bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface band bending in semimetal Td-WTe2
Authors: Chen Aixi , Li Huifang , Huang Rong , Zhao Yanfei , Liu Tong , Li Zhiyun , Wang Li , Cheng Feiyu , Ren Wei , Lu Shuai , Yang Bingjie , Huang Zengli , Ding Sunan , Li Fang-Sen
Published: December 2020

Recently, spontaneous out-of-plane electric polarization and ferroelectric switching were found in WTe2 devices. On single crystal with ferroelectric property, a built-in electric field and corresponding band bending would be expected at the surface. However, such band bending in WTe2 hasn’t directly been observed experimentally. Here, by fitting angle-dependent X-ray photoelectron spectroscopy (XPS) spectra on WTe2 surface, we clearly observed downward band bending after slightly exposure to air, verifying appearance of surface polarization. Such band bending can’t be observed on pristine WTe2 surface and will disappear on fully oxidized sample. It suggests strong correlation between surface band bending and oxidation. Ionized donors from oxide species pinned at surface may contribute to the formation of surface band bending and polarization. Our study here offers new insight to figure out the microscopic origin of ferroelectric in WTe2.
Perioperative Adherence to Continuous Positive Airway Pressure and its Effect on Postoperative Nocturnal Hypoxemia in Obstructive Sleep Apnea Patients: a Prospective Cohort Study
Authors: Suen Colin , Wong Jean , Warsame Kahiye , Subramani Yamini , Panzarella Tony , Waseem Rida , Auckley Dennis , Chaudhry Rabail , Islam Sazzadul , Chung Frances
Published: December 2020

BackgroundAlthough continuous positive airway pressure (CPAP) is the first line treatment for obstructive sleep apnea (OSA) patients, the perioperative adherence rate is unclear. The objective of this study was to determine the perioperative adherence rate of patients with OSA with a CPAP prescription and the effect of adherence on nocturnal oxygen saturation.MethodsThis prospective cohort study included adult surgical patients with a diagnosis of OSA with CPAP prescription undergoing elective non-cardiac surgery. Patients were divided into CPAP adherent and non-adherent groups based on duration of usage (≥ 4h/night). Overnight oximetry was performed preoperatively and on postoperative night 1 and 2 (N1, N2). The primary outcome was adherence rate and secondary outcomes were nocturnal oxygen saturation.ResultsOne hundred and thirty-two patients completed the study. CPAP adherence was 61% preoperatively, 58% on postoperative N1, and 59% on N2. Forty-nine percent were consistently CPAP adherent pre- and postoperatively. Using a linear fixed effects regression, oxygen desaturation index (ODI) was significantly improved by CPAP adherence (p = 0.0011). The interaction term CPAP x N1 was significant (p = 0.0015), suggesting that the effect of CPAP adherence varied on N1 vs preoperatively. There was no benefit of CPAP adherence on postoperative mean SpO2, minimum SpO2, and percentage of sleep duration with SpO2 <90%. Supplemental oxygen therapy was higher in the CPAP non-adherent group vs adherent group on N1 (47% vs 9.8%, p < 0.001).ConclusionsAmong patients with a preoperative CPAP prescription, approximately 50% were consistently adherent. CPAP adherence was associated with improved preoperative ODI and the benefit was maintained on N1 and improved pain control. These modest effects may be underestimated by a higher severity of OSA in the CPAP adherent group and a higher rate of oxygen supplementation in the non-adherent group.Trial registrationClinicalTrials.Gov registry (NCT02796846).
Exodontia-associated bacteremia in horses characterized by next generation sequencing
Authors: Townsend Kile , Johnson Philip , LaCarrubba Alison , Martin Lynn , Ericsson Aaron
Published: December 2020

Bacteremia resulting from dental surgery is increasingly recognized as a health risk, especially in older and immunocompromised patients. Dentistry-associated bacteremic showering can lead to remote infections, as exemplified by valvular endocarditis. Emerging evidence points to a novel role played by uncultivable oral cavity commensals in the pathogenesis of diabetes, respiratory disease, cardiovascular disease, and adverse pregnancy outcomes. Whether dental extraction, a commonly-undertaken procedure in old horses, causes bacteremic showering has not been reported extensively. In a prospective clinical study using next generation sequencing (based on bacterial 16S rRNA), the circulating blood microbiome was characterized before and at 1 hour following extraction of incisor, canine or cheek teeth from 29 adult horses with dental disease. 16S rRNA sequencing results from the blood microbiome were compared with those from gingival swab samples obtained prior to extraction at the location of the diseased tooth. Bacteremic showering by translocated gingival commensals was demonstrated in horses undergoing exodontia and was, in some cases, still evident one hour post-operatively.
Effectiveness of 2D Radiographs in Detecting CBCT-based Incidental Findings in Orthodontic Patients
Authors: Choi Jin-Young , Oh Song Hee , Kim Seong-Hun , Ahn Hyo-Won , Kang Yoon-Goo , Choi Yong-Suk , Kook Yoon-Ah , Nelson Gerald
Published: December 2020

