bluuebunny/crossref_metadata_2025_split huggingface dataset:
History of one’s own performance modulates evaluative processing of another’s action outcomes, but not vice versa
Authors: Ishii Chikara , Katayama Jun’ichi 
Published: January 2022

AbstractIn action monitoring, i.e., evaluating an outcome of our behavior, a reward prediction error signal is calculated as the difference between actual and predicted outcomes and is used to adjust future behavior. Previous studies demonstrate that this signal, which is reflected by an event-related brain potential called feedback-related negativity (FRN), occurs in response to not only one's own outcomes, but also those of others. However, it is still unknown if predictions of different actors' performance interact with each other. Thus, we investigated how predictions from one’s own and another’s performance history affect each other by manipulating the task difficulty for participants themselves and their partners independently. Pairs of participants performed a time estimation task, randomly switching the roles of actor and observer from trial to trial. Results show that the history of the other’s performance did not modulate the amplitude of the FRN for the evaluation of one’s own outcomes. In contrast, the amplitude of the observer FRN for the other’s outcomes differed according to the frequency of one’s own action outcomes. In conclusion, the monitoring system tracks the histories of one’s own and observed outcomes separately and considers information related to one’s own action outcomes to be more important.
Prognosis and adjuvant chemotherapy for patients with positive peritoneal cytology in stage IA endometrial cancer
Authors: Kanno Motoko , Yunokawa Mayu , Nakabayashi Makoto , Omi Makiko , Ikki Ai , Mizusaki Megumi , Nishimura Mai , Shimizu Yusuke , Okamoto Kota , Tanaka Yuji , Fusegi Atsushi , Netsu Sachiho , Kurita Tomoko , Aoki Yoichi , Tanigawa Terumi , Matoda Maki , Okamoto Sanshiro , Nomura Hidetaka , Omatsu Kohei , Sugiyama Yuko , Utsugi Kuniko , Takeshima Nobuhiro , Kanao Hiroyuki 
Published: January 2022

AbstractThis study evaluated the influence of positive peritoneal cytology (PPC) on the prognosis of patients with stage IA endometrial cancer, and the usefulness of adjuvant chemotherapy in their treatment. We retrospectively analyzed the data of patients with stage IA endometrial cancer admitted in our hospital between 2005 and 2015. Among 989 patients who underwent peritoneal cytology, 135 (13.7%) had PPC. Multivariate analysis extracted several independent risk factors for recurrence in stage IA patients, including those with PPC. Adjuvant chemotherapy did not cause a significant difference in the 5-year relapse-free survival rate in patients with PPC (p = 0.78). Similarly, the 5-year recurrence-free survival rate with or without chemotherapy was not different among type II cancer patients (p = 0.11). However, the baseline risk of 5-year relapse-free survival without chemotherapy in patients with PPC and type II was very low (66.7%). While PPC was an independent risk factor for recurrence in stage IA endometrial cancer, adjuvant chemotherapy did not influence the survival rate in patients with PPC. While it is controversial whether adjuvant chemotherapy should be administered in stage IA uterine cancer with only PPC as a prognostic factor, it should be considered for early-stage patients who have multiple risk factors for recurrence.
Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya
Authors: Phan My V. T. , Agoti Charles N. , Munywoki Patrick K. , Otieno Grieven P. , Ngama Mwanajuma , Kellam Paul , Cotten Matthew , Nokes D. James 
Published: January 2022

AbstractPneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.
Identification of vaccine and drug targets in Shigella dysenteriae sd197 using reverse vaccinology approach
Authors: Jalal Khurshid , Abu-Izneid Tareq , Khan Kanwal , Abbas Muhammad , Hayat Ajmal , Bawazeer Sami , Uddin Reaz 
Published: January 2022

