bluuebunny/crossref_metadata_2025_split huggingface dataset:
Doping effect numerical comparison of band gap energy and active region range for GaN and GaAs based semiconductor
Authors: Fajri F A A , Ahmad Noorden A F , Abdul Aziz A 
Published: May 2021

Abstract
This work reports the effect of doping concentration on the energy-band structure of semiconductor materials. The research focuses on the resultant values of bandgap energy and its depletion region (length/area), based on the initial concentrations of doping which are the donors and acceptors. The energy-band diagram is simulated by initializing the various materials’ properties of Gallium Nitride (GaN) and Gallium Arsenide (GaAs), and solving the Poisson’s equation derived from Maxwell’s equation. The equation is solved by applying the finite difference method (FDM) and using the Newton-Raphson method. Both of these materials are compared with different doping concentrations (1×1013cm−3-1×1017cm−3). Taking the GaAs properties as the controlled variable, the band structure is validated with literature findings. The measured band gap energy of GaN changes from 1.5215eV to 7.6689eV, and GaAs, from 1.1330eV to 5.6431eV. It increases with the proportion to the doping concentration increments. However, when obtaining both of the spatial active regions for GaN and GaAs, it reduce from (1.9990μm-0.0790μm)x1μm2 and from (1.9990μm-0.0890μm)x1μm2 respectively. The findings show the effect of doping concentration on the semiconductor energy-band structure. Thus, the numerical system is expected to be used as the determination of the internal quantum efficiency, and the output spectrum of light-emitting diode (LED) chip.
Effects of Ag NPs: Enhancement of Mechanical Properties of Er3+/Nd3+ Codoped Lithium Niobate Tellurite Glass via Ultrasonic Measurement
Authors: Nurhafizah H. , Nurulwahidah Z.A.S. , Anis Nazihah M.D. , Nur Hidayah A. 
Published: May 2021

Abstract
Ag NPs embedded in Er3+/Nd3+ codoped lithium niobate tellurite glasses of the form (68-x)TeO2-15Li2CO3-15Nb2O5-1Er2O3-1Nd2O3-(x)AgCl with x = 1, 2 and 3 mol% via conventional melt-quenching technique. Surface roughness and mechanical properties of the glass sample are characterized and discussed. The ultrasonic attenuation shows the rate of sound energy reduction when an ultrasonic wave is propagating in a medium which is the lithium niobate tellurite glasses. The glass attenuation depends on the grain size, viscous friction, crystal structure, porosity, and hardness. The ultrasonic acoustic impedance and attenuation coefficient of particles are estimated from an analysis of the pulse-echo technique. Simple correlation functions and the accurate scattering theory include the effects of acoustic waves, were used separately to focus on the absorption and scattering effects from spherical particles (Ag NPs) and thereby describe the structures of the medium.
Prediction of chemical reaction yields using deep learning
Authors: Schwaller Philippe , Vaucher Alain C , Laino Teodoro , Reymond Jean-Louis 
Published: May 2021

Abstract
Artificial intelligence is driving one of the most important revolutions in organic chemistry. Multiple platforms, including tools for reaction prediction and synthesis planning based on machine learning, have successfully become part of the organic chemists’ daily laboratory, assisting in domain-specific synthetic problems. Unlike reaction prediction and retrosynthetic models, the prediction of reaction yields has received less attention in spite of the enormous potential of accurately predicting reaction conversion rates. Reaction yields models, describing the percentage of the reactants converted to the desired products, could guide chemists and help them select high-yielding reactions and score synthesis routes, reducing the number of attempts. So far, yield predictions have been predominantly performed for high-throughput experiments using a categorical (one-hot) encoding of reactants, concatenated molecular fingerprints, or computed chemical descriptors. Here, we extend the application of natural language processing architectures to predict reaction properties given a text-based representation of the reaction, using an encoder transformer model combined with a regression layer. We demonstrate outstanding prediction performance on two high-throughput experiment reactions sets. An analysis of the yields reported in the open-source USPTO data set shows that their distribution differs depending on the mass scale, limiting the data set applicability in reaction yields predictions.
Quercetin for COVID-19 and DENGUE co-infection: a potential therapeutic strategy of targeting critical host signal pathways triggered by SARS-CoV-2 and DENV
Authors: Zheng Wenjiang , Wu Hui , Wang Ting , Zhan Shaofeng , Liu Xiaohong 
Published: May 2021

