bluuebunny/crossref_metadata_2025 huggingface dataset:
Combinations of deletion and missense variations of the dynein-2 DYNC2LI1 subunit found in skeletal ciliopathies cause ciliary defects
Authors: Qiu Hantian , Tsurumi Yuta , Katoh Yohei , Nakayama Kazuhisa
Published: January 2022

Cilia play crucial roles in sensing and transducing extracellular signals. Bidirectional protein trafficking within cilia is mediated by the intraflagellar transport (IFT) machinery containing IFT-A and IFT-B complexes, with the aid of kinesin-2 and dynein-2 motors. The dynein-2 complex drives retrograde trafficking of the IFT machinery after its transportation to the ciliary tip as an IFT cargo. Mutations in genes encoding the dynein-2-specific subunits (DYNC2H1, WDR60, WDR34, DYNC2LI1, and TCTEX1D2) are known to cause skeletal ciliopathies. We here demonstrate that several pathogenic variants of DYNC2LI1 are compromised regarding their ability to interact with DYNC2H1 and WDR60. When expressed in DYNC2LI1-knockout cells, deletion variants of DYNC2LI1 were unable to rescue the ciliary defects of these cells, whereas missense variants, as well as wild-type DYNC2LI1, restored the normal phenotype. DYNC2LI1-knockout cells coexpressing one pathogenic deletion variant together with wild-type DYNC2LI1 demonstrated a normal phenotype. In striking contrast, DYNC2LI1-knockout cells coexpressing the deletion variant in combination with a missense variant, which mimics the situation of cells of compound heterozygous ciliopathy individuals, demonstrated ciliary defects. Thus, DYNC2LI1 deletion variants found in individuals with skeletal ciliopathies cause ciliary defects when combined with a missense variant, which expressed on its own does not cause substantial defects.
Mechanical power normalized to lung-thorax compliance indicates weaning readiness in prolonged ventilated patients
Authors: Ghiani Alessandro , Paderewska Joanna , Walcher Swenja , Tsitouras Konstantinos , Neurohr Claus , Kneidinger Nikolaus
Published: January 2022

Since critical respiratory muscle workload is a significant determinant of weaning failure, applied mechanical power (MP) during artificial ventilation may serve for readiness testing before proceeding on a spontaneous breathing trial (SBT). Secondary analysis of a prospective, observational study in 130 prolonged ventilated, tracheotomized patients. Calculated MP’s predictive SBT outcome performance was determined using the area under receiver operating characteristic curve (AUROC), measures derived from k-fold cross-validation (likelihood ratios, Matthew's correlation coefficient [MCC]), and a multivariable binary logistic regression model. Thirty (23.1%) patients failed the SBT, with absolute MP presenting poor discriminatory ability (MCC 0.26; AUROC 0.68, 95%CI [0.59‒0.75], p = 0.002), considerably improved when normalized to lung-thorax compliance (LTCdyn-MP, MCC 0.37; AUROC 0.76, 95%CI [0.68‒0.83], p < 0.001) and mechanical ventilation PaCO2 (so-called power index of the respiratory system [PIrs]: MCC 0.42; AUROC 0.81 [0.73‒0.87], p < 0.001). In the logistic regression analysis, PIrs (OR 1.48 per 1000 cmH2O2/min, 95%CI [1.24‒1.76], p < 0.001) and its components LTCdyn-MP (1.25 per 1000 cmH2O2/min, [1.06‒1.46], p < 0.001) and mechanical ventilation PaCO2 (1.17 [1.06‒1.28], p < 0.001) were independently related to SBT failure. MP normalized to respiratory system compliance may help identify prolonged mechanically ventilated patients ready for spontaneous breathing.
Osteonecrosis development by tooth extraction in zoledronate treated mice is inhibited by active vitamin D analogues, anti-inflammatory agents or antibiotics
Authors: Soma Tomoya , Iwasaki Ryotaro , Sato Yuiko , Kobayashi Tami , Ito Eri , Matsumoto Tatsuaki , Kimura Atsushi , Miyamoto Kana , Matsumoto Morio , Nakamura Masaya , Morita Mayu , Asoda Seiji , Kawana Hiromasa , Nakagawa Taneaki , Miyamoto Takeshi
Published: January 2022

