bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings
Authors: Hwang Kyu-Baek , Lee In-Hee , Li Honglan , Won Dhong-Geon , Hernandez-Ferrer Carles , Negron Jose Alberto , Kong Sek Won
Published: March 2019

Comprehensive and accurate detection of variants from whole-genome sequencing (WGS) is a strong prerequisite for translational genomic medicine; however, low concordance between analytic pipelines is an outstanding challenge. We processed a European and an African WGS samples with 70 analytic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (VCAs), and observed remarkable differences in the number of variants called by different pipelines (max/min ratio: 1.3~3.4). The similarity between variant call sets was more closely determined by VCAs rather than by short-read aligners. Remarkably, reported minor allele frequency had a substantial effect on concordance between pipelines (concordance rate ratio: 0.11~0.92; Wald tests, P < 0.001), entailing more discordant results for rare and novel variants. We compared the performance of analytic pipelines and pipeline ensembles using gold-standard variant call sets and the catalog of variants from the 1000 Genomes Project. Notably, a single pipeline using BWA-MEM and GATK-HaplotypeCaller performed comparable to the pipeline ensembles for ‘callable’ regions (~97%) of the human reference genome. While a single pipeline is capable of analyzing common variants in most genomic regions, our findings demonstrated the limitations and challenges in analyzing rare or novel variants, especially for non-European genomes.
Prospects for Bioinspired Single-Photon Detection Using Nanotube-Chromophore Hybrids
Authors: Léonard François , Foster Michael E. , Spataru Catalin D.
Published: March 2019

The human eye is an exquisite photodetection system with the ability to detect single photons. The process of vision is initiated by single-photon absorption in the molecule retinal, triggering a cascade of complex chemical processes that eventually lead to the generation of an electrical impulse. Here, we analyze the single-photon detection prospects for an architecture inspired by the human eye: field-effect transistors employing carbon nanotubes functionalized with chromophores. We employ non-equilibrium quantum transport simulations of realistic devices to reveal device response upon absorption of a single photon. We establish the parameters that determine the strength of the response such as the magnitude and orientation of molecular dipole(s), as well as the arrangements of chromophores on carbon nanotubes. Moreover, we show that functionalization of a single nanotube with multiple chromophores allows for number resolution, whereby the number of photons in an incoming light packet can be determined. Finally, we assess the performance prospects by calculating the dark count rate, and we identify the most promising architectures and regimes of operation.
Genetic and evolutionary analysis of a new Asia-4 lineage and naturally recombinant canine distemper virus strains from Thailand
Authors: Piewbang Chutchai , Radtanakatikanon Araya , Puenpa Jiratchaya , Poovorawan Yong , Techangamsuwan Somporn
Published: March 2019

Canine distemper virus (CDV), a pathogen causing fatal disease in a wide range of carnivores, can be classified into several geographically-related lineages. It is unclear how genetic recombination contributed to the evolution and emergence of the novel CDV strains and the evolutions of these strains are not fully yet investigated. In this study, the complete genome sequences of eight CDV viruses, isolated from domestic dogs in Thailand, were investigated. Interestingly, most of the identified CDV strains (CDV1-3, -5, -8 TH/2014) clustered as a novel Asia-4 lineage, while the CDV4, -6, -7 TH/2014 belonged to the Asia-1 lineage. Recombination analysis revealed that the CDV4 TH/2014 is a putative recombinant virus from the Asia-1 and America-2 parent viruses. In contrast, no recombination events were detected in the Asia-4 lineage, indicating that it is a distinctive lineage. Evolutionary analysis suggested that the CDV Asia-4 lineage had emerged since 1924 and shared common ancestor with the America-2 lineage. Pressure analysis revealed that CDV nucleotides were under negative selection pressure for its rapid adaptation. These findings demonstrate the evolution of CDV Asia-4 lineage and identified the Asia-1 recombination event. The information regarding genetic diversity of CDVs is essential for further CDV’s research and monitoring.
Dynamic Concatenation of Quantum Error Correction in Integrated Quantum Computing Architecture
Authors: Sohn Ilkwon , Bang Jeongho , Heo Jun
Published: March 2019