Some craniofacial diseases or anatomical variations are found in radiographic images taken for other purposes. These incidental findings(IFs) can be detected in orthodontic patients, as various radiographs are required for orthodontic diagnosis. To evaluate the rates of IFs in three-dimensional(3D) cone-beam-computed tomography (CBCT) with a large field of view (FOV) and investigate the effectiveness or accuracy of two-dimensional (2D) radiographs for detecting IFs compared to CBCT, the radiographic data of 1,020-orthodontic patients were interpreted. Prevalence in five areas was measured, and sensitivity, specificity, positive predictive value (PPV), negative predictive value(NPV), and accuracy were calculated. The accuracies of various 2D-radiograph were compared through a proportion test. A total of 709-cases(69.5%) of 1,020-subjects showed one or more IFs in CBCT images. Nasal cavity was the most affected area. Based on the CBCT images as a gold standard, different accuracies of various 2D-radiographs were observed in each area of the findings. The highest accuracy was confirmed in soft tissue calcifications with comprehensive radiographs. For detecting nasal septum deviations, postero anterior cephalograms were the most accurate radiograph. A possible improvement in accuracy for detecting IFs is expected by the development of CBCT with a lower radiation dose and higher resolution.
From White to Black, from Darkness to Light: Species Delimitation and UNITE Species Hypothesis Testing in the Russula Albonigra Species Complex.
Authors: De Lange Ruben , Adamčík Slavomír , Adamčíkova Katarína , Asselman Pieter , Borovička Jan , Delgat Lynn , Hampe Felix , Verbeken Annemieke
Published: December 2020

Russula albonigra is considered a well-known species, morphologically delimited by the context of the basidiomata that is blackening without intermediate reddening, and the menthol-cooling taste of the lamellae. It is supposed to have a broad ecological amplitude and a large distribution area. A thorough molecular analysis based on four nuclear markers (ITS, LSU, RPB2 and TEF1-α) shows this traditional concept of R. albonigra s.l. represents a species complex consisting of at least five European, three North-American and one Chinese species. Morphological study shows traditional characters used to delimit R. albonigra are not always reliable. Therefore, a new delimitation of the R. albonigra lineage is proposed and a key to the described European species of R. subg. Compactae is presented. A lectotype and an epitype are designated for R. albonigra and three new European species are described: R. ambusta, R. nigrifacta and R. ustulata. UNITE species hypotheses at different thresholds were tested against the taxonomic data. The species hypotheses at the similarity threshold 0.5% give a perfect match to the phylogenetically defined species within the R. albonigra lineage. Publicly available sequence data can contribute to species delimitation and expand knowledge on ecology and distribution, but the pitfalls are short and low quality sequences. The importance of updating public taxonomic data and using correct sequence similarity thresholds is emphasised.
Increasing Rainfall and Runoff in Alpine Mountainous Areas Can't Completely Eliminate Drought Driven by Temperature Rise 
Authors: Deng Yu , Guo Zhifeng , Ni Fuquan , Xue Lianqing , Wu Yiping , Deng Ouping , Zhou Man , Hu Jian , Zhang Ying , Bu Ruihan , Ma Jie , Nie Chao , Zhang Yang
Published: December 2020

Drought research under climate change is of great scientific significance. For Land Use and Land Cover Change (LUCC), temperature and rainfall in climate change, which factor has a greater impact on runoff change in alpine mountainous areas? Can the increase of rainfall in the alpine mountainous area completely eliminate the drought driven by temperature rise? This study takes the upper reaches of Heihe River basin (URHRB) as an example, the URHRB's Soil and Water Assessment Tool (SWAT) model is constructed. Based on 58 scenarios and The Budyko Framework, here we show that a)climate change has a greater contribution to runoff than LUCC, effect of increased rainfall greater than temperature rising on runoff in alpine mountainous area; b)the drought of 57.14% of UHRRB’s sub-basins have eased, 42.86% of the sub-basins is more serious, the increase in rainfall can't completely eliminate the drought driven by temperature rise. This study coupling SWAT simulation with Budyko Framework and other methods solves the problem of lack of data in alpine mountainous areas, and more accurately quantifies the impact of climate change, LUCC on runoff changes, realizing theoretical and method innovation. The results of this study provide a scientific paradigm for solving scientific problems in similar regions in China and other countries, and have important promotion value.
Numerical Simulation of Spiral Flow and Heat Transfer in Hydrate Pipeline With Long Twisted Band
Authors: Rao Yongchao , Li Lijun , Wang Shuli , Zhao Shuhua , Zhou Shidong
Published: December 2020

The DPM model (discrete phase model) considering the motion of solid particles was used to simulate the complex spiral flow characteristics of hydrate in the pipe spinning up with long twisted band. The deposition and heat transfer characteristics of gas hydrate particles in the pipe spiral flow were studied. The velocity distribution, pressure drop distribution, heat transfer characteristics and particle settling characteristics of the flow field in the pipeline were investigated. The numerical results show that, compared with the straight flow of light pipe without twisted band, two obvious eddies are formed in the flow field under the spinning action of twisted band, and the velocities are maximum at the center of the eddies. Along the direction of the pipe, the two vortices move towards the pipe wall from near the twisted band, which can effectively carry the hydrate particles deposited on the pipe wall. With the same Reynolds number, the greater the twist ratio, the weaker the spiral strength, the smaller the tangential velocity of the spiral flow, and the smaller the pressure drop of the pipe. Therefore, the pressure loss can be reduced as much as possible while ensuring the spinning effect of the spiral flow. In a straight light pipe flow, the Nusser number is in a parabolic shape with the opening downwards. At the center of the pipe, the Nusser number gradually decreases towards the pipe wall at the maximum, and at the near wall, the attenuation gradient of Nu is large. For spiral flow, the curve presented by Nusserr number shows a trough at the center of the pipe and a peak at 1/2 of the pipe diameter. With the reduction of twist rate, the Nussel number becomes larger and larger. Therefore, the spiral flow can make the temperature distribution in the flow field in the pipeline more even, and prevent the large temperature difference resulting in the mass formation of hydrate particles in the pipeline wall. Spiral flow has a good carrying effect. Under the same working condition, the spiral flow carries hydrate particles at a distance about 3-4 times that of the straight flow.
Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry
Authors: Ito Sosuke , Ashida Keita , Aoki Kazuhiro
Published: December 2020

