chromatin interactions. Several studies have shown statistically significant relationships between gene–gene spatial contacts and their co-expression. It is desirable to uncover epigenetic mechanisms of transcriptional regulation behind such relationships using computational modeling. Existing methods for predicting gene co-expression from Hi-C data use manual feature engineering or unsupervised learning, which either limits the prediction accuracy or lacks interpretability.ResultsTo address these issues, we propose HiCoEx (Hi-C predicts gene co-expression), a novel end-to-end framework for explainable prediction of gene co-expression from Hi-C data based on graph neural network. We apply graph attention mechanism to a gene contact network inferred from Hi-C data to distinguish the importance among different neighboring genes of each gene, and learn the gene representation to predict co-expression in a supervised and task-specific manner. Then, from the trained model, we extract the learned gene embeddings as a model interpretation to distill biological insights. Experimental results show that HiCoEx can learn gene representation from 3D genomics signals automatically to improve prediction accuracy, and make the black box model explainable by capturing some biologically meaningful patterns, e.g., in a gene contact network, the common neighbors of two central genes might contribute to the co-expression of the two central genes through sharing enhancers.Availability and implementationThe source code is freely available at https://github.com/JieZheng-ShanghaiTech/HiCoEx.Supplementary informationSupplementary data are available at Bioinformatics online.
Hierarchical deep learning for predicting GO annotations by integrating protein knowledge
Authors: Merino Gabriela A , Saidi Rabie , Milone Diego H , Stegmayer Georgina , Martin Maria J 
Published: August 2022

AbstractMotivationExperimental testing and manual curation are the most precise ways for assigning Gene Ontology (GO) terms describing protein functions. However, they are expensive, time-consuming and cannot cope with the exponential growth of data generated by high-throughput sequencing methods. Hence, researchers need reliable computational systems to help fill the gap with automatic function prediction. The results of the last Critical Assessment of Function Annotation challenge revealed that GO-terms prediction remains a very challenging task. Recent developments on deep learning are significantly breaking out the frontiers leading to new knowledge in protein research thanks to the integration of data from multiple sources. However, deep models hitherto developed for functional prediction are mainly focused on sequence data and have not achieved breakthrough performances yet.ResultsWe propose DeeProtGO, a novel deep-learning model for predicting GO annotations by integrating protein knowledge. DeeProtGO was trained for solving 18 different prediction problems, defined by the three GO sub-ontologies, the type of proteins, and the taxonomic kingdom. Our experiments reported higher prediction quality when more protein knowledge is integrated. We also benchmarked DeeProtGO against state-of-the-art methods on public datasets, and showed it can effectively improve the prediction of GO annotations.Availability and implementationDeeProtGO and a case of use are available at https://github.com/gamerino/DeeProtGO.Supplementary informationSupplementary data are available at Bioinformatics online.
MICER: a pre-trained encoder–decoder architecture for molecular image captioning
Authors: Yi Jiacai , Wu Chengkun , Zhang Xiaochen , Xiao Xinyi , Qiu Yanlong , Zhao Wentao , Hou Tingjun , Cao Dongsheng 
Published: August 2022

AbstractMotivationAutomatic recognition of chemical structures from molecular images provides an important avenue for the rediscovery of chemicals. Traditional rule-based approaches that rely on expert knowledge and fail to consider all the stylistic variations of molecular images usually suffer from cumbersome recognition processes and low generalization ability. Deep learning-based methods that integrate different image styles and automatically learn valuable features are flexible, but currently under-researched and have limitations, and are therefore not fully exploited.ResultsMICER, an encoder–decoder-based, reconstructed architecture for molecular image captioning, combines transfer learning, attention mechanisms and several strategies to strengthen effectiveness and plasticity in different datasets. The effects of stereochemical information, molecular complexity, data volume and pre-trained encoders on MICER performance were evaluated. Experimental results show that the intrinsic features of the molecular images and the sub-model match have a significant impact on the performance of this task. These findings inspire us to design the training dataset and the encoder for the final validation model, and the experimental results suggest that the MICER model consistently outperforms the state-of-the-art methods on four datasets. MICER was more reliable and scalable due to its interpretability and transfer capacity and provides a practical framework for developing comprehensive and accurate automated molecular structure identification tools to explore unknown chemical space.Availability and implementationhttps://github.com/Jiacai-Yi/MICER.Supplementary informationSupplementary data are available at Bioinformatics online.
‘It just fundamentally reflects the best of social work’: Social Worker’s Practice Understandings and Experience of the Best Interests Assessor role
Authors: Buckton Wayne 
Published: August 2022