Resource overhead problem caused by concatenation in quantum error correction (QEC) is of significant importance for the realization of fault-tolerant quantum computation (FTQC). To attack this problem, we propose a novel scheme by considering integrated FTQC architecture where the concatenation level is controlled dynamically; i.e., less (or more) concatenation levels are imposed by good (or poor) performance gates—we call this scheme “dynamic concatenation” in this sense. Such a dynamic concatenation is realizable in an integrated structure of FTQC, as the information of the concatenation can be communicated between classical system elements (e.g., compiler and system organizer) and the logical qubits in real-time. We derive the effective lower and upper bounds of the length of gate decomposition in order to achieve the practical advantage, namely of reduction of the overall operation time. By considering two non-trivial examples, it is shown that the aforementioned advantage can indeed be achieved in the presented scheme. Our result also provides an important scientific message, i.e., the interplay between “classical” and “quantum” can be helpful in QEC.
Metabolic effects of leptin receptor knockdown or reconstitution in adipose tissues
Authors: Pereira Sandra , O’Dwyer Shannon M. , Webber Travis D. , Baker Robert K. , So Victor , Ellis Cara E. , Yoon Ji Soo , Mojibian Majid , Glavas Maria M. , Karunakaran Subashini , Clee Susanne M. , Covey Scott D. , Kieffer Timothy J.
Published: March 2019

The relative contribution of peripheral and central leptin signalling to the regulation of metabolism and the mechanisms through which leptin affects glucose homeostasis have not been fully elucidated. We generated complementary lines of mice with either leptin receptor (Lepr) knockdown or reconstitution in adipose tissues using Cre-lox methodology. Lepr knockdown mice were modestly lighter and had lower plasma insulin concentrations following an oral glucose challenge compared to controls, despite similar insulin sensitivity. We rendered male mice diabetic using streptozotocin (STZ) and found that upon prolonged leptin therapy, Lepr knockdown mice had an accelerated decrease in blood glucose compared to controls that was associated with higher plasma concentrations of leptin and leptin receptor. Mice with transcriptional blockade of Lepr (LeprloxTB/loxTB) were obese and hyperglycemic and reconstitution of Lepr in adipose tissues of LeprloxTB/loxTB mice resulted in males reaching a higher maximal body weight. Although mice with adipose tissue Lepr reconstitution had lower blood glucose levels at several ages, their plasma insulin concentrations during an oral glucose test were elevated. Thus, attenuation or restoration of Lepr in adipocytes alters the plasma insulin profile following glucose ingestion, modifies the glucose-lowering effect of prolonged leptin therapy in insulin-deficient diabetes, and may modulate weight gain.
Optimized pupal age of Tenebrio molitor L. (Coleoptera: Tenebrionidae) enhanced mass rearing efficiency of Chouioia cunea Yang (Hymenoptera: Eulophidae)
Authors: Li Tian-Hao , Che Peng-Fei , Yang Xiangbing , Song Li-Wei , Zhang Chao-Ran , Benelli Giovanni , Desneux Nicolas , Zang Lian-Sheng
Published: March 2019

Chouioia cunea Yang (Hymenoptera: Eulophidae) has been widely used for biological control of the fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), in China. The yellow mealworm, Tenebrio molitor L. (Coleoptera: Tenebrionidae), an important resource insect species distributed worldwide, is considered to be a potential alternative host for mass rearing of C. cunea to the Chinese oak silkworm, Antheraea pernyi (Guerin-Meneville) (Lepidoptera: Saturniidae), which is currently used. In this study, we investigated the effects of host age on C. cunea mass rearing by measuring parasitism, development and adult fertility of C. cunea on T. molitor pupae of different ages. The results showed no significant differences in the percentage of parasitized hosts and developmental time of C. cunea in pupae of different ages. However, the number of C. cunea adults (137.2–154.7 adults per host) that emerged from 0, 1, and 2-day-old pupae was significantly higher than that from 4-day-old pupae. The lowest percentages of unemerged adults were found in 2-day-old (1.2%) and 3-day-old (1.4%) pupae, which were significantly lower than that of 4-day-old pupae (10.3%). The emergence of adult females from 0 to 2-day-old pupae (120.2–142.3 per pupa) was significantly higher than that from 4-day-old hosts (64.6). Adult females emerging from 2-day-old pupae carried significantly more eggs (258.2 eggs/female) than those from 0 and 1-day-old pupae (178.4–178.9 eggs/female). Our findings indicated that 2-day-old pupae of T. molitor were most suitable to rear C. cunea. Overall, this research provided valuable information to optimize pupae for the mass rearing of C. cunea on host T. molitor.
Temporal relationship between perceptual and physiological events triggered by nociceptive heat stimuli
Authors: Castellote J. M. , Valls-Solé J.
Published: March 2019