Chemical reactions are responsible for information processing in living cells, and their accuracy and speed have been discussed from a thermodynamic viewpoint. The recent development in stochastic thermodynamics enables evaluating the thermodynamic cost of information processing. However, because experimental estimation of the thermodynamic cost based on stochastic thermodynamics requires a sufficient number of samples, it is only estimated in simple living systems, such as RNA folding and F1-ATPase. Therefore, it is challenging to estimate the thermodynamic cost of information processing by chemical reactions in living cells. Here, we evaluated the thermodynamic cost and its efficiency of information processing in living systems at the single-cell level for the first time by establishing an information-geometric method to estimate them with a relatively small number of samples. We evaluated the thermodynamic cost of the extracellular signal-regulated kinase (ERK) phosphorylation from the time series of the fluorescence imaging data by calculating the intrinsic speed in information geometry. We also evaluated a thermodynamic efficiency based on the thermodynamic speed limit, and thus this paper reports the first experimental test of thermodynamic uncertainty relations in living systems. Our evaluation revealed the change of the efficiency under the conditions of different cell densities and its robustness to the upstream pathway perturbation. Because our approach is widely applicable to other signal transduction pathways, such as the G-protein coupled receptor pathways for sensation, it would clarify efficient mechanisms of information processing in such a living system.
Early life stress induces age-dependent epigenetic changes in p11 gene expression
Authors: Seo Mi Kyoung , Lee Jung Goo , Park Sung Woo
Published: December 2020

Early life stress (ELS) causes long-lasting changes in depression-like behaviors through epigenetic mechanisms. However, little is known about the effects of ELS in adulthood, specifically across different age groups. In this study, the epigenetic modifications of p11 expression in adult mice subjected to ELS were investigated in different stages of adulthood. Pups experienced maternal separation (MS) for 3 h daily from postnatal day 1 to 21. At young and middle adulthood, behavior phenotypes, hippocampal p11 expression levels, and levels of histone acetylation and methylation and DNA methylation at the hippocampal p11 promoter were measured. Middle-aged, but not young adult, MS mice exhibited depression-like behavior in the forced swimming test. Concurrent with reduced hippocampal p11 levels, mice in both age groups showed decreases in histone acetylation and activating histone methylation as well as increases in repressive histone methylation at the p11 promoter. The extent of the reduction in gene expression and histone acetylation was much higher in middle than in young adulthood. Moreover, DNA methylation analysis of the p11 promoter revealed increased CpG methylation in middle-aged MS mice only. The results highlight the age-dependent deleterious effects of ELS on depression-like behavior and on the epigenetic modifications of p11 transcription.
Exploring Ichnofacies Distribution in Ancient Seaways: The Late Miocene Rifian Corridor as a Natural Laboratory
Authors: de Weger Wouter , Rodríguez-Tovar Francisco , Miguez-Salas Olmo
Published: December 2020

Oceanic gateways have modulated ocean circulation and have influenced climatic variations throughout the Earth´s history. During the Late Miocene (7.8 - 7.35 Ma), the Atlantic Ocean and the Mediterranean Sea were connected through the Rifian Corridor (Morocco). This gateway is one of the few examples of deep ancient seaways with a semi-continuous sedimentary record. Deposits comprise turbidites intercalated between deep-sea fine grain sediments (i.e., hemipelagites and drift deposits), channelized sandstone contourite facies, and shallow marine sandstones. Herein an ichnological analysis was conducted in these upper Miocene sediments to improve characterisation of palaeoenvironmental conditions. In addition, ichnofacies were analysed to elucidate how bottom currents control ichnofacies distribution and can modified their attributes. Turbidite deposits are typified by vertical trace fossils (i.e., Ophiomorpha), conforming the Ophiomorpha rudis ichnosubfacies. Contouritic sandstones exhibit high density and low diverse trace fossil assemblage, with predominant Macaronichnus and Scolicia, resembling a proximal expression of Cruziana ichnofacies. Shallow marine environments are dominated by vertical trace fossils (e.g., Conichnus, Ophiomorpha and Skolithos), allowing an assignation to Skolithos ichnofacies. This study reveals energy to be a major controlling factor determining ichnofacies attributes and distribution in ancient deep seaways. Within these seaways, highly energetic conditions typical of shallower settings are present in deeper environments (i.e., slope), contributing to ichnodiversity impoverishment in ichnofacies.
Depth of Anaesthesia Assessment Based on Spectral Entropy
Authors: Ra Jee Sook , Li Tianning , Li Yan
Published: December 2020

