bluuebunny/crossref_metadata_2025_split huggingface dataset:
Standing at the Border
Authors: Goyal Yogita 
Published: November 2021

Abstract
If we were to heed Edward Said’s call to see our age as “the age of the refugee, the displaced person, mass immigration,” we would need to reimagine identity, citizenship, and human rights on global and intimate scales. This essay explores how we might redefine the boundaries of our literary canons from the specific vantage point of the refugee. How do existing frames for understanding American literary history—whether those of nation and migration, slavery and segregation, Indigenous dispossession and settler colonialism—help fathom the experience of forced migration? Focusing on the African American literary tradition in particular, and guided by the efforts of Toni Morrison and Colson Whitehead, I outline how centering the figure of the refugee leads to new meanings of home and uprooting, requiring a radical rethinking of citizenship and belonging.
MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data
Authors: Song Meng-Huan , Yan Chaochao , Li Jia-Tang 
Published: November 2021

Abstract
Advances in next-generation sequencing (NGS) technologies have led to an exponential increase in the number of whole genome sequences (WGS) in databases. This wealth of WGS data has greatly facilitated the recovery of full mitochondrial genomes (mitogenomes), which are vital for phylogenetic, evolutionary and ecological studies. Unfortunately, most existing software cannot easily assemble mitogenome reference sequences conveniently or efficiently. Therefore, we developed a seed-free de novo assembly tool, MEANGS, which applies the trie-search method to extend contigs from self-discovery seeds and assemble a mitogenome from animal WGS data. We then used data from 16 species with different qualities to compare the performance of MEANGS with three other available programs. MEANGS exhibited the best overall performance since it was the only one that completed all tests, and it assembled full or partial mitogenomes for all of the tested samples while the others failed. Furthermore, MEANGS selects superior assembly sequences and annotates protein-coding genes. Thus, MEANGS can be one of the most efficient software for generating high-quality mitogenomes so far, the further use of it will benefit the study on mitogenome based on whole genome NGS data. MEANGS is available at https://github.com/YanCCscu/meangs.
Secondary structure assignment of proteins in the absence of sequence information
Authors: Khalife Sammy , Malliavin Thérèse , Liberti Leo 
Published: November 2021

Abstract

Motivation
The structure of proteins is organized in a hierarchy among which the secondary structure elements, α-helix, β-strand and loop, are the basic bricks. The determination of secondary structure elements usually requires the knowledge of the whole structure. Nevertheless, in numerous experimental circumstances, the protein structure is partially known. The detection of secondary structures from these partial structures is hampered by the lack of information about connecting residues along the primary sequence.

Results
We introduce a new methodology to estimate the secondary structure elements from the values of local distances and angles between the protein atoms. Our method uses a message passing neural network, named Sequoia, which allows the automatic prediction of secondary structure elements from the values of local distances and angles between the protein atoms. This neural network takes as input the topology of the given protein graph, where the vertices are protein residues, and the edges are weighted by values of distances and pseudo-dihedral angles generalizing the backbone angles ϕ and ψ. Any pair of residues, independently of its covalent bonds along the primary sequence of the protein, is tagged with this distance and angle information. Sequoia permits the automatic detection of the secondary structure elements, with an F1-score larger than 80% for most of the cases, when α helices and β strands are predicted. In contrast to the approaches classically used in structural biology, such as DSSP, Sequoia is able to capture the variations of geometry at the interface of adjacent secondary structure element. Due to its general modeling frame, Sequoia is able to handle graphs containing only Cα atoms, which is particularly useful on low resolution structural input and in the frame of electron microscopy development.

Availability and implementation
Sequoia source code can be found at https://github.com/Khalife/Sequoia with additional documentation.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Forced Degradation Study of Zanubrutinib: An LC–PDA and LC–MS Approach
Authors: Gollu Gowri , Gummadi Sowjanya , Vemuri Venkata Deepthi , Nalla Swathi , Mathala Nalini , Allam Sasikala 
Published: November 2021

