bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photocatalytic application of graphene oxide–ZnO nanocomposite for the reduction of methylene blue dye
Authors: Banu K Bansura , Ferdila Sr Udith , Jennifer M D Mercy 
Published: November 2021

Abstract
The graphene oxide (GO) and GO–zinc oxide (GO–ZnO) nanocomposite were prepared using simplified techniques with modified Hummer’s and solvothermal methods for photocatalytic application. In a comparative study, the optimized geometries, binding energies, electronic properties, non-linear optical properties and density of states (DOS) of GO–ZnO were calculated using density functional theory calculations with the B3LYP method and 6-31G (d,p) and LanL2DZ basis sets to examine the binding site of a methylene blue (MB) dye systematically. The result of natural bond orbital analysis revealed the effective charge transfer and also explained the mechanism and efficiency of the photocatalytic activity of GO–ZnO. DOS supported the strong interaction of MB with GO–ZnO leading to the degradation of the MB dye. The theoretical results obtained depict the existence of n → σ*, n→ n* and σ → σ* interactions, improved charge transfer, and reduced band gap which establish the use of GO–ZnO in visible light photocatalysis. Characterization methods such as x-ray diffraction (XRD), Fourier transform infrared (FTIR) and ultraviolet (UV) analysis were carried out to support our theoretical results. The XRD results confirmed the particle size of 21 nm with inter-layer spacing of 0.87 nm. FTIR spectroscopy indicated the characteristic bands related to the elements in GO–ZnO. The higher electrical conductivity was studied using UV–Vis spectral analysis. The calculated results show good agreement with experimental observations which reveal that the GO–ZnO nanocomposite has good photocatalytic behavior.
Application of integrative physiological approach to evaluate human physiological responses to the inhalation of essential oils of Japanese citrus fruits iyokan (Citrus iyo) and yuzu (Citrus junos)
Authors: Ohata Motoko , Zhou Lanxi , Ando Shiori , Kaneko Shu , Osada Kazumi , Yada Yukihiro 
Published: November 2021

ABSTRACT
This study investigated the effects of essential oil odors from Japanese citrus fruits, iyokan (Citrus iyo) and yuzu (Citrus junos), on human psychology and both the autonomic and central nervous systems. The inhalation of both essential oils significantly increased miosis rate and fingertip temperature and could induce parasympathetic dominance by suppressing sympathetic nerve activity. Oxyhemoglobin concentration in the prefrontal cortex increased after the inhalation of yuzu essential oil and decreased after the inhalation of iyokan essential oil. Subjectively, the inhalation of both essential oils reduced the feelings of fatigue and improved the feelings of refreshment, suggesting that the effect of autonomic nervous activity might involve in these psychological changes directly. Moreover, we observed that task performance improved after inhaling yuzu essential oil, which may be due to the increase in oxyhemoglobin concentration in the prefrontal cortex.
Predicting drug–drug interactions by graph convolutional network with multi-kernel
Authors: Wang Fei , Lei Xiujuan , Liao Bo , Wu Fang-Xiang 
Published: November 2021

Abstract
Drug repositioning is proposed to find novel usages for existing drugs. Among many types of drug repositioning approaches, predicting drug–drug interactions (DDIs) helps explore the pharmacological functions of drugs and achieves potential drugs for novel treatments. A number of models have been applied to predict DDIs. The DDI network, which is constructed from the known DDIs, is a common part in many of the existing methods. However, the functions of DDIs are different, and thus integrating them in a single DDI graph may overlook some useful information. We propose a graph convolutional network with multi-kernel (GCNMK) to predict potential DDIs. GCNMK adopts two DDI graph kernels for the graph convolutional layers, namely, increased DDI graph consisting of ‘increase’-related DDIs and decreased DDI graph consisting of ‘decrease’-related DDIs. The learned drug features are fed into a block with three fully connected layers for the DDI prediction. We compare various types of drug features, whereas the target feature of drugs outperforms all other types of features and their concatenated features. In comparison with three different DDI prediction methods, our proposed GCNMK achieves the best performance in terms of area under receiver operating characteristic curve and area under precision-recall curve. In case studies, we identify the top 20 potential DDIs from all unknown DDIs, and the top 10 potential DDIs from the unknown DDIs among breast, colorectal and lung neoplasms-related drugs. Most of them have evidence to support the existence of their interactions. fangxiang.wu@usask.ca
Simultaneous Determination of Voriconazole and Its Voriconazole N-Oxide Metabolite in Human Urine by Liquid Chromatography/Tandem Mass Spectrometry
Authors: Yu Yong , Yang Yu-Qing , Zeng Nv-Jin , Zhang Hong-Wen , Sun Lu-Ning , Wang Yong-Qing 
Published: November 2021