Abstract
This article explores narratives of professional social workers tasked with undertaking the formal para-legal role of Best Interests Assessor under the Deprivation of Liberty Safeguards (DoLS) scheme. Wholesale reform of this practice has been debated in recent years and legislative changes have passed through Parliament—the Liberty Protection Safeguards (LPS). The process and debate preceding this change were, however, marked by a relative marginalisation of accounts and critical opinions of Best Interests Assessors (BIAs) themselves. Semi-structured interviews were conducted with a sample group of BIAs from a variety of social work teams within a single Local Authority. These accounts are explored using a thematic analysis underpinned by Ritzer’s McDonaldization theory and Sayer’s work on Contributive Justice. The work considers the professional identities of the BIAs within and beyond their employing organisation in association with social justice and human rights. Barriers and supports to practice are considered in relation to the organisational, technological and legal contexts of assessment work under the DoLS. The study holds relevance for social workers and organisations in contemplating the transition to LPS and workforce conversions to the Approved Mental Capacity Professional.
Transthyretin cardiac amyloidosis
Authors: Porcari Aldostefano , Fontana Marianna , Gillmore Julian D 
Published: August 2022

AbstractTransthyretin cardiac amyloidosis (ATTR-CA) is an increasingly recognized cause of heart failure (HF) and mortality worldwide. Advances in non-invasive diagnosis, coupled with the development of effective treatments, have shifted ATTR-CA from a rare and untreatable disease to a relatively prevalent condition that clinicians should consider on a daily basis. Amyloid fibril formation results from age-related failure of homoeostatic mechanisms in wild-type ATTR (ATTRwt) amyloidosis (non-hereditary form) or destabilizing mutations in variant ATTR (ATTRv) amyloidosis (hereditary form). Longitudinal large-scale studies in the United States suggest an incidence of cardiac amyloidosis in the contemporary era of 17 per 100 000, which has increased from a previous estimate of 0.5 per 100 000, which was almost certainly due to misdiagnosis and underestimated. The presence and degree of cardiac involvement is the leading cause of mortality both in ATTRwt and ATTRv amyloidosis, and can be identified in up to 15% of patients hospitalized for HF with preserved ejection fraction. Associated features, such as carpal tunnel syndrome, can preceed by several years the development of symptomatic HF and may serve as early disease markers. Echocardiography and cardiac magnetic resonance raise suspicion of disease and might offer markers of treatment response at a myocardial level, such as extracellular volume quantification. Radionuclide scintigraphy with ‘bone’ tracers coupled with biochemical tests may differentiate ATTR from light chain amyloidosis. Therapies able to slow or halt ATTR-CA progression and increase survival are now available. In this evolving scenario, early disease recognition is paramount to derive the greatest benefit from treatment.
Worsening cardiac tamponade after pericardiocentesis in a patient with anterior mediastinum mass: a case report
Authors: Adi Osman , Fong Chan Pei , Ahmad Azma Haryaty , Panebianco Nova 
Published: August 2022

Abstract

Background
Mediastinal mass is an entity with variable pathology and clinical spectrum. Anterior mediastinal mass can result in severe symptoms due to involvement of surrounding vital structures such as the great vessels, trachea-bronchial tree, and heart. We highlight a case of cardiac tamponade in a patient with an anterior mediastinal mass that was paradoxically worsened after decompressive pericardiocentesis.