Abstract
Zanubrutinib is an unfamiliar second generation selective Brutson’s Tyrosine Kinase inhibitor used to treat mantle cell lymphoma. In the present analysis, a new, stability indicating reverse-phase, high performance liquid chromatography method was developed and validated for the determination of Zanubrutinib succeeding degradation studies as pert the International Conference on Harmonization guidelines. The chromatographic separation of Zanubrutinib was achieved in a C18 column (250 × 4.6 mm, 5-μm particle size) using a mobile phase of Acetonitrile: 0.1% Tri Ethyl Amine (65:35 v/v) monitored at 219 nm. The forced degradation studies were conducted by exposing the analyte to acidic, alkaline and neutral hydrolysis, oxidative, reductive, photolytic, and thermal stress conditions and the degradation behavior was studied. The analyte showed degradation under acidic, alkaline, oxidative and reductive stress conditions with additional peaks but, it was stable under neutral, photolytic and thermal stress conditions. The developed method was extended to triple quadruple mass spectrometry to characterize degradation products and to study the fragmentation pattern. Total four degradants were characterized including DP1 in acid &base hydrolysis, DP2 in oxidative and DP3, DP4 in reductive stress condition. As no substantial method was available for quantification of Zanubrutinib and to characterize zanubrutinib degradants, this method can be used for regular analysis in quality control labs.
Social relationships in children: favourable influence of activities promoting self-awareness and empathic interaction
Authors: Carro Natalia , Kuperman Marcelo , D’adamo Paola , Lozada Mariana 
Published: November 2021

Abstract
Embodied and intersubjective experience is crucial to the social cognition processes on which interpersonal relationships are based. We assessed whether promoting these processes through participation in self-awareness and empathic interaction activities can influence social integration among peers in 7- to 8-year-old children. The intervention, conducted in a school context, included mindfulness-based practices (favouring self-awareness), empathic collaboration activities and perspective-taking instances (promoting other-oriented awareness). To evaluate social integration levels, children were asked to complete a sociometric questionnaire, each listing the peers they would choose to play with (positive ties) and those they would prefer not to play with (negative ties). Based on this relational data, two types of directed networks were constructed: positive networks (PN) and negative networks (NN), in two temporal instances (pre- and post-intervention). In both the experimental and waitlist groups, pre–post intervention changes in the topology of peer social networks were evaluated by analysing global network properties such as connectivity, degree distribution, density, reciprocity, transitivity and modular structure. Our findings showed that after participating in the intervention social integration was improved, reflected in increased general interconnection of positive ties: greater average connectivity and density in PN, more equitably distributed choices (no evident leadership), greater cohesion and an increase in the number of reciprocal interactions. Additionally, we found a lower level of social rejection; that is, lower average connectivity and density in NN, the persistence of only mutual negative choices and negative ties confined to small groups. These findings were not observed in the waitlist group. This study demonstrates how participation in an intervention that promotes social cognition processes can influence the structure of peer social networks, favouring social integration. The social network analysis provides quantitative evidence of the plasticity of social relationships in children, constituting a valuable tool for the assessment of this kind of intervention at a group level.
Patching zero-day vulnerabilities: an empirical analysis
Authors: Roumani Yaman 
Published: November 2021

Abstract
Zero-day vulnerabilities remain one of the major security threats that are faced by organizations. Once a vendor learns about a zero-day vulnerability, releasing a timely patch becomes a priority given the risk of zero-day exploits. However, we still lack information on the factors that affect patch release time of such vulnerabilities. The main objective of this study is to examine the impact of other as-yet unexplored factors on the patch release time of zero-day vulnerabilities. Using zero-day vulnerability dataset captured between 2010 and 2020, we employ survival analysis technique. Our model explores the impact of vulnerability attack vector, attack complexity, privileges required, user interaction, scope, confidentiality, integrity, and availability impact on patch release timing. Findings show that a zero-day vulnerability is more likely to be patched on time if the vulnerability results in a scope change and affects more vendors, products, and versions. However, a zero-day vulnerability is less likely to be patched on time if it requires privileges and impacts confidentiality. Our sub-analyses also reveal how patch release times vary across different products and vulnerability types.
Use of rapid cardiac magnetic resonance imaging to guide chelation therapy in patients with transfusion-dependent thalassaemia in India: UMIMI study
Authors: Medina Katia Menacho , Abdel-Gadir Amna , Ganga Kartik , Ojha Vineeta , Pratap Surya , Boubertakh Redha , McGrath Louise , Augusto João B , Rikowski Alexander , Mughal Nabila , Khanna Virender Kumar , Seth Tulika , Sharma Sanjiv , Mahajan Amita , Bansal Rajiv K , Srivastava Prabhar , Mahajan Harsh , Mahajan Vidhur , Walker Judith , Seldon Tenzin , Ako Emmanuel , Moon James C , Walker John Malcolm 
Published: November 2021

Abstract

Aims
To explore the impact of incorporating a faster cardiac magnetic resonance (CMR) imaging protocol in a low–middle-income country (LMIC) and using the result to guide chelation in transfusion-dependent patients.

