bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrical control of all-optical graphene switches
Authors: Alaloul Mohammed , Khurgin Jacob B.
Published: October 2021

Graphene has emerged as an ultrafast photonic material for on-chip all-optical switching applications. However, its atomic thickness limits its interaction with guided optical modes, resulting in a high switching energy per bit. Herein, we propose a novel technique to electrically control the switching energy of an all-optical graphene switch on a silicon nitride waveguide. Using this technique, we theoretically demonstrate a 120 µm long all-optical graphene switch with an 8.9 dB extinction ratio, 2.4 dB insertion loss, a switching time of <100 fs, a fall time of <5 ps, and a 235 fJ switching energy at 2.5 V bias, where the applied voltage reduces the switching energy by

∼
16
×

. This technique paves the way for the emergence of ultra-efficient all-optical graphene switches that will meet the energy demands of next-generation photonic computing systems, and it is a promising alternative to lossy plasmon-enhanced devices.
Transfer learning assisted convolutional neural networks for modulation format recognition in few-mode fibers
Authors: Zhu Xiaorong , Liu Bo , Zhu Xu , Ren Jianxin , Ullah Rahat , Mao Yaya , Wu Xiangyu , Li Mingye , Chen Shuaidong , Bai Yu
Published: October 2021

Few-mode fiber (FMF), a mode multiplex technique, has been a candidate to provide high transmission capability in next-generation elastic optical networks (EONs), where the probabilistic shaping (PS) technology is widely used to approach Shannon limit. In this paper, we investigate a fast and accurate method of modulation format recognition (MFR) of received signals based on a transfer learning network (TLN) in PS-based FMF-EONs. TLN can apply the feature extraction ability of convolutional neural networks to the analysis of the constellations. We conduct experiments to demonstrate the effectiveness of the proposed scheme in FMF transmissions. Six modulation formats, including 16QAM, PS-16QAM, 32QAM, PS-32QAM, 64QAM and PS-64QAM, and four propagating modes, including LP01, LP11a, LP11b and LP21, are involved. In addition, comparisons of TLN with different structures of convolutional neural networks backbones are presented. In the experiment, the iterations of the TLN are one-tenth that of conventional deep learning network (DLN), and the TLN overcomes the problem of overfitting and requires less data than that of DLN. The experimental results show that the TLN is an efficient and feasible method for MFR in the PS-based FMF communication system.
Spatial resolution enhancement of coherent Doppler wind lidar using differential correlation pair technique
Authors: Zhang Yunpeng , Wu Yunbin , Xia Haiyun
Published: October 2021

A high spatial resolution coherent Doppler wind lidar (CDWL) incorporating the differential correlation pair (DCP) technique is proposed and demonstrated. By employing pulse pair with appropriate window functions, the spatial resolution can be enhanced, as the common parts of the correlation pair can be eliminated in the differential data processing. The performance of the new method is validated in the comparison experiment with the CDWLs adopting conventional schemes. Under a given peak power, the DCP technique provides higher wind velocity accuracy compared with a conventional pulsed CDWL where the laser spectral broadening caused by short pulses can be avoided and the carrier-to-noise ratio is improved. At a laser peak power of 250 W, with a spatial and temporal resolution of 3.3 m and 1 s, continuous radial wind profiling over 700 m is realized with a maximum error of 0.1 m/s.
Multiple solution solving in plasmon sensing by deep learning: determination of a layer refractive index and thickness in one experiment
Authors: Du Qian , Zhang Quan , Liu Guohua
Published: October 2021

Plasmons have received intensive attention owing to their significant spectrum shift in environmental sensing. Experimentally, the same spectral shifts may be caused by different combinations of structural parameters of a plasmonic nanoparticle. This multi-parameter problem cannot be solved by just a single feature analysis, but requires using the full scattering spectrum containing all features of the parameters. In this Letter, a deep learning method for solving multi-parameter problems is proposed based on the layer refractive index (

n

) and layer thickness (

d

) sensing of different nanorods and nanospheres. The full scattering spectrum can be theoretically simulated, precisely predicted using a well-trained deep learning method, and experimentally obtained using a homemade dark-field microscope. An error analysis of the simulation and experimental results indicates that this method is a potential way to determine

n

and

d

and further solve multi-parameter in plasmon sensing.
Simulating the performance of a high-efficiency SnS-based dual-heterojunction thin film solar cell
Authors: Kuddus Abdul , Mostaque Shaikh Khaled , Hossain Jaker
Published: October 2021

This article demonstrates a novel high efficiency ZnS/SnS/MoS2 dual-heterojunction thin film solar cell. The device has been optimized with respect to the thickness, doping concentration, and defect density of each constituent layer including working temperature and back contact metal work function using SCAPS-1D simulator. The MoS2 plays a promising role to serve as a back surface field (BSF) layer with commendatory band alignment, which provides an opportunity for higher absorption of longer wavelength photons utilizing the tail-states-assisted (TSA) two-step photon upconversion approach. The insertion of MoS2 in the ZnS/SnS pristine structure offers a significant improvement of the power conversion efficiency (PCE) within the detailed-balance limit with a rise from 20.1 to 41.4% with VOC of 0.91 V, JSC of 53.4 mA/cm2 and FF of 84.9%, respectively. This result reveals MoS2 as an effective BSF for low cost, highly efficient dual-heterojunction structure for future fabrication.
Prediction of minimal hepatic encephalopathy by using an radiomics nomogram in chronic hepatic schistosomiasis patients
Authors: Li Ying , Ju Shuai , Li Xin , Zhou Yan Li , Qiang Jin Wei
Published: October 2021

Objective

To construct an MR-radiomics nomogram to predict minimal hepatic encephalopathy (MHE) in patients with chronic hepatic schistosomiasis (CHS).

