bluuebunny/crossref_metadata_2025_split huggingface dataset:
End-to-end learning of evolutionary models to find coding regions in genome alignments
Authors: Mertsch Darvin , Stanke Mario 
Published: January 2022

AbstractMotivationThe comparison of genomes using models of molecular evolution is a powerful approach for finding, or toward understanding, functional elements. In particular, comparative genomics is a fundamental building brick in annotating ever larger sets of alignable genomes completely, accurately and consistently.ResultsWe here present our new program ClaMSA that classifies multiple sequence alignments using a phylogenetic model. It uses a novel continuous-time Markov chain machine learning layer, named CTMC, whose parameters are learned end-to-end and together with (recurrent) neural networks for a learning task. We trained ClaMSA discriminatively to classify aligned codon sequences that are candidates of coding regions into coding or non-coding and obtained four times fewer false positives for this task on vertebrate and fly alignments than existing methods at the same true positive rate. ClaMSA and the CTMC layer are general tools that could be used for other machine learning tasks on tree-related sequence data.Availability and implementationFreely from https://github.com/Gaius-Augustus/clamsa.Supplementary informationSupplementary data are available at Bioinformatics online.
massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation
Authors: Abdelmoula Walid M , Stopka Sylwia A , Randall Elizabeth C , Regan Michael , Agar Jeffrey N , Sarkaria Jann N , Wells William M , Kapur Tina , Agar Nathalie Y R 
Published: January 2022

Abstract

Motivation
Mass spectrometry imaging (MSI) provides rich biochemical information in a label-free manner and therefore holds promise to substantially impact current practice in disease diagnosis. However, the complex nature of MSI data poses computational challenges in its analysis. The complexity of the data arises from its large size, high-dimensionality and spectral nonlinearity. Preprocessing, including peak picking, has been used to reduce raw data complexity; however, peak picking is sensitive to parameter selection that, perhaps prematurely, shapes the downstream analysis for tissue classification and ensuing biological interpretation.

Results
We propose a deep learning model, massNet, that provides the desired qualities of scalability, nonlinearity and speed in MSI data analysis. This deep learning model was used, without prior preprocessing and peak picking, to classify MSI data from a mouse brain harboring a patient-derived tumor. The massNet architecture established automatically learning of predictive features, and automated methods were incorporated to identify peaks with potential for tumor delineation. The model’s performance was assessed using cross-validation, and the results demonstrate higher accuracy and a substantial gain in speed compared to the established classical machine learning method, support vector machine.

Availability and implementation
https://github.com/wabdelmoula/massNet. The data underlying this article are available in the NIH Common Fund’s National Metabolomics Data Repository (NMDR) Metabolomics Workbench under project id (PR001292) with http://dx.doi.org/10.21228/M8Q70T.

Supplementary information
Supplementary data are available at Bioinformatics online.
Berberine alleviates LPS-induced apoptosis, oxidation, and skewed lineages during mouse preimplantation development
Authors: Miao Xiaosu , Cui Wei 
Published: January 2022

Abstract
Female infertility is a heterogeneous disorder with a variety of complex causes, including inflammation and oxidative stress, which are also closely associated with the pathogenesis of polycystic ovary syndrome (PCOS). As a new treatment for PCOS, berberine (BER), a natural compound from Berberis, has been clinically applied recently. However, the mechanisms underlying the association between BER and embryogenesis are still largely unknown. In this study, effects of BER on preimplantation development were evaluated under both normal and inflammatory culture conditions induced by lipopolysaccharide (LPS) in mice. Our data first suggest that BER itself (25 nM) does not affect embryo quality or future developmental potency; however, it can effectively alleviate LPS-induced embryo damage by mitigating apoptosis via reactive oxygen species (ROS)-/caspase-3-dependent pathways and by suppressing proinflammatory cytokines via inhibition of the NF-κB signaling pathway during preimplantation embryonic development. In addition, skewed cell lineage specification in the inner cell mass (ICM) and primitive endoderm (PE) caused by LPS can also be successfully rescued with BER. In summary, these findings for the first time demonstrate the nontoxicity of low doses of BER and its antiapoptotic and antioxidative properties on embryonic cells during mammalian preimplantation development.
The placenta as a target of opioid drugs
Authors: Rosenfeld Cheryl S 
Published: January 2022

