bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recycling of buffing dust tanneries waste to prepare structural thermal insulation panels
Authors: Ulfat Wajad , Mohyuddin Ayesha , Amjad Muhammad , Saeed Shagufta , Mujahid Beenish 
Published: November 2021

Abstract
Thermal insulation panels were prepared by mixing the buffing dust obtained from tanneries waste with the polystyrene. The ratio in weight percentage of buffing dust, polystyrene and blowing agent was 20:77:3 respectively in these panels. The samples were prepared in co-twine extruder at 210 °C. Different physico-chemical properties were investigated for these samples that are required to analyze the usability of a material for construction. The composite panels showed better thermal insulation characteristics than the simple polystyrene boards. This study demonstrated that prepared composite panels have good thermal conductivity (0.029 W m−1–K−1 at 27 °C), density (300 Kg m−3), compression strength (6.25 ton) and water absorption (7.5%) without degradation of mechanical properties. Thermogravimetric analysis depicted that composite panels were thermally stable from 200 °C to 412 °C. FTIR analysis showed that composite has carbonyl and free amino functional groups. The SEM study explained that voids were created in the composite and homogeneousity was decreased after the addition of buffing dust. The composite had 62% of carbon and 0.2% of chromium as determined by EDX analysis. The results suggested that the prepared composite panels can be used as thermal insulation boards in building sector which will help in the recycling of waste produced by leather industry and consequently a reduction in environmental pollution.
Towards efficient description of type-C London dispersion forces between low-dimensional metallic nanostructures
Authors: Dobson John F 
Published: November 2021

Abstract
This paper concerns one of the remaining difficulties encountered in efficient modelling schemes for dispersion forces between nanostructures. Dispersion (van der Waals, vdW) interactions between molecules and nanostructures can be reliably described in principle by computationally intensive high-level theory, but this is often not computationally feasible in practice, so more efficient methods are continually being developed. Progress has been made with nonlocal density functionals (vdW-DFs) and with atom-based schemes (D4, MBD, uMBD). In such efficient schemes, the effects beyond additive two-atom terms have been categorized as ‘type A’, ‘type B’ and ‘type C’ non-additivity (see Dobson (2014 Int. J. Quantum Chem.
114 1157)). Atom-based models using coupled-harmonic-oscillator theory (MBD) now deal adequately with type A and type B non-additivity, but type-C effects, related to gapless collective electronic excitations, can occur in low-dimensional metals, and these are not correctly described by the efficient schemes mentioned above.
From analytic work within the direct random phase approximation (dRPA), type-C effects have long been known to cause the vdW interaction between well-separated low-d metals to fall off much more slowly with separation than is predicted by the above-mentioned efficient schemes. The slower decay means that type-C effects dominate in this asymptotic large-separation regime. It has not been clear, however, whether type-C physics contributes significantly to the vdW interaction of low-d metals near to contact, where the forces are much larger.
The present work uses recent semi-analytic dRPA results to provide some evidence that type-C effects are indeed significant near to contact between metallic carbon nanotubes, and between doped graphene sheets.
Some guidelines are therefore suggested for ways to combine the semi-analytic dRPA approach, here termed ‘SAM-dRPA’, with the existing efficient vdW algorithms described above.
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses
Authors: García-Jimeno Luis , Fustero-Torre Coral , Jiménez-Santos María José , Gómez-López Gonzalo , Di Domenico Tomás , Al-Shahrour Fátima 
Published: November 2021

Abstract

Summary
bollito is an automated, flexible and parallelizable computational pipeline for the comprehensive analysis of single-cell RNA-seq data. Starting from FASTQ files or preprocessed expression matrices, bollito performs both basic and advanced tasks in single-cell analysis integrating &gt;30 state-of-the-art tools. This includes quality control, read alignment, dimensionality reduction, clustering, cell-marker detection, differential expression, functional analysis, trajectory inference and RNA velocity. bollito is built using the Snakemake workflow management system, which easily connects each execution step and facilitates the reproducibility of results. bollito’s modular design makes it easy to incorporate other packages into the pipeline enabling its expansion with new functionalities.