Abstract
A convenient and sensitive liquid chromatography–tandem mass spectrometry method was established to simultaneously quantify voriconazole (VRZ) and its metabolite, voriconazole N-oxide (VNO), in human urine. Voriconazole-d3 and voriconazole-d3 N-oxide were used as isotopic internal standards. Samples were processed by protein precipitation and separated using a ZORBAX SB-Aq column (1.8 μm, 2.1 × 50 mm). Mass spectrometry was performed using an API 4000 mass spectrometry by positive electrospray ionization. The flow rate was 0.6 mL/min. Gradient elution was performed with methanol and 0.1% formic acid as the organic and water phase, respectively. The VRZ and VNO calibration curves ranged from 20.0 to 7200 ng/mL in human urine. The specificity, matrix effect, extraction recovery, intra/inter-run precision, accuracy and stability were validated for both VRZ and VNO in human urine. The developed method was used to study urinary excretion after intravenous injection of 4 mg/kg VRZ in healthy Chinese subjects.
DCMP: database of cancer mutant protein domains
Authors: Emerson Isaac Arnold , Chitluri Kiran Kumar 
Published: November 2021

Abstract
Protein domains are functional and structural units of proteins. They are responsible for a particular function that contributes to protein’s overall role. Because of this essential role, the majority of the genetic variants occur in the domains. In this study, the somatic mutations across 21 cancer types were mapped to the individual protein domains. To map the mutations to the domains, we employed the whole human proteome to predict the domains in each protein sequence and recognized about 149 668 domains. A novel Perl-API program was developed to convert the protein domain positions into genomic positions, and users can freely access them through GitHub. We determined the distribution of protein domains across 23 chromosomes with the help of these genomic positions. Interestingly, chromosome 19 has more number of protein domains in comparison with other chromosomes. Then, we mapped the cancer mutations to all the protein domains. Around 46–65% of mutations were mapped to their corresponding protein domains, and significantly mutated domains for all the cancer types were determined using the local false discovery ratio (locfdr). The chromosome positions for all the protein domains can be verified using the cross-reference ensemble database.
Database URL:http://dcmp.vit.ac.in/
Transcatheter aortic valve replacement in mixed aortic valve disease: a systematic review and meta-analysis
Authors: Guddeti Raviteja R , Gill Gauravpal S , Garcia-Garcia Hector M , Alla Venkata Mahesh 
Published: November 2021

Abstract

Background
Utilization of transcatheter aortic valve replacement (TAVR) has expanded from high-risk patients to intermediate- and select low-risk candidates with severe aortic stenosis (AS). TAVR is currently not indicated for patients with aortic insufficiency, and its outcomes in mixed aortic valve disease (MAVD) are unclear.

Methods
A systematic search of PubMed, Medline, CINHAL, and Cochrane databases was performed to identify studies comparing TAVR outcomes in patients with AS vs. MAVD. Primary outcomes included 30-day and late all-cause mortality, and paravalvular regurgitation (PVR). Secondary outcomes were major bleeding, vascular complications, device implantation success, permanent pacemaker, and stroke. Pooled odds ratios (OR) and 95% confidence intervals (CIs) were calculated using Der Simonian-Laird random-effects model.

Results
Six observational studies with 58 879 patients were included in the analysis. There was no significant difference in 30-day all-cause mortality [OR 1.03 (95% CI 0.92–1.15); P = 0.63], however, MAVD group had higher odds of moderate-to-severe PVR [1.81 (1.41–2.31); P &lt; 0.01]. MAVD patients had lower odds of device implantation success [0.60 (0.40–0.91); P = 0.02] while other secondary outcomes were similar in the two groups.