Case summary
A 21-year-old male presented to the emergency department (ED) with breathlessness and hypotension. Bedside focused cardiac ultrasound revealed cardiac tamponade which was made worse with an anterior mediastinal mass compressing the right heart chambers. The patient was intubated for respiratory failure, following which an ultrasound-guided pericardiocentesis was performed. Unexpectedly, his hemodynamic status worsened after aspiration of 1000 mL of pericardial fluid. A repeat focused cardiac ultrasound showed reduced pericardial effusion, but worsening of right heart chambers compression by the mediastinal mass. Re-expansion of the pericardium space with 600 mL of normal saline improved the patient’s vital signs, and reduced the right heart compression. Computed tomography was deferred due to the patient’s hemodynamic instability. Despite resuscitation with fluids and initiation of vasopressor, the patient’s condition deteriorated. He succumbed to his illness due to obstructive shock causing multi-organ failure. The autopsy showed a large anterior mediastinal mass, and histopathological examination confirmed the diagnosis of lymphoma.

Discussion
This case demonstrated the therapeutic challenges of managing a shock patient with anterior mediastinal mass, and massive pericardial effusion causing cardiac tamponade.
Cardiac remodelling in the highest city in the world: effects of altitude and chronic mountain sickness
Authors: Doutreleau Stéphane , Ulliel-Roche Mathilde , Hancco Ivan , Bailly Sébastien , Oberholzer Laura , Robach Paul , Brugniaux Julien V , Pichon Aurélien , Stauffer Emeric , Perger Elisa , Parati Gianfranco , Verges Samuel 
Published: August 2022

Abstract

Aims
A unique Andean population lives in the highest city of the world (La Rinconada, 5100 m, Peru) and frequently develops a maladaptive syndrome, termed chronic mountain sickness (CMS). Both extreme altitude and CMS are a challenge for the cardiovascular system. This study aims to evaluate cardiac remodelling and pulmonary circulation at rest and during exercise in healthy and CMS highlanders.

Methods and results
Highlanders living permanently at 3800 m (n = 23) and 5100 m (n = 55) with (n = 38) or without CMS (n = 17) were compared with 18 healthy lowlanders. Rest and exercise echocardiography were performed to describe cardiac remodelling, pulmonary artery pressure (PAP), and pulmonary vascular resistance (PVR). Total blood volume (BV) and haemoglobin mass were determined in all people. With the increase in the altitude of residency, the right heart dilated with an impairment in right ventricle systolic function, while the left heart exhibited a progressive concentric remodelling with Grade I diastolic dysfunction but without systolic dysfunction. Those modifications were greater in moderate–severe CMS patients. The mean PAP was higher both at rest and during exercise in healthy highlanders at 5100 m. The moderate–severe CMS subjects had a higher PVR at rest and a larger increase in PAP during exercise. The right heart remodelling was correlated with PAP, total BV, and SpO2.

Conclusion
Healthy dwellers at 5100 m exhibit both right heart dilatation and left ventricle concentric remodelling with diastolic dysfunction. Those modifications are even more pronounced in moderate–severe CMS subjects and could represent the limit of the heart's adaptability before progression to heart failure.
Bordetella pertussis outer membrane vesicles as virulence factor vehicles that influence bacterial interaction with macrophages
Authors: Blancá Bruno , Alvarez Hayes Jimena , Surmann Kristin , Hugo Valdez , Hentschker Christian , Lamberti Yanina , Völker Uwe , Rodriguez María Eugenia 
Published: August 2022

ABSTRACT
Gram-negative pathogenic bacteria constitutively shed outer membrane vesicles (OMVs) which play a significant role in the host–pathogen interaction, eventually determining the outcome of the infection. We previously found that Bordetella pertussis, the etiological agent of whooping cough, survives the innate interaction with human macrophages remaining alive inside these immune cells. Adenylate cyclase (CyaA), one of the main toxins of this pathogen, was found involved in the modulation of the macrophage defense response, eventually promoting bacterial survival within the cells. We here investigated whether B. pertussis OMVs, loaded with most of the bacterial toxins and CyaA among them, modulate the macrophage response to the bacterial infection. We observed that the pre-incubation of macrophages with OMVs led to a decreased macrophage defense response to the encounter with the bacteria, in a CyaA dependent way. Our results suggest that CyaA delivered by B. pertussis OMVs dampens macrophages protective function by decreasing phagocytosis and the bactericidal capability of these host cells. By increasing the chances of bacterial survival to the innate encounter with the macrophages, B. pertussis OMVs might play a relevant role in the course of infection, promoting bacterial persistence within the host and eventually, shaping the whole infection process.
Risks of Melanoma and Nonmelanoma Skin Cancers Pre– and Post–Inflammatory Bowel Disease Diagnosis
Authors: Narous Mariam , Nugent Zoann , Singh Harminder , Bernstein Charles N 
Published: August 2022