Availability and implementation
Source code is freely available at https://gitlab.com/bu_cnio/bollito under the MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Limits and potential of combined folding and docking
Authors: Pozzati Gabriele , Zhu Wensi , Bassot Claudio , Lamb John , Kundrotas Petras , Elofsson Arne 
Published: November 2021

Abstract

Motivation
In the last decade, de novo protein structure prediction accuracy for individual proteins has improved significantly by utilising deep learning (DL) methods for harvesting the co-evolution information from large multiple sequence alignments (MSAs). The same approach can, in principle, also be used to extract information about evolutionary-based contacts across protein–protein interfaces. However, most earlier studies have not used the latest DL methods for inter-chain contact distance prediction. This article introduces a fold-and-dock method based on predicted residue-residue distances with trRosetta.

Results
The method can simultaneously predict the tertiary and quaternary structure of a protein pair, even when the structures of the monomers are not known. The straightforward application of this method to a standard dataset for protein–protein docking yielded limited success. However, using alternative methods for generating MSAs allowed us to dock accurately significantly more proteins. We also introduced a novel scoring function, PconsDock, that accurately separates 98% of correctly and incorrectly folded and docked proteins. The average performance of the method is comparable to the use of traditional, template-based or ab initio shape-complementarity-only docking methods. Moreover, the results of conventional and fold-and-dock approaches are complementary, and thus a combined docking pipeline could increase overall docking success significantly. This methodology contributed to the best model for one of the CASP14 oligomeric targets, H1065.

Availability and implementation
All scripts for predictions and analysis are available from https://github.com/ElofssonLab/bioinfo-toolbox/ and https://gitlab.com/ElofssonLab/benchmark5/. All models joined alignments, and evaluation results are available from the following figshare repository https://doi.org/10.6084/m9.figshare.14654886.v2.

Supplementary information
Supplementary data are available at Bioinformatics online.
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications
Authors: Bevilacqua Martina , Paladin Lisanna , Tosatto Silvio C E , Piovesan Damiano 
Published: November 2021

AbstractSummaryBiological data is ever-increasing in amount and complexity. The mapping of this data to biological entities such as nucleotide and amino acid sequences supports biological data analysis, classification and prediction. Sequence alignments and comparison allow the transfer of knowledge to evolutionary-related entities, the mapping of functional domains, the identification of binding and modification sites. To support these types of studies, we developed ProSeqViewer, a tool to visualize annotation on single sequences and multiple sequence alignments. This state-of-the-art multifunctional library was developed as a modular component to be integrated into static or dynamic web resources and support intuitive visualization of sequence features. ProseSeqViewer is extremely lightweight, fast, interactive, dynamic, responsive and works at any screen size. It generates pure HTML which is compatible with any browser and operating system. ProSeqViewer can exchange events with other visualization components and is already used by multiple biological databases.Availability and implementationProSeqViewer is an open-source TypeScript library compatible with state-of-the-art website environments. The source code and an extensive documentation including use cases are available from the URL: https://github.com/BioComputingUP/ProSeqViewer.
Effect of primary tumour resection without curative intent in patients with metastatic neuroendocrine tumours of the small intestine and right colon: meta-analysis
Authors: Van Den Heede Klaas , Chidambaram Swathikan , Van Slycke Sam , Brusselaers Nele , Warfvinge Carl Fredrik , Ohlsson Håkan , Nordenström Erik , Almquist Martin 
Published: November 2021

Abstract

Background
Patients with small intestinal neuroendocrine tumours (siNETs) usually present with advanced disease. Primary tumour resection without curative intent is controversial in patients with metastatic siNETs. The aim of this meta-analysis was to investigate survival after primary tumour resection without curative intent compared with no resection in patients with metastatic siNETs.