Methods

From July 2017 to July 2020, 236 CHS patients with non-HE (n = 140) and MHE (n = 96) were retrospective collected and randomly divided into training group and testing group. Radiomics features were extracted from substantia nigra-striatum system of a brain diffusion weighted images (DWI) and combined with clinical predictors to build a radiomics nomogram for predicting MHE in CHS patients. The ROC curve was used to evaluate the predicting performance in training group and testing group. The clinical decisive curve (CDC) was used to assess the clinical net benefit of using radiomics nomogram in predicting MHE.

Results

Low seralbumin (P < 0.05), low platelet count (P < 0.05) and high plasma ammonia (P < 0.05) was the significant clinical predictors for MHE in CHS patients. The AUC, specificity and sensitivity of the radiomics nomogram were 0.89, 0.90 and 0.86 in the training group, and were 0.83, 0.85 and 0.75 in the training group. The CDC analysis showed clinical net benefits for the radiomics nomogram in predicting MHE.

Conclusions

The radiomics nomogram combining DWI radiomics features and clinical predictors could be useful tool to predict MHE in CHS patients.
Association of abnormal pulmonary vasculature on CT scan for COVID-19 infection with decreased diffusion capacity in follow up: A retrospective cohort study
Authors: Salerno Daniel , Oriaku Ifeoma , Darnell Melinda , Lanclus Maarten , De Backer Jan , Lavon Ben , Gupta Rohit , Jaffe Fredric , Vega Sanchez Maria Elena , Kim Victor ,   on behalf of the Temple University Covid-19 Research Group
Published: October 2021

Background

Coronavirus Disease 2019 (COVID-19) is a respiratory viral illness causing pneumonia and systemic disease. Abnormalities in pulmonary function tests (PFT) after COVID-19 infection have been described. The determinants of these abnormalities are unclear. We hypothesized that inflammatory biomarkers and CT scan parameters at the time of infection would be associated with abnormal gas transfer at short term follow-up.

Methods

We retrospectively studied subjects who were hospitalized for COVID-19 pneumonia and discharged. Serum inflammatory biomarkers, CT scan and clinical characteristics were assessed. CT images were evaluated by Functional Respiratory Imaging with automated tissue segmentation algorithms of the lungs and pulmonary vasculature. Volumes of the pulmonary vessels that were ≤5mm (BV5), 5-10mm (BV5_10), and ≥10mm (BV10) in cross sectional area were analyzed. Also the amount of opacification on CT (ground glass opacities). PFT were performed 2–3 months after discharge. The diffusion capacity of carbon monoxide (DLCO) was obtained. We divided subjects into those with a DLCO <80% predicted (Low DLCO) and those with a DLCO ≥80% predicted (Normal DLCO).

Results

38 subjects were included in our cohort. 31 out of 38 (81.6%) subjects had a DLCO<80% predicted. The groups were similar in terms of demographics, body mass index, comorbidities, and smoking status. Hemoglobin, inflammatory biomarkers, spirometry and lung volumes were similar between groups. CT opacification and BV5 were not different between groups, but both Low and Normal DLCO groups had lower BV5 measures compared to healthy controls. BV5_10 and BV10 measures were higher in the Low DLCO group compared to the normal DLCO group. Both BV5_10 and BV10 in the Low DLCO group were greater compared to healthy controls. BV5_10 was independently associated with DLCO<80% in multivariable logistic regression (OR 1.29, 95% CI 1.01, 1.64). BV10 negatively correlated with DLCO% predicted (r = -0.343, p = 0.035).

Conclusions

Abnormalities in pulmonary vascular volumes at the time of hospitalization are independently associated with a low DLCO at follow-up. There was no relationship between inflammatory biomarkers during hospitalization and DLCO. Pulmonary vascular abnormalities during hospitalization for COVID-19 may serve as a biomarker for abnormal gas transfer after COVID-19 pneumonia.
Revisiting the hybridization processes in the Triatoma brasiliensis complex (Hemiptera, Triatominae): Interspecific genomic compatibility point to a possible recent diversification of the species grouped in this monophyletic complex
Authors: Pinotti Heloisa , de Oliveira Jader , Ravazi Amanda , Madeira Fernanda Fernandez , dos Reis Yago Visinho , de Oliveira Ana Beatriz Bortolozo , Azeredo-Oliveira Maria Tercília Vilela de , Rosa João Aristeu da , Alevi Kaio Cesar Chaboli
Published: October 2021