Anaesthesia is a state of temporary controlled loss of awareness induced for medical purposes. An accurate assessment of the depth of anaesthesia (DoA) has always been required. However, the current DoA algorithms have limitations such as inaccuracy or inflexibility. In this study, for more reliable DoA assessment, pre-denoised electroencephalograph (EEG) signals are divided into ten frequency bands (α, β1, β2, β3, β4, β, βγ, γ, δ and θ), and the basic complexity measure is done by using spectral entropy (SE). SE from beta-gamma frequency band (21.5 - 38.5 Hz) and SE from beta frequency band show the highest R squared value (0.8458 and 0.7312, respectively) with currently the most popular DoA index, bispectral index (BIS). A new DoA index is developed based on these two SE values for monitoring the DoA and evaluated by comparing with the BIS index. The highest Pearson correlation coefficient is 0.918, and the average is 0.80. In addition, the proposed index shows an earlier reaction than BIS index when the patient from deep anaesthesia to moderate anaesthesia, and the consistency in the case of poor signal quality (SQ) while the BIS Index exhibits inflexibility with cases of poor SQ.
Photocurrent-driven transient symmetry breaking in the Weyl semimetal TaAs
Authors: Sirica Nicolas , Orth Peter , Scheurer Matthias , Dai Yaomin , Lee Min-Cheol , Padmanabhan Prashant , Mix LaMoyne , Teitelbaum Samuel , Trigo Mariano , Zhao Lingxiao , Chen Genfu , Xu Bing , Yang Run , Shen Bing , Hu Chaowei , Lee Chi-Cheng , Lin Hsin , Cochran Tyler , Trugman Stuart , Zhu Jian-Xin , Hasan M , Ni Ni , Qiu Xianggang , Taylor Antoinette , Yarotski Dmitry , Prasankumar Rohit
Published: December 2020

Symmetry plays a central role in conventional and topological phases of matter, making the ability to optically drive symmetry changes a critical step in developing future technologies that rely on such control. Topological materials, like the newly discovered topological semimetals, are particularly sensitive to a breaking or restoring of time-reversal and crystalline symmetries, which affect both bulk and surface electronic states. While previous studies have focused on controlling symmetry via coupling to the crystal lattice, we demonstrate here an all-electronic mechanism based on photocurrent generation. Using second-harmonic generation spectroscopy as a sensitive probe of symmetry changes, we observe an ultrafast breaking of time-reversal and spatial symmetries following femtosecond optical excitation in the prototypical type-I Weyl semimetal TaAs. Our results show that optically driven photocurrents can be tailored to explicitly break electronic symmetry in a generic fashion, opening up the possibility of driving phase transitions between symmetry protected states on ultrafast time scales.
Effect of Shape on the Magnitude of the Delboeuf Illusion
Authors: Li Shujie , Zhang Xiaolin , Yin Keli
Published: December 2020

Three experiments to discuss the applicability of the contour attraction and the parallel attraction to different shapes in the Delboeuf illusion. The contour attraction suggests that the contours of the test figure and the inducer have an effect of interattraction in the Delboeuf illusion, and the parallel attraction suggests that the attraction between non-intersecting contours was maximal when they were parallel. In Experiment 1, the shape of the test figures and the inducers changed simultaneously and formed parallel lines. In Experiment 2, the test figures remained circles while the inducers changed shape. Experiment 3 was identical to Experiment 2 except that the areas of the inducers remained equal. The results demonstrated that the illusion is influenced by shape. Importantly, the effect of shape on the magnitude of the Delboeuf illusion is based on the contour attraction and the parallel attraction. Configurations with circles or shapes more similar to a circle were related more to the contour attraction, whereas shapes that were dissimilar to a circle were related more to the parallel attraction. We suggest that the contour attraction may be a circular modality of the parallel attraction.
A Zero-field Nuclear Magnetic Resonance Spectroscopy Study on the Structure Property Relationship in Co thin Films
Authors: Fritsch Patrizia , Lucassen Juriaan , Swagten Henk , Büchner Bernd , Lavrijsen Reinoud , Wurmehl Sabine
Published: December 2020

The interfacial Dzyaloshinskii-Moriya interaction (iDMI) was investigated in Co thin-films with different combinations of seeding and capping layers in previous works. The variations in the local magnetic out-of-plane (oop) anisotropy K as a function of film thickness t lead to additional contributions that make the quantification of the iDMI more challenging. These additional contributions were specifically attributed to the transition of fcc Co to hcp Co at a critical thickness tcr. In this work we clarify this issue by investigating the local structure and local magnetic stiffness and their contribution to the oop anisotropy K in two Pt/Co(t)/Ir film stacks with t = 10 nm and t = 25 nm. Zero-field nuclear magnetic resonance spectroscopy (ZF NMR) is the method of choice as it is a non-destructive and sensitive probe to examine structure and magnetic properties of nano-sized samples. We describe the evolution of the Co allotropes (fcc & hcp) and stacking fault disorder with the increase of t and illustrate the structure-property relationship between the local environments of Co and their respective magnetic stiffness.
Conversion and Validation of Rectal Constraints for Prostate Carcinoma Receiving Hypofractionated Carbon-ion Radiotherapy With a Local Effect Model
Authors: Wang Weiwei , Li Ping , Sheng Yinxiangzi , Huang Zhijie , Zhao Jingfang , Hong Zhengshan , Shahnazi Kambiz , Jiang Guoliang , Zhang Qing
Published: December 2020

