bluuebunny/crossref_metadata_2025 huggingface dataset:
Mosaic chromosome Y loss is associated with alterations in blood cell counts in UK Biobank men
Authors: Lin Shu-Hong , Loftfield Erikka , Sampson Josh N. , Zhou Weiyin , Yeager Meredith , Freedman Neal D. , Chanock Stephen J. , Machiela Mitchell J.
Published: February 2020

Mosaic loss of Y chromosome (mLOY) is the most frequently detected somatic copy number alteration in leukocytes of men. In this study, we investigate blood cell counts as a potential mechanism linking mLOY to disease risk in 206,353 UK males. Associations between mLOY, detected by genotyping arrays, and blood cell counts were assessed by multivariable linear models adjusted for relevant risk factors. Among the participants, mLOY was detected in 39,809 men. We observed associations between mLOY and reduced erythrocyte count (−0.009 [−0.014, −0.005] × 1012 cells/L, p = 2.75 × 10−5) and elevated thrombocyte count (5.523 [4.862, 6.183] × 109 cells/L, p = 2.32 × 10−60) and leukocyte count (0.218 [0.198, 0.239] × 109 cells/L, p = 9.22 × 10−95), particularly for neutrophil count (0.174 × [0.158, 0.190]109 cells/L, p = 1.24 × 10−99) and monocyte count (0.021 [0.018 to 0.024] × 109 cells/L, p = 6.93 × 10−57), but lymphocyte count was less consistent (0.016 [0.007, 0.025] × 109 cells/L, p = 8.52 × 10−4). Stratified analyses indicate these associations are independent of the effects of aging and smoking. Our findings provide population-based evidence for associations between mLOY and blood cell counts that should stimulate investigation of the underlying biological mechanisms linking mLOY to cancer and chronic disease risk.
Whole embryo culture, transcriptomics and RNA interference identify TBX1 and FGF11 as novel regulators of limb development in the mouse
Authors: Tejedor Gautier , Laplace-Builhé Béryl , Luz-Crawford Patricia , Assou Said , Barthelaix Audrey , Mathieu Marc , Kissa Karima , Jorgensen Christian , Collignon Jérôme , Chuchana Paul , Djouad Farida
Published: February 2020

Identifying genes involved in vertebrate developmental processes and characterizing this involvement are daunting tasks, especially in the mouse where viviparity complicates investigations. Attempting to devise a streamlined approach for this type of study we focused on limb development. We cultured E10.5 and E12.5 embryos and performed transcriptional profiling to track molecular changes in the forelimb bud over a 6-hour time-window. The expression of certain genes was found to diverge rapidly from its normal path, possibly reflecting the activation of a stress-induced response. Others, however, maintained for up to 3 hours dynamic expression profiles similar to those seen in utero. Some of these resilient genes were known regulators of limb development. The implication of the others in this process was either unsuspected or unsubstantiated. The localized knockdown of two such genes, Fgf11 and Tbx1, hampered forelimb bud development, providing evidence of their implication. These results show that combining embryo culture, transcriptome analysis and RNA interference could speed up the identification of genes involved in a variety of developmental processes, and the validation of their implication.
Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction
Authors: Gliozzo Jessica , Perlasca Paolo , Mesiti Marco , Casiraghi Elena , Vallacchi Viviana , Vergani Elisabetta , Frasca Marco , Grossi Giuliano , Petrini Alessandro , Re Matteo , Paccanaro Alberto , Valentini Giorgio
Published: February 2020

Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel network-based approach named Patient-Net (P-Net) in which biomolecular profiles of patients are modeled in a graph-structured space that represents gene expression relationships between patients. Then a kernel-based semi-supervised transductive algorithm is applied to the graph to explore the overall topology of the graph and to predict the phenotype/clinical outcome of patients. Experimental tests involving several publicly available datasets of patients afflicted with pancreatic, breast, colon and colorectal cancer show that our proposed method is competitive with state-of-the-art supervised and semi-supervised predictive systems. Importantly, P-Net also provides interpretable models that can be easily visualized to gain clues about the relationships between patients, and to formulate hypotheses about their stratification.
Characterization of a Species E Adenovirus Vector as a Zika virus vaccine
Authors: Bullard Brianna L. , Corder Brigette N. , Gordon David N. , Pierson Theodore C. , Weaver Eric A.
Published: February 2020

The development of a safe and efficacious Zika virus (ZIKV) vaccine remains a global health priority. In our previous work, we developed an Adenovirus vectored ZIKV vaccine using a low-seroprevalent human Adenovirus type 4 (Ad4-prM-E) and compared it to an Ad5 vector (Ad5-prM-E). We found that vaccination with Ad4-prM-E leads to the development of a strong anti-ZIKV T-cell response without eliciting significant anti-ZIKV antibodies, while vaccination with Ad5-prM-E leads to the development of both anti-ZIKV antibody and T-cell responses in C57BL/6 mice. However, both vectors conferred protection against ZIKV infection in a lethal challenge model. Here we continued to characterize the T-cell biased immune response observed in Ad4 immunized mice. Vaccination of BALB/c mice resulted in immune correlates similar to C57BL/6 mice, confirming that this response is not mouse strain-specific. Vaccination with an Ad4 expressing an influenza hemagglutinin (HA) protein resulted in anti-HA T-cell responses without the development of significant anti-HA antibodies, indicating this unique response is specific to the Ad4 serotype rather than the transgene expressed. Co-administration of a UV inactivated Ad4 vector with the Ad5-prM-E vaccine led to a significant reduction in anti-ZIKV antibody development suggesting that this serotype-specific immune profile is capsid-dependent. These results highlight the serotype-specific immune profiles elicited by different Adenovirus vector types and emphasize the importance of continued characterization of these alternative Ad serotypes.
Prevalence and clinical features of hearing loss caused by EYA4 variants
Authors: Shinagawa Jun , Moteki Hideaki , Nishio Shin-ya , Ohyama Kenji , Otsuki Koshi , Iwasaki Satoshi , Masuda Shin , Oshikawa Chie , Ohta Yumi , Arai Yasuhiro , Takahashi Masahiro , Sakuma Naoko , Abe Satoko , Sakurai Yuika , Sakaguchi Hirofumi , Ishino Takashi , Uehara Natsumi , Usami Shin-ichi
Published: February 2020