Abstract
Opioid drugs are analgesics increasingly being prescribed to control pain associated with a wide range of causes. Usage of pregnant women has dramatically increased in the past decades. Neonates born to these women are at risk for neonatal abstinence syndrome (also referred to as neonatal opioid withdrawal syndrome). Negative birth outcomes linked with maternal opioid use disorder include compromised fetal growth, premature birth, reduced birthweight, and congenital defects. Such infants require lengthier hospital stays necessitating rising health care costs, and they are at greater risk for neurobehavioral and other diseases. Thus, it is essential to understand the genesis of such disorders. As the primary communication organ between mother and conceptus, the placenta itself is susceptible to opioid effects but may be key to understanding how these drugs affect long-term offspring health and potential avenue to prevent later diseases. In this review, we will consider the evidence that placental responses are regulated through an endogenous opioid system. However, maternal consumption of opioid drugs can also bind and act through opioid receptors express by trophoblast cells of the placenta. Thus, we will also discuss the current human and rodent studies that have examined the effects of opioids on the placenta. These drugs might affect placental hormones associated with maternal recognition of pregnancy, including placental lactogens and human chorionic gonadotropin in rodents and humans, respectively. A further understanding of how such drugs affect the placenta may open up new avenues for early diagnostic and remediation approaches.
Predicting postoperative complications and their impact on quality of life and functional status in older patients with breast cancer
Authors: Lemij A A , van der Plas-Krijgsman W G , Bastiaannet E , Merkus J W S , van Dalen T , Vulink A J E , van Gerven L , Guicherit O R , Linthorst-Niers E M H , Lans T E , van der Pol C C , Wyld L , Morgan J L , Portielje J E A , de Glas N A , Liefers G J 
Published: January 2022

Abstract

Background
The percentage of older patients undergoing surgery for early-stage breast cancer has decreased over the past decade. This study aimed to develop a prediction model for postoperative complications to better inform patients about the benefits and risks of surgery, and to investigate the association between complications and functional status and quality of life (QoL).

Methods
Women aged at least 70 years who underwent surgery for Tis–3 N0 breast cancer were included between 2013 and 2018. The primary outcome was any postoperative complication within 30 days after surgery. Secondary outcomes included functional status and QoL during the first year after surgery, as assessed by the Groningen Activity Restriction Scale and the European Organisation for Research and Treatment of Cancer QLQ-C30 and QLQ-BR23 questionnaires. A prediction model was developed using multivariable logistic regression and validated externally using data from the British Bridging the Age Gap Study. Linear mixed models were used to assess QoL and functional status over time.

Results
The development and validation cohorts included 547 and 2727 women respectively. The prediction model consisted of five predictors (age, polypharmacy, BMI, and type of breast and axillary surgery) and performed well in internal (area under curve (AUC) 0.76, 95 per cent c.i. 0.72 to 0.80) and external (AUC 0.70, 0.68 to 0.72) validations. Functional status and QoL were not affected by postoperative complication after adjustment for confounders.

Conclusion
This validated prediction model can be used to counsel older patients with breast cancer about the postoperative phase. Postoperative complications did not affect functional status nor QoL within the first year after surgery even after adjustment for predefined confounders.
Effect of Maternal Immunization With 10-Valent Pneumococcus Conjugate Vaccine (PCV-10), 23-Valent Pneumococcus Polysaccharide Vaccine, or Placebo on the Immunogenicity of PCV-10 in Human Immunodeficiency Virus–Exposed Uninfected Infants: A Randomized Clinical Trial
Authors: Mussi-Pinhata Marisa M , Ward Shawn , Laimon Lauren , Pelton Stephen I , Canniff Jennifer , Golner Amanda , Bone Frederic , Newton Lassallete , Muresan Petronella , Fenton Terence , Johnson Michael J , João Esau C , Santos Breno R , Pilotto Jose H , Oliveira Ricardo H , Pinto Jorge A , Dal Bó Andrea G B L , Kreitchmann Regis , Chakhtoura Nahida , Duarte Geraldo , Weinberg Adriana 
Published: January 2022

Abstract

Background
The effect of pneumococcal vaccination of mothers with human immunodeficiency virus (HIV) on infant responses to childhood vaccination has not been studied. We compared the immunogenicity of 10-valent pneumococcus conjugate vaccine (PCV-10) in HIV-exposed uninfected infants born to mothers who received PCV-10, 23-valent pneumococcus polysaccharide vaccine (PPV-23), or placebo during pregnancy.

