bluuebunny/crossref_metadata_2025_split huggingface dataset:
Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning
Authors: Jiang Dejun , Sun Huiyong , Wang Jike , Hsieh Chang-Yu , Li Yuquan , Wu Zhenxing , Cao Dongsheng , Wu Jian , Hou Tingjun 
Published: December 2021

AbstractAccurate prediction of atomic partial charges with high-level quantum mechanics (QM) methods suffers from high computational cost. Numerous feature-engineered machine learning (ML)-based predictors with favorable computability and reliability have been developed as alternatives. However, extensive expertise effort was needed for feature engineering of atom chemical environment, which may consequently introduce domain bias. In this study, SuperAtomicCharge, a data-driven deep graph learning framework, was proposed to predict three important types of partial charges (i.e. RESP, DDEC4 and DDEC78) derived from high-level QM calculations based on the structures of molecules. SuperAtomicCharge was designed to simultaneously exploit the 2D and 3D structural information of molecules, which was proved to be an effective way to improve the prediction accuracy of the model. Moreover, a simple transfer learning strategy and a multitask learning strategy based on self-supervised descriptors were also employed to further improve the prediction accuracy of the proposed model. Compared with the latest baselines, including one GNN-based predictor and two ML-based predictors, SuperAtomicCharge showed better performance on all the three external test sets and had better usability and portability. Furthermore, the QM partial charges of new molecules predicted by SuperAtomicCharge can be efficiently used in drug design applications such as structure-based virtual screening, where the predicted RESP and DDEC4 charges of new molecules showed more robust scoring and screening power than the commonly used partial charges. Finally, two tools including an online server (http://cadd.zju.edu.cn/deepchargepredictor) and the source code command lines (https://github.com/zjujdj/SuperAtomicCharge) were developed for the easy access of the SuperAtomicCharge services.
The developmentally dynamic microRNA transcriptome of Glossina pallidipes tsetse flies, vectors of animal trypanosomiasis
Authors: Naitore Careen , Villinger Jandouwe , Kibet Caleb K , Kalayou Shewit , Bargul Joel L , Christoffels Alan , Masiga Daniel K 
Published: December 2021

Abstract

Summary
MicroRNAs (miRNAs) are single stranded gene regulators of 18–25 bp in length. They play a crucial role in regulating several biological processes in insects. However, the functions of miRNA in Glossina pallidipes, one of the biological vectors of African animal trypanosomosis in sub-Saharan Africa, remain poorly characterized. We used a combination of both molecular biology and bioinformatics techniques to identify miRNA genes at different developmental stages (larvae, pupae, teneral and reproductive unmated adults, gravid females) and sexes of G. pallidipes. We identified 157 mature miRNA genes, including 12 novel miRNAs unique to G. pallidipes. Moreover, we identified 93 miRNA genes that were differentially expressed by sex and/or in specific developmental stages. By combining both miRanda and RNAhybrid algorithms, we identified 5550 of their target genes. Further analyses with the Gene Ontology term and KEGG pathways for these predicted target genes suggested that the miRNAs may be involved in key developmental biological processes. Our results provide the first repository of G. pallidipes miRNAs across developmental stages, some of which appear to play crucial roles in tsetse fly development. Hence, our findings provide a better understanding of tsetse biology and a baseline for exploring miRNA genes in tsetse flies.

Availability and implementation
Raw sequence data are available from NCBI Sequence Read Archives (SRA) under Bioproject accession number PRJNA590626.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
C5a receptor inhibitor avacopan in immunoglobulin A nephropathy—an open-label pilot study
Authors: Bruchfeld Annette , Magin Hasan , Nachman Patrick , Parikh Samir , Lafayette Richard , Potarca Antonia , Miao Shichang , Bekker Pirow 
Published: December 2021

ABSTRACT

Background
Improvement of proteinuria as a marker for disease activity is associated with a better renal outcome in immunoglobulin A nephropathy (IgAN). Complement is an effector pathway in IgA-mediated kidney injury. Avacopan, a selective C5a receptor inhibitor, has previously shown efficacy in anti-neutrophil cytoplasmic antibody–associated vasculitis. The aim of this study was to evaluate the safety and efficacy of avacopan in patients with IgAN with persistent proteinuria despite a maximally tolerated dose of renin–angiotensin–aldosterone system blockade. The efficacy evaluation was based on the change in proteinuria.