Variants in the EYA4 gene are known to lead to autosomal dominant non-syndromic hereditary hearing loss, DFNA10. To date, 30 variants have been shown to be responsible for hearing loss in a diverse set of nationalities. To better understand the clinical characteristics and prevalence of DFNA10, we performed genetic screening for EYA4 mutations in a large cohort of Japanese hearing loss patients. We selected 1,336 autosomal dominant hearing loss patients among 7,408 unrelated Japanese hearing loss probands and performed targeted genome enrichment and massively parallel sequencing of 68 target genes for all patients. Clinical information of cases with mutations in EYA4 was gathered and analyzed from medical charts. Eleven novel EYA4 variants (three frameshift variants, three missense variants, two nonsense variants, one splicing variant, and two single-copy number losses) and two previously reported variants were found in 12 probands (0.90%) among the 1,336 autosomal dominant hearing loss families. The audiometric configuration of truncating variants tends to deteriorate for all frequencies, whereas that of non-truncating variants tends to show high-frequency hearing loss, suggesting a new correlation between genotype and phenotype in DFNA10. The rate of hearing loss progression caused by EYA4 variants was considered to be 0.63 dB/year, as found in this study and previous reports.
Global mapping of freshwater nutrient enrichment and periphyton growth potential
Authors: McDowell R. W. , Noble A. , Pletnyakov P. , Haggard B. E. , Mosley L. M.
Published: February 2020

Periphyton (viz. algal) growth in many freshwater systems is associated with severe eutrophication that can impair productive and recreational use of water by billions of people. However, there has been limited analysis of periphyton growth at a global level. To predict where nutrient over-enrichment and undesirable periphyton growth occurs, we combined several databases to model and map global dissolved and total nitrogen (N) and phosphorus (P) concentrations, climatic and catchment characteristics for up to 1406 larger rivers that were analysed between 1990 and 2016. We predict that 31% of the global landmass contained catchments may exhibit undesirable levels of periphyton growth. Almost three-quarters (76%) of undesirable periphyton growth was caused by P-enrichment and mapped to catchments dominated by agricultural land in North and South America and Europe containing 1.7B people. In contrast, undesirable periphyton growth due to N-enrichment was mapped to parts of North Africa and parts of the Middle East and India affecting 280 M people. The findings of this global modelling approach can be used by landowners and policy makers to better target investment and actions at finer spatial scales to remediate poor water quality owing to periphyton growth.
Multimodal imaging reveals transient liver metabolic disturbance and sinusoidal circulation obstruction after a single administration of ketamine/xylazine mixture
Authors: Chen Fang-Hsin , Yu Ching-Fang , Yang Chung-Lin , Lin Yu-Chun , Lin Gigin , Wang Chun-Chieh , Yu Huang-Ping , Fang Jui , Chang Ning-Fang , Hong Ji-Hong
Published: February 2020

A ketamine/xylazine (K/X) mixture is widely used before and during experiments in rodents. However, the impact of short-term use of K/X mixture and its influences on data interpretation have rarely been discussed. In this study, we administered one shot of a K/X mixture and examined acute hepatic responses using biochemical analysis, histopathological examination, and non-invasive imaging to determine the delay required prior to further assessment of the liver to avoid confounding effects triggered by anaesthesia. After the K/X injection, aspartate aminotransferase (AST) in serum was significantly elevated from 3 to 48 h. Obstructed sinusoidal circulation lasting for 24 or 36 h was revealed by DCE-MRI and drug distribution analysis, respectively. Metabolic alterations were detected at 3 h by NMR analysis and FDG-PET. Moreover, ultrasonography showed that lipid droplet accumulation increased from 1 to 16 h and declined thereafter. Taken together, our findings show that the K/X mixture induces acute hepatotoxicity and metabolic disturbance, and these disturbances cause hemodynamical disorders in the liver. The required time interval for recovery from K/X impact was dependent on the chosen assay. It took at least 16 h for metabolic recovery and 36 h for recovery of sinusoidal circulation. However, the liver was not fully recovered from the injury within 48 h.
A phylogenetic comparative analysis on the evolution of sequential hermaphroditism in seabreams (Teleostei: Sparidae)
Authors: Pla Susanna , Benvenuto Chiara , Capellini Isabella , Piferrer Francesc
Published: February 2020

