bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tensor-structured algorithm for reduced-order scaling large-scale Kohn–Sham density functional theory calculations
Authors: Lin Chih-Chuen , Motamarri Phani , Gavini Vikram 
Published: April 2021

AbstractWe present a tensor-structured algorithm for efficient large-scale density functional theory (DFT) calculations by constructing a Tucker tensor basis that is adapted to the Kohn–Sham Hamiltonian and localized in real-space. The proposed approach uses an additive separable approximation to the Kohn–Sham Hamiltonian and an L1 localization technique to generate the 1-D localized functions that constitute the Tucker tensor basis. Numerical results show that the resulting Tucker tensor basis exhibits exponential convergence in the ground-state energy with increasing Tucker rank. Further, the proposed tensor-structured algorithm demonstrated sub-quadratic scaling with system-size for both systems with and without a gap, and involving many thousands of atoms. This reduced-order scaling has also resulted in the proposed approach outperforming plane-wave DFT implementation for systems beyond 2000 electrons.
Neutrophil subtypes shape HIV-specific CD8 T-cell responses after vaccinia virus infection
Authors: Di Pilato Mauro , Palomino-Segura Miguel , Mejías-Pérez Ernesto , Gómez Carmen E. , Rubio-Ponce Andrea , D’Antuono Rocco , Pizzagalli Diego Ulisse , Pérez Patricia , Kfuri-Rubens Raphael , Benguría Alberto , Dopazo Ana , Ballesteros Iván , Sorzano Carlos Oscar S. , Hidalgo Andrés , Esteban Mariano , Gonzalez Santiago F. 
Published: April 2021

AbstractNeutrophils are innate immune cells involved in the elimination of pathogens and can also induce adaptive immune responses. Nα and Nβ neutrophils have been described with distinct in vitro capacity to generate antigen-specific CD8 T-cell responses. However, how these cell types exert their role in vivo and how manipulation of Nβ/Nα ratio influences vaccine-mediated immune responses are not known. In this study, we find that these neutrophil subtypes show distinct migratory and motility patterns and different ability to interact with CD8 T cells in the spleen following vaccinia virus (VACV) infection. Moreover, after analysis of adhesion, inflammatory, and migration markers, we observe that Nβ neutrophils overexpress the α4β1 integrin compared to Nα. Finally, by inhibiting α4β1 integrin, we increase the Nβ/Nα ratio and enhance CD8 T-cell responses to HIV VACV-delivered antigens. These findings provide significant advancements in the comprehension of neutrophil-based control of adaptive immune system and their relevance in vaccine design.
Cephalometric measures correlate with polysomnography parameters in individuals with midface deficiency
Authors: Bittar Renato Fortes , Duailibi Sílvio Eduardo , Prado Gabriela Pereira Ribeiro , Ferreira Lydia Masako , Pereira Max Domingues 
Published: April 2021

AbstractTo determine the association between cephalometric measurements and polysomnographic parameters in Brazilian patients with midface deficiency. This was a primary, clinical, observational, longitudinal, retrospective, analytical, and single-center study. Forty-eight patients with midface deficiency were divided into two groups as follows: those who underwent surgically assisted rapid palatal expansion (SARME) and those who received maxillary advancement (MA). Pre- and post-operative cephalometric and polysomnography measurements were obtained. Pearson's correlation was used to verify the presence of any significant associations between PSG scores and cephalometric measurements. Associations between BMI (Body Mass Index) and AHI (Apnea Hypopnea Index) as well as arousals were observed. In the SARME group, associations between AHI and SNA, UAS and MP-H, arousals and SNA, and Co-A and MP-H were noted. Associations between AHI and Co-A, PoOr-A and MP-H, arousals and UAS, and between minimum saturation of O2 and SNA, SNB, and Co-A were observed in the MA group. This study demonstrates the alterations in the middle third of the face that were related to sleep disturbance. In addition, it shows the associations between the polysomnographic parameters and the cephalometric representations corresponding to the analyzed deformities and transverse or anteroposterior maxillary deficiencies.
Fitness for purpose of stabilized stool samples for bile acid metabolite analyses
Authors: Neuberger-Castillo Lorie , Ammerlaan Wim , Betsou Fay 
Published: April 2021