Conclusions
TAVR in MAVD is associated with increased odds of paravalvular regurgitation and lower odds of device implantation success when compared to severe aortic stenosis.
A Domain Based Approach to Semantic Lexicon Expansion
Authors: Prentice Sheryl , Rayson Paul , Knight Jo , El-Haj Mahmoud , Elstein Solly 
Published: November 2021

Abstract
Current approaches to the expansion of semantic lexicons for corpus annotation are somewhat ad hoc in nature and do not generally offer a systematic means of identifying areas for development within one’s lexicon. The present paper sets forward a domain based approach to semantic lexicon expansion, targeting UCREL’s Semantic Analysis System (USAS). First, an updated version of the lexicon is compared to representative corpora to ascertain areas of underrepresentation in a novel method which we call K-FLUX analysis. Second, an example set of underrepresented types are targeted for development using domain specific corpora. Collectively, the results show that some corpora are more successful than others in supplementing the existing USAS lexicon. The paper discusses the various factors that should be borne in mind when utilising the proposed method before concluding with how findings might inform future developments of the lexicon, and crucially, the semantic system on which it is based.
Assessment of water, sanitation and hygiene practices for prevention and control of COVID-19 in Kenya
Authors: Mwai J , Nyole D , Abdi M , Ahmed I , Mutai J , Kaduka L , Ndemwa P , Omogi J 
Published: November 2021

Abstract

Background
Safely managed water, sanitation and hygiene (WASH) services are an essential part of preventing and protecting human health during infectious disease outbreaks, including the current coronavirus disease 2019 (COVID-19) pandemic. Additionally, adherence to COVID-19 measures, including washing hands using soap and proper waste disposal, no doubt can improve containment of the virus.

Methods
A cross-sectional survey was conducted in Kilifi and Mombasa Counties in Kenya. A total of 612 quantitative data were collected using a mobile data collection tool Open Data Kit. Parametric and non-parametric tests were used to examine factors associated with WASH practices and control of COVID-19 in Kenya.

Results
More than half of the respondents were from Kilifi, 431 (70.4%) were female and the mean age was 38.2±14.8 y. Households in Kilifi were most likely not to have enough water, while Mombasa households were more likely to pay for water. Sanitation coverage was 47.6%, with more than half sharing sanitation facilities. Sharing of latrines was significantly associated with county and income level. Accessing soap was worse compared with the month prior to the survey, only 3.9% had their garbage collected by formal service providers and only 17% reported wearing any protective gear while handling waste at home.

Conclusions
Water is disproportionately available in the two counties, with low sanitation coverage. There is low knowledge on hand washing and inadequate waste disposal services.
Inference-based correction of multi-site height and weight measurement data in the All of Us research program
Authors: Khan Mirza S , Carroll Robert J 
Published: November 2021

Abstract

Objective
Measurement and data entry of height and weight values are error prone. Aggregation of medical record data from multiple sites creates new challenges prompting the need to identify and correct errant values. We sought to characterize and correct issues with height and weight measurement values within the All of Us (AoU) Research Program.

Materials and Methods
Using the AoU Researcher Workbench, we assessed site-level measurement value distributions to infer unit types. We also used plausibility checks with exceptions for conditions with possible outlier values, eg obesity, and assessed for excess deviation within individual participant’s records.

Results
15.8% of height and 22.4% of weight values had missing unit type information.

Discussion
We identified several measurement unit related issues: the use of different units of measure within and between sites, missing units, and incorrect labeling of units. Failure to account for these in patient data repositories may lead to erroneous study results and conclusions.

Conclusion
Discrepancies in height and weight measurement data may arise from missing or mislabeled units. Using site- and participant-level analyses while accounting for outlier value-associated clinical conditions, we can infer measurement units and apply corrections. These methods are adaptable and expandable within AoU and other data repositories.
Relationship of tissue dimensions and three captive bolt placements on cadaver heads from mature swine (Sus scrofa domesticus) &gt; 200 kg body weight
Authors: Anderson Karly N , Allen Kaysie J , Baysinger Angela , Benjamin Madonna , Berger Jennifer , Claus James R , Greco Brian J , Massie Emily A , O’Brien Brett , Ramirez Alejandro , Rendahl Aaron K , Reyes Arquimides A , Zhitnitskiy Perle E , Vogel Kurt D 
Published: November 2021