The Sparids are an ideal group of fishes in which to study the evolution of sexual systems since they exhibit a great sexual diversity, from gonochorism (separate sexes) to protandrous (male-first) and protogynous (female-first) sequential hermaphroditism (sex change). According to the size-advantage model (SAM), selection should favour sex change when the second sex achieves greater reproductive success at a larger body size than the first sex. Using phylogenetic comparative methods and a sample of 68 sparid species, we show that protogyny and protandry evolve from gonochorism but evolutionary transitions between these two forms of sequential hermaphroditism are unlikely to happen. Using male gonadosomatic index (GSI) as a measure of investment in gametes and proxy for sperm competition, we find that, while gonochoristic and protogynous species support the predictions of SAM, protandrous species do not, as they exhibit higher GSI values than expected even after considering mating systems and spawning modes. We suggest that small males of protandrous species have to invest disproportionally more in sperm production than predicted not only when spawning in aggregations, with high levels of sperm competition, but also when spawning in pairs due to the need to fertilize highly fecund females, much larger than themselves. We propose that this compensatory mechanism, together with Bateman’s principles in sequential hermaphrodites, should be formally incorporated in the SAM.
A microparticulate based formulation to protect therapeutic enzymes from proteolytic digestion: phenylalanine ammonia lyase as case study
Authors: Pereira de Sousa Irene , Gourmel Charlotte , Berkovska Olena , Burger Michael , Leroux Jean-Christophe
Published: February 2020

Phenylketonuria is a genetic disorder affecting the metabolism of phenylalanine (phe) due to a deficiency in the enzyme phenylalanine hydroxylase. This disorder is characterized by an elevated phe blood level, which can lead to severe intellectual disabilities in newborns. The current strategy to prevent these devastating consequences is limited to a life-long phe-free diet, which implies major lifestyle changes and restrictions. Recently, an injectable enzyme replacement therapy, Pegvaliase, has been approved for treating phenylketonuria, but is associated with significant side-effects. In this study a phe-metabolizing system suitable for oral delivery is designed to overcome the need for daily injections. Active phenylalanine ammonia-lyase (PAL), an enzyme that catalyses phe metabolism, is loaded into mesoporous silica microparticles (MSP) with pore sizes ranging from 10 to 35 nm. The surface of the MSP is lined with a semipermeable barrier to allow permeation of phe while blocking digestive enzymes that degrade PAL. The enzymatic activity can be partially preserved in vitro by coating the MSP with poly(allylamine) and poly(acrylic acid)-bowman birk (protease inhibitor) conjugate. The carrier system presented herein may provide a general approach to overcome gastro-intestinal proteolytic digestion and to deliver active enzymes to the intestinal lumen for prolonged local action.
Imaging Cherenkov emission for quality assurance of high-dose-rate brachytherapy
Authors: Yogo Katsunori , Matsushita Akihiro , Tatsuno Yuya , Shimo Takahiro , Hirota Seiko , Nozawa Marika , Ozawa Shuichi , Ishiyama Hiromichi , Yasuda Hiroshi , Nagata Yasushi , Hayakawa Kazushige
Published: February 2020

With advances in high-dose-rate (HDR) brachytherapy, the importance of quality assurance (QA) is increasing to ensure safe delivery of the treatment by measuring dose distribution and positioning the source with much closer intervals for highly active sources. However, conventional QA is time-consuming, involving the use of several different measurement tools. Here, we developed simple QA method for HDR brachytherapy based on the imaging of Cherenkov emission and evaluated its performance. Light emission from pure water irradiated by an 192Ir γ-ray source was captured using a charge-coupled device camera. Monte Carlo calculations showed that the observed light was primarily Cherenkov emissions produced by Compton-scattered electrons from the γ-rays. The uncorrected Cherenkov light distribution, which was 5% on average except near the source (within 7 mm from the centre), agreed with the dose distribution calculated using the treatment planning system. The accuracy was attributed to isotropic radiation and short-range Compton electrons. The source positional interval, as measured from the light images, was comparable to the expected intervals, yielding spatial resolution similar to that permitted by conventional film measurements. The method should be highly suitable for quick and easy QA investigations of HDR brachytherapy as it allows simultaneous measurements of dose distribution, source strength, and source position using a single image.
Plantaricin NC8 αβ exerts potent antimicrobial activity against Staphylococcus spp. and enhances the effects of antibiotics
Authors: Bengtsson Torbjörn , Selegård Robert , Musa Amani , Hultenby Kjell , Utterström Johanna , Sivlér Petter , Skog Mårten , Nayeri Fariba , Hellmark Bengt , Söderquist Bo , Aili Daniel , Khalaf Hazem
Published: February 2020

The use of conventional antibiotics has substantial clinical efficacy, however these vital antimicrobial agents are becoming less effective due to the dramatic increase in antibiotic-resistant bacteria. Novel approaches to combat bacterial infections are urgently needed and bacteriocins represent a promising alternative. In this study, the activities of the two-peptide bacteriocin PLNC8 αβ were investigated against different Staphylococcus spp. The peptide sequences of PLNC8 α and β were modified, either through truncation or replacement of all L-amino acids with D-amino acids. Both L- and D-PLNC8 αβ caused rapid disruption of lipid membrane integrity and were effective against both susceptible and antibiotic resistant strains. The D-enantiomer was stable against proteolytic degradation by trypsin compared to the L-enantiomer. Of the truncated peptides, α1–22, β7–34 and β1–20 retained an inhibitory activity. The peptides diffused rapidly (2 min) through the bacterial cell wall and permeabilized the cell membrane, causing swelling with a disorganized peptidoglycan layer. Interestingly, sub-MIC concentrations of PLNC8 αβ substantially enhanced the effects of different antibiotics in an additive or synergistic manner. This study shows that PLNC8 αβ is active against Staphylococcus spp. and may be developed as adjuvant in combination therapy to potentiate the effects of antibiotics and reduce their overall use.
Disrupted principal network organisation in multiple sclerosis relates to disability
Authors: Charalambous Thalis , Clayden Jonathan D. , Powell Elizabeth , Prados Ferran , Tur Carmen , Kanber Baris , Chard Declan , Ourselin Sebastien , Wheeler-Kingshott Claudia A. M. Gandini , Thompson Alan J. , Toosy Ahmed T.
Published: February 2020