AbstractBiobanks and cohort studies are increasingly utilizing chemical stabilizers to collect and store stool samples for downstream DNA-based microbiome analyses. While stabilizers permit ambient-temperature collection and storage of samples for gut microbiome studies, the use of the same sample type for downstream metabolomics assays has not been explored. Microbiome-metabolomics analysis of fecal samples is increasingly getting attention to further elucidate the mechanisms by which the gut microbiota influences the host. In this study, we evaluated fitness-for-purpose of OMNIgene-GUT-collected stool samples for downstream metabolomics assays in the scope of fecal bile acids (BA) quantification. Biocrates Bile Acids Kit was used for the quantification of BA from eight healthy donors’ samples collected in (1) OMNIgene-GUT kit and (2) snap frozen in −80 °C in duplicates. A highly selective reversed phase LC–MS/MS analysis method in negative ion multiple reaction monitoring (MRM) detection mode was applied to determine the BA concentrations in each sample.Total fecal BA levels were detectable in OMNIgene-GUT-collected samples (range: 29.9–903.7 pmol/mg). Paired t-test confirmed that there was a significant difference in the total BAs between the OMNIgene-GUT and snap frozen samples (p < 0.05). Extractions from snap frozen samples resulted in higher concentrations of total BAs (range: 243.7–1136.2 pmol/mg). Qualitative differences between individual donors’ BA profiles were detectable using the two sample collection methods. No significant difference was found in the relative concentrations of primary (CA, CDCA) or secondary (DCA, LCA, UDCA) unconjugated BAs to the total BA concentrations in OMNIgene-GUT-collected samples as compared with the snap frozen samples (Wilcoxon-Mann–Whitney test, p > 0.05). Passing-Bablok method comparison and correlation analyis showed a high degree of correlation in the relative concentrations of CA, CDCA, DCA and LCA between OMNIgene-GUT and snap frozen samples. For these four bile acids, the two methods are comparable at an acceptability bias of 30%. We conclude that the OMNIgene-GUT-collected stool samples are fit-for-purpose for downstream fecal bile acids analysis.
Frailty is associated with susceptibility and severity of pneumonia in older adults (A JAGES multilevel cross-sectional study)
Authors: Iwai-Saito Kousuke , Shobugawa Yugo , Aida Jun , Kondo Katsunori 
Published: April 2021

AbstractPneumonia is a leading cause of mortality among older adults worldwide. Recently, several studies reported that frailty was associated with mortality among older adults hospitalized due to respiratory infectious diseases, including pneumonia. However, it is unknown whether frailty is associated with susceptibility to and severity of pneumonia in functionally-independent community-dwelling older adults. In this study, we examined whether frailty increased the susceptibility to pneumonia and hospitalization in older adults. We used cross-sectional data from the Japan Gerontological Evaluation Study; the data was collected by using mail-based, self-reported questionnaires from 177,991 functionally-independent community-dwelling older adults aged ≥ 65 years. Our results showed that frailty was significantly associated with both occurrence of and hospitalization due to pneumonia after adjustments with covariates; (Preference ratio {PR} 1.92, 95% confidence interval {95% CI} [1.66–2.22] and PR 1.80, 95% CI [1.42–2.28], respectively, p < 0.001 for the both). Pre-frailty was associated only with the occurrence of pneumonia. Besides, the instrumental activity of daily living, physical strength, nutrition status, oral function, homeboundness, and depression status in frail older adults were associated with either or both occurrence of and hospitalization due to pneumonia. Our results suggest that frailty influenced the susceptibility to and severity of pneumonia in older adults.
Application of DBN and GWO-SVM in analog circuit fault diagnosis
Authors: Su Xiyuan , Cao Changqing , Zeng Xiaodong , Feng Zhejun , Shen Jingshi , Yan Xu , Wu Zengyan 
Published: April 2021