Methods
A systematic literature search was performed, using MEDLINE® (PubMed), Embase®, Web of Science, and the Cochrane Library up to 25 February 2021. Studies were included if survival after primary tumour resection versus no resection in patients with metastatic siNETs was reported. Results were pooled in a random-effects meta-analysis, and are reported as hazard ratios (HRs) with 95 per cent confidence intervals. Sensitivity analyses were undertaken to enable comment on the impact of important confounders.

Results
After screening 3659 abstracts, 16 studies, published between 1992 and 2021, met the inclusion criteria, with a total of 9428 patients. Thirteen studies reported HRs adjusted for important confounders and were included in the meta-analysis. Median overall survival was 112 (i.q.r. 82–134) months in the primary tumour resection group compared with 60 (74–88) months in the group without resection. Five-year overall survival rates were 74 (i.q.r. 67–77) and 44 (34–45) per cent respectively. Primary tumour resection was associated with improved survival compared with no resection (HR 0.55, 95 per cent c.i. 0.47 to 0.66). This effect remained in sensitivity analyses.

Conclusion
Primary tumour resection is associated with increased survival in patients with advanced, metastatic siNETs, even after adjusting for important confounders.
Cognitive Evolution and China’s International Development Cooperation
Authors: Yu Bowen 
Published: November 2021

Abstract
China’s approach to International Development Cooperation (IDC) has been one of continuous evolution. The 2000s version of Chinese IDC applied a request-/project-centrism methodology, focused on the infrastructure sector, and mixed aid with business. Since the launch of the Belt and Road Initiative (BRI), the methodological dimension of the existing IDC model has changed by virtue of a growing emphasis on top-level design, sectoral programmes, and high standards for project implementation. How to explain these changes? Different from the conventional material-functionalist approaches, this article attributes the development of China’s IDC to cognitive evolution—an intra-community collective learning mechanism that drives changes in norms and practices. Cognitive evolution consists of the following three interconnected processes: uncertainty build-up; experimentation; and selection. Three factors that may shape the trajectories of cognitive evolution are as follows: the legacy of orthodox norms; the availability of transferable local ideas; and the communal interpretation of candidate ideas’ performance. The IDC model of the 2000s was constructed based on critical reflections on the internationalist foreign aid model of the Mao era and on the IDC policy community’s interpretation and transplantation of China’s development experience. The methodology of this IDC model—request-/project-centrism—has come under new pressure for change due to the BRI’s ambition to engender more substantial and sustainable developmental impact.
Playing together, laughing together: rapid facial mimicry and social sensitivity in lowland gorillas
Authors: Bresciani Chiara , Cordoni Giada , Palagi Elisabetta 
Published: November 2021

AbstractIn nonhuman animals, the phenomenon of rapid facial mimicry (RFM)—the automatic, involuntary, and rapid (&lt;1 s) replication of others’ facial expressions—has been mainly investigated in the playful domain. In immature lowland gorillas Gorilla gorilla gorilla both play face (PF) and full PF (FPF) are rapidly mimicked between the players. This makes the species suitable to test hypotheses on the factors influencing RFM during play. The observations on 3 captive groups of lowland gorillas (N = 27) revealed that contrary to expectations, the closeness of social bond negatively influenced the occurrence of RFM but it did not affect either RFM latency or its overlapping index (OVERLAP). RFM was affected by the degree of symmetry of play fighting: the more balanced the session, the higher the occurrence of RFM. Players of the same sex class responded faster than players of different sex. These findings suggest that RFM may help synchronizing behaviors of playmates matching in size (same-sex) and promote symmetric playful interactions. “Laughing together” (measured by the RFM OVERLAP) lasted longer when the responder perfectly mirrored the partner expression (PF→PF; FPF→FPF). If PF and FPF convey information on the different play roughness degree, through “laughing together” the players could coordinate their actions and share positive moods and playful intensity. If the perfect congruency in the motor resonance, also known as social sensitivity, can foster a possible emotional dialogue between gorillas remains to be investigated.
Characteristics of Psychologists Assessing Deaf and Hard of Hearing Clients
Authors: Wilkins Alexander M , Morere Donna A , Pick Lawrence H , Day Lori A , Anderson Melissa L 
Published: November 2021