A combined assessment tool for the perceptual-motor aspects of pain processing will be valuable to clinicians. Fifteen healthy subjects were exposed to contact-heat stimulation (Pathway, Medoc, Israel) to assess perception through a simple task (motor response or conscious appraisal of the time the stimulus was felt) or with a dual task (both responses). The outcome measure was the temporal relationship between contact heat evoked potentials (CHEPS), reaction time (RT) and conscious awareness (AW). There were different temporal profiles for CHEPs, RT and AW to changes in stimulus intensity, AW being the least affected. Performing the dual task led to a significantly more pronounced effect on RT than on AW, while CHEPS were not influenced by task performance. Our results support the dissociation between physiological, behavioral and cognitive events elicited by nociceptive stimuli. The time of conscious appraisal of stimulus occurrence is a complementary information to other responses such as evoked potentials or behavioral tasks. The combined assessment of physiological and behavioral aspects of pain processing may provide clinicians with information on the different paths followed by nociceptive afferent inputs in the central nervous system.
Pelota-interacting G protein Hbs1 is required for spermatogenesis in Drosophila
Authors: Li Zhaohui , Yang Fu , Xuan Yang , Xi Rongwen , Zhao Rui
Published: March 2019

Hbs1, which is homologous to the GTPase eRF3, is a small G protein implicated in mRNA quality control. It interacts with a translation-release factor 1-like protein Dom34/Pelota to direct decay of mRNAs with ribosomal stalls. Although both proteins are evolutionarily conserved in eukaryotes, the biological function of Hbs1 in multicellular organisms is yet to be characterized. In Drosophila, pelota is essential for the progression through meiosis during spermatogenesis and germline stem cell maintenance. Here we show that homozygous Hbs1 mutant flies are viable, female-fertile, but male-sterile, which is due to defects in meiosis and spermatid individualization, phenotypes that are also observed in pelota hypomorphic mutants. In contrast, Hbs1 mutants have no obvious defects in germline stem cell maintenance. We show that Hbs1 genetically interacts with pelota during spermatid individualization. Furthermore, Pelota with a point mutation on the putative Hbs1-binding site cannot substitute the wild type protein for normal spermatogenesis. These data suggest that Pelota forms a complex with Hbs1 to regulate multiple processes during spermatogenesis. Our results reveal a specific requirement of Hbs1 in male gametogenesis in Drosophila and indicate an essential role for the RNA surveillance complex Pelota-Hbs1 in spermatogenesis, a function that could be conserved in mammals.
A Portion of the Apomixis Locus of Paspalum Simplex is Microsyntenic with an Unstable Chromosome Segment Highly Conserved Among Poaceae
Authors: Galla Giulio , Siena Lorena A. , Ortiz Juan Pablo A. , Baumlein Helmut , Barcaccia Gianni , Pessino Silvina C. , Bellucci Michele , Pupilli Fulvio
Published: March 2019

The introgression of apomixis in major seed crops, would guarantee self-seeding of superior heterotic seeds over generations. In the grass speciesPaspalum simplex, apomixis is controlled by a single locus in which recombination is blocked. In the perspective of isolating the genetic determinants of apomixis, we report data on sequencing,in silicomapping and expression analysis of some of the genes contained in two cloned genomic regions of the apomixis locus ofP.simplex.In silicomapping allowed us to identify a conserved synteny group homoeologous to the apomixis locus, located on a telomeric position of chromosomes 12, 8, 3 and 4 of rice,Sorghum bicolor,Setaria italicaandBrachypodium distachyum, respectively, and on a more centromeric position of maize chromosome 1. Selected genes of the apomixis locus expressed sense and antisense transcripts in reproductively committed cells of sexual and apomictic ovules. Some of the genes considered here expressed apomixis-specific allelic variants which showed partial non-overlapping expression patterns with alleles shared by sexual and apomictic reproductive phenotypes. Our findings open new routes for the isolation of the genetic determinants of apomixis and, in perspective, for its introgression in crop grasses.
Evaluation of focal damage in the retinal pigment epithelium layer in serous retinal pigment epithelium detachment
Authors: Miura Masahiro , Makita Shuichi , Azuma Shinnosuke , Yasuno Yoshiaki , Ueda Shunichiro , Sugiyama Satoshi , Mino Toshihiro , Yamaguchi Tatsuo , Sandhu Harpal S. , Kaplan Henry J. , Iwasaki Takuya , Goto Hiroshi
Published: March 2019