Triatomines are hematophagous insects of great epidemiological importance, since they are vectors of the protozoanTrypanosoma cruzi, the etiological agent of Chagas disease.Triatoma brasiliensiscomplex is a monophyletic group formed by two subspecies and six species:T.b.brasiliensis,T.b.macromelasoma,T.bahiensis,T.juazeirensis,T.lenti,T.melanica,T.petrocchiaeandT.sherlocki. The specific status of several species grouped in theT.brasiliensiscomplex was confirmed from experimental crossing and analysis of reproductive barriers. Thus, we perform interspecific experimental crosses betweenT.lentiand other species and subspecies of theT.brasiliensiscomplex and perform morphological analysis of the gonads and cytogenetic analysis in the homeologous chromosomes of the hybrids of first generation (F1). Besides that, we rescue all the literature data associated with the study of reproductive barriers in this monophyletic complex of species and subspecies. For all crosses performed betweenT.b.brasiliensis,T.b.macromelasoma,T.juazeirensisandT.melanicawithT.lenti, interspecific copulas occurred (showing absence of mechanical isolation), hybrids were obtained, none of the male hybrids presented the phenomenon of gonadal dysgenesis and 100% pairing between the chromosomes homeologous of the hybrids was observed. Thus, we demonstrate that there are no pre-zygotic reproductive barriers installed betweenT.lentiand the species and subspecies of theT.brasiliensiscomplex. In addition, we demonstrate that the hybrids obtained between these crosses have high genomic compatibility and the absence of gonadal dysgenesis. These results point to reproductive compatibility betweenT.lentiand species and subspecies of theT.brasiliensiscomplex (confirming its inclusion in the complex) and lead us to suggest a possible recent diversification of the taxa of this monophyletic group.
Ventricular outflow tract obstruction: An in-silico model to relate the obstruction to hemodynamic quantities in cardiac paediatric patients
Authors: Comunale Giulia , Padalino Massimo , Maiorana Carmelo , Di Salvo Giovanni , Susin Francesca M.
Published: October 2021

Background

Right (R) or left (L) ventricular outflow tract (VOT) obstruction can be either a dynamic phenomenon or a congenital anatomic lesion, which requires a prompt and optimal timing of treatment to avoid a pathological ventricular remodelling.

Objective

To develop a simple and reliable numerical tool able to relate the R/L obstruction size with the pressure gradient and the cardiac output. To provide indication of the obstruction severity and be of help in the clinical management of patients and designing the surgical treatment for obstruction mitigation.

Methods

Blood flow across the obstruction is described according to the classical theory of one-dimensional flow, with the obstruction uniquely characterized by its size. Hemodynamics of complete circulation is simulated according to the lumped parameter approach. The case of a 2 years-old baby is reproduced, with the occlusion placed in either the R/ or the L/VOT. Conditions from wide open to almost complete obstruction are reproduced.

Results

Both R/LVOT obstruction in the in-silico model resulted in an increased pressure gradient and a decreased cardiac output, proportional to the severity of the VOT obstruction and dependent on the R/L location of the obstruction itself, as it is clinically observed.

Conclusion

The in-silico model of ventricular obstruction which simulates pressure gradient and/or cardiac output agrees with clinical data, and is a first step towards the creation of a tool that can support the clinical management of patients from diagnosis to surgical treatments.
Association mapping for general combining ability with yield, plant height and ear height using F1 population in maize
Authors: Zheng Yunxiao , Han Xintong , Zhao Yongfeng , Zhu Liying , Huang Yaqun , Jia Xiaoyan , Zhang Zhongqin , Chen Jingtang , Guo Jinjie
Published: October 2021

General combining ability (GCA) is an important index for inbred lines breeding of maize. To identify the genetic loci of GCA and associated agronomic traits, an association analysis with 195 SSRs was made in phenotypic traits of 240 F1 derived from 120 elite inbred lines containing current breeding resources of maize crossed with 2 testers (Zheng58 and Chang7-2) in two places in 2018. All of the 20 association loci detected for grain yield (GY), plant height (PH), ear height (EH) and GCA for the three traits in two places could explain a phenotypic variation range of 7.31%-9.29%. Among the 20 association loci, 9 (7.31%-9.04%) were associated with GY, 4 (7.22%-8.91%) were related to GCA of GY, 1 (7.56%) was associated with PH, and 3 (7.53%-8.96%) were related to EH. In addition, 3 loci (9.14%-9.29%) were associated with GCA of PH whereas no locus was identified for GCA of EH. In the comparison of the association loci detected in Baoding and Handan, interestingly, one locus (7.69% and 8.11%) was identified in both environments and one locus (7.52% and 7.82%) was identified for yield and GCA of yield. Therefore, the identification of GY-, PH-, EH- and GCA-related association loci could not only provide references for high yield breeding of maize, but also help us comprehend the relationships among GY, agricultural traits and GCA.
Why we habitually engage in null-hypothesis significance testing: A qualitative study
Authors: Stunt Jonah , van Grootel Leonie , Bouter Lex , Trafimow David , Hoekstra Trynke , de Boer Michiel
Published: October 2021

Background

Null Hypothesis Significance Testing (NHST) is the most familiar statistical procedure for making inferences about population effects. Important problems associated with this method have been addressed and various alternatives that overcome these problems have been developed. Despite its many well-documented drawbacks, NHST remains the prevailing method for drawing conclusions from data. Reasons for this have been insufficiently investigated. Therefore, the aim of our study was to explore the perceived barriers and facilitators related to the use of NHST and alternative statistical procedures among relevant stakeholders in the scientific system.