AbstractFor large-scale integrated electronic equipment, the complex operating mechanisms make fault detection very difficult. Therefore, it is important to accurately identify analog circuit faults in a timely manner. To overcome this problem, this paper proposes a novel fault diagnosis method based on the deep belief network (DBN) and restricted Boltzmann machine (RBM) optimized by the gray wolf optimization (GWO) algorithm. First, DBN is used to extract the deep features of the analog circuit output signal. Then, GWO is used to optimize the penalty factor c and kernel parameter g of support vector machine (SVM). Finally, GWO-SVM is used to diagnose the signal features extracted by the DBN. Fault diagnosis simulation was conducted for the Sallen–Key band-pass filter and a four-opamp biquad highpass filter. The experimental results show that compared with the existing algorithms, the algorithm proposed in this paper improves the accuracy of Sallen–Key bandpass filter circuit to 100% and shortens the fault diagnosis time by about 90%; for four-opamp biquad highpass filter, the accuracy rate has increased to 99.68%, and the fault diagnosis time has been shortened by approximately 75%, and reduce hundreds of iterations. Moreover, the experimental results reveal that the proposed fault diagnosis method greatly improves the accuracy of analog circuit fault diagnosis, which solves a major problem in analog circuitry and has great significance for the future development of relevant applications.
The FCGR3A 158 V/V-genotype is associated with decreased survival of renal allografts with chronic active antibody-mediated rejection
Authors: Litjens Nicolle , Peeters Annemiek , Gestel Judith Kal-van , Klepper Mariska , Betjes Michiel 
Published: April 2021

AbstractNatural killer (NK) cells express the Fc-gamma receptor CD16 (FCGR3A) and could therefore mediate renal endothelial cell damage in cases of chronic-active antibody mediated rejection (c-aABMR). The V/V-genotype of the FCGR3A 158 F/V polymorphism is associated with increased CD16 expression and cytotoxicity by NK cells. This study evaluated whether this genotype is associated with the diagnosis of c-aABMR and renal allograft loss. The distribution of the FGCR3A 158 F/V-genotypes was not different for c-aABMR cases (N = 133) compared to control kidney transplant recipients (N = 116, P = 0.65). The V-allele was associated with increased median fluorescence intensity (MFI) of CD16 by NK cells (MFI 3.5 × 104 versus 1.3 × 104 for V/V and F/F-genotype, P < 0.001). Increased expression of CD16 correlated with CD16-dependent degranulation of NK cells (R = 0.4; P = 0.02). Moreover, the V/V-genotype was significantly associated with a higher glomerulitis score and an independent risk factor (HR 1.98; P = 0.04) for decreased allograft survival. Death-censored graft survival in c-aABMR cases at 3 years follow-up was 33% for the FCGR3A 158 V/V-genotype versus 62% for the F/F-genotype. In conclusion, the FCGR3A V/V-genotype increases CD16-mediated NK cell cytotoxicity and is associated with a higher glomerulitis score and decreased graft survival in cases with c-aABMR.
COPD significantly increases cerebral and cardiovascular events in hypertensives
Authors: Perticone Maria , Maio Raffaele , Caroleo Benedetto , Suraci Edoardo , Corrao Salvatore , Sesti Giorgio , Perticone Francesco 
Published: April 2021

AbstractEssential hypertension and chronic obstructive pulmonary disease often coexist in the same patient. The aim of this study was to evaluate whether the addition of chronic obstructive pulmonary disease modifies the risk of cardiovascular events in hypertensives. We enrolled 1728 hypertensives. Study outcomes included fatal and non-fatal cardiovascular stroke and myocardial infarction, and cardiovascular death. During a mean follow-up of 57 months there were 205 major adverse cardiovascular events (2.47 per 100 pts/yr): cardiac (n117; 1.41 per 100 pts/yr) and cerebrovascular (n = 77; 0.93 per 100 pts/yr). In hypertensives with chronic obstructive pulmonary disease we observed a greater number of cardiovascular events than in hypertensives without respiratory disease (133 [5.55 per 100 pts/yr) vs 72 [1.22 per 100 pts/yr], respectively. The addition of chronic obstructive pulmonary disease to hypertension increased the incidence of total and non-fatal stroke of more than nine- (2.42 vs 0.32 per 100 pts/yr) and 11-fold (2.09 vs 0.22 per 100 pts/yr), respectively. The same trend was observed for total (2.88 vs 0.81 per 100 pts/yr) and non-fatal (2.67 vs 0.79 per 100 pts/y) myocardial infarction. The presence of chronic obstructive pulmonary disease in hypertensives significantly increases the risk of stroke, myocardial infarction and major adverse cardiovascular events.
Matrix model for collective phenomena in electron beam’s longitudinal phase space
Authors: Perosa Giovanni , Di Mitri Simone 
Published: April 2021