Purpose: The study objective was to convert the microdosimetric kinetic model (MKM) rectum constraints for 16-fraction carbon-ion radiotherapy (CIRT) to local effect model (LEM) constraints for 12-fraction, 8-fraction, and 4-fraction CIRT for prostate carcinoma patients (PCAs).Methods: Two strategies were employed. To understand the fractionation effects, MKM linear-quadric (LQ) strategy first converted MKM rectum constraints for 16-fraction CIRT to 12-fraction, 8-fraction, and 4-fraction CIRT. To examine the differences in the biophysical models, MKM constraints were converted to LEM constraints using an RBE-conversion model. The LEM LQ strategy first converted MKM rectum constraints for 16-fraction CIRT to LEM constraints using the RBE-conversion model. Then, the LEM constraints converted the 16-fraction constraints to the rectum constraints for 12-fraction, 8-fraction, and 4-fraction CIRT using the LQ model. The LEM rectum constraints for 16 and 12-fraction CIRTs were compared to the rectum doses and the clinical follow-ups in 40 patients.Results: The 16-fraction NIRS rectum constraint Dmax < 60.8 Gy(RBE) and CNAO rectum constraint D1cc < 66.00 Gy(RBE) were converted by MKM LQ strategy to LEM constraints 58.01 and 55.97 Gy(RBE) (12fx), 45.47 and 43.97 Gy(RBE) (8fx), and 29.64 and 28.67 Gy(RBE) (4fx) and by LEM LQ strategy to 61.73 and 59.69 Gy(RBE) (12fx), 53.03 and 51.33 Gy(RBE) (8fx), and 40.10 and 38.88 Gy(RBE) (4fx). Differences of 36.13% were found. No late rectum complications were reported.Conclusions: The LEM rectum constraints from MKM LQ strategy were more conservative and can be used as the reference constraints for starting the hypofractionated CIRT.
Foot Arch Posture Development in Children and Adolescents aged 6 to 19 Years: A Cross-sectional Descriptive Study
Authors: Mahmoudzadeh Yousef , Alipour Roghayyeh
Published: December 2020

Background: The arch height index (AHI) is a commonly used method for measuring foot arch posture. However, there are little studies have investigated the natural growth and normative values of the foot arch using the AHI. The objective of this study was to establish normative and cut-off values for foot arch posture and to identify factors influencing foot arch posture across childhood and adolescence. Methods: In this cross-sectional study, a sample of 3532 healthy children and adolescents (1804 boys, 1728 girls; aged 6 to 19 years) was recruited for the navicular height (NH) and AHI measurements and anthropometry assessment (weight, height, BMI and foot length). Data were explored descriptively and graphically, comparisons between groups used t-tests or ANOVA model as appropriate and a multiple regressions was conducted. The 95% and 68% prediction intervals were used as cut-off values. Results : approximately 69% had a normal AHI range, 12% low arched foot, 3% severely low arched, 14% high arched and 1.8% severely high arched foot. The mean (SD) AHI was 15.16 (2.61). Very little gender bias was found for AHI values, being higher in males 15.32 (2.54) than in females 15.0 (2.68) ( p = .019). Regression showed approximately 3%, 0.3% and 2% of the AHI change was explained by age, BMI and foot length, respectively. The mean NH significantly increased from the age of 6 (2.62 cm) to 19 (4.20 cm). Conclusions: This study confirms that the ‘flexible flatfoot’ or low arched foot decreases with age. Simultaneously, increase of high arched foot type and shift in foot posture towards more normal foot type are also confirmed. BMI does not seem to be an important determinant of children foot arch posture. Keywords: Foot posture, Navicular height, Arch height index, Normative values, Medial longitudinal arch, Foot arch development, Children, Adolescents
Systematic Identification and Characterization of Five Transcription Factors Mediating the Oxidative Stress Response in Candida Albicans
Authors: Cui YingChao , Wang DaoSheng , Nobile Clarissa J. , Dong Danfeng , Ni Qi , Su Tongxuan , Jiang Cen , Peng Yibing
Published: December 2020

BackgroundCandida albicans is an opportunistic human fungal pathogen that can cause both superficial and systemic infections, especially in immunocompromised individuals. In response to C. albicans infections, innate immune cells of the host produce and accumulate reactive oxygen species (ROS) that can lead to irreversible damage and apoptosis of fungal cells. Prior studies have identified several transcription factors involved in the oxidative stress response of C. albicans. However, a systematic study to identify transcription factors mediating the oxidative response had not been previously conducted. ResultsIn this study, we screened a comprehensive transcription factor mutant library consisting of 211 transcription factor deletion mutant strains in the presence and absence of H2O2, a potent inducer of ROS, and identified five transcription factors (Skn7, Dpb4, Cap1, Dal81 and Stp2) involved in the response to H2O2. Genome-wide transcriptional profiling revealed that H2O2 induced a discreet set of genes differentially regulated in common among the five transcription factor mutant strains identified. Functional enrichment analysis identified KEGG pathways pertaining to glycolysis/gluconeogenesis, amino sugar and nucleotide sugar metabolism, and ribosome synthesis as the most enriched pathways. Furthermore, among the most common differentially expressed genes, hexose catabolism and iron transport were the most enriched GO terms.ConclusionsOur study is the first to systematically identify and characterize transcription factors involved in the response to H2O2. Based on the transcription factors identified, we found that exposure to H2O2 modulates several downstream gene classes involved in fungal virulence. Overall, this study sheds new light on the metabolism, physiological functions and cellular processes involved in the H2O2-induced oxidative stress response in C. albicans.
Weighted Gene Co-Expression Network Analysis Revealed The Cellular Senescence Signaling Pathway Associated With Non-Obstructive Azoospermia
Authors: Wang Ye Copper , Xia Leilei , Yi Xingpeng , Lu Jianping , Shen Dan
Published: December 2020