Abstract

Background
The clinical consequences of SARS-CoV-2 and DENGUE virus co-infection are not promising. However, their treatment options are currently unavailable. Current studies have shown that quercetin is both resistant to COVID-19 and DENGUE; this study aimed to evaluate the possible functional roles and underlying mechanisms of action of quercetin as a potential molecular candidate against COVID-19 and DENGUE co-infection.

Methods
We used a series of bioinformatics analyses to understand and characterize the biological functions, pharmacological targets and therapeutic mechanisms of quercetin in COVID-19 and DENGUE co-infection.

Results
We revealed the clinical characteristics of COVID-19 and DENGUE, including pathological mechanisms, key inflammatory pathways and possible methods of intervention, 60 overlapping targets related to the co-infection and the drug were identified, the protein–protein interaction (PPI) was constructed and TNFα, CCL-2 and CXCL8 could become potential drug targets. Furthermore, we disclosed the signaling pathways, biological functions and upstream pathway activity of quercetin in COVID-19 and DENGUE. The analysis indicated that quercetin could inhibit cytokines release, alleviate excessive immune responses and eliminate inflammation, through NF-κB, IL-17 and Toll-like receptor signaling pathway.

Conclusions
This study is the first to reveal quercetin as a pharmacological drug for COVID-19 and DENGUE co-infection. COVID-19 and DENGUE co-infection remain a potential threat to the world’s public health system. Therefore, we need innovative thinking to provide admissible evidence for quercetin as a potential molecule drug for the treatment of COVID-19 and DENGUE, but the findings have not been verified in actual patients, so further clinical drug trials are needed.
Topology-based sparsification of graph annotations
Authors: Danciu Daniel , Karasikov Mikhail , Mustafa Harun , Kahles André , Rätsch Gunnar 
Published: May 2021

Abstract

Motivation
Since the amount of published biological sequencing data is growing exponentially, efficient methods for storing and indexing this data are more needed than ever to truly benefit from this invaluable resource for biomedical research. Labeled de Bruijn graphs are a frequently-used approach for representing large sets of sequencing data. While significant progress has been made to succinctly represent the graph itself, efficient methods for storing labels on such graphs are still rapidly evolving.

Results
In this article, we present RowDiff, a new technique for compacting graph labels by leveraging expected similarities in annotations of vertices adjacent in the graph. RowDiff can be constructed in linear time relative to the number of vertices and labels in the graph, and in space proportional to the graph size. In addition, construction can be efficiently parallelized and distributed, making the technique applicable to graphs with trillions of nodes. RowDiff can be viewed as an intermediary sparsification step of the original annotation matrix and can thus naturally be combined with existing generic schemes for compressed binary matrices. Experiments on 10 000 RNA-seq datasets show that RowDiff combined with multi-BRWT results in a 30% reduction in annotation footprint over Mantis-MST, the previously known most compact annotation representation. Experiments on the sparser Fungi subset of the RefSeq collection show that applying RowDiff sparsification reduces the size of individual annotation columns stored as compressed bit vectors by an average factor of 42. When combining RowDiff with a multi-BRWT representation, the resulting annotation is 26 times smaller than Mantis-MST.