Methods
Antibody levels against 7 serotypes were measured at birth, before the first and second doses of PCV-10m and after completion of the 2-dose regimen in 347 infants, including 112 born to mothers who received PPV-23, 112 who received PCV-10, and 119 who received placebo during pregnancy. Seroprotection was defined by antibody levels ≥0.35 µg/mL.

Results
At birth and at 8 weeks of life, antibody levels were similar in infants born to PCV-10 or PPV-23 recipients and higher than in those born to placebo recipient. After the last dose of PCV-10, infants in the maternal PCV-10 group had significantly lower antibody levels against 5 serotypes than those in the maternal PPV-23 group and against 3 serotypes than those in the maternal placebo group, and they did not have higher antibody levels against any serotype. The seroprotection rate against 7 serotypes was 50% in infants in the maternal PCV-10 group, compared with 71% in both of the maternal PPV-23 and placebo groups (P &lt; .001).

Conclusions
Administration of PCV-10 during pregnancy was associated with decreased antibody responses to PCV-10 and seroprotection rates in infants. Considering that PCV-10 and PPV-23 had similar immunogenicity in pregnant women with HIV and that administration of PPV-23 did not affect the immunogenicity of PCV-10 in infants, PPV-23 in pregnancy may be preferred over PCV-10.
Outcomes of the management of corrosive injuries of the upper digestive tract in a tertiary care center
Authors: Biswas Ravi Shankar , Ray Dipankar 
Published: January 2022

Summary
Esophageal stricture is the most common delayed sequelae of aerodigestive tract corrosive injuries. Early endoscopic dilatation is an integral part of corrosive injury management. Self-dilatation of the esophagus is effective in preventing stricture recurrence. In this prospective study, we included patients with corrosive aerodigestive tract injury from January 2009 to December 2020. We analyzed the outcome of the endoscopic dilatation and self-dilatation treatments administered to patients with a corrosive esophageal stricture. Among 295 patients, 164 had an esophageal injury, 73 had esophago-gastric injury, 55 had a gastric injury, and 3 had the pharyngeal injury. Of the 295 patients, 194 (81.85%) underwent dilatation, and 13 patients with diffuse esophageal injury underwent upfront surgery. Successful dilatation was performed in 169 (87.11%) patients. Of the 68 patients undergoing self-dilatation, 63 patients achieved nutritional autonomy by 28 days. Early endoscopic dilatation effectively prevents surgery, and self-dilatation appears promising to prevent recurrent esophageal stricture.
The Effect of Concealed-Carry and Handgun Restrictions on Gun-Related Deaths: Evidence from the Sullivan Act of 1911
Authors: Depew Briggs , Swensen Isaac 
Published: January 2022

AbstractThe 1911 New York State Sullivan Act outlawed carrying concealable firearms without a licence, established strict licencing rules and regulated the sale and possession of handguns. We analyse the effects of the Sullivan Act using historical data on mortality rates, pistol permits and citations for illegal carrying. Our analysis of pistol permits and citations reveal clear initial effects of the Sullivan Act on gun-related behaviours. Using synthetic control and difference-in-differences methodologies, our main analyses show no effects on overall homicide rates, evidence of a reduction in overall suicide rates and strong evidence of a large and sustained decrease in gun-related suicide rates.
Impact of hospital mergers: a systematic review focusing on healthcare quality measures
Authors: Mariani Marco , Sisti Leuconoe Grazia , Isonne Claudia , Nardi Angelo , Mete Rosario , Ricciardi Walter , Villari Paolo , De Vito Corrado , Damiani Gianfranco 
Published: January 2022

Abstract

Background
Despite mergers have increasingly affected hospitals in the recent decades, literature on the impact of hospitals mergers on healthcare quality measures (HQM) is still lacking. Our research aimed to systematically review evidence regarding the impact of hospital mergers on HQM focusing especially on process indicators and clinical outcomes.