Methods
This open-label pilot trial enrolled adult patients with biopsy-proven IgAN, urinary protein:creatinine ratio (UPCR) &gt;1 g/g creatinine and an estimated glomerular filtration rate (eGFR) &gt;60 mL/min/1.73 m2 or &gt;45 mL/min/1.73 m2 if eGFR has not declined &gt;10 mL/min/1.73 m2 over the previous 24 weeks. If the UPCR remained at &gt;1 g/g creatinine after an 8-week run-in period, patients started avacopan 30 mg twice daily. The primary efficacy endpoint was the change in the slope of the UPCR from the 8-week run-in period to the slope in the 12-week avacopan dosing period.

Results
A total of 10 of 15 screened patients entered the run-in period. Seven patients with a UPCR &gt;1 g/g creatinine received avacopan. Six of seven patients had numerical improvement in the UPCR during the avacopan treatment period, three of whom had a numerical improvement of ∼50% at week 12. At week 24, five of seven patients still showed numerical improvement in the UPCR compared with baseline. The urinary monocyte chemoattractant protein-1:creatinine ratio decreased numerically 30% by week 8, possibly reflecting the anti-inflammatory activity of avacopan. Avacopan was well tolerated. There was one serious adverse event of unstable angina, which was deemed to be unrelated to avacopan.

Conclusions
This short-term pilot study showed an improvement in the slope of the UPCR, with ∼50% improvement in three of seven patients with IgAN. Longer avacopan treatment duration may be indicated for maximal benefit.
Neoadjuvant chemoradiotherapy, chemotherapy, and radiotherapy do not significantly increase the incidence of anastomotic leakage after esophageal cancer surgery: a meta-analysis
Authors: Jin Zixian , Zhang Jian , Chen Dong , Wu Sikai , Xue Penglai , Zhu Kanghao , Xu Congcong , Zhu Chengchu , Zhang Bo 
Published: December 2021

Summary
This study investigated whether neoadjuvant therapies, such as neoadjuvant chemoradiotherapy (NCRT), neoadjuvant chemotherapy (NCT), and neoadjuvant radiotherapy (NRT), would affect the incidence of anastomotic leakage (AL) after esophageal cancer surgery. Published randomized controlled trials were reviewed, and the incidence of AL after esophageal cancer was statistically analyzed in each study. Meta-analysis was performed using Revman and Stata software. A total of 17 randomized controlled trials with 2874 patients were reviewed showing that, in general, preoperative neoadjuvant therapies were not significant risk factors for AL after esophageal cancer surgery (relative risk [RR] = 0.82, 95% CI = 0.64–1.04). NCRT and NRT did not significantly increase the risk of postoperative AL in patients with esophageal cancer (RR = 0.81, 95% CI = 0.63–1.05; RR = 0.64, 95% CI = 0.14–2.97, respectively). Moreover, NCT has no significant correlation with the occurrence of AL (RR = 1.01, 95% CI = 0.57–1.80). NCRT, NCT, and NRT do not significantly increase the incidence of gastroesophageal AL after esophageal cancer surgery.
Assessing the Economic Viability of the Mechanized Removal of Understory Beech during a Shelterwood Harvest
Authors: Weyrens Josh , Germain Rene 
Published: December 2021