Abstract
Psychological assessment plays a large part in the practice of psychology. Over the years, steps have been taken towards ensuring ethical and culturally sensitive psychological assessment for underserved populations, but little is known about the current state of the field of assessment of deaf and hard-of-hearing (DHH) individuals. An exploratory survey of school and clinical psychologists who work with DHH clients (n = 30) was conducted to obtain a snapshot of the state of the field. The current article focuses on sociodemographic characteristics, clinical training, clinical experiences, and language abilities of clinical psychologists who work with DHH clients. Participants averaged 15 years of assessment experience and almost all participants had some type of specialized training in assessing DHH clients. More than half of participants reported their ability to use multiple languages and communication approaches as either excellent or good. Current findings were compared with a similar survey from nearly 50 years ago (Levine, E. S. (1974). Psychological tests and practices with the deaf: A survey of the state of the art. Volta Review, 76, 298–319), and significant differences were found in participants’ self-reported experience with DHH clients, training, and methods of communication.
Intravascular ultrasound-guided drug-coated balloon venoplasty for in-stent restenosis in pulmonary veins stenosis: a case report
Authors: Portero-Portaz Juan J , Córdoba-Soriano Juan G , Gallardo-López Arsenio , Jiménez-Mazuecos Jesús M 
Published: November 2021

Abstract

Background
Pulmonary veins stenosis (PVS) after atrial fibrillation radiofrequency ablation is an uncommon complication. When it occurs, percutaneous treatment is the preferred approach. There is a lack of standardized procedures, and when stenting restenosis is relatively common.

Case summary
We present a young patient with recurrence of PVS after first percutaneous treatment. The recurrence of haemoptysis and dyspnoea after treatment in PVS allowed the diagnosis of significant stenosis again in our patient. In the Heart Team, we opted for a new percutaneous treatment, using intravascular ultrasound (IVUS) to optimize the final result.

Discussion
Nowadays, percutaneous approach is preferred and among percutaneous treatments for PVS, stenting has shown better results than balloon angioplasty (BA). Despite this, experience in in-stent restenosis is limited, and there is a lack of adequate and specific material for its approach. In this case, we present the possible role of the IVUS and the drug-coated BA in this entity.
Long-term outcomes following rheumatic heart disease diagnosis in Australia
Authors: Stacey Ingrid , Hung Joseph , Cannon Jeff , Seth Rebecca J , Remenyi Bo , Bond-Smith Daniela , Griffiths Kalinda , Sanfilippo Frank , Carapetis Jonathan , Murray Kevin , Katzenellenbogen Judith M 
Published: November 2021

AbstractAims Rheumatic heart disease (RHD) is a major contributor to cardiac morbidity and mortality globally. This study aims to estimate the probability and predictors of progressing to non-fatal cardiovascular complications and death in young Australians after their first RHD diagnosis.Methods and results This retrospective cohort study used linked RHD register, hospital, and death data from five Australian states and territories (covering 70% of the whole population and 86% of the Indigenous population). Progression from uncomplicated RHD to all-cause death and non-fatal cardiovascular complications (surgical intervention, heart failure, atrial fibrillation, infective endocarditis, and stroke) was estimated for people aged &lt;35 years with first-ever RHD diagnosis between 2010 and 2018, identified from register and hospital data. The study cohort comprised 1718 initially uncomplicated RHD cases (84.6% Indigenous; 10.9% migrant; 63.2% women; 40.3% aged 5–14 years; 76.4% non-metropolitan). The composite outcome of death/cardiovascular complication was experienced by 23.3% (95% confidence interval: 19.5–26.9) within 8 years. Older age and metropolitan residence were independent positive predictors of the composite outcome; history of acute rheumatic fever was a negative predictor. Population group (Indigenous/migrant/other Australian) and sex were not predictive of outcome after multivariable adjustment.Conclusion This study provides the most definitive and contemporary estimates of progression to major cardiovascular complication or death in young Australians with RHD. Despite access to the publically funded universal Australian healthcare system, one-fifth of initially uncomplicated RHD cases will experience one of the major complications of RHD within 8 years supporting the need for programmes to eradicate RHD.
What Is Acting?
Authors: Guo Yuchen 
Published: November 2021