Methods
The search was carried out until January 2020 using the Population, Intervention, Comparison and Outcome model, querying electronic databases (MEDLINE, Scopus, Web Of Science) and refining the search with hand search. Studies that assessed HQM of hospitals that have undergone a merger were included. HQMs were analyzed through a narrative synthesis and a strength of the evidence analysis based on the quality of the studies and the consistency of the findings.

Results
The 16 articles, included in the narrative synthesis, reported inconsistent findings and few statistically significant results. All indicators analyzed showed an insufficient strength of evidence to achieve conclusive results. However, a tendency in the decrease of the number of beds, hospital staff and inpatient admissions and an increase in both mortality and readmission rate for acute myocardial infarction and stroke emerged in our analysis.

Conclusions
In our study, there is no strong evidence of improvement or worsening of HQM in hospital mergers. Since a limited amount of studies currently exists, additional studies are needed. In the meanwhile, hospital managers involved in mergers should adopt a clear evaluation framework with indicators that help to periodically and systematically assess HQM ascertaining that mergers ensure and primarily do not reduce the quality of care.
Anti-malarial plants in Ethiopia and their activities on drug-resistant malaria
Authors: Sema Yimeslal Atnafu , Waktola Teshale Areda 
Published: January 2022

AbstractIn Ethiopia, the impacts of malaria continue to cause a many number of morbidity and mortality that accounts to most-outpatient observations. Ethiopia recently designed to attain nationwide malaria control by 2030 by beginning sub-national elimination in districts with low malaria transmission. However, the rise of drug-resistant parasites, especially Plasmodium falciparum hinder the malaria-containment strategies. Plasmodium falciparum and Plasmodium vivax are dispersed all over Ethiopia, and account for 60% and 40% of malaria cases, respectively. The aim of this report was to overview the phytochemical constituents, diversity, and effect of some compound extracts on drug-resistant plasmodium species. Many plant species, a total 200 identified by 82 studies, are used in traditional malaria treatments throughout the country. Allium sativum, Croton macrostachyus, and Carica papaya were the more frequently used medicinal plant species. There are so many phytochemical constituents found in medicinal plants used to treat malaria. Alkaloids, flavonoids, phenolics, terpenoids, and glycosides are the most-reported for their effective activity on drug-resistant malaria.
Bactericidal efficacy of slightly acidic electrolyzed water (SAEW) against Listeria monocytogenes planktonic cells and biofilm on food-contact surfaces
Authors: Hao Jianxiong , Zhang Junyi , Zheng Xueqi , Zhao Dandan 
Published: January 2022

Abstract
In the present study, the bactericidal efficacy of slightly acidic electrolyzed water (SAEW) against Listeria monocytogenes (L. monocytogenes) planktonic cells and biofilm on food-contact surfaces including stainless steel and glass was systematically evaluated. The results showed that SAEW (pH 5.09 and available chlorine concentration (ACC) of 60.33 mg/L) could kill L. monocytogenes on food-contact surfaces completely in 30 s, a disinfection efficacy equal to that of NaClO solutions (pH 9.23 and ACC of 253.53 mg/L). The results showed that long exposure time and high ACC contributed to the enhancement of the disinfection efficacy of SAEW on L. monocytogenes on food-contact surfaces. Moreover, the log reduction of SAEW treatment presented an increasing tendency within the prolonging of treatment time when SAEW was used to remove the L. monocytogenes biofilm formed on stainless steel and glass surfaces, which suggested that SAEW could remove L. monocytogenes biofilm effectively and its disinfection efficacy is equal to (in the case of stainless steel) or higher than (in the case of glass) that of high-ACC NaClO solutions. In addition, the results of the crystal violet staining and scanning electron microscopy also demonstrated that SAEW treatment could remove the L. monocytogenes biofilm on food-contact surfaces.
Reconstructing the Roles of Human Rights Treaty Organs under the ‘Two-Tiered Bounded Deliberative Democracy’ Theory
Authors: Takata Hinako 
Published: January 2022