Availability and implementation
RowDiff is implemented in C++ within the MetaGraph framework. The source code and the data used in the experiments are publicly available at https://github.com/ratschlab/row_diff.
Quantification and Validation of Stability-Indicating RP-HPLC Method for Efavirenz in Bulk and Tablet Dosage Form using Quality by Design (QbD): A Shifting Paradigm
Authors: Gurumukhi Vishal C , Bari Sanjaykumar B 
Published: May 2021

Abstract
The present study endeavors quality by design (QbD) assisted chromatographic method for the quantification of Efavirenz (ERZ) in bulk and tablet dosage form. Analytical QbD instigated with assignment of analytical target profile (ATP) and critical analytical attributes (CAAs). Risk assessment studies and factor screening studies facilitate to identify the critical method parameters (CMPs). Optimization was performed by employing 32 full factorial design using identified CMPs i.e., flow rate (X1) and pH of buffer (X2) at three different levels and evaluating selected CAAs i.e., retention time (Y1) and peak area (Y2). The individual and interactive influence of CMPs on CAAs were tested by statistical data and response surface plots. Analysis of variance (ANOVA) confirmed that method parameters are significant (P &lt; 0.05). Chromatographic separation was achieved using methanol, 10 mM ammonium acetate buffer (70:30 v/v), pH adjusted at 3.1 with 0.05% ortho-phosphoric acid as a mobile phase at flow rate 1.0 mL/min, and a Nucleosil C18 (4.6 mm I.D. × 250 mm, 5 μm) column with UV detection at 247 nm. The method validation and subsequent stresses degradation studies according to ICH guidelines supported the method to be highly efficient for regular drug analysis and its degradation products. The proposed method was successfully demonstrated QbD based approach for the development of highly sensitive, reliable and suitable for routine analysis, and clinical applications.
Geometric morphometrics of mandibles for dietary differentiation of Bovidae (Mammalia: Artiodactyla)
Authors: Wang Bian , Zelditch Miriam , Badgley Catherine 
Published: May 2021

Abstract
The mammalian family Bovidae has been widely studied in ecomorphological research, with important applications to paleoecological and paleohabitat reconstructions. Most studies of bovid craniomandibular features in relation to diet have used linear measurements. In this study, we conduct landmark-based geometric-morphometric analyses to evaluate whether different dietary groups can be distinguished by mandibular morphology. Our analysis includes data for 100 species of extant bovids, covering all bovid tribes and 2 dietary classifications. For the first classification with 3 feeding categories, we found that browsers (including frugivores), mixed feeders, and grazers are moderately well separated using mandibular shape. A finer dietary classification (frugivore, browser, browser–grazer intermediate, generalist, variable grazer, and obligate grazer) proved to be more useful for differentiating dietary extremes (frugivores and obligate grazers) but performed equally or less well for other groups. Notably, frugivorous bovids, which belong in tribe Cephalophini, have a distinct mandibular shape that is readily distinguished from all other dietary groups, yielding a 100% correct classification rate from jackknife cross-validation. The main differences in mandibular shape found among dietary groups are related to the functional needs of species during forage prehension and mastication. Compared with browsers, both frugivores and grazers have mandibles that are adapted for higher biomechanical demand of chewing. Additionally, frugivore mandibles are adapted for selective cropping. Our results call for more work on the feeding ecology and functional morphology of frugivores and offer an approach for reconstructing the diet of extinct bovids.
Cover Crop Soil Legacies Alter Phytochemistry and Resistance to Fall Armyworm (Lepidoptera: Noctuidae) in Maize
Authors: Davidson-Lowe Elizabeth , Ray Swayamjit , Murrell Ebony , Kaye Jason , Ali Jared G 
Published: May 2021