Abstract

Background
We compared risks of nonmelanoma skin cancers (NMSCs) and melanoma preceding and following a diagnosis of inflammatory bowel disease (IBD) and to evaluate the effect of thiopurines and anti-tumor necrosis factor α (anti-TNF-α) on skin cancer risk in IBD.

Methods
This was a retrospective, historical cohort study using the population-based University of Manitoba IBD Epidemiology Database (11 228 IBD cases and 104 725 matched controls) linked to the Manitoba Cancer Registry. Logistic and Cox regression analyses were performed to calculate skin cancer risks prior to and after IBD diagnosis.

Results
Persons with ulcerative colitis (UC) were more likely to have basal cell carcinoma (BCC) predating their UC diagnosis (odds ratio, 1.32; 95% confidence interval [CI], 1.08-1.60). Risks of squamous cell carcinoma (SCC), other NMSCs, or melanoma prior to IBD diagnosis were not significantly increased. Post-IBD diagnosis, risks of BCC (hazard ratio, 1.53; 95% CI, 1.37-1.70) and SCC (hazard ratio, 1.61; 95% CI, 1.29-2.01) were significantly increased across all IBD groups except for SCC in UC. There was no significant association between melanoma and IBD post–IBD diagnosis. The risks of BCC and melanoma were increased in thiopurine and anti-TNF users, and risk of SCC was increased in only thiopurine users. Nested cohort analysis of persons with IBD with censoring at both thiopurines and anti-TNF use confirmed a higher baseline risk of BCC and no effect on SCC, comparable to pre-IBD diagnosis findings.

Conclusions
The risk of BCC preceding a diagnosis of UC is higher than in non-UC controls, compared with a generally increased risk of all NMSCs post–IBD diagnosis. Thiopurine and anti-TNF therapy increase the risks for skin cancers in persons with IBD after their diagnoses.
Utilization of Community Science Data to Explore Habitat Suitability of Basal Termite Genera
Authors: Goodman Aaron , Allen Jonah , Brim Jinna , Codella Alessa , Hahn Brittney , Jojo Hassan , BondocGawa Mafla-Mills Zoila , Bondoc Mafla Salka’Tuwa , Oduro Agnes , Wilson Megan , Ware Jessica 
Published: August 2022

AbstractThe advent of community-science databases in conjunction with museum specimen locality information has exponentially increased the power and accuracy of ecological niche modeling (ENM). Increased occurrence data has provided colossal potential to understand the distributions of lesser known or endangered species, including arthropods. Although niche modeling of termites has been conducted in the context of invasive and pest species, few studies have been performed to understand the distribution of basal termite genera. Using specimen records from the American Museum of Natural History (AMNH) as well as locality databases, we generated ecological niche models for 12 basal termite species belonging to six genera and three families. We extracted environmental data from the Worldclim 19 bioclimatic dataset v2, along with SoilGrids datasets and generated models using MaxEnt. We chose Optimal models based on partial Receiving Operating characteristic (pROC) and omission rate criterion and determined variable importance using permutation analysis. We also calculated response curves to understand changes in suitability with changes in environmental variables. Optimal models for our 12 termite species ranged in complexity, but no discernible pattern was noted among genera, families, or geographic range. Permutation analysis revealed that habitat suitability is affected predominantly by seasonal or monthly temperature and precipitation variation. Our findings not only highlight the efficacy of largely community-science and museum-based datasets, but our models provide a baseline for predictions of future abundance of lesser-known arthropod species in the face of habitat destruction and climate change.