Abstract
Beech bark disease is a pathogenic complex that has been spreading throughout the American beech’s range since the 1800s. A litany of negative consequences have manifested from the infestation of this disease, many of which deteriorate the ecological functions of forestland. This case study sought to analyze the cost structure for removing a recalcitrant beech understory via mechanized shelterwood harvesting. High-resolution data regarding the day-to-day operation of harvesting equipment was collected using daily production journals. Interviews were conducted with the logging company owner and maintenance supervisor to gather additional information required to calculate machine costs, overhead, job specific costs, and trucking costs. The yield from this harvest was 527 metric tonnes of sawtimber and 4,893 tonnes of clean chips. The total harvesting cost equated to $4,651/ha, with the cost attributed to removing beech at $204/ha. Despite the additional cost of beech removal, the logger generated a total profit of $5,965 and a return on investment of 7.5%, allowing us to conclude that mechanized harvesting can be a viable beech removal strategy given the forest stocking and market conditions that are in place.
From Model Organisms to Humans, the Opportunity for More Rigor in Methodologic and Statistical Analysis, Design, and Interpretation of Aging and Senescence Research
Authors: Chusyd Daniella E , Austad Steven N , Brown Andrew W , Chen Xiwei , Dickinson Stephanie L , Ejima Keisuke , Fluharty David , Golzarri-Arroyo Lilian , Holden Richard , Jamshidi-Naeini Yasaman , Landsittel Doug , Lartey Stella , Mannix Edward , Vorland Colby J , Allison David B 
Published: December 2021

AbstractThis review identifies frequent design and analysis errors in aging and senescence research and discusses best practices in study design, statistical methods, analyses, and interpretation. Recommendations are offered for how to avoid these problems. The following issues are addressed: (a) errors in randomization, (b) errors related to testing within-group instead of between-group differences, (c) failing to account for clustering, (d) failing to consider interference effects, (e) standardizing metrics of effect size, (f) maximum life-span testing, (g) testing for effects beyond the mean, (h) tests for power and sample size, (i) compression of morbidity versus survival curve squaring, and (j) other hot topics, including modeling high-dimensional data and complex relationships and assessing model assumptions and biases. We hope that bringing increased awareness of these topics to the scientific community will emphasize the importance of employing sound statistical practices in all aspects of aging and senescence research.
Associations Between Life-Course Socioeconomic Conditions and the Pace of Aging
Authors: Schrempft Stephanie , Belsky Daniel W , Draganski Bogdan , Kliegel Matthias , Vollenweider Peter , Marques-Vidal Pedro , Preisig Martin , Stringhini Silvia 
Published: December 2021

Abstract

Background
Socioeconomic disadvantage is a well-established predictor of morbidity and mortality, and is thought to accelerate the aging process. This study examined associations between life-course socioeconomic conditions and the Pace of Aging, a longitudinal measure of age-related physiological decline.

Methods
Data were drawn from a Swiss population-based cohort of individuals originally recruited between 2003 and 2006, and followed up for 11 years (2 834 women, 2 475 men aged 35–75 years [mean 52]). Pace of Aging was measured using 3 repeated assessments of 12 biomarkers reflecting multiple body systems. Analysis tested associations of socioeconomic conditions with physiological status at baseline and with the Pace of Aging.

Results
Participants with more life-course socioeconomic disadvantage were physiologically older at baseline and experienced faster Pace of Aging. Effect sizes (β) for associations of childhood socioeconomic disadvantage with baseline physiological status ranged from 0.1 to 0.2; for adulthood socioeconomic disadvantage, effect sizes ranged from 0.2 to 0.3. Effect sizes were smaller for associations with the Pace of Aging (&lt;0.05 for childhood disadvantage, 0.05–0.1 for adulthood disadvantage). Those who experienced disadvantaged socioeconomic conditions from childhood to adulthood aged 10% faster over the 11 years of follow-up as compared with those who experienced consistently advantaged socioeconomic conditions. Covariate adjustment for health behaviors attenuated associations, but most remained statistically significant.