Methods

Individual semi-structured interviews and focus groups were conducted with junior and senior researchers, lecturers in statistics, editors of scientific journals and program leaders of funding agencies. During the focus groups, important themes that emerged from the interviews were discussed. Data analysis was performed using the constant comparison method, allowing emerging (sub)themes to be fully explored. A theory substantiating the prevailing use of NHST was developed based on the main themes and subthemes we identified.

Results

Twenty-nine interviews and six focus groups were conducted. Several interrelated facilitators and barriers associated with the use of NHST and alternative statistical procedures were identified. These factors were subsumed under three main themes: the scientific climate, scientific duty, and reactivity. As a result of the factors, most participants feel dependent in their actions upon others, have become reactive, and await action and initiatives from others. This may explain why NHST is still the standard and ubiquitously used by almost everyone involved.

Conclusion

Our findings demonstrate how perceived barriers to shift away from NHST set a high threshold for actual behavioral change and create a circle of interdependency between stakeholders. By taking small steps it should be possible to decrease the scientific community’s strong dependence on NHST and p-values.
Determinants of quality of life in women immediately following the completion of primary treatment of breast cancer: A cross-sectional study
Authors: Park Jin-Hee , Jung Yong Sik , Kim Ji Young , Bae Sun Hyoung
Published: October 2021

Backgrounds

Many breast cancer patients experience significant distress immediately following the completion of primary treatment. Women who report low levels of quality of life (QOL) early in this phase of transitional survivorship tend to experience diminished long-term adjustment. However, since most of the prior studies on survivors were conducted on patients at various times, studies on QOL of women during the end of primary treatment have been insufficient. This study aimed to identify determinants of QOL in women with breast cancer immediately following the completion of treatment.

Methods

A cross-sectional study was conducted on 140 disease-free breast cancer patients who had completed therapy in the past 1 month at university hospitals. Functional Assessment of Cancer Therapy-Breast (FACT-B), Memorial Symptom Assessment Scale-Short Form (MSAS-SF), Self-Efficacy Scale for Self-Management of Breast Cancer (SESSM-B), and Interpersonal Support Evaluation List-12 (ISEL-12) scales were used to assess predictors and QOL. The data were analyzed using the Pearson correlation, t-test, ANOVA, and hierarchical multiple regression.

Results

The mean score of QOL for breast cancer survivors was 97.23 (±20.01). Chemotherapy and perceived economic status were significantly associated with QOL in terms of sociodemographic and disease/treatment-related characteristics. Physical and psychological symptoms and social support had a significant association with QOL. The regression analyses showed that physical and psychological symptoms and belonging support were statistically significant in predicting the QOL of breast cancer survivors.

Conclusions

The variables of symptom experience and social support must be acknowledged when improving women’s QOL immediately after their completion of primary breast cancer treatment. Greater focus on the reduction of symptom distress and increasing a sense of belonging could improve QOL among breast cancer survivors.
Cost-effectiveness of patient navigation programs for stroke patients–A systematic review
Authors: Kass Benjamin , Dornquast Christina , Meisel Andreas , Holmberg Christine , Rieckmann Nina , Reinhold Thomas
Published: October 2021

Objective

Stroke remains a leading cause of premature death, impairment and reduced quality of life. Its aftercare is performed by numerous different health care service providers, resulting in a high need for coordination. Personally delivered patient navigation (PN) is a promising approach for managing pathways through health care systems and for improving patient outcomes. Although PN in stroke care is evolving, no summarized information on its cost-effectiveness in stroke survivors is available. Hence, the aim of this systematic review is to analyze the level of evidence on the cost-effectiveness of PN for stroke survivors.

Methods

A systematic literature search without time limitations was carried out in PubMed, EMBASE, CENTRAL, CINAHL as well as PsycINFO and supplemented by a manual search. Randomized controlled trials published prior to April 2020 in English or German were considered eligible if any results regarding the cost-effectiveness of PN for stroke survivors were reported. The review was conducted according to PRISMA guidelines. Quality of included studies was assessed with the RoB2 tool. Main study characteristics and cost-effectiveness results were summarized and discussed.

Results

The search identified 1442 records, and two studies met the inclusion criteria. Quality of included studies was rated moderate and high. Programs, settings and cost-effectiveness results were heterogeneous, with one study showing a 90% probability of being cost-effective at a willingness to pay of $25600 per QALY (health/social care perspective) and the other showing similar QALYs and higher costs.

Conclusions

Since only two studies were eligible, this review reveals a large gap in knowledge regarding the cost-effectiveness of PN for stroke survivors. Furthermore, no conclusive statement about the cost-effectiveness can be made. Future attempts to evaluate PN for stroke survivors are necessary and should also involve cost-effectiveness issues.
Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks
Authors: Alachram Halima , Chereda Hryhorii , Beißbarth Tim , Wingender Edgar , Stegmaier Philip
Published: October 2021