Structural network-based approaches can assess white matter connections revealing topological alterations in multiple sclerosis (MS). However, principal network (PN) organisation and its clinical relevance in MS has not been explored yet. Here, structural networks were reconstructed from diffusion data in 58 relapsing-remitting MS (RRMS), 28 primary progressive MS (PPMS), 36 secondary progressive (SPMS) and 51 healthy controls (HCs). Network hubs’ strengths were compared with HCs. Then, PN analysis was performed in each clinical subtype. Regression analysis was applied to investigate the associations between nodal strength derived from the first and second PNs (PN1 and PN2) in MS, with clinical disability. Compared with HCs, MS patients had preserved hub number, but some hubs exhibited reduced strength. PN1 comprised 10 hubs in HCs, RRMS and PPMS but did not include the right thalamus in SPMS. PN2 comprised 10 hub regions with intra-hemispheric connections in HCs. In MS, this subnetwork did not include the right putamen whilst in SPMS the right thalamus was also not included. Decreased nodal strength of the right thalamus and putamen from the PNs correlated strongly with higher clinical disability. These PN analyses suggest distinct patterns of disruptions in MS subtypes which are clinically relevant
Different dynamical behaviors induced by slow excitatory feedback for type II and III excitabilities
Authors: Zhao Zhiguo , Li Li , Gu Huaguang
Published: February 2020

Neuronal excitability is classified as type I, II, or III, according to the responses of electronic activities, which play different roles. In the present paper, the effect of an excitatory autapse on type III excitability is investigated and compared to type II excitability in the Morris-Lecar model, based on Hopf bifurcation and characteristics of the nullcline. The autaptic current of a fast-decay autapse produces periodic stimulations, and that of a slow-decay autapse highly resembles sustained stimulations. Thus, both fast- and slow-decay autapses can induce a resting state for type II excitability that changes to repetitive firing. However, for type III excitability, a fast-decay autapse can induce a resting state to change to repetitive firing, while a slow-decay autapse can induce a resting state to change to a resting state following a transient spike instead of repetitive spiking, which shows the abnormal phenomenon that a stronger excitatory effect of a slow-decay autapse just induces weaker responses. Our results uncover a novel paradoxical phenomenon of the excitatory effect, and we present potential functions of fast- and slow-decay autapses that are helpful for the alteration and maintenance of type III excitability in the real nervous system related to neuropathic pain or sound localization.
Epithelial-mesenchymal transition gene signature is associated with prognosis and tumor microenvironment in head and neck squamous cell carcinoma
Authors: Jung Ah Ra , Jung Chan-Hun , Noh Joo Kyung , Lee Young Chan , Eun Young-Gyu
Published: February 2020

In this study we assessed the clinical significance of an epithelial-mesenchymal transition (EMT) gene signature and explored its association with the tumor microenvironment related to immunotherapy in patients with head and neck squamous cell carcinoma (HNSCC). Genes were selected when mRNA levels were positively or negatively correlated with at least one well-known EMT marker. We developed an EMT gene signature consisting of 82 genes. The patients were classified into epithelial or mesenchymal subgroups according to EMT signature. The clinical significance of the EMT signature was validated in three independent cohorts and its association with several immunotherapy-related signatures was investigated. The mesenchymal subgroup showed worse prognosis than the epithelial subgroup, and significantly elevated PD-1, PD-L1, and CTLA-4 levels, and increased interferon-gamma, cytolytic, T cell infiltration, overall immune infiltration, and immune signature scores. The relationship between PD-L1 expression and EMT status in HNSCC after treatment with TGF-β was validated in vitro. In conclusion, the EMT gene signature was associated with prognosis in HNSCC. Additionally, our results suggest that EMT is related to immune activity of the tumor microenvironment with elevated immune checkpoint molecules.
A novel microfluidic paper-based analytical device based on chemiluminescence for the determination of β-agonists in swine hair
Authors: Li Wei , Luo Yong , Yue Xiqing , Wu Junrui , Wu Rina , Qiao Yu , Peng Qing , Shi Bo , Lin Bingcheng , Chen Xu
Published: February 2020

β-Agonists are illegal feed additives in the feed industries of many countries, especially China.
Insights into the uptake, distribution, and efflux of arsenite associated with nano-TiO2 in determining its toxicity on Daphnia magna
Authors: Luo Zhuanxi , Wang Zhenhong , Xing Baoshan
Published: February 2020