Conclusions
Socioeconomic inequalities contribute to a faster Pace of Aging, partly through differences in health behaviors. Intervention to slow aging in at-risk individuals is needed by midlife, before etiology of aging-related diseases become established.
Two-step full waveform inversion of diving and reflected waves with the diffraction-angle-filtering-based scale-separation technique
Authors: Kim Donggeon , Hwang Jongha , Min Dong-Joo , Oh Ju-Won , Alkhalifah Tariq 
Published: December 2021

SUMMARYFull waveform inversion (FWI) is a highly non-linear optimization problem that aims to reconstruct high-resolution subsurface structures. The success of FWI in reflection seismology relies on appropriate updates of low-wavenumber background velocity structures, which are generally driven by the diving waves in conventional FWI. On the other hand, the reflected waves mainly contribute to updating high-wavenumber components rather than low-wavenumber components. To extract low-wavenumber information from the reflected waves in addition to the diving waves, we propose a two-step FWI strategy that separates a given model into the reflectivity and background velocity models and then alternately update them using the scale-separation technique based on diffraction-angle filtering (DAF; which was proposed to effectively control wavenumber components of the FWI gradient). Our strategy first inverts the high-wavenumber reflectivity model by suppressing energy at large diffraction angles, which are necessary to compute the reflection wave paths (i.e. the rabbit-ears-shaped kernels) for low-wavenumber updates in the subsequent stage. Then, we extract low-wavenumber components due to the diving (banana-shaped kernels) and reflected waves (rabbit-ears-shaped kernels) from the gradient by suppressing energy at small diffraction angles. Our strategy is similar to reflection waveform inversion (RWI) in that it separates a given model into high- and low-wavenumber components and uses the rabbit-ears-shaped kernels for low-wavenumber updates. The main difference between our strategy and RWI is that our strategy adopts the DAF-based scale-separation technique in the space domain, which makes our algorithm of using both the banana-shaped and rabbit-ears-shaped kernels computationally attractive. By applying our two-step inversion strategy to the synthetic data for the Marmousi-II model and the real ocean-bottom cable data from the North sea, we demonstrate that our method properly reconstructs low-wavenumber structures even if initial models deviate from the true models.
Numerical simulation of the graphite effect on the electrical conductivity of the upper mantle
Authors: Guo Yingxing , Zheng Jun , Zhu Aiyu , Zhu Tao 
Published: December 2021

SUMMARY
The origin of high-conductivity anomalies in the deep Earth is one of the hot issues in geoscience research. The presence of graphite is a possible reason, but the effects of the volume fraction and geometry of graphite on the high-conductivity anomaly in the upper mantle are still controversial. Based on the possible morphology of graphite in the uppermost mantle, graphite–olivine–orthopyroxene assemblage models are constructed and their conductivities are calculated by a finite-element method. The results show that when graphite is isolated from each other, temperature is the main factor that leads to a change in electrical conductivity. When graphite is in contact with each other, increases in the diameter/thickness ratio (β), orientation arrangement along the direction of conduction, and a mixture of powdered and disc-shaped graphite can significantly cause an increase in electrical conductivity. We found that a threshold value of graphite content exists at which the model conductivity suddenly increases. The threshold decreases significantly with increasing β. A model with β larger than 25 could explain the high-conductivity anomaly in the upper mantle.
Neutralizing Response Against SARS-CoV-2 Variants 8 Months After BNT162b2 Vaccination in Naive and COVID-19–Convalescent Individuals
Authors: Luczkowiak Joanna , Labiod Nuria , Rivas Gonzalo , Rolo Marta , Lasala Fátima , Lora-Tamayo Jaime , Mancheno-Losa Mikel , Rial-Crestelo David , Pérez-Rivilla Alfredo , Folgueira María Dolores , Delgado Rafael 
Published: December 2021

Abstract
We have investigated the evolution of the neutralizing response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants at 8 months after Pfizer-BNT162b2 vaccination in coronavirus disease 2019 (COVID-19)–naive (n = 21) and COVID-19–convalescent (n = 21) individuals. Neutralizing levels declined for all variants (range 2- to 3.7-fold). Eight months after vaccination, a significant proportion (4/21) of naive individuals lacked detectable neutralizing activity against the highly transmissible SARS-CoV-2 delta variant. In the convalescent group, the impressive high initial humoral response resulted in detectable neutralizing antibody levels against all variants throughout this period.
Nosological Diagnosis, Theories of Categorization, and Argumentations by Analogy
Authors: Gagliardi Francesco 
Published: December 2021