Methods and results
A prospective UK–India collaborative cohort study was conducted in two cities in India. Two visits 13 months apart included clinical assessment and chelation therapy recommendations based on rapid CMR results. Participants were recruited by the local patient advocate charity, who organized the patient medical camps. The average scanning time was 11.3 ± 2.5 min at the baseline and 9.8 ± 2.4 min (P &lt; 0.001) at follow-up. The baseline visit was attended by 103 patients (mean age 25 years) and 83% attended the second assessment. At baseline, 29% had a cardiac T2* &lt; 20 ms, which represents significant iron loading, and 12% had left ventricular ejection fraction &lt;60%, the accepted lower limit in this population. Only 3% were free of liver iron (T2* ≥ 17 ms). At 13 months, more patients were taking intensified dual chelation therapy (43% vs. 55%, P = 0.002). In those with cardiac siderosis (baseline T2* &lt; 20 ms), there was an improvement in T2*—10.9 ± 5.9 to 13.5 ± 8.7 ms, P = 0.005—and fewer were classified as having clinically important cardiac iron loading (T2* &lt; 20 ms, 24% vs. 16%, P &lt; 0.001). This is the first illustration in an LMIC that incorporating CMR results into patient management plans can improve cardiac iron loading.

Conclusion
For thalassaemia patients in an LMIC, a simplified CMR protocol linked to therapeutic recommendation via the patient camp model led to enhanced chelation therapy and a reduction in cardiac iron in 1 year.
Statin use and risk of dementia or Alzheimer’s disease: a systematic review and meta-analysis of observational studies
Authors: Olmastroni Elena , Molari Giulia , De Beni Noemi , Colpani Ornella , Galimberti Federica , Gazzotti Marta , Zambon Alberto , Catapano Alberico L , Casula Manuela 
Published: November 2021

AbstractAimsAs the potential impact of statins on cognitive decline and dementia is still debated, we conducted a meta-analysis of observational studies to examine the effect of statin use on the risk of Alzheimer’s disease (AD) and dementia.Methods and resultsPubMed, Cochrane, and EMBASE were searched since inception to January 2021. Inclusion criteria were: (i) cohort or case–control studies; (ii) statin users compared to non-users; and (iii) AD and/or dementia risk as outcome. Estimates from original studies were pooled using restricted maximum-likelihood random-effect model. Measure of effects were reported as odds ratio (OR) and 95% confidence intervals (CIs). In the pooled analyses, statins were associated with a decreased risk of dementia [36 studies, OR 0.80 (CI 0.75–0.86)] and of AD [21 studies, OR 0.68 (CI 0.56–0.81)]. In the stratified analysis by sex, no difference was observed in the risk reduction of dementia between men [OR 0.86 (CI 0.81–0.92)] and women [OR 0.86 (CI 0.81–0.92)]. Similar risks were observed for lipophilic and hydrophilic statins for both dementia and AD, while high-potency statins showed a 20% reduction of dementia risk compared with a 16% risk reduction associated with low-potency statins, suggesting a greater efficacy of the former, although a borderline statistical significance (P = 0.05) for the heterogeneity between estimates.ConclusionThese results confirm the absence of a neurocognitive risk associated with statin treatment and suggest a potential favourable role of statins. Randomized clinical trials with an ad hoc design are needed to explore this potential neuroprotective effect.
What does antimicrobial stewardship look like where you are? Global narratives from participants in a massive open online course
Authors: Nampoothiri Vrinda , Bonaconsa Candice , Surendran Surya , Mbamalu Oluchi , Nambatya Winnie , Ahabwe Babigumira Peter , Ahmad Raheelah , Castro-Sanchez Enrique , Broom Alex , Szymczak Julia , Zingg Walter , Gilchrist Mark , Holmes Alison , Mendelson Marc , Singh Sanjeev , McLeod Monsey , Charani Esmita 
Published: November 2021

Abstract

Background
Whilst antimicrobial stewardship (AMS) is being implemented globally, contextual differences exist. We describe how the use of a massive open online course (MOOC) platform provided an opportunity to gather diverse narratives on AMS from around the world.