This study provides new insights into the “Trojan horse” effects of nano-TiO2 on arsenite (As(iii)) bioaccumulation in Daphnia magna.
The crucial roles of guest water in a biocompatible coordination network in the catalytic ring-opening polymerization of cyclic esters: a new mechanistic perspective
Authors: Chen Sheng-Chun , Zhang Fei-Hang , Huang Kun-Lin , Tian Feng , Zhang Zhi-Hui , Zhou Renxian , Feng Xue-Jun , Zhou Xiaoying , He Ming-Yang , Gu Jiande , Chen Qun , Wu Chuan-De
Published: February 2020

A new ring-opening polymerization mechanism is unveiled based on synergistic catalysis involving Brønsted and Lewis acid centers in a coordination framework.
Pre-mounted dry TAVI valve with improved endothelialization potential using REDV-loaded PEGMA hydrogel hybrid pericardium
Authors: Yang Li , Huang Xueyu , Deng Lu , Ma Xiaoxiao , Jiang Honglin , Ning Qinggong , Liang Zhen , Lei Yang , Wang Yunbing
Published: February 2020

Schematic diagram for the preparation of hydrogel hybrid dry valve.
Oxygen incorporated solution-processed high-κ La2O3 dielectrics with large-area uniformity, low leakage and high breakdown field comparable with ALD deposited films
Authors: Yan Longsen , He Waner , Liang Xiaoci , Liu Chuan , Lu Xihong , Luo Chunlai , Zhang Aihua , Tao Ruiqiang , Fan Zhen , Zeng Min , Ning Honglong , Zhou Guofu , Lu Xubing , Liu Junming
Published: February 2020

Oxygen incorporated solution-processed high-κ La2O3 dielectrics exhibit large-area uniformity, low leakage and high breakdown field comparable with ALD deposited films.
Understanding the emulsion copolymerization kinetics of vinyl acetate and vinyl silanes
Authors: Barquero Aitor , Ruipérez Fernando , Barandiaran María Jesús , Leiza Jose Ramon
Published: February 2020

Radical entry affected by alkoxysilane monomers in free radical emulsion copolymerization with vinyl acetate.
Mono- and dimeric zinc(ii) complexes for PLA production and degradation into methyl lactate – a chemical recycling method
Authors: Payne Jack , McKeown Paul , Mahon Mary F. , Emanuelsson Emma A. C. , Jones Matthew D.
Published: February 2020

A series of well-defined mono- and dimeric Zn(ii)-complexes were prepared and fully characterised by X-ray crystallography and NMR spectroscopy.
Synthesis of tricyclo[7.2.1.09,10]dodecan-11-one core ring systems of norditerpenoid alkaloids and racemulosine
Authors: Cao Su-Yan , Yue Hui-Jie , Zhu Meng-Qian , Xu Liang
Published: February 2020

A synthetic strategy involving [2 + 2] enyne cycloaddition and pinacol rearrangement to construct common BCD ring systems of norditerpenoid alkaloids and racemulosine was developed.
A nitronyl nitroxide and its two 1D chain Cu–Tb complexes: synthesis, structures, and magnetic properties
Authors: Yang Meng , Liang Xiaohong , Zhang Yandie , Ouyang Zhijian , Dong Wen
Published: February 2020

A new nitronyl nitroxide and two types of one-chain Cu–Tb complexes have been successfully synthesized, and the molecular structures have been elucidated via single-crystal X-ray structural analysis.
Effects of natamycin and Lactobacillus plantarum on the chemical composition, microbial community, and aerobic stability of Hybrid pennisetum at different temperatures
Authors: Shah Assar Ali , Qian Chen , Wu Juanzi , Liu Zhiwei , Khan Salman , Tao Zhujun , Zhang Xiaomin , Khan Irfan Ullah , Zhong Xiaoxian
Published: February 2020

The inoculation of L. plantarum and natamycin influenced the fermentation quality. Natamycin and L. plantarum reduced the undesirable microbial community. During ensiling process, the LA and LABs was significantly enhanced.
Physical properties of phospholipids and integral proteins and their biofunctional roles in pulmonary surfactant from molecular dynamics simulation
Authors: Hadrioui Nourddine , Lemaalem Mohammed , Derouiche Abdelali , Ridouane Hamid
Published: February 2020

This work deals with a quantitative investigation of the physical properties of pulmonary surfactant near melting temperature.
A novel porous egg-white (EW)/titania composite photocatalytic material for efficient photodegradation applications
Authors: Feng Guo , Jiang Feng , Hu Zi , Jiang Weihui , Liu Jianmin , Zhang Quan , Wu Qian , Hu Qing , Miao Lifeng , Cheng Si
Published: February 2020

A novel porous egg-white (EW)/titania composite material was prepared via a facile nonaqueous precipitation method with EW as the porous skeleton.
Simple, scalable mechanosynthesis of metal–organic frameworks using liquid-assisted resonant acoustic mixing (LA-RAM)
Authors: Titi Hatem M. , Do Jean-Louis , Howarth Ashlee J. , Nagapudi Karthik , Friščić Tomislav
Published: February 2020

We present a rapid and readily scalable methodology for the mechanosynthesis of diverse metal–organic frameworks (MOFs) in the absence of milling media typically required for other types of mechanochemical syntheses.
Intra- and intermolecular Fe-catalyzed dicarbofunctionalization of vinyl cyclopropanes
Authors: Liu Lei , Lee Wes , Yuan Mingbin , Acha Chris , Geherty Michael B. , Williams Brandon , Gutierrez Osvaldo
Published: February 2020