Invasive dental treatment such as tooth extraction following treatment with strong anti-bone resorptive agents, including bisphosphonates and denosumab, reportedly promotes osteonecrosis of the jaw (ONJ) at the extraction site, but strategies to prevent ONJ remain unclear. Here we show that in mice, administration of either active vitamin D analogues, antibiotics or anti-inflammatory agents can prevent ONJ development induced by tooth extraction during treatment with the bisphosphonate zoledronate. Specifically, tooth extraction during treatment with zoledronate induced osteonecrosis in mice, but administration of either 1,25(OH)2D3 or ED71, both active vitamin D analogues, significantly antagonized osteonecrosis development, even under continuous zoledronate treatment. 1,25(OH)2D3 or ED71 administration also significantly inhibited osteocyte apoptosis induced by tooth extraction and bisphosphonate treatment. Administration of either active vitamin D analogue significantly inhibited elevation of serum inflammatory cytokine levels in mice in response to injection of lipopolysaccharide, an infection mimetic. Furthermore, administration of either anti-inflammatory or antibiotic reagents significantly blocked ONJ development following tooth extraction and zoledronate treatment. These findings suggest that administration of active vitamin D, anti-inflammatory agents or antibiotics could prevent ONJ development induced by tooth extraction in patients treated with zoledronate.
Study of risk factors for healthcare-associated infections in acute cardiac patients using categorical principal component analysis (CATPCA)
Authors: Renes Carreño Emilio , Escribá Bárcena Almudena , Catalán González Mercedes , Álvarez Lerma Francisco , Palomar Martínez Mercedes , Nuvials Casals Xavier , Jaén Herreros Felisa , Montejo González Juan Carlos
Published: January 2022

Using categorical principal component analysis, we aimed to determine the relationship between health care-associated infections (HAIs) and diagnostic categories (DCs) in patients with acute heart disease using data collected in the Spanish prospective ENVIN-HELICS intensive care registry over a 10-year period (2005–2015). A total of 69,876 admissions were included, of which 5597 developed HAIs. Two 2-component CATPCA models were developed. In the first model, all cases were included; the first component was determined by the duration of the invasive devices, the ICU stay, the APACHE II score and the HAIs; the second component was determined by the type of admission (medical or surgical) and by the DCs. No clear association between DCs and HAIs was found. Cronbach’s alpha was 0.899, and the variance accounted for (VAF) was 52.5%. The second model included only admissions that developed HAIs; the first component was determined by the duration of the invasive devices and the ICU stay; the second component was determined by the inflammatory response, the mortality in the ICU and the HAIs. Cronbach’s alpha value was 0.855, and VAF was 46.9%. These findings highlight the role of exposure to invasive devices in the development of HAIS in patients with acute heart disease.
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

In 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

This 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

Pneumonia 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

Shigellosis 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

Non-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

Diabetes 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

Isotopic 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

Depression 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

To 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

The 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

Breast 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

Burkholderia 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

The 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

A 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.
Magnetic capsulate triboelectric nanogenerators
Authors: Jiao Pengcheng , Matin Nazar Ali , Egbe King-James Idala , Barri Kaveh , Alavi Amir H.
Published: January 2022

Triboelectric nanogenerators have received significant research attention in recent years. Structural design plays a critical role in improving the energy harvesting performance of triboelectric nanogenerators. Here, we develop the magnetic capsulate triboelectric nanogenerators (MC-TENG) for energy harvesting under undesirable mechanical excitations. The capsulate TENG are designed to be driven by an oscillation-triggered magnetic force in a holding frame to generate electrical power due to the principle of the freestanding triboelectrification. Experimental and numerical studies are conducted to investigate the electrical performance of MC-TENG under cyclic loading in three energy harvesting modes. The results indicate that the energy harvesting performance of the MC-TENG is significantly affected by the structure of the capsulate TENG. The copper MC-TENG systems are found to be the most effective design that generates the maximum mode of the voltage range is 4 V in the closed-circuit with the resistance of 10 GΩ. The proposed MC-TENG concept provides an effective method to harvest electrical energy from low-frequency and low-amplitude oscillations such as ocean wave.
Jointly modeling marine species to inform the effects of environmental change on an ecological community in the Northwest Atlantic
Authors: Roberts Sarah M. , Halpin Patrick N. , Clark James S.
Published: January 2022