Methods
A free 3 week MOOC titled ‘Tackling antimicrobial resistance: a social science approach’ was launched in November 2019. Learners were asked specific questions about their experiences of AMS via 38 optional free-text prompts dispersed throughout the modules. Content analysis was used to identify key emerging themes from the learners’ responses in the first three runs of the MOOC.

Results
Between November 2019 and July 2020, 1464 learners enrolled from 114 countries. Overall, 199 individual learners provided a total of 1097 responses to the prompts. The diverse perspectives describe unique challenges present in different contexts including ill-defined roles for pharmacists and nurses in AMS; inadequate governance and policy inconsistencies in surveillance for antibiotic consumption and antimicrobial resistance (AMR) in some countries; lack of ownership of antibiotic decision-making and buy-in from different clinical specialties; and human resource and technological constraints. Patients’ knowledge, experiences and perspectives were recognized as a valuable source of information that should be incorporated in AMS initiatives to overcome cultural barriers to the judicious use of antibiotics.

Conclusions
Analysis of learner comments and reflections identified a range of enablers and barriers to AMS implementation across different healthcare economies. Common challenges to AMS implementation included the role of non-physician healthcare workers, resource limitations, gaps in knowledge of AMR, and patient engagement and involvement in AMS.
CircRPPH1 promotes cell proliferation, migration and invasion of non-small cell lung cancer via the PI3K/AKT and JAK2/STAT3 signalling axes
Authors: Xiong Jian-wen , Song Si-bei , Xiong Lin-min , Duan Chuan-hui , Song Qian , Yu Dong-liang , Zhang Xiao-qiang 
Published: November 2021

Abstract
Non-small cell lung cancer (NSCLC) has markedly increased morbidity and mortality rates worldwide. Circular RNAs were shown to regulate NSCLC progression. But the underlying pathways of the circRPPH1-mediated regulation of NSCLC still need further exploration. We evaluated circRPPH1 levels in NSCLC tissues and cell lines via qRT-PCR. Moreover, using ectopic plasmid incorporation and siRNA assays, we analysed the circRPPH1-mediated regulation of cell proliferation (CP), cell migration (CM) and cell invasion (CI) in NSCLC cell lines (H1975 and A549 cells), using CCK-8, colony forming, scratch wound and transwell assays, respectively. CircRPPH1 levels were remarkably high in the NSCLC tissues and cell lines. The transfection experiments showed that circRPPH1 overexpression was able to promote CP, CM and CI of NSCLC cells, while CP, CM and CI were significantly restrained by the knockdown of circRPPH1. We also displayed that circRPPH1 knockdown suppressed the cell progression via inactivating the PI3K/AKT and JAK2/STAT3 signalling axes. Subsequently, in vivo experiment in nude mice was demonstrated that the inhibition of circRPPH1 could reduce the tumour growth of NSCLC. circRPPH1 may accelerate the growth and metastasis of NSCLC, in culture conditions and in animal models, by stimulating the PI3K/AKT and JAK2/STAT3 signalling axes, thus promoting the development of NSCLC.
Review of the southern African Leptestheriidae (Branchiopoda: Spinicaudata), II: Diagnoses and key
Authors: Rogers D Christopher , Meyer-Milne Elizabeth 
Published: November 2021

AbstractWe review and revise the southern African species of Leptestheria Daday, 1913 (Leptestheriidae) based on type specimens when possible as well as on new material. We recognise four species out of the six hitherto reported from the region south of the Kunene, Okavango, and Zambezi rivers. Leptestheria inermis (Barnard, 1929) is shown to be a junior synonym of L. calcarata (Wolf in Daday, 1923), L. striatoconchaBarnard, 1924, and L. rubidgei (Baird, 1862) junior synonyms of L. siliqvaSars, 1898. Leptestheria setosa (Barnard, 1935) is clearly defined with quantifiable diagnostic characters. A key to the species of Leptestheria of southern Africa is presented as an aid to additional surveys and conservation efforts.
Anchored hybrid enrichment resolves the phylogeny ofLacunicambarusHobbs, 1969 (Decapoda: Astacidea: Cambaridae)
Authors: Glon Mael G , Broe Michael B , Crandall Keith A , Daly Meg , Kong Sungsik , Thoma Roger F , Freudenstein John V 
Published: November 2021