Design and implementation of the first (asymmetric) Fe-catalyzed intra- and intermolecular difunctionalization of vinyl cyclopropanes (VCPs) with alkyl halides and aryl Grignard reagents has been realized via a mechanistically driven approach.
Supertough and ultrasensitive flexible electronic skin based on nanocellulose/sulfonated carbon nanotube hydrogel films
Authors: Xu Haiyu , Xie Yuanyuan , Zhu Enwen , Liu Yan , Shi Zhuqun , Xiong Chuanxi , Yang Quanling
Published: February 2020

Flexible TOCN/SCNT hydrogel film E-skin prepared by a simple method exhibited excellent sensing performance and high strength, indicating potential application for wearable electronic devices, health monitoring, and artificial intelligence.
Planarized intramolecular charge transfer on triphenylamine-modified pyrazine and its application in organic light-emitting diodes
Authors: Zhang Bing , Wu Haozhong , Wang Zhiming , Qin Anjun , Tang Ben Zhong
Published: February 2020

PLICT molecules have twisted structures in the ground state, which are conducive to transport, while the planar conformations of the excited states facilitate radiation. Based on these advantages, they can serve as excellent emitters and hosts in OLEDs.
Optimisation of the duplex D2D network: a deep learning approach
Authors: Liu Xian
Published: February 2020

For wireless networks, it is highly desirable to design a quality‐of‐service‐promotion strategy to allocate the transmission power. In this study, the authors apply the deep learning methodology to solve such a problem in a duplex device‐to‐device network. The model is formulated as a constrained non‐linear programming problem. The training data are generated by a standard optimisation tool. Then, an artificial neural network is designed to learn the system from the training data. Simulation results show the effectiveness of deep leaning.
Repeater coil‐based wireless power transfer system powering multiple gate drivers of series‐connected IGBTs
Authors: Cheng Chenwen , Wang Chao , Zhou Zhe , Li Weiguo , Deng Zhanfeng , Mi Chunting Chris
Published: February 2020

It is challenging to power a large number of gate drivers of the series‐connected insulated gate bipolar transistors (IGBTs) in a high‐voltage application because multiple isolated power supplies are needed. In this study, a novel wireless power transfer (WPT) system using repeater coils is designed to solve this problem. Every two repeater coils form a repeater unit, which transfers power to one load. With multiple repeater units in the system, multiple loads can obtain power simultaneously. To eliminate undesirable magnetic couplings between these coils, bipolar coils are used and the two bipolar coils in the same repeater unit are placed perpendicularly. It is derived that constant voltage can be obtained for all the loads, which is especially suitable for powering the IGBT's gate driver. Moreover, the variation of one load power will not affect others. The receiving circuit is designed to transform the received power to the DC voltage compatible with the driving circuits. An experimental setup with six loads has been constructed to validate the proposed WPT system.
Solution combustion synthesis and sorption properties of nanoscale amorphous AlPO4
Authors: Bai Jiahai , Piao Jiasi
Published: February 2020

Nanoscale amorphous AlPO4 was synthesised via a solution combustion process using C2H5NO2 (glycine) as fuel and NH4NO3 as oxidant. The effects of molar ratios of C2H5NO2 to NH4NO3 on characteristics and sorption properties of the amorphous AlPO4 were also studied. The experimental results showed that the Brunauer–Emmett–Teller specific surface areas of the amorphous AlPO4 and the sorption capacities of Pb2+ ions on AlPO4 decreased appreciably with the molar ratio of C2H5NO2 to NH4NO3 varying from 1:9 to 1:12, while the average particle size of the amorphous AlPO4 exhibited no appreciable change.
Silymarin-Extrakt aus Silybum marianum (L.) Gaertn. gegen alimentär-toxische Leberschäden?
Authors: Jobst Detmar , Kraft Karin , Feistel Björn , Fürst Robert
Published: February 2020

Die nichtalkoholische Fettlebererkrankung (NAFLD) zählt zu den häufigsten Lebererkrankungen weltweit. Wesentliche Risikofaktoren sind eine durch Fehl- und Überernährung hervorgerufene Adipositas, Fettstoffwechselstörungen und Insulinresistenz. Silymarin-Präparate zeigten hier in jüngeren Studien uneinheitliche Ergebnisse.
Health-Related Quality of Life – an Underestimated Factor to Evaluate the Treatment Success after Open Wedge HTO Surgery: Prospective 6-Years Follow-Up
Authors: Herbst Moritz , Kuwashima Umito , Ahrend Marc-Daniel , Gueorguiev Boyko Guergov , Schröter Steffen , Ihle Christoph
Published: February 2020

Background The subjective health related quality of life in patients with degenerative joint diseases is an important variable to evaluate the treatment outcome. In this study, mid-term results of open wedge HTO were analysed and compared to the subjective quality of life (SF 36) of the general population. Furthermore, the relationships of preoperative assessed subscales of the health-related quality of life (SF 36) and the conversion to knee arthroplasty were analysed.

Methods The cohort consisted of 120 patients who were prospectively followed-up after open wedge HTO. At five follow-up points of time, patients were examined and asked about their subjective, health-related quality of life using the SF 36 score.