BackgroundNon-obstructive azoospermia (NOA) in males is a disease commonly associated with infertility, and is characterized by a disorder in spermogenesis, which may be caused by chromosomal abnormalities, orchitis, or chemical therapy. Spermogenesis is a process tightly regulated by precise gene expression patterns. However, the key genes and signaling pathways contributing to NOA remain unclear.MethodsIn this study, weighted gene co-expression network analysis was performed to identify NOA-associated gene clusters, and combined with the KEGG pathway assay and biological research.ResultsOur results revealed that the cellular senescence signaling pathway may play important roles in NOA. Indeed, cellular senescence is a complex biological process, often associated with disorder in cellular function. Using different expression genes (DEGs), the core, NOA-associated gene set in the cellular senescence pathway was identified; it contained SMAD2, which was upregulated, and HIPK4, which was downregulated. Consequently, the database was divided based on the expression levels of SMAD2 and HIPK4, and the GSEA (Gene Set Enrichment Analysis) assay, as well as the GO and KEGG assays of genes co-expressing with SMAD2 and HIPK4, showed that these two genes may take part in the regulation of cellular senescence, sperm differentiation and development, and energy metabolism.ConclusionsThe two genes, SMAD2 and HIPK4, took part in the regulation of senescence, and indicated that the cellular senescence of sertoli cells may play important roles in the NOA. This research can help us understand the mechanisms underlying NOA, and suggest anti-senescence therapeutic approaches that target these associated genes, especially SMAD2 and HIPK4.
Strategy for Mass Production of Lytic Staphylococcus Aureus Bacteriophage pSa-3: Contribution of Multiplicity of Infection
Authors: Kim Sang Guen , Kwon Jun , Giri Sib Sankar , Yun Saekil , Kim Hyoun Joong , Kim Sang Wha , Kang Jung Woo , Lee Sung Bin , Jung Won Joon , Park Se Chang
Published: December 2020

BackgroundAntibiotic-resistant bacteria have emerged as a serious problem; bacteriophages have, therefore, been proposed as a therapeutic alternative to antibiotics. Several authorities, such as pharmacopeia, FDA, have confirmed their safety, and some bacteriophages are commercially available worldwide. The demand for bacteriophages is expected to increase exponentially in the future; hence, there is an urgent need to mass-produce bacteriophages economically. Unlike the replication of non-lytic bacteriophages, lytic bacteriophages are replicated by lysing host bacteria, which leads to the termination of phage production; hence, strategies that can prolong the lysis of host bacteria in bacteria-bacteriophage co-cultures are required.ResultsIn the current study, we manipulated the inoculum concentrations of Staphylococcus aureus and phage pSa-3 (multiplicity of infection, MOI), and their energy sources to delay the bactericidal effect while optimizing phage production. We examined an increasing range of bacterial inoculum concentration (2 × 108 to 2 × 109 CFU/mL) to decrease the lag phase, in combination with a decreasing range of phage inoculum (from MOI 0.01 to 0.00000001) to delay the lysis of the host. Bacterial concentration of 2 × 108 CFU/mL and phage MOI of 0.0001 showed the maximum final phage production rate (1.68 × 1010 plaque forming unit (PFU)/mL). With this combination of phage-bacteria inoculum, we selected glycerol, glycine, and calcium as carbon, nitrogen, and divalent ion sources, respectively, for phage production. After optimization using response surface methodology, the final concentration of lytic Staphylococcus phage was 8.63 × 1010 ± 9.71 × 109 PFU/mL (5.13 fold increase).ConclusionsTherefore, Staphylococcus phage pSa-3 production can be maximized by increasing the bacterial inoculum and reducing the seeding phage MOI, which this combinatorial strategy could decrease phage production time. Further, we suggest that response surface methodology has the potential for optimizing mass production of lytic bacteriophages.
The Dynamic Landscape of Parasitaemia Dependent Intestinal Microbiota Shifting at Species Level and the Correlated Gut Transcriptome During Plasmodium Yoelii Infection
Authors: Zong Yawen , Cheng Lei , Cheng Xiangyun , Liao Binyou , Ye Xingchen , Liu Taiping , Li Jiyao , Zhou Xuedong , Xu Wenyue , Ren Biao
Published: December 2020

BackgroundMalaria, caused by Plasmodium infection, is a global life-threatening infection disease especially during the COVID-19 pandemic. However, it is still unclear about the dynamic change and the interactions of the intestinal microbiota and immunity during the whole parasite infection. Here, we investigated the change of intestinal microbiome and transcriptome during the whole Plasmodium infection process in mice to analyze the dynamic landscape of parasitaemia dependent intestinal microbiota shifting and related to host immunity.ResultsThere were significant parasitaemia dependent changes of intestinal microbiota and transcriptome, and the microbiota was significantly correlated to the intestinal immunity. We found that (i) the diversity and composition of the intestinal microbiota represented a significant correlation along with the Plasmodium infection in family, genus and species level; (ii) particularly, Erysipelotrichaceae bacterium canine oral taxon 255, Sutterella*, Ruminococcus 1* and Eubacterium plexicaudatum ASF492 were specific during the parasitaemia rising state, while Eubacterium nodatum group* was specific in the recovering phase at species level; (iii) the up-regulated genes from the intestinal transcriptome were mainly enriched in immune cell differentiation pathways along with the malaria development, particularly, naive CD4+ T cells differentiated into Th1, Th2 and Tfh cells in the early immune response and into Th17 cells in the later response, while B cells were activated during the whole Plasmodium infection process; (iv) the abundance of the parasitaemia phase-specific microbiota represented a high correlation with the phase-specific immune cells development, particularly, Th1 cell with family Bacteroidales BS11 gut group, genera Prevotella 9, Ruminococcaceae UCG 008, Moryella and specie Sutterella* , Th2 cell with specie Sutterella*, Th17 cell with family Peptococcaceae , genus Lachnospiraceae FCS020 group and spices Ruminococcus 1*, Ruminococcus UGG 014* and Eubacterium plexicaudatum ASF492, Tfh and B cell with genera Moryella and species Erysipelotrichaceae bacterium canine oral taxon 255.Conclusion﻿There were a remarkable dynamic landscape of the parasitaemia dependent shifting of intestinal microbiota and immunity, and a notable correlation between the abundance of intestinal microbiota, especially at species level, and immune cells.
Data Quality Assessment and Subsampling Strategies to Correct Distributional Bias in Prevalence Studies.
Authors: D'Ambrosio Angelo , Garlasco Jacopo , Quattrocolo Francesca , Vicentini Costanza , Zotti Carla Maria
Published: December 2020