AbstractThe taxonomy of North American crayfishes has recently experienced a boom in interest as these crustaceans have become increasingly imperiled. Improving taxonomic resolution can inform and facilitate conservation efforts but has proven challenging for crayfishes due to the limited number of molecular tools available to resolve species complexes and delimit species. The burrowing crayfish LacunicambarusHobbs, 1969 has a particularly convoluted taxonomic history that epitomizes many of the challenges of crayfish taxonomy. Recent studies using mitochondrial DNA (mtDNA) data to resolve this genus have had mixed results: mtDNA data have successfully resolved species-clades within Lacunicambarus but have failed to resolve interspecific relationships. This has precluded research on evolutionary history and biogeography. Our goal was to resolve the phylogeny of Lacunicambarus using anchored hybrid enrichment (AHE) data, a new source of additional molecular markers for estimating phylogenetic relationships. We present the best resolved phylogeny for Lacunicambarus to date and explore discrepancies between this phylogeny and past ones based on mtDNA data. We use this new phylogeny to explore interspecific relationships within Lacunicambarus and redescribe L. erythrodactylus (Simon & Morris, 2014) and L. nebrascensis (Girard, 1852) comb. nov. Our study demonstrates the tremendous contributions that next-generation sequencing methods like AHE can make to crayfish taxonomy and conservation.
Plasma VP8∗-Binding Antibodies in Rotavirus Infection and Oral Vaccination in Young Bangladeshi Children
Authors: Lee Benjamin , Colgate E Ross , Carmolli Marya , Dickson Dorothy M , Gullickson Soyeon , Diehl Sean A , Ara Rifat , Alam Masud , Kibria Golam , Abdul Kader Md , Afreen Sajia , Ferdous Tahsin , Haque Rashidul , Kirkpatrick Beth D 
Published: November 2021

Abstract

Background
Despite the availability and success of live-attenuated oral vaccines, rotavirus (RV) remains the leading cause of pediatric gastroenteritis worldwide. Next-generation vaccines targeting RV VP8∗ are under evaluation, but the role of VP8∗-specific antibodies in human immunity to RV and their potential as immune correlates of protection remains underexplored.

Methods
We measured plasma RV VP8∗-binding antibodies in 2 cohorts of young children in Dhaka, Bangladesh. Plasma from a cohort study of 137 unvaccinated children aged 6-24 months old hospitalized with acute gastroenteritis was assessed for VP8∗ antibody seropositivity. VP8∗ antibodies were compared with the current standard for RV immunity, total RV-specific IgA (RV-IgA). Additionally, VP8∗ antibody responses were measured as part of an immunogenicity trial of a monovalent, oral, live-attenuated RV vaccine (Rotarix).

Results
Fewer children with acute RV gastroenteritis were seropositive for VP8∗-binding IgA or IgG antibodies at hospital admission compared with RV-IgA, suggesting that the absence of VP8∗-binding antibodies more accurately predicts susceptibility to RV gastroenteritis than RV-IgA in unvaccinated children. However, when present, these antibodies appeared insufficient to protect fully from disease and no threshold antibody level for protection was apparent. In vaccinated children, these antibodies were very poorly induced by Rotarix vaccine, suggesting that VP8∗-specific antibodies alone are not necessary for clinical protection following oral vaccination.

Conclusions
This work suggests that VP8∗-binding antibodies may not be sufficient or necessary for protection from RV gastroenteritis following prior RV infection or oral vaccination; the role of VP8∗ antibodies induced by parenteral vaccination with non-replicating vaccines remains to be determined.
Double aortic arch: a rare cause of stridor in infants
Authors: Aladham Youssef , Bonduelle Quentin , Yaro John , Ahmed Omar 
Published: November 2021

Abstract
Double aortic arch is the most common vascular ring anomaly. It usually presents with symptoms related to tracheal and oesophageal compression. The constricting vascular ring may lead to stridor in infants and young children, which could be mistaken for upper respiratory tract infections or foreign body aspiration. It is therefore prudent to have a high index of suspicion when evaluating cases of paediatric stridor. Contrast-enhanced computed tomography and cardiac magnetic resonance imaging are the diagnostic modalities of choice to investigate vascular rings. We report a case of a stridulous infant with a double aortic arch.