Results 104 patients were included and evaluated until the last follow-up (mean: 81.2 ± 11.3 months after open wedge HTO; follow-up rate: 86.7%). Six years after open wedge HTO, similar values in several psychologic subscales of the SF 36 (BP, GH, V, MH) and the mental health component summary score (MCS) compared to the general population were found. The physical health component summary score (PCS) showed a significant improvement relative to the preoperative values. Nine out of 104 patients (8.7%) received a knee arthroplasty (50.1 ± 25.0 months). Low preoperative values of the subscales “physical functioning” (PF) and “bodily pain” (BP) were identified as risk factors in terms of conversion to a total knee arthroplasty.

Conclusions Patients with medial unicompartimental knee osteoarthrosis treated with open wedge HTO showed very good results. The health-related quality of life was nearly as high as in the general population. Patients with preoperative low physical function and high pain values have a higher risk to have a conversion to knee arthroplasty. Surgeons should be aware of these factors if an open wedge HTO is considered.
A Three Point Assessment Protocol for Tympanoplasty Outcomes: A Retrospective Analysis
Authors: Naina P. , Pokharel Apar , Syed Kamran Asif , John Mary , Varghese Ajoy Mathew , Kurien Mary
Published: February 2020

Introduction The surgical outcome of chronic otitis media (COM) of the mucosal type in the pediatric population with high rates of recurrent tympanic membrane perforation is indeed a concern for the attending surgeon.

Objective The present study was done to evaluate the outcome of tympanoplasty in children with chronic otitis media mucosal type.

Methods A retrospective analysis of the medical records of all children, aged < 16 years old, who underwent tympanoplasty for COM of the mucosal type was performed. These patients were addressed by a three-point assessment, for predicting outcome of tympanoplasty, which included the age of the patient, addressing the nasal/pharyngeal issues, and the status of the COM (discharging or dry). Surgical success was assessed in terms of graft uptake and improvement of hearing. Factors affecting the surgical outcome were also analyzed.

Results A total of 90 children underwent type 1 tympanoplasty; 7 were lost to follow-up and 10 had incomplete audiometric results. In the 73 tympanoplasties analyzed, graft uptake was seen in 91.7% of the patients. Children with longer duration of ear discharge (> 8 years) had greater hearing loss. Children aged > 8 years old showed statistically significant higher chance of graft uptake (p = 0.021). Five of the six children who had graft rejection had bilateral disease.

Conclusion A three-point assessment in the management of pediatric COM of the mucosal type offers good outcomes with post-tympanoplasty graft uptake rates > 90%.
Experiments and simulations on the magnetization of transparent Co-Fe-Ta-B-O heteroamorphous films
Authors: Xiong Chengyue , Zhang Xiaozhong
Published: February 2020

Inducing oxygen into Co-Fe-Ta-B amorphous alloy system makes the transparent amorphous magnetic thin film (Co20Fe47Ta20B13)1-xOx. Oxygen content plays a major role in the magnetization properties of the films. Samples with x=0.41 have a large coercivity ∼1000 Oe, which is 20 times larger than the low oxygen content samples. The forming of a set of single domain magnetic granules rather than continuous magnetic film makes the different magnetization mechanisms. The deviation from Bloch law of saturation magnetization with temperature indicates the Bose-Einstein condensation occurring in magnetic nanostructures. According to the superparamagnetic theory, magnetic phase diagram of the system has been obtained. Monte-Carlo method is used for the simulation of the magnetization of a single domain magnetic granular system at a finite temperature. The simulation results match the experiment to some extent in magnetization-filed curve and field-cooling and zero-field-cooling magnetization curve. This work provides a systematical study of transparent amorphous magnetic thin film system and helps us to know better of this material.
Polymer foil windows for gas–vacuum separation in accelerator applications
Authors: Engel J. , Gross M. , Koss G. , Lishilin O. , Loisch G. , Philipp S. , Richter D. , Stephan F.
Published: February 2020

Various applications in modern particle accelerators or experiments involving high energy particle beams require a gas atmosphere or involve the production of big amounts of residual gas. Among these are, e.g., gas cells for plasma acceleration, gas jet targets, or plasma lenses. As high beam quality and stable operation of RF-accelerator cavities demand for ultra-high vacuum (UHV) conditions, a separation between high pressure and UHV beamline sections is needed. Commonly, this is realized by differential pumping or thin windows, the main advantages of the latter being a simple and compact setup. Nevertheless, the interaction between the window and the beam particles reduces the beam quality via scattering. In this paper, low scattering, low permeability polymer foils that can withstand pressure differences up to 1 bar are investigated as electron beam windows. Measurements, analytical considerations, and simulations on the gas permeation, radiation, and UV resistivity as well as electron beam scattering are presented.
Electronic and optical properties of zinc based hybrid organic-inorganic compounds
Authors: Sahoo Trilochan , Anene Uchenna A , Nayak Sanjeev K , Alpay S Pamir
Published: February 2020