Biomedical and life science literature is an essential way to publish experimental results. With the rapid growth of the number of new publications, the amount of scientific knowledge represented in free text is increasing remarkably. There has been much interest in developing techniques that can extract this knowledge and make it accessible to aid scientists in discovering new relationships between biological entities and answering biological questions. Making use of theword2vecapproach, we generated word vector representations based on a corpus consisting of over 16 million PubMed abstracts. We developed a text mining pipeline to produce word2vec embeddings with different properties and performed validation experiments to assess their utility for biomedical analysis. An important pre-processing step consisted in the substitution of synonymous terms by their preferred terms in biomedical databases. Furthermore, we extracted gene-gene networks from two embedding versions and used them as prior knowledge to train Graph-Convolutional Neural Networks (CNNs) on large breast cancer gene expression data and on other cancer datasets. Performances of resulting models were compared to Graph-CNNs trained with protein-protein interaction (PPI) networks or with networks derived using other word embedding algorithms. We also assessed the effect of corpus size on the variability of word representations. Finally, we created a web service with a graphical and a RESTful interface to extract and explore relations between biomedical terms using annotated embeddings. Comparisons to biological databases showed that relations between entities such as known PPIs, signaling pathways and cellular functions, or narrower disease ontology groups correlated with higher cosine similarity. Graph-CNNs trained with word2vec-embedding-derived networks performed sufficiently good for the metastatic event prediction tasks compared to other networks. Such performance was good enough to validate the utility of our generated word embeddings in constructing biological networks. Word representations as produced by text mining algorithms like word2vec, therefore are able to capture biologically meaningful relations between entities. Our generated embeddings are publicly available athttps://github.com/genexplain/Word2vec-based-Networks/blob/main/README.md.
Identifying disease-gene associations using a convolutional neural network-based model by embedding a biological knowledge graph with entity descriptions
Authors: Choi Wonjun , Lee Hyunju
Published: October 2021

Understanding the role of genes in human disease is of high importance. However, identifying genes associated with human diseases requires laborious experiments that involve considerable effort and time. Therefore, a computational approach to predict candidate genes related to complex diseases including cancer has been extensively studied. In this study, we propose a convolutional neural network-based knowledge graph-embedding model (KGED), which is based on a biological knowledge graph with entity descriptions to infer relationships between biological entities. As an application demonstration, we generated gene-interaction networks for each cancer type using gene-gene relationships inferred by KGED. We then analyzed the constructed gene networks using network centrality measures, including betweenness, closeness, degree, and eigenvector centrality metrics, to rank the central genes of the network and identify highly correlated cancer genes. Furthermore, we evaluated our proposed approach for prostate, breast, and lung cancers by comparing the performance with that of existing approaches. The KGED model showed improved performance in predicting cancer-related genes using the inferred gene-gene interactions. Thus, we conclude that gene-gene interactions inferred by KGED can be helpful for future research, such as that aimed at future research on pathogenic mechanisms of human diseases, and contribute to the field of disease treatment discovery.
Differential STAT gene expressions of Penaeus monodon and Macrobrachium rosenbergii in response to white spot syndrome virus (WSSV) and bacterial infections: Additional insight into genetic variations and transcriptomic highlights
Authors: Soo Tze Chiew Christie , Bhassu Subha
Published: October 2021

Diseases have remained the major issue for shrimp aquaculture industry for decades by which different shrimp species demonstrated alternative disease resistance or tolerance. However, there had been insufficient studies on the underlying host mechanisms of such phenomenon. Hence, in this study, the main objective involves gaining a deeper understanding into the functional importance of shrimp STAT gene from the aspects of expression, sequence, structure, and associated genes. STAT gene was selected primarily because of its vital signalling roles in stress, endocrine, and immune response. The differential gene expressions ofMacrobrachium rosenbergiiSTAT (MrST) andPenaeus monodonSTAT (PmST) under White Spot Syndrome Virus (WSSV) andVibrio parahaemolyticus/VpAHPNDinfections were identified through qPCR analysis. Notably, during both pathogenic infections,MrSTdemonstrated significant gene expression down-regulations (during either early or later post-infection time points) whereasPmSTshowed only significant gene expression up-regulations. Important sequence conservation or divergence was highlighted through STAT sequence comparison especially amino acid alterations at 614 aa [K (Lysine) to E (Glutamic Acid)] and 629 aa [F (Phenylalanine) to V (Valine)] from PmST (AY327491.1) to PmST (disease tolerant strain). There were significant differences observed between in silico characterized structures of MrST and PmST proteins. Important functional differentially expressed genes (DEGs) in the aspects of stress, endocrine, immune, signalling, and structural were uncovered through comparative transcriptomic analysis. The DEGs associated with STAT functioning were identified including inositol 1,4,5-trisphosphate receptor, hsp90, caspase, ATP binding cassette transmembrane transporter, C-type Lectin, HMGB, ALF1, ALF3, superoxide dismutase, glutathione peroxidase, catalase, and TBK1. The main findings of this study are STAT differential gene expression patterns, sequence divergence, structural differences, and associated functional DEGs. These findings can be further utilized for shrimp health or host response diagnostic studies. STAT gene can also be proposed as a suitable candidate for future studies of shrimp innate immune enhancement.
High affinity associations with α-SNAP enable calcium entry via Orai1 channels
Authors: Ramanagoudr-Bhojappa Ramanagouda , Miao Yong , Vig Monika
Published: October 2021