The purpose of this study was to evaluate focal damage in the retinal pigment epithelium (RPE) layer in serous retinal pigment epithelium detachment (PED) with multi-contrast optical coherence tomography (OCT), which is capable of simultaneous measurement of OCT angiography, polarization-sensitive OCT and standard OCT images. We evaluated 37 eyes with age-related macular degeneration that had serous PED. Focal RPE damage was indicated by hyper-transmission beneath the RPE-Bruch’s membrane band in standard OCT images. Distribution of RPE melanin was calculated using the dataset from multi-contrast OCT. Twenty-four points with hyper-transmission were detected in 21 of the 37 eyes. Standard OCT images failed to show disruption of the RPE-Bruch’s membrane band at 5 of the 24 hyper-transmission points. Conversely, multi-contrast OCT images clearly showed melanin defects in the RPE-Bruch’s membrane band at all points. Areas of melanin defects with disruption of the RPE-Bruch’s membrane band were significantly larger than those without disruption. The volume of intraretinal hyper-reflective foci was significantly larger in eyes with hyper-transmission than that in eyes without hyper-transmission. Multi-contrast OCT is more sensitive than standard OCT for displaying changes at the RPE-Bruch’s membrane band when there are small areas of RPE damage.
Limited available evidence supports theoretical predictions of reduced vaccine efficacy at higher exposure dose
Authors: Langwig Kate E. , Gomes M. Gabriela M. , Clark Mercedes D. , Kwitny Molly , Yamada Steffany , Wargo Andrew R. , Lipsitch Marc
Published: March 2019

Understanding the causes of vaccine failure is important for predicting disease dynamics in vaccinated populations and planning disease interventions. Pathogen exposure dose and heterogeneity in host susceptibility have both been implicated as important factors that may reduce overall vaccine efficacy and cause vaccine failure. Here, we explore the effect of pathogen dose and heterogeneity in host susceptibility in reducing efficacy of vaccines. Using simulation-based methods, we find that increases in pathogen exposure dose decrease vaccine efficacy, but this effect is modified by heterogeneity in host susceptibility. In populations where the mode of vaccine action is highly polarized, vaccine efficacy decreases more slowly with exposure dose than in populations with less variable protection. We compared these theoretical results to empirical estimates from a systematic literature review of vaccines tested over multiple exposure doses. We found that few studies (nine of 5,389) tested vaccine protection against infection over multiple pathogen challenge doses, with seven studies demonstrating a decrease in vaccine efficacy with increasing exposure dose. Our research demonstrates that pathogen dose has potential to be an important determinant of vaccine failure, although the limited empirical data highlight a need for additional studies to test theoretical predictions on the plausibility of reduced host susceptibility and high pathogen dose as mechanisms responsible for reduced vaccine efficacy in high transmission settings.
The Grande Rose of the Reims Cathedral: an eight-century perspective on the colour management of medieval stained glass
Authors: Capobianco Natan , Hunault Myrtille O. J. Y. , Balcon-Berry Sylvie , Galoisy Laurence , Sandron Dany , Calas Georges
Published: March 2019