Single species distribution models (SSDMs) are typically used to understand and predict the distribution and abundance of marine fish by fitting distribution models for each species independently to a combination of abiotic environmental variables. However, species abundances and distributions are influenced by abiotic environmental preferences as well as biotic dependencies such as interspecific competition and predation. When species interact, a joint species distribution model (JSDM) will allow for valid inference of environmental effects. We built a joint species distribution model of marine fish and invertebrates of the Northeast US Continental Shelf, providing evidence on species relationships with the environment as well as the likelihood of species to covary. Predictive performance is similar to SSDMs but the Bayesian joint modeling approach provides two main advantages over single species modeling: (1) the JSDM directly estimates the significance of environmental effects; and (2) predicted species richness accounts for species dependencies. An additional value of JSDMs is that the conditional prediction of species distributions can use not only the environmental associations of species, but also the presence and abundance of other species when forecasting future climatic associations.
Dynamics of camel and human hemoglobin revealed by molecular simulations
Authors: Ali Amanat , Soman Soja Saghar , Vijayan Ranjit
Published: January 2022

Hemoglobin is one of the most widely studied proteins genetically, biochemically, and structurally. It is an oxygen carrying tetrameric protein that imparts the characteristic red color to blood. Each chain of hemoglobin harbors a heme group embedded in a hydrophobic pocket. Several studies have investigated structural variations present in mammalian hemoglobin and their functional implications. However, camel hemoglobin has not been thoroughly explored, especially from a structural perspective. Importantly, very little is known about how the heme group interacts with hemoglobin under varying conditions of osmolarity and temperature. Several experimental studies have indicated that the tense (T) state is more stable than the relaxed (R) state of hemoglobin under normal physiological conditions. Despite the fact that R state is less stable than the T state, no extensive structural dynamics studies have been performed to investigate global quaternary transitions of R state hemoglobin under normal physiological conditions. To evaluate this, several 500 ns all-atom molecular dynamics simulations were performed to get a deeper understanding of how camel hemoglobin behaves under stress, which it is normally exposed to, when compared to human hemoglobin. Notably, camel hemoglobin was more stable under physiological stress when compared to human hemoglobin. Additionally, when compared to camel hemoglobin, cofactor-binding regions of hemoglobin also exhibited more fluctuations in human hemoglobin under the conditions studied. Several differences were observed between the residues of camel and human hemoglobin that interacted with heme. Importantly, distal residues His58 of α hemoglobin and His63 of β hemoglobin formed more sustained interactions, especially at higher temperatures, in camel hemoglobin. These residues are important for oxygen binding to hemoglobin. Thus, this work provides insights into how camel and human hemoglobin differ in their interactions under stress.
Cryopreservation of Anopheles stephensi embryos
Authors: James Eric R. , Wen Yingda , Overby James , Pluchino Kristen , McTighe Shane , Matheny Stephen , Eappen Abraham , Hoffman Stephen L. , Billingsley Peter F.
Published: January 2022

The ability to cryopreserve mosquitoes would revolutionize work on these vectors of major human infectious diseases by conserving stocks, new isolates, lab-bred strains, and transgenic lines that currently require continuous life cycle maintenance. Efforts over several decades to develop a method for cryopreservation have, until now, been fruitless: we describe here a method for the cryopreservation of Anopheles stephensi embryos yielding hatch rates of ~ 25%, stable for > 5 years. Hatched larvae developed into fertile, fecund adults and blood-fed females, produced fully viable second generation eggs, that could be infected with Plasmodium falciparum at high intensities. The key components of the cryopreservation method are: embryos at 15–30 min post oviposition, two incubation steps in 100% deuterated methanol at − 7 °C and − 14.5 °C, and rapid cooling. Eggs are recovered by rapid warming with concomitant dilution of cryoprotectant. Eggs of genetically modified A. stephensi and of A. gambiae were also successfully cryopreserved. This enabling methodology will allow long-term conservation of mosquitoes as well as acceleration of genetic studies and facilitation of mass storage of anopheline mosquitoes for release programs.
Approximate reinforcement learning to control beaconing congestion in distributed networks
Authors: Aznar-Poveda J. , García-Sánchez A.-J. , Egea-López E. , García-Haro J.
Published: January 2022