Molecular steps that activate store-operated calcium entry (SOCE) via Orai channel supramolecular complex remain incompletely defined. We have earlier shown that α-SNAP regulates the on-site functional assembly and calcium selectivity of Orai1 channels. Here we investigate the molecular basis of its association with Orai, Stim and find that the affinity of α-SNAP for Orai and Stim is substantially higher than previously reported affinities between Stim and Orai sub-domains. α-SNAP binds the coiled-coil 3 (CC3) sub-domain of Stim1. Mutations of Tryptophan 430 in Stim1-CC3 disrupted α-SNAP association and SOCE, demonstrating a novel α-SNAP dependent function for this crucial subdomain. Further, α-SNAP binds the hinge region near the C-terminus of Orai1 and an additional broad region near the N-terminus and Valine 262 and Leucine 74 were necessary for these respective interactions, but not Orai, Stim co-clustering. Thus, high affinity interactions with α-SNAP are necessary for imparting functionality to Stim, Orai clusters and induction of SOCE.
Tau fibril with membrane lipids: Insight from computational modeling and simulations
Authors: Barredo Prechiel A. , Fernandez Marvin Jose F. , Ambe Christopher E. , Balanay Mannix P.
Published: October 2021

The microtubule-binding protein tau has been the center of researches concerning Alzheimer’s disease (AD) due to several clinical trials of β-amyloid therapies failing recently. The availability of the tau fibril structure from AD brain enables computational modeling studies to calculate binding affinities with different ligands. In this study, the tau paired helical filaments (PHF-Tau) (PDB ID: 5O3L) was used as receptor and interactions with the lipids: 3-alpha-cholesterol; 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; and C18:1 sphingomyelin, were explored with molecular docking, molecular dynamics, and natural bond orbital analysis. Docking sites upon solvation of the protein with transferable interatomic potential-3 points reveal the amphipathic nature of PHF-Tau and molecular dynamics simulations show that the embedded phosphocholine at the tail side gives high potential energy values with some amino acids forming H-bond interactions.
Radiological correlates of vocal fold bowing as markers of Parkinson’s disease progression: A cross-sectional study utilizing dynamic laryngeal CT
Authors: Ma Andrew , Lau Kenneth K. , Thyagarajan Dominic
Published: October 2021

Objective

To determine whether arytenoid cartilage position and dynamics change with advancing duration and severity (as graded by MDS-UPDRS part III scores) in Parkinson’s disease, in a cross-sectional study design, we performed laryngeal four-dimensional computed tomography (4D-CT) in people with Parkinson’s disease and controls.

Methods

31 people with Parkinson’s disease covering a range of disease duration and severity and 19 controls underwent laryngeal 4D-CT whilst repeatedly vocalizing. We measured on each CT volume the glottic area (GA), inter-arytenoid distance (IAD), IAD-Area index (IAI) and arytenoid cartilage velocity (av→).

Results

People with Parkinson’s disease had reductions in the mean/effective minimum IAD when compared to controls, while mean/effective minimum GA and mean/effective maximum IAI were increased. Arytenoid cartilage velocities showed no difference. On Spearman correlation analyses, advancing disease duration and severity of PD showed moderately strong and significant correlations with increasing mean/effective minimum GA, increasing mean/effective maximum IAI and decreasing effective minimum IAD. Linear mixed models which considered the effects of intra and inter-individual variation showed that both disease duration (b = -0.011, SEb = 0.053, 95% CI [-0.022, 0], t(27) = -2.10, p = 0.045) and severity (b = -0.069, SEb = 0.032, 95% CI [-0.14,-0.0039], t(27) = -2.17, p = 0.039) were significant predictors for IAD, and also for transformed values of the GA and IAI.

Conclusions

There are progressive alterations in phonatory posturing as Parkinson’s disease advances. The increases in GA despite reductions in IAD are concordant with prior observations of vocal fold bowing. Our study provides a basis for using laryngeal 4D-CT to assess disease progression in Parkinson’s disease.
Unusual features and localization of the membrane kinome of Trypanosoma brucei
Authors: Jensen Bryan C. , Vaney Pashmi , Flaspohler John , Coppens Isabelle , Parsons Marilyn
Published: October 2021

In many eukaryotes, multiple protein kinases are situated in the plasma membrane where they respond to extracellular ligands. Ligand binding elicits a signal that is transmitted across the membrane, leading to activation of the cytosolic kinase domain. Humans have over 100 receptor protein kinases. In contrast, our search of theTrypanosoma bruceikinome showed that there were only ten protein kinases with predicted transmembrane domains, and unlike other eukaryotic transmembrane kinases, seven are predicted to bear multiple transmembrane domains. Most of the ten kinases, including their transmembrane domains, are conserved in bothTrypanosoma cruziandLeishmaniaspecies. Several possess accessory domains, such as Kelch, nucleotide cyclase, and forkhead-associated domains. Surprisingly, two contain multiple regions with predicted structural similarity to domains in bacterial signaling proteins. A few of the protein kinases have previously been localized to subcellular structures such as endosomes or lipid bodies. We examined the localization of epitope-tagged versions of seven of the predicted transmembrane kinases inT.bruceibloodstream forms and show that five localized to the endoplasmic reticulum. The last two kinases are enzymatically active, integral membrane proteins associated with the flagellum, flagellar pocket, or adjacent structures as shown by both fluorescence and immunoelectron microscopy. Thus, these kinases are positioned in structures suggesting participation in signal transduction from the external environment.
Hantaviruses use the endogenous host factor P58IPK to combat the PKR antiviral response
Authors: Wang Zekun , Ren Songyang , Li Qiming , Royster Austin D. , lin Lei , Liu Sichen , Ganaie Safder S. , Qiu Jianming , Mir Sheema , Mir Mohammad A.
Published: October 2021