The Grande Rose of Reims Cathedral (France), a UNESCO Cultural Heritage Monument from the 13th century, underwent several restoration works during the 20th century. Its colours result from centuries of colour management from which little information remain. We used non-destructive and portable optical absorption spectroscopy to quantify glass colour and determine the colouring species on a large-scale study of this monumental window. We found six distinct colour groups, each containing both medieval and modern glasses, with colouring processes specific to each colour. This illustrates medieval glassmakers’ mastering of glass colouring and modern glassmakers’ management to reproduce medieval glasses colours. Full UV-visible-NIR energy range is necessary for determining the contribution of colouring elements as Fe2+ and Cu2+. Systematic thickness measurements reveal an average glass thickness of 3 mm and demonstrate the major control of chromophore concentration on glass colour. Yellow, red and purple colours arise from a single chromophore each, suggesting the use of well-defined glassmaking techniques leading to robust colour reproducibility. By contrast, blue and green glasses show different chromophore combinations depending on production time, which suggests more diversity in glassmaking techniques.
Early hospital readmissions after ABO- or HLA- incompatible living donor kidney transplantation
Authors: Lee Juhan , Kim Deok Gie , Kim Beom Seok , Kim Myoung Soo , Il Kim Soon , Kim Yu Seun , Huh Kyu Ha
Published: March 2019

Early hospital readmission (EHR) after kidney transplantation (KT) is associated with adverse outcomes and significant healthcare costs. Despite survival benefits, ABO- and HLA-incompatible (ABOi and HLAi) KTs require desensitization and potent immunosuppression that increase risk of EHR. However, little data exist regarding EHR after incompatible KT. We defined EHR as admission for any reason within 30 days of discharge from the index hospitalization. Patients who underwent living donor KT from 2010–2017 were classified into one of three groups (control, ABOi KT, or HLAi KT). Our study included 732 patients, 96 (13.1%) of who experienced EHR. HLAi KT patients had a significantly higher incidence of EHR than other groups (26.6%; P < 0.001). In addition, HLAi KT (HR, 2.26; 95% CI, 1.35–3.77; P = 0.002) and advanced age (≥60 years) (HR, 1.93; 95% CI, 1.20–3.12; P = 0.007) were independent risk factors for EHR. Patients with EHR showed 1.5 times and 3 times greater risk of late hospital readmission and death-censored graft loss, respectively, and consistently exhibited inferior renal function compared to those without EHR, regardless of immunologic incompatibilities. We recommend that KT recipients experiencing EHR or its risk factors be managed with extreme care due to their increased susceptibility to adverse outcomes.
Predicting seasonal influenza epidemics using cross-hemisphere influenza surveillance data and local internet query data
Authors: Zhang Yuzhou , Yakob Laith , Bonsall Michael B. , Hu Wenbiao
Published: March 2019

Can early warning systems be developed to predict influenza epidemics? Using Australian influenza surveillance and local internet search query data, this study investigated whether seasonal influenza epidemics in China, the US and the UK can be predicted using empirical time series analysis. Weekly national number of respiratory cases positive for influenza virus infection that were reported to the FluNet surveillance system in Australia, China, the US and the UK were obtained from World Health Organization FluNet surveillance between week 1, 2010, and week 9, 2018. We collected combined search query data for the US and the UK from Google Trends, and for China from Baidu Index. A multivariate seasonal autoregressive integrated moving average model was developed to track influenza epidemics using Australian influenza and local search data. Parameter estimates for this model were generally consistent with the observed values. The inclusion of search metrics improved the performance of the model with high correlation coefficients (China = 0.96, the US = 0.97, the UK = 0.96, p < 0.01) and low Maximum Absolute Percent Error (MAPE) values (China = 16.76, the US = 96.97, the UK = 125.42). This study demonstrates the feasibility of combining (Australia) influenza and local search query data to predict influenza epidemics a different (northern hemisphere) scales.
Dye-coupling between neonatal spinal motoneurons and interneurons revealed by prolonged back-filling of a ventral root with a low molecular weight tracer in the mouse
Authors: Blivis Dvir , Falgairolle Melanie , O’Donovan Michael J.
Published: March 2019