Abstract
Growing concern for the democratic legitimacy of human rights treaty organs calls for the construction of an autonomous conception of ‘democracy’ as a constitutional principle of human rights treaties, and the reconstruction of the roles of treaty organs per that conception. This study responds to this call by proposing an original ‘two-tiered bounded deliberative democracy’ theory that harmonizes human rights with democracy globally. This theory gives priority to national deliberations while setting certain frameworks and limits on them based on the principles and values that have been firmly established through international deliberations, including human rights treaty standards. The theory not only appropriately explains the roles of treaty organs within the conception of democracy but also offers a comprehensive normative framework to guide their roles and interactions with other actors. Even for those who champion different versions of democracy, it offers a solid basis for constructive discussions and fruitful engagement.
Cloud services and government digital sovereignty in Australia and beyond
Authors: Mitchell Andrew D , Samlidis Theodore 
Published: January 2022

Abstract
The Australian government has expressed concerns about various ‘data challenges’ confronting the public sector. Similar concerns are reverberating throughout the globe. Other governments continue to voice and act upon their own apprehensions about the threats posed to public and private society by attenuations to their nations’ ‘digital sovereignty’. This article critically examines the Australian government’s potential justifications, particularly under international trade law, for introducing digital sovereignty policies explicitly targeted at protecting government cyber systems and government data. We explore the risks and vulnerabilities of hosting government data offshore or with foreign cloud providers onshore. We find that Australia has sufficient latitude under its existing trade commitments, and within its current procurement framework, to introduce legitimate and proportionate digital sovereignty measures for the public sector.
Priming effect of colour on aiding the attentional reorientation in sequential presentations of temporal data vizualisation: evidence from eye-tracking
Authors: Peng Ningyue , Xue Chengqi , Wang Haiyan , Niu Yafeng , Wu Lei 
Published: January 2022

Abstract
The paper by Ningyue Peng, Chengqi Xue, Haiyan Wang, Yafeng Niu and Lei Wu, published in Interacting with Computers (August 2021), explores the use of colour to influence behavioural performance using eye-tracking.
WebGIS approach of entity-oriented search to visualize historical and cultural events
Authors: Wei Tong , Sang Yuchen , Chen Shufen , Wang Letian , Wang Rui , Wang Jun , Huang Qi , Wang Jun 
Published: January 2022

Abstract
The chronological biography or ‘Nianpu’ is a special style of Chinese historical writing formed by a person’s life events in time order. It provides significant records for the research of historical events. However, from syntactic collation, structural, and semantic aspects, the heterogeneousness of Nianpu materials caused the lack of systematical information collation, which could hinder the research of historical events. The article presents a semantic WebGIS platform based on an entity-oriented search and visualization system to reorganize unstructured information. It delivers: (1) a Chinese historical event database to store and manage Chinese historical information derived from the chronological biography; (2) an ontology to integrate different historical datasets; and (3) a web geographic information system to visualize and analyze information of historical events. This platform achieves the reorganization of historical event information at spatial and temporal levels by the Web. It enables humanities researchers to explore the relationships of historical entities and their evolution visually and interactively. The platform is available at https://nianpu.pkudh.org/.
Running the gauntlet – survival of small circumbinary planets migrating through destabilizing resonances
Authors: Martin David V , Fitzmaurice Evan 
Published: January 2022

ABSTRACT
All of the known circumbinary planets are large (Rp ≥ 3 R⊕). Whilst observational biases may account for this dearth of small planets, in this paper we propose a theoretical explanation. Most of the known planets are near the stability limit, interspersed between potentially unstable 5:1, 6:1, and 7:1 mean motion resonances with the binary. It is believed that these planets did not form in situ, but rather migrated from farther out in the disc, and hence passed through these resonances. Planets are expected to migrate at a speed proportional to their mass, and a slower rate makes resonant capture and subsequent ejection more likely. Therefore, whilst large planets may be able to successfully ‘run the gauntlet’, small planets may be imperilled. This hypothesis is tested using N-body integrations of migration in a truncated and turbulent disc. We discover that surprisingly none of the known planets exist interior to a fully unstable resonance. We demonstrate that resonant ejection of migrating planets may occur in nature, and that it does indeed disproportionately affect small planets, but it requires a highly turbulent disc and its efficiency is likely too low to fully explain a dearth of Rp &lt; 3 R⊕ planets.