Abstract
Three penetrating captive bolt (PCB) placements were tested on cadaver heads from swine with estimated body weight (BW) &gt;200 kg (sows = 232.9 ± 4.1 kg; boars = 229.3 ± 2.6 kg). The objectives were to determine tissue depth, cross-sectional brain area, visible brain damage (BD), regions of BD, and bolt–brain contact; and determine relationships between external head dimensions and tissue depth at each placement. A Jarvis PAS-Type P 0.25R PCB with a Long Stunning Rod Nosepiece Assembly and 3.5 g power loads was used at the following placements on heads from 111 sows and 46 boars after storage at 2 to 4 °C for ~62 h before treatment: FRONTAL (F)—3.5 cm superior to the optic orbits at midline, TEMPORAL (T)—at the depression posterior to the lateral canthus of the eye within the plane between the lateral canthus and the base of the ear, or BEHIND EAR (BE)—directly caudal to the pinna of the ear on the same plane as the eyes and targeting the middle of the opposite eye. For sows, the bolt path was in the plane of the brain for 42/42 (100%, 95% confidence interval [CI]: 91.6% to 100.0%) F heads, 39/40 (97.5%, 95% CI: 86.8% to 99.9%) T heads, and 34/39 (87.5%, 95% CI: 72.6% to 95.7%) BE heads; for the heads that could reliably be assessed for BD damage was detected in 25/26 (96.2%, 95% CI: 80.4% to 99.9%) F heads, 24/35 (68.6%, 95% CI: 50.7% to 83.2%) T heads, and 5/40 (12.5%, 95% CI: 4.2% to 26.8%) BE heads. For boars, the bolt path was in the plane of the brain for 17/17 (100.0%, 95% CI: 80.5% to 100.0%) F heads, 18/18 (100.0%, 95% CI: 81.5% to 100.0%) T heads, and 14/14 (100.0%, 95% CI: 76.8% to 100.0%) BE heads; damage was detected in 11/12 (91.7%, 95% CI: 61.5% to 99.8%) F heads, 2/15 (13.3%, 95% CI: 1.7% to 40.5%) T heads, and 7/14 (50.0%, 95% CI: 23.0% to 77.0%) BE heads. Tissue depth was reported as mean ± standard error followed by 95% one-sided upper reference limit (URL). For sows, total tissue thickness was different (P &lt; 0.05) between placements (F: 52.7 ± 1.0 mm, URL: 64.1 mm; T: 69.8 ± 1.4 mm, URL: 83.9 mm; BE: 89.3 ± 1.5 mm, URL: 103.4 mm). In boars, total tissue thickness was different (P &lt; 0.05) between placements (F: 41.2 ± 2.1 mm, URL: 56.3 mm; T: 73.2 ± 1.5 mm, URL: 83.4 mm; BE: 90.9 ± 3.5 mm, URL: 113.5 mm). For swine &gt; 200 kg BW, F placement may be more effective than T or BE due to less soft tissue thickness, which may reduce concussive force. The brain was within the plane of bolt travel for 100% of F heads with BD for 96.2% and 91.7% of F sow and boar heads, respectively.
Successful laparoscopic extraction of trichobezoar due to Rapunzel syndrome: first reported case in Kuwait
Authors: Al-Mulla Ahmad E , Altabeekh Ali , Al-Jafar Ahmad , Dashti Shaimaa 
Published: November 2021

Abstract
Rapunzel syndrome is a rare condition typically found in young female patients with mental or psychiatric disorders. It manifests as a large trichobezoar extending beyond the pylorus into the small intestine and leads to various adverse conditions. Early diagnosis and prompt management are crucial to avoiding complications. These bezoars are extracted endoscopically, laparoscopically and via open surgery (most common). In this current report, we discuss a successful laparoscopic extraction of a trichobezoar in a 12-year-old girl with acute abdominal pain due to small-bowel obstruction. We describe our technique compared with others’ techniques and include a literature review on this topic.
The proteome of developing barley anthers during meiotic prophase I
Authors: Lewandowska Dominika , Orr Jamie , Schreiber Miriam , Colas Isabelle , Ramsay Luke , Zhang Runxuan , Waugh Robbie 
Published: November 2021

Abstract
Flowering plants reproduce sexually by combining a haploid male and female gametophyte during fertilization. Male gametophytes are localized in the anthers, each containing reproductive (meiocyte) and non-reproductive tissue necessary for anther development and maturation. Meiosis, where chromosomes pair and exchange their genetic material during a process called recombination, is one of the most important and sensitive stages in breeding, ensuring genetic diversity. Most anther development studies have focused on transcript variation, but very few have been correlated with protein abundance. Taking advantage of a recently published barley anther transcriptomic (BAnTr) dataset and a newly developed sensitive mass spectrometry-based approach to analyse the barley anther proteome, we conducted high-resolution mass spectrometry analysis of barley anthers, collected at six time points and representing their development from pre-meiosis to metaphase. Each time point was carefully staged using immunocytology, providing a robust and accurate staging mirroring our previous BAnTr dataset. We identified &gt;6100 non-redundant proteins including 82 known and putative meiotic proteins. Although the protein abundance was relatively stable throughout prophase I, we were able to quantify the dynamic variation of 336 proteins. We present the first quantitative comparative proteomics study of barley anther development during meiotic prophase I when the important process of homologous recombination is taking place.
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length
Authors: Bohlen Jonathan , Roiuk Mykola , Teleman Aurelio A 
Published: November 2021