BackgroundHealthcare-associated infections (HAIs) represent a major Public Health issue. Hospital-based prevalence studies are a common tool of HAI surveillance, but data quality problems and non-representativeness can undermine their reliability.MethodsThis study proposes three algorithms that, given a convenience sample and variables relevant for the outcome of the study, select a subsample with specific distributional characteristics, boosting either representativeness (Probability and Distance procedures) or risk factors' balance (Uniformity procedure). A "Quality Score" (QS) was also developed to grade sampled units according to data completeness and reliability. The methodologies were evaluated through bootstrapping on a convenience sample of 135 hospitals collected during the 2016 Italian Point Prevalence Survey (PPS) on HAIs.ResultsThe QS highlighted wide variations in data quality among hospitals (median QS 52.9 points, range 7.98-628, lower meaning better quality), with most problems ascribable to ward and hospital-related data reporting. Both Distance and Probability procedures produced subsamples with lower distributional bias (Log-likelihood score increased from 7.3 to 29 points). The Uniformity procedure increased the homogeneity of the sample characteristics (e.g., -58.4% in geographical variability). The procedures selected hospitals with higher data quality, especially the Probability procedure (lower QS in 100% of bootstrap simulations). The Distance procedure produced lower HAI prevalence estimates (6.98% compared to 7.44% in the convenience sample), more in line with the European median.ConclusionsThe QS and the subsampling procedures proposed in this study could represent effective tools to improve the quality of prevalence studies, decreasing the biases that can arise due to non-probabilistic sample collection.
A Novel Graphical Evaluation of Agreement
Authors: Kim Jongphil , Lee Ji-Hyun
Published: December 2020

Background: The Bland-Altman plot with limit of agreement has been widely used as a visual tool for assessing test-retest reliability or reproducibility between two measurements. We have observed, however, that in certain circumstances the limit of agreement approach may mislead practitioners. Particularly, if the acceptable difference is not available and two readers are highly concordant but the common variance of the data is large, the broad width of the limit of agreement plot may incorrectly indicate a lack of agreement. Methods: This paper proposes a novel, scaled index-based guidance for graphical evaluation of reproducibility or reliability. We create a reference band from two measurements, which is based on the concordance correlation coefficient.Results: Simulation studies have been carried out to demonstrate the benefits of our method over the limit of agreement. We also consider the application to the real examples, including the peak expiratory flow rate data in Bland and Altman's paper and the test-retest reproducibility data of Radiomics study.Conclusions: In absence of acceptable difference, we found that the limit of agreement seems to derive subjective inference and may not be consistent with concordance correlation coefficient. Our simulation study results and real data application show that the proposed method can provide practitioners with a novel graphical evaluation method which is consistent with results from concordance correlation coefficient approach than the limit of agreement approach.
The Feasibility of Selective High-Risk Area Irradiation for Supraglottic Laryngeal Carcinoma With Positive Lymph Nodes Only in Areas II and IIIThe Feasibility of Selective High-Risk Area Irradiation for Supraglottic Laryngeal Carcinoma With Positive Lymph Nodes Only in Areas II and III
Authors: zhou jianfeng , Wang hongyong , Bian li , Wang tiejun
Published: December 2020

ObjectiveTo study the prognosis of patients with positive lymph nodes in area II and III after supraglottic laryngocarcinoma surgery and to evaluate the feasibility of selective irradiation of a high-risk area. MethodsFrom February 2010 to March 2015, the complete clinical data for 181 patients treated for supraglottic laryngeal cancer at the Radiotherapy Department of the Second Hospital of Jilin University were analysed retrospectively. Among them, 100 patients were treated with whole neck prophylactic irradiation and 81 patients were treated with selective high-risk irradiation; i.e., lymph drainage of areas II and III. ResultsThe median follow-up time was 38.5 months; the 5-year OS, PFS, and NFS were 67.9%,58.1%,64.6% respectively. Among them, there were 6 cases of lymph node recurrence, 4 cases of local recurrence, 8 cases of distant metastasis and 58 deaths. However, there was no significant difference in recurrence between the selective high-risk radiation group and the total neck prophylactic radiation group. The OS, PFS and NFS of the two groups were 67.9% vs. 68%, 58.02% and 58%, and 62.9% and 66%, respectively, and the P values were 0.9161, 0.8916 and 0.7333,respectively. For late toxicity resulting from radiotherapy, the incidence of cervical fibrosis (2.47% vs. 10%, P = 0.043) and the incidence of throat mucosa injury (6.17% vs. 24%, P = 0.001) in patients in the selective high-risk area irradiation group were reduced. ConclusionThe preliminary data show that selective high-risk area irradiation is safe and feasible for patients with supraglottic laryngeal cancer accompanied by positive lymph nodes only in areas II and III, and the treatment can reduce the long-term adverse reactions and improve the quality of life. However, more evidence is needed.
Effect of Prenatal Phthalate Exposure on Childhood Atopic Dermatitis: a Systematic Review and a Meta-analysis of Birth Cohort Studies
Authors: Jung Minyoung , Kim Min-ji , Kim Seonwoo , Kyung Yechan , Kim Minji , Lee Ji Young , Jeong Hye-In , Lee Bo Ra , Kim Jihyun , Ahn Kangmo , Park Yong Mean
Published: December 2020