Hantavirus nucleocapsid protein (NP) inhibits protein kinase R (PKR) dimerization by an unknown mechanism to counteract its antiviral responses during virus infection. Here we demonstrate that NP exploits an endogenous PKR inhibitor P58IPKto inhibit PKR. The activity of P58IPKis normally restricted in cells by the formation of an inactive complex with its negative regulator Hsp40. On the other hand, PKR remains associated with the 40S ribosomal subunit, a unique strategic location that facilitates its free access to the downstream target eIF2α. Although both NP and Hsp40 bind to P58IPK, the binding affinity of NP is much stronger compared to Hsp40. P58IPKharbors an NP binding site, spanning to N-terminal TPR subdomains I and II. The Hsp40 binding site on P58IPKwas mapped to the TPR subdomain II. The high affinity binding of NP to P58IPKand the overlap between NP and Hsp40 binding sites releases the P58IPKfrom its negative regulator by competitive inhibition. The NP-P58IPKcomplex is selectively recruited to the 40S ribosomal subunit by direct interaction between NP and the ribosomal protein S19 (RPS19), a structural component of the 40S ribosomal subunit. NP has distinct binding sites for P58IPKand RPS19, enabling it to serve as bridge between P58IPKand the 40S ribosomal subunit. NP mutants deficient in binding to either P58IPKor RPS19 fail to inhibit PKR, demonstrating that selective engagement of P58IPKto the 40S ribosomal subunit is required for PKR inhibition. Cells deficient in P58IPKmount a rapid PKR antiviral response and establish an antiviral state, observed by global translational shutdown and rapid decline in viral load. These studies reveal a novel viral strategy in which NP releases P58IPKfrom its negative regulator and selectively engages it on the 40S ribosomal subunit to promptly combat the PKR antiviral responses.
Fracture Resistance and Strain Analysis of Zirconia Copings With Vertical Knife Edge and Three Horizontal Finish Line Designs; Chamfer, Deep Chamfer and Shoulder With Two Cementation Techniques
Authors: Emam Marwa , El-Etreby Amr , Younis Jihan Farouk
Published: October 2021

Objective: The purpose of this in vitro study is to evaluate the effect of four finish line configurations and two cement types on the fracture resistance of zirconia copings. Material and Methods: Forty yttrium tetragonal zirconia polycrystals copings were manufactured on epoxy resin dies with four preparation designs: knife edge, chamfer, deep chamfer 0.5, 1 mm and shoulder 1 mm. The copings were cemented with two cement types (glass ionomer and resin cement); (n = 5). Two strain gauges were attached on each coping before they were vertically loaded till fracture with a universal testing machine. Data were analyzed by 2-way analysis of variance ANOVA (p < .05). Fractured specimens were examined for mode of failure with digital microscope. Results: Knife edge showed the highest mean fracture resistance (987.04 ± 94.18) followed by Chamfer (883.28 ± 205.42) followed by Shoulder (828.64 ± 227.79) and finally Deep chamfer finish line (767.66 ± 207.09) with no statistically significant difference. Resin cemented copings had higher mean Fracture resistance (911.76 ± 167.95) than glass ionomer cemented copings (821.55 ± 224.24) with no statistically significant difference. Knife edge had the highest strain mean values on the buccal (374.04 ± 195.43) and lingual (235.80 ± 103.46) surface. Shoulder finish line showed the lowest mean strain values on the buccal (127.47 ± 40.32) and lingual (68.35 ± 80.68) with no statistically significant difference. Resin cemented copings had higher buccal (295.05 ± 167.92) and lingual (197.38 ± 99.85) mean strain values  than glass ionomer copings (149.14 ± 60.94) and (90.27 ± 55.62) with no statistically significant difference. Conclusion: Vertical knife edge finish line is a promising alternative and either adhesive or conventional cementation can be used with zirconia copings.
 
KEYWORDS
Cementation; Flexural strength; Prosthodontics; Tooth preparation; Zirconium.
Enamel Deproteinization: Will It Save The Shear Bond Strength For The Sake Of Preventing White Spot Lesions?
Authors: Elhiny Omnia A. , El-Refai Dina A.
Published: October 2021

Objective: This study attempted to investigate the effect of enamel deproteinization using citric acid, PEG 400 and NaOCL on the shear bond strength of orthodontic brackets to enamel using nano-silver modified resin for the prevention of white spot lesions. Material and Methods: 68 premolars were used in the study; nano-silver modified adhesive resin was used to bond orthodontic brackets to the enamel. Specimens were divided into 4 groups according to the applied surface treatment before bonding. Group I (control): acid etching with 37% phosphoric acid. Group II: deproteinization using 5.25% sodium hypochlorite (NaOCl) before acid etching. Group III:deproteinization using 10% citric acid before acid etching. Group IV:deproteinization using 5% polyethylene glycol (PEG 400) before acid etching. The specimens were then thermo- cycled for 6000 cycles. They were examined for surface roughness, shear bond strength and using electron microscope. electron microscope Results: In both surface roughness and shear bond strength tests, Group III (citric acid) showed the highest values, followed by Group II (sodium hypochlorite); (p < 0.001). The least values were shown for Groups I (control) and IV (PEG 400), with no statistically significant difference between them (p = 0.948). SEM revealed etching pattern type 1 and 2 in the citric acid group while PEG 400 showed shallower micro- porosities. Conclusions: Deproteinization of enamel using either NaOCl or citric acid increased the bond strength of nano-sliver modified resin to enamel, with citric acid showing greater increase in bond strength. Deproteinization using PEG 400 did not increase the bond strength.
 