Abstract
Phosphorylation of Ribosomal Protein S6 (RPS6) was the first post-translational modification of the ribosome to be identified and is a commonly-used readout for mTORC1 activity. Although the cellular and organismal functions of RPS6 phosphorylation are known, the molecular consequences of RPS6 phosphorylation on translation are less well understood. Here we use selective ribosome footprinting to analyze the location of ribosomes containing phosphorylated RPS6 on endogenous mRNAs in cells. We find that RPS6 becomes progressively dephosphorylated on ribosomes as they translate an mRNA. As a consequence, average RPS6 phosphorylation is higher on mRNAs with short coding sequences (CDSs) compared to mRNAs with long CDSs. We test whether RPS6 phosphorylation differentially affects mRNA translation based on CDS length by genetic removal of RPS6 phosphorylation. We find that RPS6 phosphorylation promotes translation of mRNAs with short CDSs more strongly than mRNAs with long CDSs. Interestingly, RPS6 phosphorylation does not promote translation of mRNAs with 5′ TOP motifs despite their short CDS lengths, suggesting they are translated via a different mode. In sum this provides a dynamic view of RPS6 phosphorylation on ribosomes as they translate mRNAs and the functional consequence on translation.
The SARS-CoV-2 RNA polymerase is a viral RNA capping enzyme
Authors: Walker Alexander P , Fan Haitian , Keown Jeremy R , Knight Michael L , Grimes Jonathan M , Fodor Ervin 
Published: November 2021

Abstract
SARS-CoV-2 is a positive-sense RNA virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic, which continues to cause significant morbidity, mortality and economic strain. SARS-CoV-2 can cause severe respiratory disease and death in humans, highlighting the need for effective antiviral therapies. The RNA synthesis machinery of SARS-CoV-2 is an ideal drug target and consists of non-structural protein 12 (nsp12), which is directly responsible for RNA synthesis, and numerous co-factors involved in RNA proofreading and 5′ capping of viral RNAs. The formation of the 5′ 7-methylguanosine (m7G) cap structure is known to require a guanylyltransferase (GTase) as well as a 5′ triphosphatase and methyltransferases; however, the mechanism of SARS-CoV-2 RNA capping remains poorly understood. Here we find that SARS-CoV-2 nsp12 is involved in viral RNA capping as a GTase, carrying out the addition of a GTP nucleotide to the 5′ end of viral RNA via a 5′ to 5′ triphosphate linkage. We further show that the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase) domain performs this reaction, and can be inhibited by remdesivir triphosphate, the active form of the antiviral drug remdesivir. These findings improve understanding of coronavirus RNA synthesis and highlight a new target for novel or repurposed antiviral drugs against SARS-CoV-2.
Taiji-reprogram: a framework to uncover cell-type specific regulators and predict cellular reprogramming cocktails
Authors: Wang Jun , Liu Cong , Chen Yue , Wang Wei 
Published: November 2021

AbstractCellular reprogramming is a promising technology to develop disease models and cell-based therapies. Identification of the key regulators defining the cell type specificity is pivotal to devising reprogramming cocktails for successful cell conversion but remains a great challenge. Here, we present a systems biology approach called Taiji-reprogram to efficiently uncover transcription factor (TF) combinations for conversion between 154 diverse cell types or tissues. This method integrates the transcriptomic and epigenomic data to construct cell-type specific genetic networks and assess the global importance of TFs in the network. Comparative analysis across cell types revealed TFs that are specifically important in a particular cell type and often tightly associated with cell-type specific functions. A systematic search of TFs with differential importance in the source and target cell types uncovered TF combinations for desired cell conversion. We have shown that Taiji-reprogram outperformed the existing methods to better recover the TFs in the experimentally validated reprogramming cocktails. This work not only provides a comprehensive catalog of TFs defining cell specialization but also suggests TF combinations for direct cell conversion.