bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evangelicalism: A Very Short Introduction
Authors: Stackhouse Jr. John G. 
Published: May 2022

Abstract
Evangelicalism: A Very Short Introduction examines the heart of the evangelical phenomenon. Evangelicalism encompasses many Protestant denominations that share core tenets of Christianity. It is foremost defined by its fervent worship, its regard for the Bible as the ultimate theological and ethical authority, the desire to evangelize, and the insistence on religious conversion known as being “born again.” As the Evangelical movement has grown rapidly, so has its influence on the political stage. This VSI tells the evangelical story from the preacher-led revivals of the eighteenth century, through the frontier camp meetings of the nineteenth, to the mass urban rallies of the twentieth and the global megachurches of the twenty-first.
Uracil-auxotrophic marker recycling system for multiple gene disruption in Pseudozyma antarctica
Authors: Sameshima-Yamashita Yuka , Yarimizu Tohru , Uenishi Hirohide , Tanaka Takumi , Kitamoto Hiroko 
Published: May 2022

Abstract
The basidiomycetous yeast Pseudozyma antarctica, which has multiple auxotrophic markers, was constructed, without inserting a foreign gene, as the host strain for the introduction of multiple useful genes. P. antarctica was more resistant to ultraviolet (UV) irradiation than the model yeast Saccharomyces cerevisiae, and a Paura3 mutant (C867T) was obtained after 3 min of UV exposure. A uracil-auxotrophic marker (URA3) recycling system developed in ascomycetous yeasts and fungi was applied to the P. antarctica Paura3 strain. The PaLYS12 and PaADE2 loci were disrupted via site-directed homologous recombination of PaURA3 (pop-in), followed by the removal of PaURA3 (pop-out). In the obtained double auxotrophic strain (Palys12Δ, Paura3), PaADE2 was further disrupted, and PaURA3 was removed to obtain the triple auxotrophic strain PGB800 (Paura3, Palys12Δ, Paade2Δ). The whole-genome sequence of the PGB800 strain did not contain foreign genes used for genetic manipulation and disrupted PaADE2 and PaLYS12 and removed PaURA3, as planned.
Does Down syndrome influence the outcomes of congenital cardiac surgery? A systematic review and meta-analysis
Authors: Wang Benjamen , Verrocchi Justin , Liew Danny , Zentner Dominica 
Published: May 2022

Abstract

Background
Congenital cardiac surgery for individuals with Down syndrome (DS) has historically occurred at a reduced frequency. Little data are available regarding long-term post-congenital cardiac surgical outcomes. Limited sample sizes and clinical heterogeneity require a pooled analysis approach.

Aims
To compare long-term outcomes post-congenital heart surgery between adults with and without DS.

Methods
Databases (Medline, Embase, and PubMed) were searched utilizing terms related to DS and congenital heart disease.
Studies that enrolled adults (&gt;18 years) with operated congenital heart disease and compared long-term outcomes with respect to DS presence were included. All study designs were included, but those with limited/peri-operative follow-up, non-English texts, case studies, and literature reviews were excluded.
Blinded screening, data extraction, and quality assessment were independently conducted by two reviewers. QUIPS criteria were used for risk of bias analysis. Both random- and fixed-effects models were used for meta-analysis.

Results
A total of 23 studies (n = 10 466) were included. Risk of bias was frequently high due to unblinded retrospective study designs and analyses limited in adjustment for other prognostic factors.
Meta-analysis demonstrated no effect of DS on long-term mortality [hazard ratio (HR) 0.86, 95% confidence interval (95% CI) 0.6–1.23], to a maximum described follow-up of 38 years. Lower cardiac reoperation risk (HR 0.6, 95% CI 0.46–0.78) for individuals with DS was found on pooled analysis. Meta-analysis was limited by between-study variation.