Background: The association between prenatal exposure to phthalate and childhood atopic dermatitis (AD) has been previously investigated; however, the results are inconsistent. We aimed to perform a systematic review and meta-analysis of birth cohort studies to investigate whether prenatal exposure to phthalate increases the risk of developing AD in children.Methods: We performed an electronic search of the MEDLINE, Embase, and Cochrane library databases. Studies were critically appraised, and meta-analyses were performed.Results: Among 129 articles identified, 11 studies met the eligibility criteria. Included studies originated from Europe (n = 5), USA (n = 4), and Asia (n = 2). The study sample size ranged from 147 to 1024 mother-child pairs. Quality assessment using the Newcastle–Ottawa scale of all studies had scores of six or greater. A meta-analysis of data from eight selected studies suggested that monobenzyl phthalate (MBzP) exposure was significantly associated with the risk of AD development (odds ratio 1.16, 95% confidence interval 1.04-1.31, I2 = 17.36%). However, AD development was not associated with other phthalate metabolites such as mono-(2-ethylhexyl) phthalate, monoethyl phthalate, mono-isobutyl phthalate, mono-n-butyl phthalate, and the sum of di-[2-ethylhexyl] phthalate on the development of AD (all P-values > 0.05).Conclusions: Our study suggests a positive association between prenatal exposure to MBzP and the development of childhood AD.
The Effect of Adenomyosis on the Outcome of Fresh Embryo Transfer in ICSI Cycles: a Retrospective Case-control Study
Authors: Nagireddy Siddhartha , Reddy Nellepalli Sanjeeva , Pandurangi Monna , Vembu Radha , Muthusamy Tamizharasi , Kasinathan Kanomozhi
Published: December 2020

Background: Adenomyosis is known to cause reduced clinical pregnancies and increased miscarriage rates in ART (Assisted Reproductive Technology) cycles. The detrimental effect was found to be enhanced if these women would undergo fresh embryo transfer without optimal suppression by GnRH agonist treatment. Several mechanisms were proposed as causative factors such as increased myometrial contractions, decreased implantation and altered endometrial receptivity. But the conclusions from previous studies were mutually conflicting. To ensure adequate regression of the disease prior to embryo transfer, these women would commonly undergo freeze-all and subsequent frozen embryo transfer. On contrary to this, fresh embryo transfer may be necessary in certain justifiable clinical situations. The present study was designed as a retrospective case-control study to compare the ICSI-fresh embryo transfer outcomes of women with adenomyosis to those with tubal factor infertility. This study is aimed to find the extent to which adenomyosis compromises the outcomes of fresh embryo transfer in ICSI cycles. Methods: The data of the eligible patients as per the study criteria, was obtained from the hospital medical records of a tertiary care University teaching hospital, in Chennai, South India. The study groups (Group A: women with adenomyosis, GroupB; women with tubal factor infertility) were compared for the fresh embryo transfer outcomes such as pregnancy rate, clinical pregnancy rate, miscarriage and live birth rates. SPSS version 17 software was used and and P<0.05 was considered statistically significant.Results: The data of 89 women included in the study (Group A: 47, and Group B: 42) were analysed. The data analysis showed significantly reduced pregnancy, clinical pregnancy, implantation and live birth rates in Group A compared to Group B (25.7 vs. 52.4%; 23.4 vs. 52.4%; 7.6% vs. 26.2%; 17.0 vs. 47.6%, respectively).Conclusions: We found that adenomyosis is associated with a less favourable outcome in ICSI -fresh embryo transfer. Though these results are justifiable if performed with appropriate indications, the cost-effectiveness and indications of such an approach needs to be evaluated on a larger prospective data.
Successful Birth After Preimplantation Genetic Testing for a Couple With Two Different Reciprocal Translocations and Review of the Literature
Authors: Liu Dun , Chen Chuangqi , Zhang Xiqian , Dong Mei , He Tianwen , Dong Yunqiao , Lu Jian , Yu Lihua , Yang Chuanchun , Liu Fenghua
Published: December 2020

Background: Preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) is widely applied in couples with single reciprocal translocation to increase the chance for a healthy live birth. However, limited knowledge is known on the data of PGT-SR when both parents have a reciprocal translocation. Here, we for the first time present a rare instance of PGT-SR for a non-consanguineous couple in which both parents carried an independent balanced reciprocal translocation and show how relevant genetic counseling data can be generated.Methods: The precise translocation breakpoints were identified by whole genome low-coverage sequencing (WGLCS) and Sanger sequencing. Next-generation sequencing (NGS) combining with breakpoint-specific polymerase chain reaction (PCR) was used to define 24-chromosome and the carrier status of the euploid embryos.Results: Surprisingly, 66.7% day-5 blastocysts were found to be balanced for maternal reciprocal translocation while being normal for paternal translocation and thus transferable. The transferable embryo rate was significantly higher than that which would be expected theoretically. Transfer of one balanced embryo resulted in the birth of a healthy boy. Conclusion(s): Our data of PGT-SR together with a systematic review of the literature should help in providing couples carrying two different reciprocal translocations undergoing PGT-SR with more appropriate genetic counseling.