AbstractThe possibility to predict, characterize and minimize the presence of spurious harmonic content in the longitudinal profile of high brightness electron beams, namely the microbunching instability, has become vital to ensure accurate modeling and reliable operation of radiofrequency and plasma-based linear accelerators such as those driving free-electron lasers. Recently, the impact of intrabeam scattering (IBS) on the instability has been experimentally demonstrated by the authors. This work complements that experimental study by extending existing theories in a self-consistent, piece-wise calculation of IBS in single pass linacs and multi-bend transfer lines. New expressions for the IBS are introduced in two different semi-analytical models of microbunching. The accuracy of the proposed models and the range of beam parameters to which they apply is discussed. The overall modeling turns out to be a fast comprehensive tool for the optimization of linac-driven free-electron lasers.
Enhancement in physicochemical parameters and microbial populations of mushrooms as influenced by nano-coating treatments
Authors: Sami Rokayya , Elhakem Abeer , Almushhin Amina , Alharbi Mona , Almatrafi Manal , Benajiba Nada , Fikry Mohammad , Helal Mahmoud 
Published: April 2021

AbstractWhite button mushrooms are greatly high perishable and can deteriorate within a few days after harvesting due to physicomechanical damage, respiration, microbial growth of the delicate epidermal structure. For that reason, the present research work was applied to evaluate the effect of chitosan combination with nano-coating treatments on physicochemical parameters and microbial populations on button mushrooms at chilling storage. Nano coating with the addition of nisin 1% (CHSSN/M) established the minimum value for weight loss 12.18%, maintained firmness 11.55 N, and color index profile. Moreover, O2% rate of (CHSSN/M) mushrooms was the lowest at 1.78%; while the highest rate was reported for CO2 24.88% compared to the untreated samples (Control/M) on day 12. Both pH and total soluble solid concentrations increased during storage. Results reported that the (CHSS/M) mushroom significantly (P < 0.05) reduced polyphenol oxidase activity (24.31 U mg−1 Protein) compared with (Control/M) mushrooms that increased faster than the treated samples. (CHSSN/M) treatment was the most efficient in the reduction of yeast and mold, aerobic plate microorganisms (5.27–5.10 log CFU/g), respectively. The results established that nano-coating film might delay the aging degree and accompany by marked prolongation of postharvest mushroom freshness.
A non-volatile cryogenic random-access memory based on the quantum anomalous Hall effect
Authors: Alam Shamiul , Hossain Md Shafayat , Aziz Ahmedullah 
Published: April 2021

AbstractThe interplay between ferromagnetism and topological properties of electronic band structures leads to a precise quantization of Hall resistance without any external magnetic field. This so-called quantum anomalous Hall effect (QAHE) is born out of topological correlations, and is oblivious of low-sample quality. It was envisioned to lead towards dissipation-less and topologically protected electronics. However, no clear framework of how to design such an electronic device out of it exists. Here we construct an ultra-low power, non-volatile, cryogenic memory architecture leveraging the QAHE phenomenon. Our design promises orders of magnitude lower cell area compared with the state-of-the-art cryogenic memory technologies. We harness the fundamentally quantized Hall resistance levels in moiré graphene heterostructures to store non-volatile binary bits (1, 0). We perform the memory write operation through controlled hysteretic switching between the quantized Hall states, using nano-ampere level currents with opposite polarities. The non-destructive read operation is performed by sensing the polarity of the transverse Hall voltage using a separate pair of terminals. We custom design the memory architecture with a novel sensing mechanism to avoid accidental data corruption, ensure highest memory density and minimize array leakage power. Our design provides a pathway towards realizing topologically protected memory devices.
A next-generation sequencing study on mechanisms by which restraint and social instability stresses of male mice alter offspring anxiety-like behavior
Authors: Kong Qiao-Qiao , Tian Xiao-Dan , Wang Jia , Yuan Hong-Jie , Ning Shu-Fen , Luo Ming-Jiu , Tan Jing-He 
Published: April 2021