Conclusion
DS does not affect post-congenital cardiac surgical survival in adulthood. Reduced reoperation may reflect challenges in assessing functional and symptomatic status and/or concerns regarding perceived reoperation difficulties or likely benefits.
Career Pressures and Organizational Evil: A Novel Perspective on the Study of Organized Violence
Authors: Scharpf Adam , Gläßel Christian 
Published: May 2022

AbstractDictators, rebel commanders, and mafia bosses frequently delegate gruesome and immoral tasks to their subordinates. However, most individuals want to avoid such work. This analytical essay proposes an institutional logic to understand how dictatorships, insurgent organizations, and criminal gangs get their evil work done nonetheless. We argue that common features of organizations produce mundane career pressures that incentivize subordinates to zealously execute reprehensible tasks. Subordinates may come under pressure for six distinct reasons: incompetence, misconduct, origin, isolation, organizational backlog, and shrinkage. Superiors, in turn, can exploit that pressured subordinates hope to improve their prospects for advancement by loyally executing the organization’s evil tasks. Empirically, we illustrate how Nazi Germany utilized each of the suggested career pressures to staff the units in charge of the Holocaust. We highlight that our logic might also apply to less extreme forms of organizational evil. Together, the essay offers a novel perspective to demystify radical behavior in state and non-state organizations with important implications for our understanding of transnational terrorist violence and underworld crimes.
Alignment of the central galaxies with the environment
Authors: Rodriguez Facundo , Merchán Manuel , Artale M Celeste 
Published: May 2022

ABSTRACT
In this work, we combine ellipticity and major axis position angle measurements from the Sloan Digital Sky Server Data Release 16 with the group finder algorithm of Rodriguez & Merchán to determine the alignment of the central galaxies with the surrounding structures and satellite galaxies lying in their group. We use two independent methods: a modified version of the two-point cross-correlation function and the angle between the central galaxy orientation and the satellite galaxies relative position. The first method allows us to study the inner and outer regions of the cluster, while the second method provides information within the haloes. Our results show that central galaxies present anisotropy in the correlation function up to $\sim 10 \, h^{-1}~{\rm Mpc}$, which becomes ∼10 per cent stronger for the brightest ones (0.1Mr &lt; −21.5). When we split the galaxy sample by colour, we find that red central galaxies are the main contributors to this anisotropy. We also show that this behaviour does not depend on the group mass or central galaxy ellipticity. Finally, our results are in agreement with previous findings, showing that the two-point cross-correlation function is a good tracer of the galaxy alignments using all galaxies and not only those of the group to which it belongs. In addition, this feature allows us to explore the behaviour of the alignment on larger scales.
On the effect of surface bipolar magnetic regions on the convection zone dynamo
Authors: Pipin V V 
Published: May 2022

ABSTRACTWe investigate the effect of surface bipolar magnetic regions (BMRs) on the large-scale dynamo distributed in the bulk of the convection zone. The study employs the non-linear three-dimensional mean-field dynamo model. We model the emergence of the BMRs on the surface through the non-axisymmetric magnetic buoyancy effect, which acts on the large-scale toroidal magnetic field in the upper half of the convection zone. The non-axisymmetric magnetic field that results from this mechanism is shallow. On the surface, the effect of the BMRs on the magnetic field generation is dominant. However, because of the shallow distribution of BMRs, its effect on the global dynamo is less compared with the effect on the convective zone dynamo. We find that the mean-field α-effect, which acts on the non-axisymmetric magnetic field of the BMRs, provides the greater contribution to the dynamo process than the tilt of the BMRs. Even so, the fluctuations of the tilt of the BMRs lead to parity braking in the global dynamo. At the surface, the non-axisymmetric magnetic fields, which are generated because of the activity of the BMRs, show a tendency for the bihelical spectrum with positive sign for the low ℓ modes during the maximum of the magnetic activity cycle.
Narrative Assessments in Higher Education: A Scoping Review to Identify Evidence-Based Quality Indicators
Authors: Chakroun Molk , Dion Vincent R. , Ouellet Kathleen , Graillon Ann , Désilets Valérie , Xhignesse Marianne , St-Onge Christina 
Published: May 2022