There is significant interest in hybrid organic-inorganic (HOI) compounds since these materials offer multiple functionalities and properties that can be tailored at the mesoscopic and nanoscale levels. HOIs investigated for photovoltaic applications typically contain lead or mercury. There is considerably less work done on Zn-based HOIs. These could potentially be considered in biomedical applications due to presence of organic components and the biocompatibility of Zn cations. Using a systematic materials selection approach, we have carried out a detailed search of Zn-HOI compounds in two comprehensive experimental crystallographic repositories: Inorganic Crystal Structure Database and American Mineralogist Crystal Structure Database. Thirteen Zn-HOI compounds are discovered: CuZnO2(CO3), Zn(C2O4), ((CH3)2NH2)Zn3(PO4)(HPO4)2, (CH3NH3)Zn4(PO4)3, Zn(N(CH2PO3H)3)(H2O)3, (CH3NH3)Zn(HCO2)3, Zn4(CO3)2, Zn8(HPO4)16(C2H8N)8, Zn5(CO3)2, (Mg2Zn)8(CO3)2(OH), Zn7(CO3)2(OH)10, Ca3Zn2(PO4)CO3(OH).2H2O, and Zn(CO3). We have then performed first principles calculations via density functional theory with hybrid functional treatment to determine the electronic band gap and optical response of these materials. Our computations show that eleven of the thirteen compounds have insulating properties with band gaps ranging from 2.8 eV to 6.9 eV. Ten of these are found to have a high absorbance in the far ultra-violet (FUV) region of 200–112 nm wavelength. For example, the absorption coefficient of (CH3NH3)Zn(HCO2)3 is ∼0.75 × 105 cm−1 for F2 excimer laser energy (wavelength ∼157 nm) which is more than three orders higher than the average tissue absorbance (∼101.5 cm−1) and the refractive index of 1.85 is larger than typical biological matter which is in the range 1.36–1.49. These results suggest that Zn-HOIs could potentially find applications in photothermolysis and UV protection.
MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors
Authors: Schwarz Michael , Welzel Marius , Kabdullayeva Tolganay , Becker Anke , Freisleben Bernd , Heider Dominik
Published: February 2020

The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes.

Availability and implementation

MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim.

Contact

dominik.heider@uni-marburg.de

Supplementary information

Supplementary data are available at Bioinformatics online.
Supervised learning is an accurate method for network-based gene classification
Authors: Liu Renming , Mancuso Christopher A , Yannakopoulos Anna , Johnson Kayla A , Krishnan Arjun
Published: February 2020

Background

Assigning every human gene to specific functions, diseases and traits is a grand challenge in modern genetics. Key to addressing this challenge are computational methods, such as supervised learning and label propagation, that can leverage molecular interaction networks to predict gene attributes. In spite of being a popular machine-learning technique across fields, supervised learning has been applied only in a few network-based studies for predicting pathway-, phenotype- or disease-associated genes. It is unknown how supervised learning broadly performs across different networks and diverse gene classification tasks, and how it compares to label propagation, the widely benchmarked canonical approach for this problem.

Results

In this study, we present a comprehensive benchmarking of supervised learning for network-based gene classification, evaluating this approach and a classic label propagation technique on hundreds of diverse prediction tasks and multiple networks using stringent evaluation schemes. We demonstrate that supervised learning on a gene’s full network connectivity outperforms label propagaton and achieves high prediction accuracy by efficiently capturing local network properties, rivaling label propagation’s appeal for naturally using network topology. We further show that supervised learning on the full network is also superior to learning on node embeddings (derived using node2vec), an increasingly popular approach for concisely representing network connectivity. These results show that supervised learning is an accurate approach for prioritizing genes associated with diverse functions, diseases and traits and should be considered a staple of network-based gene classification workflows.

Availability and implementation

The datasets and the code used to reproduce the results and add new gene classification methods have been made freely available.

Contact

arjun@msu.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Fast and robust ancestry prediction using principal component analysis
Authors: Zhang Daiwei , Dey Rounak , Lee Seunggeun
Published: February 2020

Motivation

Population stratification (PS) is a major confounder in genome-wide association studies (GWAS) and can lead to false-positive associations. To adjust for PS, principal component analysis (PCA)-based ancestry prediction has been widely used. Simple projection (SP) based on principal component loadings and the recently developed data augmentation, decomposition and Procrustes (ADP) transformation, such as LASER and TRACE, are popular methods for predicting PC scores. However, the predicted PC scores from SP can be biased toward NULL. On the other hand, ADP has a high computation cost because it requires running PCA separately for each study sample on the augmented dataset.

Results

We develop and propose two alternative approaches: bias-adjusted projection (AP) and online ADP (OADP). Using random matrix theory, AP asymptotically estimates and adjusts for the bias of SP. OADP uses a computationally efficient online singular value decomposition algorithm, which can greatly reduce the computation cost of ADP. We carried out extensive simulation studies to show that these alternative approaches are unbiased and the computation speed can be 16–16 000 times faster than ADP. We applied our approaches to the UK Biobank data of 488 366 study samples with 2492 samples from the 1000 Genomes data as the reference. AP and OADP required 0.82 and 21 CPU hours, respectively, while the projected computation time of ADP was 1628 CPU hours. Furthermore, when inferring sub-European ancestry, SP clearly showed bias, unlike the proposed approaches.

Availability and implementation

The OADP and AP methods, as well as SP and ADP, have been implemented in the open-source Python software FRAPOSA, available at github.com/daviddaiweizhang/fraposa.

Contact

leeshawn@umich.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
In Their Own Words: Joel Cracraft
Authors: Verdier James M
Published: February 2020

In Their Own Words chronicles the stories of scientists who have made great contributions to their fields, particularly within the biological sciences. These short oral histories provide our readers a way to learn from and share their experiences. Each month, we will publish in the pages of BioScience and in our podcast, BioScience Talks (http://bioscienceaibs.libsyn.com), the results of these conversations. This oral history is with Joel Cracraft, curator in the Department of Ornithology at the American Museum of Natural History. He previously served as president of the American Institute of Biological Sciences. Note: Both the text and audio versions have been edited for clarity and length.