AbstractPlant-soil feedbacks can mediate aboveground plant–herbivore interactions by impacting plant chemistry. Given that soil legacies and agricultural practices are closely tied, a better understanding of soil legacy cascades and their application in pest management are needed. We tested how cover crop legacies alter resistance to fall armyworm (Spodoptera frugiperda Smith, Lepidoptera: Noctuidae) in maize (Zea mays L., Poales: Poaceae). We compared herbivore performance and behavior of fall armyworm larvae on maize grown after four cover crop treatments: a leguminous mycorrhizal cover crop (pea: Pisum sativum L., Fabales: Fabaceae), a nonleguminous mycorrhizal cover crop (triticale: x Triticosecale Wittm. Ex A. Camus, Poales: Poaceae), a nonleguminous nonmycorrhizal cover crop (radish: Raphanus sativus L., Brassicales: Brassicaceae), and no cover crops (fallow). Soil inorganic N was highest in pea treatments and lowest in triticale treatments, while maize AMF colonization was greatest when grown after mycorrhizal cover crops compared to nonmycorrhizal or no cover crops. Cover crop legacies altered the emission of maize volatiles and fall armyworm larvae oriented toward odors emitted by maize grown after radish more frequently than triticale in olfactometer assays. Additionally, larvae performed better and consumed more leaf tissue when feeding on maize grown after radish and poorest on plants grown after triticale. When damaged by fall armyworm, maize grown after triticale expressed higher levels of lipoxygenase-3 (lox3), while plants grown after radish upregulated maize proteinase inhibitor (mpi) gene expression. Our results highlight the importance of appropriate cover crop selection and suggest that triticale could strengthen maize resistance to fall armyworm.
More than words: methods to elicit talk in interviews
Authors: Thille Patricia H , Rotteau Leahora , Webster Fiona 
Published: May 2021

Lay Summary
In health services and primary care research, semi-structured interviews are a very common method of generating data. These interviews have a pre-determined set of topics, with questions and prompts written in advance, though there is flexibility to adjust the interview to match the direction set by the participant. Like all methods, semi-structured interviews have limits, some of which can be addressed through adaptation. In the social sciences, some interview methods include prompts beyond verbal questions to participants, called elicitation tools. Visuals (e.g. photos), videos, audio excerpts and texts can be brought into interviews to orient the discussion. Another type of interview—mobile interview—happens in places meaningful to the participants. Depending on the research question, elicitation methods can enrich semi-structured interviews. This methods brief will introduce interviewing with elicitation tools, and outline strengths of such methods.
Cut-off value of ulcerative colitis endoscopic index of severity (UCEIS) score for predicting the need for pouch construction in ulcerative colitis: results of a multicenter study with long-term follow-up
Authors: Xu Weimin , Ou Weijun , Fu Jihong , Gu Yubei , Cui Long , Zhong Jie , Du Peng 
Published: May 2021

Abstract

Background
Total proctocolectomy with ileal pouch–anal anastomosis (IPAA) was the first choice for the surgical treatment of the ulcerative colitis (UC) patients. The data on the predictive value of the ulcerative colitis endoscopic index of severity (UCEIS) for the need for IPAA in UC patients is scarce. We aimed to establish the UCEIS cut-off value to further analyse whether the UCEIS cut-off was suitable for predicting the need for IPAA in UC patients.

Methods
The clinical data of UC patients from June 1986 to March 2020 at our institute were retrospectively assessed. The UCEIS scores recorded at the time of the first colonoscopy after hospitalization were used in the study. Receiver operating characteristic curve analysis was performed to determine the UCEIS cut-off value for predicting the need for IPAA.

Results
A total of 283 UC patients were included in the study, with a median UCEIS of 4. During a median follow-up of 13 years, 80 patients (28.3%) received surgery invention, among whom 75 (93.8%) underwent IPAA surgery and 5 (6.2%) received subtotal colectomy with permanent ostomy. A UCEIS cut-off of 6 had the most significant area under the curve of 0.769 for predicting the need for IPAA (P &lt; 0.001), with a sensitivity of 72.0% and specificity of 81.8%. UCEIS ≥6 was an independent predictive factor for the need for IPAA (P &lt; 0.001) and malignant transformation (P = 0.010). Patients with UCEIS ≥6 had a significantly shorter IPAA-free survival time than those with UCEIS &lt;6 (P &lt; 0.001).