PurposeNarrative comments are increasingly used in assessment to document trainees’ performance and to make important decisions about academic progress. However, little is known about how to document the quality of narrative comments, since traditional psychometric analysis cannot be applied. The authors aimed to generate a list of quality indicators for narrative comments, to identify recommendations for writing high-quality narrative comments, and to document factors that influence the quality of narrative comments used in assessments in higher education.MethodThe authors conducted a scoping review according to Arksey & O’Malley’s framework. The search strategy yielded 690 articles from 6 databases. Team members screened abstracts for inclusion and exclusion, then extracted numerical and qualitative data based on predetermined categories. Numerical data were used for descriptive analysis. The authors completed the thematic analysis of qualitative data with iterative discussions until they achieved consensus for the interpretation of the results.ResultsAfter the full-text review of 213 selected articles, 47 were included. Through the thematic analysis, the authors identified 7 quality indicators, 12 recommendations for writing quality narratives, and 3 factors that influence the quality of narrative comments used in assessment. The 7 quality indicators are (1) describes performance with a focus on particular elements (attitudes, knowledge, skills); (2) provides a balanced message between positive elements and elements needing improvement; (3) provides recommendations to learners on how to improve their performance; (4) compares the observed performance with an expected standard of performance; (5) provides justification for the mark/score given; (6) uses language that is clear and easily understood; and (7) uses a nonjudgmental style.ConclusionsAssessors can use these quality indicators and recommendations to write high-quality narrative comments, thus reinforcing the appropriate documentation of trainees’ performance, facilitating solid decision making about trainees’ progression, and enhancing the impact of narrative feedback for both learners and programs.
Functional and Patient-reported Outcomes following Transmetatarsal Amputation in High-risk Limb Salvage Patients
Authors: Deldar Romina , Cach Gina , Sayyed Adaah A. , Truong Brian N. , Kim Emily , Atves Jayson N. , Steinberg John S. , Evans Karen K. , Attinger Christopher E. 
Published: May 2022

Background:
Transmetatarsal amputation (TMA) is performed in patients with nonhealing wounds of the forefoot. Compared with below-knee amputations, healing after TMA is less reliable, and often leads to subsequent higher-level amputation. The aim of this study was to evaluate the functional and patient-reported outcomes of TMA.

Methods:
A retrospective review of patients who underwent TMA from 2013 to 2021 at our limb-salvage center was conducted. Primary outcomes included postoperative complications, secondary proximal lower extremity amputation, ambulatory status, and mortality. Univariate and multivariate analyses were performed to evaluate independent risk factors for higher-level amputation after TMA. Patient-reported outcome measures for functionality and pain were also obtained.

Results:
A total of 146 patients were identified. TMA success was achieved in 105 patients (72%), and 41 patients (28%) required higher-level amputation (Lisfranc: 31.7%, Chopart: 22.0%, below-knee amputations: 43.9%). There was a higher incidence of postoperative infection in patients who subsequently required proximal amputation (39.0 versus 9.5%, P < 0.001). At mean follow-up duration of 23.2 months (range, 0.7–97.6 months), limb salvage was achieved in 128 patients (87.7%) and 83% of patients (n = 121) were ambulatory. Patient-reported outcomes for functionality corresponded to a mean maximal function of 58.9%. Pain survey revealed that TMA failure patients had a significantly higher pain rating compared with TMA success patients (P = 0.016).

Conclusions:
TMA healing remains variable, and many patients will eventually require a secondary proximal amputation. Multi-institutional studies are warranted to identify perioperative risk factors for higher-level amputation and to further evaluate patient-reported outcomes.
Intravenous immunoglobulin and treatment in COVID-19 patients: case series
Authors: Mohtadi Negar , Ghaysouri Abas , Nazari Ali , Feizi Jalil , Tavan Hamed 
Published: May 2022

Introduction:
Intravenous immunoglobulin (IVIG) is one of the drugs used to treat COVID-19. The aim of this study was to evaluate the role of IVIG in the treatment of COVID-19 in hospitalized patients.

Materials and methods:
The patients received IVIG before being intubated. The patients’ symptoms, disease severity, clinical features, and chest computed tomography findings were compared between before and after the treatment.

Results:
Out of 62 patients who received IVIG, 35 patients (56.5%) were male, and 27 patients (43.5%) were female. Overall, 13 (21%) patients died, and 49 (79%) recovered and were discharged from the hospital.