AbstractShigellosis is characterized as diarrheal disease that causes a high mortality rate especially in children, elderly and immunocompromised patients. More recently, the World Health Organization advised safe vaccine designing against shigellosis due to the emergence of Shigella dysenteriae resistant strains. Therefore, the aim of this study is to identify novel drug targets as well as the design of the potential vaccine candidates and chimeric vaccine models against Shigella dysenteriae. A computational based Reverse Vaccinology along with subtractive genomics analysis is one of the robust approaches used for the prioritization of drug targets and vaccine candidates through direct screening of genome sequence assemblies. Herein, a successfully designed peptide-based novel highly antigenic chimeric vaccine candidate against Shigella dysenteriae sd197 strain is proposed. The study resulted in six epitopes from outer membrane WP_000188255.1 (Fe (3+) dicitrate transport protein FecA) that ultimately leads to the construction of twelve vaccine models. Moreover, V9 construct was found to be highly immunogenic, non-toxic, non-allergenic, highly antigenic, and most stable in terms of molecular docking and simulation studies against six HLAs and TLRS/MD complex. So far, this protein and multiepitope have never been characterized as vaccine targets against Shigella dysenteriae. The current study proposed that V9 could be a significant vaccine candidate against shigellosis and to ascertain that further experiments may be applied by the scientific community focused on shigellosis.
Antimicrobial susceptibility of commensal Neisseria in a general population and men who have sex with men in Belgium
Authors: Laumen Jolein Gyonne Elise , Van Dijck Christophe , Abdellati Saïd , De Baetselier Irith , Serrano Gabriela , Manoharan-Basil Sheeba Santhini , Bottieau Emmanuel , Martiny Delphine , Kenyon Chris 
Published: January 2022

AbstractNon-pathogenic Neisseria are a reservoir of antimicrobial resistance genes for pathogenic Neisseria meningitidis and Neisseria gonorrhoeae. Men who have sex with men (MSM) are at risk of co-colonization with resistant non-pathogenic and pathogenic Neisseria. We assessed if the antimicrobial susceptibility of non-pathogenic Neisseria among MSM differs from a general population and if antimicrobial exposure impacts susceptibility. We recruited 96 participants at our center in Belgium: 32 employees, 32 MSM who did not use antibiotics in the previous 6 months, and 32 MSM who did. Oropharyngeal Neisseria were cultured and identified with MALDI-TOF–MS. Minimum inhibitory concentrations for azithromycin, ceftriaxone and ciprofloxacin were determined using E-tests® and compared between groups with non-parametric tests. Non-pathogenic Neisseria from employees as well as MSM were remarkably resistant. Those from MSM were significantly less susceptible than employees to azithromycin and ciprofloxacin (p < 0.0001, p < 0.001), but not ceftriaxone (p = 0.3). Susceptibility did not differ significantly according to recent antimicrobial exposure in MSM. Surveilling antimicrobial susceptibility of non-pathogenic Neisseria may be a sensitive way to assess impact of antimicrobial exposure in a population. The high levels of antimicrobial resistance in this survey indicate that novel resistance determinants may be readily available for future transfer from non-pathogenic to pathogenic Neisseria.
Identifying diabetes from conjunctival images using a novel hierarchical multi-task network
Authors: Li Xinyue , Xia Chenjie , Li Xin , Wei Shuangqing , Zhou Sujun , Yu Xuhui , Gao Jiayue , Cao Yanpeng , Zhang Hong 
Published: January 2022

AbstractDiabetes can cause microvessel impairment. However, these conjunctival pathological changes are not easily recognized, limiting their potential as independent diagnostic indicators. Therefore, we designed a deep learning model to explore the relationship between conjunctival features and diabetes, and to advance automated identification of diabetes through conjunctival images. Images were collected from patients with type 2 diabetes and healthy volunteers. A hierarchical multi-tasking network model (HMT-Net) was developed using conjunctival images, and the model was systematically evaluated and compared with other algorithms. The sensitivity, specificity, and accuracy of the HMT-Net model to identify diabetes were 78.70%, 69.08%, and 75.15%, respectively. The performance of the HMT-Net model was significantly better than that of ophthalmologists. The model allowed sensitive and rapid discrimination by assessment of conjunctival images and can be potentially useful for identifying diabetes.
Soil δ13C and δ15N baselines clarify biogeographic heterogeneity in isotopic discrimination of European badgers (Meles meles)
Authors: Mullineaux Shay T. , Kostka Berit , Rock Luc , Ogle Neil , Marks Nikki J. , Doherty Rory , Harrod Chris , Montgomery W. Ian , Scantlebury D. Michael 
Published: January 2022