AbstractPathophysiological mechanisms for depression/anxiety are largely unknown. Evidence for transgenerational transmission of acquired epigenetic marks remains limited. We bred unstressed (US) female mice with adolescently restraint-stressed (RS), social instability-stressed (SI) or US males to produce RS, SI and control F1 offspring, respectively. Compared to controls, while paternal RS decreased anxiety-like behavior (ALB) in both female and male offspring, paternal SI increased ALB only in female offspring. Next-generation sequencing and bioinformatics using RS and SI female offspring identified 5 candidate anxiety-transmitting (CAT) genes; each showed a consistent pattern of DNA methylation from F0 spermatozoa through F1 blastocysts to fetal and adult hippocampi. Further analyses validated 4 CAT genes, demonstrated that paternal SI caused ALB differences between male and female offspring through modifying the CAT genes, and indicated a strong correlation between inflammation and ALB pathogenesis and an important function for intronic DNA methylation in regulating ALB-related genes. In conclusion, this study identified important CAT genes and suggested the possibility that stresses on males might alter offspring’s ALB by modifying sperm DNA methylation.
Description of optochin-resistant Streptococcus pneumoniae due to an uncommon mutation in the atpA gene and comparison with previously identified atpC mutants from Brazil
Authors: Souza Aline R. V. , de Pina Sandrine E. C. M. , Costa Natália S. , Neves Felipe P. G. , Merquior Vânia L. C. , Peralta José Mauro , Pinto Tatiana C. A. , Teixeira Lúcia M. 
Published: April 2021

AbstractOptochin susceptibility testing is a major assay used for presumptive identification of Streptococcus pneumoniae. Still, atypical optochin-resistant (Optr) pneumococci have been reported and this phenotype has been attributed to nucleotide substitutions in the genes coding for the F0F1ATPase. While substitutions in the atpC gene (c-subunit of ATPase) are more common and better characterized, data on mutations in the atpA (a-subunit) are still limited. We have characterized five Optr isolates presenting alterations in the atpA (Trp206Cys in four isolates and Trp206Ser in one isolate), constituting the first report of such mutations in Brazil. Most of the Optr isolates consisted of heterogeneous populations. Except for Opt MICs and the nucleotide changes in the atpA gene, Optr and Opts subpopulations originating from the same culture had identical characteristics. In addition, we compared phenotypic and genetic characteristics of these atpA mutants with those of atpC mutants previously identified in Brazil. No structural alterations were detected among predicted proteins, regardless of mutations in the coding gene, suggesting that, despite the occurrence of mutations, protein structures tend to be highly conserved, ensuring their functionalities. Phylogenetic analysis revealed that atypical Optr strains are true pneumococci and Opt resistance does not represent any apparent selective advantage for clinical isolates.
Undulation of a moving fluid membrane pushed by filament growth
Authors: Noguchi Hiroshi , Pierre-Louis Olivier 
Published: April 2021

AbstractBiomembranes experience out-of-equilibrium conditions in living cells. Their undulation spectra are different from those in thermal equilibrium. Here, we report on the undulation of a fluid membrane pushed by the stepwise growth of filaments as in the leading edge of migrating cells, using three-dimensional Monte Carlo simulations. The undulations are largely modified from equilibrium behavior. When the tension is constrained, the low-wave-number modes are suppressed or enhanced at small or large growth step sizes, respectively, for high membrane surface tensions. In contrast, they are always suppressed for the tensionless membrane, wherein the wave-number range of the suppression depends on the step size. When the membrane area is constrained, in addition to these features, a specific mode is excited for zero and low surface tensions. The reduction of the undulation first induces membrane buckling at the lowest wave-number, and subsequently, other modes are excited, leading to a steady state.
Prediction of ambulatory outcome in patients with corona radiata infarction using deep learning
Authors: Kim Jeoung Kun , Choo Yoo Jin , Shin Hyunkwang , Choi Gyu Sang , Chang Min Cheol 
Published: April 2021

AbstractDeep learning (DL) is an advanced machine learning approach used in diverse areas such as bioinformatics, image analysis, and natural language processing. Here, using brain magnetic resonance imaging (MRI) data obtained at early stages of infarcts, we attempted to develop a convolutional neural network (CNN) to predict the ambulatory outcome of corona radiata infarction at six months after onset. We retrospectively recruited 221 patients with corona radiata infarcts. A favorable outcome of ambulatory function was defined as a functional ambulation category (FAC) score of ≥ 4 (able to walk without a guardian’s assistance), and a poor outcome of ambulatory function was defined as an FAC score of < 4. We used a CNN algorithm. Of the included subjects, 69.7% (n = 154) were assigned randomly to the training set and the remaining 30.3% (n = 67) were assigned to the validation set to measure the model performance. The area under the curve was 0.751 (95% CI 0.649–0.852) for the prediction of ambulatory function with the validation dataset using the CNN model. We demonstrated that a CNN model trained using brain MRIs captured at an early stage after corona radiata infarction could be helpful in predicting long-term ambulatory outcomes.