Abstract
We can portray or take on the role of someone whom we are not. For example, a professional actor can play the role of a fictional character who does not exist in the real world, although she believes she is not that person. This behavior is named “acting.” My aim here is to locate the necessary and sufficient conditions of acting. In my view, acting is a process of communication between actors and audiences. One of its necessary components is that actors use their own features to represent those features that their characters have; another is that actors intend to make their audiences imagine that they are themselves identical to their characters. In this article, I specify these two components, critique other views of the definition of acting and distinguish acting from other similar processes.
Immunodeficiency and Autoantibodies to Cytokines
Authors: Knight Vijaya 
Published: November 2021

AbstractBackgroundAnti-cytokine autoantibodies (AAbs) associated with an infectious phenotype are now included along with anti-complement AAbs and somatic pathogenic gene variants as a distinct category termed ‘phenocopies of primary immunodeficiencies’ in the classification of inborn errors of immunity. Anti-cytokine AAbs target specific cytokine pathways, leading to inordinate susceptibility to specific organisms, generally in the setting of immunocompetence.ContentAnti-cytokine AAbs are detected in the majority of healthy individuals and may play a regulatory role in limiting exaggerated responses to cytokines. While it is not well understood why some individuals with anti-cytokine AAbs develop increased susceptibility to organisms of low pathogenicity and others do not, it is likely that genetics and environment play a role. To date, AAbs to interferon gamma (IFNγ), interferon alpha (IFNα), interleukins-17 and 22 (IL-17/IL-22), interleukin-6 and granulocyte macrophage colony stimulating factor (GM-CSF) and their association with increased susceptibility to nontuberculous mycobacteria and other intracellular organisms, viral infections, Candida albicans, Staphylococcus aureus and other pyogenic organisms, and fungal infections respectively, have been described. The clinical phenotype of these patients is very similar to that of individuals with pathogenic gene variants in the specific cytokine pathway that the autoantibody targets, hence the term ‘phenocopy.’ Recognition of anti-cytokine AAbs as a distinct cause of immunodeficiency or immune dysregulation is important for appropriate management of such patients.SummaryUnderstanding the roles that anti-cytokine AAbs play in health and disease continues to be a fascinating area of research. Evaluating generally immunocompetent individuals who present with chronic, treatment refractory, or unusual infections for anti-cytokine AAbs is critical as it may direct therapy and disease management.
Needle in a haystack: a case report of splenic foreign body-associated sepsis
Authors: Turner Benedict R H , Barnacle James , Sheth Hemant 
Published: November 2021

Abstract
Instances of foreign bodies impacted in solid organs are rare, and rarer still are reports of objects in the spleen. A 42-year-old presented septic with abdominal pain, high inflammatory markers and haemodynamic instability. She was found to have a splenic haematoma and a 4-cm hyperdense foreign body within the spleen. Ultrasound-guided drainage of the haematoma isolated Streptococcus anginosus and conservative management with intravenous antibiotics avoided the need for emergency splenectomy. The bacterium isolated was the same cultured 9 months previously from the patient’s empyema fluid. The origin of the foreign body was not identified, though is made of metal and pre-dates any hospital admissions. The case raised the question of how an object might penetrate the spleen without knowledge of the patient and highlighted the risks of foreign body-associated sepsis, the risks and benefits of emergency splenectomy and management of complex cases with paucity of evidence.