Conclusion:
IVIG can be used as an effective drug to save patients’ lives before they enter the intubation phase.
SARS-CoV-2 NSP3, NSP4 and NSP6 mutations and Epistasis during the pandemic in the world: Evolutionary Trends and Natural Selections in Six Continents
Authors: fooladinezhad Haniyeh , Shahidi Maryamsadat , Mahmanzar Mohammadamin , Mahdavi Bahar , Tokhanbigli Samaneh , Sisakht Mahsa Mollapour , Moradi Bahman , Ganjalikhany Mohamad Reza , Rahimian Karim , Ganjalikhani-Hakemi Mazdak 
Published: May 2022

AbstractBackgroundThe Coronavirus 2019 (COVID-19) was named by the World Health Organization (WHO) due to its rapid transmittable potential and high mortality rate. Based on the critical role of None Structural Proteins (NSP), NSP3, NSP4, and NSP6 in COVID-19, this study attempts to investigate the superior natural selection mutations and Epistasis among these none structural proteins.MethodsApproximately 6.5 million SARS-CoV-2 protein sequences of each NSP3, NSP4, and NSP6 nonstructural protein were analyzed from January 2020 to January 2022. Python programming language was utilized to preprocess and apply inclusion criteria on the FASTA file to prepare a list of suitable samples. NSP3, NSP4, and NSP6 were aligned to the reference sequence to compare and identify mutation patterns categorized based on frequency, geographical zone distribution, and date. To discover epistasis situations, linear regression between mutation frequency and date among candidate genes was performed to determine correlations.ResultsThe rate of NSP3, NSP4, and NSP6 mutations in divided geographical areas was different. Based on continental studies, P1228L (54.48%), P1469S (54.41%), and A488S (53.86%) mutations in NSP3, T492I (54.84%), and V167L (52.81%) in NSP4 and T77A (69.85%) mutation in NSP6 increased over time, especially in recent months. For NSP3, Europe had the highest P1228L, P1469S, and A488S mutations. For NSP4, Oceania had the highest T492I and V167L mutations, and for NSP6, Europe had the highest T77A mutation. Hot spot regions for NSP3, NSP4, and NSP6 were 1358 to 1552 AA, 150 to 200 AA, and 58 to 87 AA, respectively. Our results showed a significant correlation and co-occurrence between NSP3, NSP4, and NSP6 mutations.ConclusionWe conclude that the effect of mutations on virus stability and replication can be predicted by examining the amino acid changes of P1228L, P1469S, A488S, T492I, V167L and T77A mutations. Also, these mutations can possibly be effective on the function of proteins and their targets in the host cell.
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide
Authors: Chi L. América , Asgharpour Somayeh , Correa-Basurto José , Bandala Cindy Rodríguez , Martínez-Archundia Marlet 
Published: May 2022

AbstractNew therapies that allow natural healing processes are required. Such as the endogenous peptide called Angiotensin-(1-7), a safe and eff e drug, which is able to re-balance the Renin-Angiotensin system affected during several pathologies, including the new COVID-19; cardiovascular, renal, and pulmonary disease; diabetes; neuropathic pain; Alzheimer and cancer. However, one of the limiting factors for its application is its unfavorable pharmacokinetic profile. In this work, we propose the coupling of Angiotensin-(1-7) to PAMAM dendrimers in order to evaluate the capacity of the nanocarrier to improve isolated peptide features and to gain insight into the structural as well as the energetic basis of its molecular binding. The In Silico tests were performed in acidic and neutral pH conditions as well as amino-terminated and hydroxyl-terminated PAMAM dendrimers. High-rigor computational approaches, such as molecular dynamics and metadynamics simulations were used. We found that, at neutral pH, PAMAM dendrimers with both terminal types are able to interact stably with 3 Angioteinsin-(1-7) peptides through ASP1, TYR4 and PRO7 key aminoacids, however, there are some differences in the binding sites of the peptides. In general, they bind on the surface in the case of the hydroxyl-terminated compact dendrimer and in the internal zone in the case of the amino-terminated open dendrimer. At acidic pH, PAMAM dendrimers with both terminal groups are still able to interact with peptides either internalized or in its periphery, however, the number of contacts, the percentage of coverage and the number of HBs are lesser than at neutral pH, suggesting a state for peptide release. In summary, amino-terminated PAMAM dendrimer showed slightly better features to bind, load and protect Angiotensin-(1-7) peptides.
Detection of latent Epstein-Barr virus gene expression in single-cell sequencing of peripheral blood mononuclear cells
Authors: Bäckerholm Alan , Tian Yarong , Holmqvist Isak , Xie Guojiang , Vracar Diana , Abrahamsson Sanna , Guibentif Carolina , Tang Ka-Wei 
Published: May 2022