AbstractIsotopic techniques have been used to study phenomena in the geological, environmental, and ecological sciences. For example, isotopic values of multiple elements elucidate the pathways energy and nutrients take in the environment. Isoscapes interpolate isotopic values across a geographical surface and are used to study environmental processes in space and time. Thus, isoscapes can reveal ecological shifts at local scales, and show distribution thresholds in the wider environment at the macro-scale. This study demonstrates a further application of isoscapes, using soil isoscapes of13C/12C and15N/14N as an environmental baseline, to understand variation in trophic ecology across a population of Eurasian badgers (Meles meles) at a regional scale. The use of soil isoscapes reduced error, and elevated the statistical signal, where aggregated badger hairs were used, and where individuals were identified using genetic microarray analysis. Stable isotope values were affected by land-use type, elevation, and meteorology. Badgers in lowland habitats had diets richer in protein and were adversely affected by poor weather conditions in all land classes. It is concluded that soil isoscapes are an effective way of reducing confounding biases in macroscale, isotopic studies. The method elucidated variation in the trophic and spatial ecology of economically important taxa at a landscape level. These results have implications for the management of badgers and other carnivores with omnivorous tendencies in heterogeneous landscapes.
Evaluation of animal model congruence to human depression based on large-scale gene expression patterns of the CNS
Authors: Gammie Stephen C. 
Published: January 2022

AbstractDepression is a complex mental health disorder that is difficult to study. A wide range of animal models exist and for many of these data on large-scale gene expression patterns in the CNS are available. The goal of this study was to evaluate how well animal models match human depression by evaluating congruence and discordance of large-scale gene expression patterns in the CNS between almost 300 animal models and a portrait of human depression created from male and female datasets. Multiple approaches were used, including a hypergeometric based scoring system that rewards common gene expression patterns (e.g., up-up or down-down in both model and human depression), but penalizes opposing gene expression patterns. RRHO heat maps, Uniform Manifold Approximation Plot (UMAP), and machine learning were used to evaluate matching of models to depression. The top ranked model was a histone deacetylase (HDAC2) conditional knockout in forebrain neurons. Also highly ranked were various models for Alzheimer’s, including APPsa knock-in (2nd overall), APP knockout, and an APP/PS1 humanized double mutant. Other top models were the mitochondrial gene HTRA2 knockout (that is lethal in adulthood), a modified acetylcholinesterase, a Huntington’s disease model, and the CRTC1 knockout. Over 30 stress related models were evaluated and while some matched highly with depression, others did not. In most of the top models, a consistent dysregulation of MAP kinase pathway was identified and the genes NR4A1, BDNF, ARC, EGR2, and PDE7B were consistently downregulated as in humans with depression. Separate male and female portraits of depression were also evaluated to identify potential sex specific depression matches with models. Individual human depression datasets were also evaluated to allow for comparisons across the same brain regions. Heatmap, UMAP, and machine learning results supported the hypergeometric ranking findings. Together, this study provides new insights into how large-scale gene expression patterns may be similarly dysregulated in some animals models and humans with depression that may provide new avenues for understanding and treating depression.
Research on the rapid combustion process of butane under microwave discharge
Authors: Tang Qiang , Hu Zhibin , Tao Zechao , Ye Dan , Tang Jau 
Published: January 2022