Conclusions
UCEIS ≥6 may be a threshold value for decision-making for IPAA and should be recommended for UC patients for reducing the incidence of malignant transformation.
Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction
Authors: Skejo Josip , Garg Sriram G , Gould Sven B , Hendriksen Michael , Tria Fernando D K , Bremer Nico , Franjević Damjan , Blackstone Neil W , Martin William F 
Published: May 2021

AbstractModern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, and polykaryons) are surprisingly common across eukaryotic supergroups. Here, we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA’s multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other’s lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia but have so far gone unrecognized.
Biomonitoring and Digital Data Technology as an Opportunity for Enhancing Animal Study Translation
Authors: Defensor Erwin B , Lim Maria A , Schaevitz Laura R 
Published: May 2021

Abstract
The failure of animal studies to translate to effective clinical therapeutics has driven efforts to identify underlying cause and develop solutions that improve the reproducibility and translatability of preclinical research. Common issues revolve around study design, analysis, and reporting as well as standardization between preclinical and clinical endpoints. To address these needs, recent advancements in digital technology, including biomonitoring of digital biomarkers, development of software systems and database technologies, as well as application of artificial intelligence to preclinical datasets can be used to increase the translational relevance of preclinical animal research. In this review, we will describe how a number of innovative digital technologies are being applied to overcome recurring challenges in study design, execution, and data sharing as well as improving scientific outcome measures. Examples of how these technologies are applied to specific therapeutic areas are provided. Digital technologies can enhance the quality of preclinical research and encourage scientific collaboration, thus accelerating the development of novel therapeutics.
What Will Fall Armyworm (Lepidoptera: Noctuidae) Cost Western Australian Agriculture?
Authors: Cook David C , Gardiner Peter S , Spafford Helen 
Published: May 2021

Abstract
Following the detection of fall armyworm Spodoptera frugiperda (J.E. Smith, Lepidoptera: Noctuidae) in Western Australia in early 2020 and the lack of government response action, we estimate the impact it is likely to have on the state’s agriculture. A bioeconomic model is used to estimate cost and revenue implications for broadacre cropping and horticulture industries. We assume permanent S. frugiperda populations are likely to establish in areas of the state’s north and mid-west over the next decade, and other regions may experience sporadic outbreaks over single seasons. Over 0.8 million hectares of host crops could be permanently affected, while sporadic outbreaks may affect a further 150,000 hectares. Expressed in Australian dollars (A$), S. frugiperda is likely to add a A$14.2–39.3 million burden to agricultural producers per annum by year 10 of the outbreak. Approximately 55% of these damage costs are attributable to yield loss and 45% to increased variable production costs.
Evidence for Vertical Transmission ofBabesia odocoilei(Piroplasmida: Babesiidae) inIxodes scapularis(Acari: Ixodidae)
Authors: Zembsch T E , Bron G M , Paskewitz S M 
Published: May 2021

AbstractLimited evidence suggests that the cervid parasite, Babesia odocoilei, is transovarially transmitted from adult female Ixodes scapularis Say to offspring. The prevalence of B. odocoilei in unfed larval I. scapularis and whether vertical transmission is crucial to pathogen maintenance are currently unknown. To investigate these questions, 275 unfed larvae from two Wisconsin counties were tested for B. odocoilei genetic material. Sixteen of 29 pools were positive for the parasite. The maximum likelihood estimation for overall larval infection prevalence was 7.8% (95% confidence interval: 4.7–12). This vertically acquired infection appears to be sustained transstadially in nymphal ticks the following year; however, our relatively small sample and replicate size warrants additional evaluation. Our study revealed further evidence of vertical transmission, a low and consistent infection prevalence in larvae, and the potential importance of vertical transmission in B. odocoilei maintenance.
Prophylactic laparoscopic total gastrectomy in a patient with situs inversus totalis
Authors: Sivakumar Jonathan , Crosthwaite Gary 
Published: May 2021

Abstract
A rare case was demonstrated whereby a prophylactic laparoscopic total gastrectomy was performed in a 29-year-old male with a CDH1 gene mutation in the context of rare anatomical anomaly, situs inversus totalis (SIT).
This report provides radiological and laparoscopic images detailing the patient’s unique anatomy. We also describe the operative approach and technical challenges whilst accounting for the patient’s anatomical anomaly.
This is the first known case of a laparoscopic total gastrectomy for a CDH1 gene mutation in a patient with SIT. With sufficient pre-operative evaluation and meticulous intra-operative caution, this technically complex operation is safe and feasible in patients with mirror-image anatomy as seen in SIT.