Keywords
Deproteinization; Sodium hypochlorite; Citric acid; PEG 400; Nano- silver modified adhesives.
Awareness of medical emergencies among dental practitioners in three Egyptian Dental Schools: A cross-sectional study
Authors: Hussein Heba , A. Abdelbaqy Mohamed , A. Ibrahim Abdelrahman , Farid Shahenda , Ibrahim Suzan
Published: October 2021

Objectives: To evaluate the awareness of medical emergencies among dental practitioners in three dental schools. Material and methods: The study group included 384 dental practitioners, including dental staff members, post-graduate students, and dental interns. These professionals were attending three dental educational institutions in Egypt. Two of them were governmental and one was a private school. The educational model is almost the same in most Egyptian dental schools. Results: The response rate was 100%. Most of the participants worked in private academia (44.16%) or practice (42.34%) and 65.20% of them were females. The participants recorded medical history and filled a form (91.17%, 80.52 % respectively) while only 41.82% obtained the vital signs. Among the participants, 48.57 % were confident about handling medical emergency and 74.29 % reported their capability of intramuscular injection while only 25.71 % for intravenous injection and 49.35% knew about emergency kits. Management knowledge of airway obstruction and prosthetic heart valve patients was reported by 80.27 % and 71.94 % respectively, while less percentage for activation of EMS, chest compression, CPR ratio, and infant rescue breathing. The mean preparedness percent score was 54.57% and it was inversely correlated to the years of experiences and directly correlated to the degree of confidence in their ability to manage the dental emergency. Conclusion: The current study results reflected a deficiency in the dental practitioner awareness about the medical emergency especially the practical part.
   
Keywords
Dentists; Cross-sectional studies; Emergencies; Educational models; Dental schools.
Assessing knowledge, practices, use and raising awareness of antibiotics and antibiotic resistance among dental patients before and after educational sessions
Authors: Farghaly Mahassen , Badran Amira , Keraa Khaled
Published: October 2021

Abstract

Objectives: Education and awareness-raising are global health policy tools to modify public behavior towards antibiotic resistance. Considering the high frequency of antibiotic use and self-medication in Egypt, together with the lack of an awareness agenda, our objectives were to assess the knowledge and practices related to antibiotic use and resistance among patients attending dental clinics, and to evaluate the changes in knowledge following a specially designed one to one educational session. Methodology: A convenience sample of 310 dental patients participated in this study. A modified questionnaire was used to assess knowledge and practices related to antibiotic use and resistance. Second-year dental students were trained to administer the questionnaire and to use the educational materials they designed to raise awareness. Following the education session, patients completed another similar questionnaire to assess the changes in their knowledge. Results: Increasing awareness of antibiotic resistance can be an effective way to address the antibiotic resistance crisis. More than half of the participants (55.6%) did not know whether antibiotics treat diseases caused by bacterial or viral infections. The majority of participants (85.5%) had taken antibiotics during the last year, and (50.5%) of them had taken the same antibiotic more than once. Higher educational levels of the participants were significantly associated with a higher level of knowledge. Statistically significant increases in the percentages of correct answers to all questions were observed after the educational session. Conclusion: The one to one educational session is an effective approach to address the antibiotic resistance crisis.

Keywords

Antibiotic use, antibiotic resistance, knowledge, practices, dental patients, awareness and education, SDGs.
Prevalence of cleft lip and palate in Bauru, SP – concordance among registries of HRAC/USP, DNV and SINASC
Authors: Molena Kelly Fernanda , Winckler Vivian Patricia Saldias Vargas , Dalben Gisele da Silva
Published: October 2021

Objective: Congenital defects, including cleft lip and palate, increase the morbidity and mortality in the affected population. This study aimed to determine the prevalence of cleft lip and palate in the city of Bauru, Brazil, by evaluation of registry in the Brazilian Livebirth Certificate (DNV) and the Information System on Livebirths (SINASC), and analyzed the concordance of diagnosis compared with registries of the Hospital for Rehabilitation of Craniofacial Anomalies (HRAC/USP), located in the same city. Material and Methods: This retrospective observational study comprised analysis of all DNVs and identification of individuals with clefts born and living in Bauru, comparing with data from HRAC/USP. The prevalence was calculated by dividing the number of children born with clefts in the study period by the total number of livebirths registered. The reporting of different types of clefts was compared by the chi-square test. Results: Overall, 50,898 DNV were evaluated, among which there were 25 reported cases of cleft lip and/or palate. In the same period, HRAC/USP registered 77 cases born in Bauru, representing 67.5% of underreporting of the occurrence of clefts. Cleft palate was the most prevalent (34.9%), followed by cleft lip and palate (31.7%) and cleft lip (30.2%), mostly affecting males (58.5%). The reporting of cleft palate (16.12%) was lower compared to cleft lip (43.75%) and cleft lip and palate (54.54%). Conclusion: The study revealed predominance of cleft palate, with significant underreporting of clefts in the public health system, especially for cleft palate as compared to cleft lip and cleft lip and palate.
Keywords
Cleft lip; Cleft palate; Epidemiology; Prevalence; Reporting.