AbstractEpstein-Barr virus (EBV) DNA is regularly found in the blood of patients with EBV associated diseases and occasionally in healthy individuals. However, EBV infected primary B-lymphocytes have not yet been detected using scRNA seq. Here, we screened the viral transcriptome in single cell RNA sequencing datasets from peripheral blood to identify virus infected cells. Whereas EBV RNA was detected in an immunocompromised patient, EBV associated nasopharyngeal carcinoma and multiple sclerosis samples did not display any levels of circulating EBV RNA. We further screened whole-blood samples from a cohort of immunosuppressed patients for viral transcripts using a custom enhanced RT-qPCR panel and detected latency programs dominated by noncoding RNAs (EBERs and RPMS1). To explore the interplay between the EBV and the host-cell transcriptome profile, we used enriched B-lymphocytes from a splenectomy patient with 30% EBER positivity estimated by in situ hybridization and performed 5’ single-cell RNA sequencing with paired VDJ profiling. The EBV expression pattern of the patients’ B-lymphocytes confirmed the RT-qPCR assay with RPMS1 and LMP-1/BNLF2a/b significantly dominating the sequenced EBV polyadenylated RNA. A comparison between the expression profile of EBV positive B-lymphocytes and healthy controls B-lymphocytes revealed the upregulation in genes involved in cell population proliferation when infected with EBV. This is further supported by a measurable polyclonal expansion in the patient, as compared to a control, emphasizing EBV’s role in a host-cell’s tendency for cellular expansion. However, when contrasting to cells that have undergone malignant transformation, the primary EBV infected cells display a rather dissimilar expression profile, even to cells that are supposed to simulate primary EBV infection (I.e. Lymphoblastoid Cell Lines). This implies that during primary infection of EBV, the host-cell enters a state of premalignancy rather than a complete oncogenic transformation at the initial time of infection
Gram-positive bacteria evade phage predation through endolysin-mediated L-form conversion
Authors: Wohlfarth Jan C. , Feldmüller Miki , Schneller Alissa , Kilcher Samuel , Burkolter Marco , Pilhofer Martin , Schuppler Markus , Loessner Martin J. 
Published: May 2022

AbstractBacteriophages kill bacteria by osmotic lysis towards the end of the lytic cycle. In the case of Gram-positive bacteria, peptidoglycan-degrading endolysins released at the end of infection cycle cause explosive cell lysis not only of the infected host, but can also attack non-infected bystander cells. Here, we show that in osmotically stabilized environments, Listeria monocytogenes can evade phage predation by transient conversion to a cell wall-deficient L-form state. This L-form escape is triggered by endolysins disintegrating the cell wall from without, leading to turgor-driven extrusion of wall-deficient, yet viable L-form cells. Remarkably, in absence of phage predation, we show that L-forms can quickly revert to the walled state. These findings suggest that L-form conversion represents a population-level persistence mechanism to evade complete eradication by phage attack. Importantly, we also demonstrate phage-mediated L-form switching of the urinary tract pathogen Enterococcus faecalis in human urine, which underscores that this escape route may be widespread and has important implications for phage- and endolysin-based therapeutic interventions.
The substrate scopes of enzymes: a general prediction model based on machine and deep learning
Authors: Kroll Alexander , Ranjan Sahasra , Engqvist Martin K. M. , Lercher Martin J. 
Published: May 2022

ABSTRACTFor a comprehensive understanding of metabolism, it is necessary to know all potential substrates for each enzyme encoded in an organism’s genome. However, for most proteins annotated as enzymes, it is unknown which primary and/or secondary reactions they catalyze [1], as experimental characterizations are time-consuming and costly. Machine learning predictions could provide an efficient alternative, but are hampered by a lack of information regarding enzyme non-substrates, as available training data comprises mainly positive examples. Here, we present ESP, a general machine learning model for the prediction of enzyme-substrate pairs, with an accuracy of over 90% on independent and diverse test data. This accuracy was achieved by representing enzymes through a modified transformer model [2] with a trained, task-specific token, and by augmenting the positive training data by randomly sampling small molecules and assigning them as non-substrates. ESP can be applied successfully across widely different enzymes and a broad range of metabolites. It outperforms recently published models designed for individual, well-studied enzyme families, which use much more detailed input data [3, 4]. We implemented a user-friendly web server to predict the substrate scope of arbitrary enzymes, which may support not only basic science, but also the development of pharmaceuticals and bioengineering processes.