AbstractTo study the combustion process of fuel in the microwave plasma torch, we designed a butane microwave plasma device exploiting a tungsten rod as an electrode. Through analysis of the image record by high-speed camera, we found that the discharge of butane microwave plasma torch is a cyclic process at atmospheric pressure at a frequency of around 100 Hz. During the discharge, the active particles continuously diffuse from the electrode to the outside like the bloom of the flower. Then, the variation of plasma torch of jet height and temperature with microwave power is obtained. In addition, we studied the effects of different butane flow rates on the plasma torch. The results illustrate that excessive butane will lead to carbon deposition on the electrode. All in all, this work provides a new understanding of the combustion of the microwave plasma torch, which is conducive to the further development of microwave plasma in the fields of waste gas treatment, fuel combustion, and plasma engine.
In-situ twistable bilayer graphene
Authors: Hu Cheng , Wu Tongyao , Huang Xinyue , Dong Yulong , Chen Jiajun , Zhang Zhichun , Lyu Bosai , Ma Saiqun , Watanabe Kenji , Taniguchi Takashi , Xie Guibai , Li Xiaojun , Liang Qi , Shi Zhiwen 
Published: January 2022

AbstractThe electrical and optical properties of twisted bilayer graphene (tBLG) depend sensitively on the twist angle. To study the angle dependent properties of the tBLG, currently it is required fabrication of a large number of samples with systematically varied twist angles. Here, we demonstrate the construction of in-situ twistable bilayer graphene, in which the twist angle of the two graphene monolayers can be in-situ tuned continuously in a large range with high precision. The controlled tuning of the twist angle is confirmed by a combination of real-space and spectroscopic characterizations, including atomic force microscopy (AFM) identification of crystal lattice orientation, scanning near-field optical microscopy (SNOM) imaging of superlattice domain walls, and resonant Raman spectroscopy of the largely enhanced G-mode. The developed in-situ twistable homostructure devices enable systematic investigation of the twist angle effects in a single device, thus could largely advance the research of twistronics.
Biomarker dynamics and prognosis in breast cancer after neoadjuvant chemotherapy
Authors: Zarotti Cristina , Papassotiropoulos Bärbel , Elfgen Constanze , Dedes Konstantin , Vorburger Denise , Pestalozzi Bernhard , Trojan Andreas , Varga Zsuzsanna 
Published: January 2022

AbstractBreast cancer is a biologically diverse disease with treatment modalities selected based on tumor stage and tumor biology. Distinct intrinsic subtypes and surrogate biomarker profiles play a major role for therapeutic decisions. Response rates to systemic and local treatments as well as the interaction with epidemiological risk factors have been validated in clinical trials and translational studies. This retrospective study addresses the question how biomarker profiles and treatment modalities in the neoadjuvant chemotherapy setting have changed during the past 15 years and what prognostic impact these changes implicate. 342 female breast cancer stage I-IV patients receiving neoadjuvant chemotherapy between 2003 and 2017 were analyzed. Overall survival (OS) was correlated with preoperative clinical stage, postoperative pathological stage, treatment modalities and tumor biology before and after chemotherapy. Two subgroups were separated using an arbitrary cut-off year at 2009/2010, due to 2010 when platinum containing regimens were first administered. Median follow-up was 54 months. 57 (17%) patients died; recurrences occurred in 103 of 342 (30%) patients. Nodal stage and intrinsic subtypes (pre- and postoperative) significantly correlated with OS (p < 0.001). Preoperative histological grading lacked prognostic power. When comparing the patient characteristics of the subgroups, we found significant difference in the following characteristics: cT, ypT, ypN, pCR and chemotherapy regimens (p < 0.001). There was no difference in OS when comparing the two subgroups. Pathological complete response (pCR) rates had a significant impact on OS and disease-free survival (DFS) in HER2+ and triple negative subtypes (p = 0.03). In multivariate analysis, high proliferation index (> 30%), clinical metastatic stage and pathological tumor stage had prognostic impact on OS (p < 0.001, p = 0.0001, p = 0.002). Clinico-pathological factors and distinct therapy regiments especially in triple negative and HER2+ subtypes have prognostic impact on pCR, OS and DFS after neoadjuvant chemotherapy.
The NarX-NarL two-component system regulates biofilm formation, natural product biosynthesis, and host-associated survival in Burkholderia pseudomallei
Authors: Mangalea Mihnea R. , Borlee Bradley R. 
Published: January 2022