In vehicular communications, the increase of the channel load caused by excessive periodical messages (beacons) is an important aspect which must be controlled to ensure the appropriate operation of safety applications and driver-assistance systems. To date, the majority of congestion control solutions involve including additional information in the payload of the messages transmitted, which may jeopardize the appropriate operation of these control solutions when channel conditions are unfavorable, provoking packet losses. This study exploits the advantages of non-cooperative, distributed beaconing allocation, in which vehicles operate independently without requiring any costly road infrastructure. In particular, we formulate the beaconing rate control problem as a Markov Decision Process and solve it using approximate reinforcement learning to carry out optimal actions. Results obtained were compared with other traditional solutions, revealing that our approach, called SSFA, is able to keep a certain fraction of the channel capacity available, which guarantees the delivery of emergency-related notifications with faster convergence than other proposals. Moreover, good performance was obtained in terms of packet delivery and collision ratios.
SVBE: searchable and verifiable blockchain-based electronic medical records system
Authors: Alrebdi Norah , Alabdulatif Abdulatif , Iwendi Celestine , Lian Zhuotao
Published: January 2022

Central management of electronic medical systems faces a major challenge because it requires trust in a single entity that cannot effectively protect files from unauthorized access or attacks. This challenge makes it difficult to provide some services in central electronic medical systems, such as file search and verification, although they are needed. This gap motivated us to develop a system based on blockchain that has several characteristics: decentralization, security, anonymity, immutability, and tamper-proof. The proposed system provides several services: storage, verification, and search. The system consists of a smart contract that connects to a decentralized user application through which users can transact with the system. In addition, the system uses an interplanetary file system (IPFS) and cloud computing to store patients’ data and files. Experimental results and system security analysis show that the system performs search and verification tasks securely and quickly through the network.
Lateral forces determine dimensional accuracy of the narrow-kerf sawing of wood
Authors: Orlowski Kazimierz A. , Chuchala Daniel , Szczepanski Marcin , Migda Wojciech , Wojnicz Wiktoria , Sandak Jakub
Published: January 2022

The shrinking global forest area limits the supply of industrially usable raw resources. This, in combination with the ever-increasing consumption of timber due to population growth can lead to the lack of a positive balance between the annual volumetric growth and consumption of wood. An important innovation toward increasing environmental and economic sustainability of timber production is to reduce the volume of wood residues by minimizing the sawing kerf. It results in higher material yield but may impact the dimensional accuracy of derived products. Therefore, the cutting tool geometry as well as the sawing process as a whole must be carefully optimized to assure optimal use of resources. The goal of this study is to better understand the causes of machining errors that occur when sawing wood with saws of varying thickness of kerf, with a special focus on re-sawing thin lamellae performed on the gang saw. Numerical simulations were tested against experimental results, considering influence of diverse components of cutting forces, in addition to the initial and operating stiffness coefficients of the saw blade. It has been demonstrated that asymmetric loads from the cutting process for the scraper saw blade can cause sawing inaccuracies. The simulation methodology developed in this research can be straightforwardly extended towards determination of optimal geometry of other cutting tools, particularly with the reduced sawing kerf. This may lead to more sustainable use of natural resources as well as an increase in economic gain for the wood processing industries.
Photosynthetic efficiency, growth and secondary metabolism of common buckwheat (Fagopyrum esculentum Moench) in different controlled-environment production systems
Authors: Hornyák Marta , Dziurka Michał , Kula-Maximenko Monika , Pastuszak Jakub , Szczerba Anna , Szklarczyk Marek , Płażek Agnieszka
Published: January 2022

Light-emitting diodes (LEDs) and high-pressure sodium lamps (HPS) are among the most commonly used light sources for plant cultivation. The objective of this study was to evaluate the effect of two controlled-environment production systems differing in light sources on growth, photosynthetic activity, and secondary metabolism of common buckwheat. We hypothesized that LED light with the majority of red and blue waves would increase physiological and biochemical parameters compared to sunlight supplemented with HPS lamps. The experiment was performed in a phytotronic chamber (LEDs) and in a greenhouse (solar radiation supplemented with HPS lamps as a control). The effects were analyzed at the flowering phase with biometric measurements, leaf chlorophyll index, the kinetics of chlorophyll a fluorescence, content of soluble carbohydrates and phenolics in the leaves. Applied LED light decreased the biomass but stimulated the production of phenolics compared to control plants. In control plants, a positive correlation between flavonoid content and energy dissipation from photosystem II (DIo/CSm) was found, while in plants under LEDs total pool of phenolic content correlated with this parameter and the quantum yield of electron transport (φ Ro and ψ Ro) was lower than that of the control, probably affecting buckwheat biomass.
Efficacy analysis of one-stage posterior-only surgical treatment for thoracic spinal tuberculosis in the T4–6 segments with minimum 5-year follow-up
Authors: Zhan Yi , Kang Xin , Gao Wenjie , Zhang Xinliang , Kong Lingbo , Hao Dingjun , Wang Biao
Published: January 2022