AbstractThe nosological diagnosis is a particular type of nontheoretical diagnosis consisting of identifying the disease that afflicts the patient without explaining the underlying etiopathological mechanisms. Its origins are within the essentialist point of view on the nature of diseases, which dates back at least to 18th-century taxonomy studies. In this article, we propose a model of nosological diagnosis as a two-phase process composed of the categorization of inductive inferences and argumentations by analogy. In the inductive phase, disease entities are identified by means of typicality-based categorization processes, and meaningful clinical samples are learned (abstract clinical cases, i.e., syndromes and actual cases); in the subsequent phase, those samples are used as the bases of argumentations by analogy to obtain a diagnosis for a given patient. This model extends the prototype resemblance theory of disease including also the exemplar theory proposed in cognitive science and, moreover, it frames the clinical activity of nosological diagnosis and how it can be explained within the theory of argumentation. According to it, diagnosis based on the recognition of a typical syndrome is explained in terms of the prototype theory of categorization and the antisymmetrical argumentation by analogy, while diagnosis based on a comparison with a previous clinical case is explained by the exemplar theory of categorization and by the symmetrical argumentation by analogy.
Engagement with risk-exposed neighbours: the track record of nuclear newbuild and newcomer states
Authors: Yao Lixia , Andrews-Speed Philip 
Published: December 2021

Abstract
Several international norms oblige governments of countries planning to build nuclear installations to proactively consult potentially affected countries in a timely manner. These norms arise from customary international law, the Convention on Nuclear Safety (CNS), the guidelines of the International Atomic Energy Agency (IAEA) and regional treaties and international environmental law. This study has examined 15 examples to assess (i) the extent to which such consultation has taken place and (ii) the effectiveness of measures taken by potentially affected countries in those cases where prior consultation had not taken place. Examples range in vintage from the 1960s to the present day and include both newbuild and newcomer countries. In only 3 of these 15 cases, prior consultation had taken place and all the involved nations had good bilateral relations and/or common interests in the project. Nevertheless, disputes arose later in two of these cases. In the other examples, the degree of success of the potentially affected state in changing the behaviour of the newbuild or newcomer state depended on a number of factors; for example, the state of bilateral relations, the availability of a regional organization to resolve the dispute, the validity of the arguments of both parties and the goodwill of the newbuild or newcomer state. Whilst the CNS and the actions of the IAEA have raised nuclear safety standards substantially over recent decades, the unwillingness of most nations to adhere to the obligation to consult would seem to be a significant weakness.
Computed Tomography of the Chest as a Screening Tool for Low Bone Mineral Density
Authors: Vanier Alan T , Colantonio Donald , Saxena Sameer K , Rodkey Daniel , Wagner Scott 
Published: December 2021

ABSTRACTIntroductionComputed tomography (CT) Hounsfield units (HU) recently emerged as a promising screening tool for low bone mineral density (BMD). We hypothesized that CT HU measurements of the thoracic spine would significantly and positively correlate with dual X-ray absorptiometry (DXA) BMD scans of the femoral neck.Materials and methodsThe study included patients with DXA scans and thoracic CT scans at the Walter Reed National Military Medical Center. One author, blinded to the DXA scans, measured HU from the cancellous bone in T4 vertebrae. Another author statistically compared femoral neck DXA T-scores to the CT HU measurements.ResultsThe study included 145 patients with CT scans and femoral neck DXAs. The osteoporotic and osteopenic groups had a significant difference in HU measurements compared to the normal group within the study (P &lt; .0001 and .002, respectively). A low BMD screening value of 231 HU provided a sensitivity of 90.1% and negative predictive value of 85.7%.ConclusionThoracic vertebrae HU measurements correlate with a low BMD of the femoral neck as determined by DXA T-scores. A high sensitivity and negative predictive value was achieved with a screening value of 231 HU. Utilization of chest or thoracic spine CT imaging as a screening method provides a quick and available screening tool for assessing low BMD in patients with these scans.Level of Evidence: III (Diagnostic)