AbstractBurkholderia pseudomallei is a saprophytic bacterium endemic throughout the tropics causing severe disease in humans and animals. Environmental signals such as the accumulation of inorganic ions mediates the biofilm forming capabilities and survival of B. pseudomallei. We have previously shown that B. pseudomallei responds to nitrate and nitrite by inhibiting biofilm formation and altering cyclic di-GMP signaling. To better understand the roles of nitrate-sensing in the biofilm inhibitory phenotype of B. pseudomallei, we created in-frame deletions of narX (Bp1026b_I1014) and narL (Bp1026b_I1013), which are adjacent components of a conserved nitrate-sensing two-component system. We observed transcriptional downregulation in key components of the biofilm matrix in response to nitrate and nitrite. Some of the most differentially expressed genes were nonribosomal peptide synthases (NRPS) and/or polyketide synthases (PKS) encoding the proteins for the biosynthesis of bactobolin, malleilactone, and syrbactin, and an uncharacterized cryptic NRPS biosynthetic cluster. RNA expression patterns were reversed in ∆narX and ∆narL mutants, suggesting that nitrate sensing is an important checkpoint for regulating the diverse metabolic changes occurring in the biofilm inhibitory phenotype. Moreover, in a macrophage model of infection, ∆narX and ∆narL mutants were attenuated in intracellular replication, suggesting that nitrate sensing contributes to survival in the host.
The flow of the Berry curvature vector field
Authors: Stejskal Ondřej , Veis Martin , Hamrle Jaroslav 
Published: January 2022

AbstractThe concept of Berry phase and Berry curvature has become ubiquitous in solid state physics as it relates to variety of phenomena, such as topological insulators, polarization, and various Hall effects. It is well known that large Berry curvatures arise from close proximity of hybridizing bands, however, the vectorial nature of the Berry curvature is not utilized in current research. On bulk bcc Fe, we demonstrate the flow of the Berry curvature vector field which features not only monopoles but also higher dimensional structures with its own topological features. They can provide a novel unique view on the electronic structure in all three dimensions. This knowledge is also used to quantify particular contributions to the intrinsic anomalous Hall effect in a simple analytical form.
Endoscopic ultrasound-guided fine-needle biopsy as a tool for studying the intra-tumoral microbiome in pancreatic ductal adenocarcinoma: a pilot study
Authors: Chu Chia-Sheng , Yang Chi-Ying , Yeh Chun-Chieh , Lin Ro-Ting , Chen Chi-Ching , Bai Li-Yuan , Hung Mien-Chie , Lin Chun-Che , Wu Chun-Ying , Lin Jaw-Town 
Published: January 2022

AbstractA new approach by investigating the intra-tumoral microbiome raised great interest because they may influence the host immune response and natural history of the disease. However, previous studies on the intra-tumoral microbiome of pancreatic ductal adenocarcinoma (PDAC) were mostly based on examining the formalin-fixed paraffin-embedded tumor specimens. This study aims to investigate the feasibility of using endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) as a complementary procedure of surgical biopsy to obtain adequate fresh pancreatic cancer tissue for intra-tumoral microbial research. This was a prospective pilot study performed at a single tertiary referral center. We obtained pancreatic cancer tissue by EUS-FNB and surgical biopsy, respectively. We amplified the V3-V4 hyper-variable region of bacterial 16S ribosomal ribonucleic acid (rRNA) genes, constructed a pair-end library, and performed high-throughput sequencing. From August 2020 to November 2020, nine eligible patients with PDAC were enrolled in this study. The intra-tumoral microbiome profile was successfully generated from the PDAC cancer tissue obtained by EUS-FNB as well as by surgical biopsy. There was no significant difference in intra-tumoral alpha-diversity or bacterial taxonomic composition between tissues obtained by EUS-FNB and by surgical biopsy. EUS-FNB can collect sufficient fresh cancer tissue for microbiome analyses without complication. The intra-tumoral microbiome profile in tissues obtained by EUS-FNB had similar alpha-diversity and taxonomic profiles with those obtained by surgical biopsy. It implicated, except for surgical biopsy, EUS-FNB can be another valid and valuable tool for studying intra-tumoral microbiome in patients with resectable and unresectable PDAC.