In recent years, with the in-depth research on spinal tuberculosis, posterior surgery alone has been praised highly by more and more surgeons due to the better correction of kyphosis, better maintenance of spinal physiological curvature, smaller surgical trauma and fewer surgical complications. However, there is currently lack of relevant reports about the efficacy of posterior surgery alone in the treatment of tuberculosis in the T4–6 segments. This study aimed to evaluate the clinical study efficacy and feasibility of one-stage posterior-only surgical treatment for thoracic spinal tuberculosis in the T4–6 segments. 67 patients with tuberculosis in T4–6 segments who underwent one-stage posterior-only surgery were included in this study. The clinical efficacy was evaluated using statistical analysis based on the data about erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), Oswestry Dability Index (ODI) score, Visual Analogue Scale (VAS) score and Cobb angle before surgery, after surgery and at the last follow-up. All patients completed fusion during the follow-up period of 6–9 months. ESR and CRP were returned to normal for all patients at 6 months follow-up. In the meanwhile, among the 27 patients combined with neurological impairment, neurological functions of 22 cases (81.48%) recovered completely at the last follow-up (P < 0.05). Cobb angle of the kyphosis was improved from preoperative 34.8 ± 10.9° to postoperative 9.6 ± 2.8°, maintaining at 11.3 ± 3.2° at the last follow-up, The ODI and VAS scores were improved by 77.10% and 81.70%, respectively. This 5-year follow-up study shows that better clinical efficacy can be achieved for tuberculosis in T4–6 segments using one-stage posterior-only approach by costotransverse debridement in combination with bone graft and internal fixation. The posterior surgical method cannot only effectively accomplish debridement, obtain satisfactory clinical results, but also well correct kyphotic deformity and maintain it.
Association between plasma glycocalyx component levels and poor prognosis in severe influenza type A (H1N1)
Authors: Huang Xiao , Lu Feng , Tian Huanhuan , Hu Haoran , Ning Fangyu , Shang Quanmei , Hao Dong , Zhu Weiwei , Kong Guiqing , Ma Xiaohong , Feng Jiali , Wang Tao , Wang Xiaozhi
Published: January 2022

Influenza A virus infection causes a series of diseases, but the factors associated with disease severity are not fully understood. Disruption of the endothelial glycocalyx contributes to acute lung injury in sepsis, but has not been well studied in H1N1 influenza. We aim to determine whether the plasma glycocalyx components levels are predictive of disease severity in H1N1 influenza. This prospective observational study included 53 patients with influenza A (H1N1) during the influenza season, and 30 healthy controls in our hospital. Patients were grouped by severity and survival. We collected clinical data and blood samples at admission. Inflammatory factors (tumor necrosis factor-α, interleukin-6, interleukin-10) and endothelial glycocalyx components (syndecan-1, hyaluronan, heparan sulfate) were measured. The plasma levels of syndecan-1, hyaluronan, and heparan sulfate were significantly higher in patients with severe influenza A (H1N1) than in mild cases. Syndecan-1 and hyaluronan were positively correlated with disease severity, which was indicated by the APACHE II and SOFA scores and lactate levels, and negatively correlated with albumin levels. At a cutoff point ≥ 173.9 ng/mL, syndecan-1 had a 81.3% sensitivity and 70.3% specificity for predicting of 28-day mortality. Kaplan–Meier analysis demonstrated a strong association between syndecan-1 levels and 28-day mortality (log-rank 11.04,P = 0.001). Elevated plasma levels of syndecan-1 has a potential role in systemic organ dysfunction and may be indicative of disease severity in patients with influenza A (H1N1).