We investigated dye-coupling between motoneurons in the L6 segment of the neonatal mouse spinal cord that contains limb-innervating motoneurons and sexually dimorphic motor nuclei. Using an isolated spinal cord preparation, we back-filled the cut, L6 ventral root with the small molecule Neurobiotin, or the much larger dextran-conjugated fluorophores for 16–24 hours. Motoneurons and parasympathetic preganglionic neurons were filled with both markers, but dye-coupling was only seen with Neurobiotin fills. Following a neurobiotin fill, fluorescence was observed in contralateral motoneurons, in motoneurons innervating adjacent ventral roots, and in ChAT-negative, putative interneurons outside of the motoneuron pools in addition to the directly back-labeled L6 motoneurons. It is known that the gap junction protein connexin-36 is widely expressed in the sexually dimorphic motoneurons of the L6 segment, suggesting that the dye-coupling is mediated by gap junctions. The technique has revealed previously unknown connections of motoneurons in the neonatal mouse cord that are likely to play important roles in the development and function of spinal circuits.
TBA225, a fusion toxoid vaccine for protection and broad neutralization of staphylococcal superantigens
Authors: Venkatasubramaniam Arundhathi , Adhikari Rajan P. , Kort Thomas , Liao Grant C. , Conley Shawn , Abaandou Laura , Kailasan Shweta , Onodera Yoshikuni , Krishnan Subramaniam , Djagbare Didier M. , Holtsberg Frederick W. , Karauzum Hatice , Aman M. Javad
Published: March 2019

Superantigens (SAgs) play a major role in the pathogenesis of Staphylococcus aureus and are associated with several diseases, including food poisoning, bacterial arthritis, and toxic shock syndrome. Monoclonal antibodies to these SAgs, primarily TSST-1, SEB and SEA have been shown to provide protection in animal studies and to reduce clinical severity in bacteremic patients. Here we quantify the pre-existing antibodies against SAgs in many human plasma and IVIG samples and demonstrate that in a major portion of the population these antibody titers are suboptimal and IVIG therapy only incrementally elevates the anti-SAg titers. Our in vitro neutralization studies show that a combination of antibodies against SEA, SEB,and TSST-1 can provide broad neutralization of staphylococcal SAgs. We report a single fusion protein (TBA225) consisting of the toxoid versions of TSST-1, SEB and SEA and demonstrate its immunogenicity and protective efficacy in a mouse model of toxic shock. Antibodies raised against this fusion vaccine provide broad neutralization of purified SAgs and culture supernatants of multiple clinically relevant S. aureus strains. Our data strongly supports the use of this fusion protein as a component of an anti-virulence based multivalent toxoid vaccine against S. aureus disease.
Automated detection of koalas using low-level aerial surveillance and machine learning
Authors: Corcoran Evangeline , Denman Simon , Hanger Jon , Wilson Bree , Hamilton Grant
Published: March 2019

Effective wildlife management relies on the accurate and precise detection of individual animals. These can be challenging data to collect for many cryptic species, particularly those that live in complex structural environments. This study introduces a new automated method for detection using published object detection algorithms to detect their heat signatures in RPAS-derived thermal imaging. As an initial case study we used this new approach to detect koalas (Phascolarctus cinereus), and validated the approach using ground surveys of tracked radio-collared koalas in Petrie, Queensland. The automated method yielded a higher probability of detection (68–100%), higher precision (43–71%), lower root mean square error (RMSE), and lower mean absolute error (MAE) than manual assessment of the RPAS-derived thermal imagery in a comparable amount of time. This new approach allows for more reliable, less invasive detection of koalas in their natural habitat. This new detection methodology has great potential to inform and improve management decisions for threatened species, and other difficult to survey species.
Highly Sensitive Active-Matrix Driven Self-Capacitive Fingerprint Sensor based on Oxide Thin Film Transistor
Authors: Jeon Guk-Jin , Lee Seung-Hwan , Lee Seung Hee , Shim Jun-Bo , Ra Jong-Hyun , Park Kyoung Woo , Yeom Hye-In , Nam Yunyong , Kwon Oh-Kyong , Park Sang-Hee Ko
Published: March 2019

The fingerprint recognition has been widely used for biometrics in mobile devices. Existing fingerprint sensors have already been commercialized in the field of mobile devices using primarily Si-based technologies. Recently, mutual-capacitive fingerprint sensors have been developed to lower production costs and expand the range of application using thin-film technologies. However, since the mutual-capacitive method detects the change of mutual capacitance, it has high ratio of parasitic capacitance to ridge-to-valley capacitance, resulting in low sensitivity, compared to the self-capacitive method. In order to demonstrate the self-capacitive fingerprint sensor, a switching device such as a transistor should be integrated in each pixel, which reduces a complexity of electrode configuration and sensing circuits. The oxide thin-film transistor (TFT) can be a good candidate as a switching device for the self-capacitive fingerprint sensor. In this work, we report a systematic approach for self-capacitive fingerprint sensor integrating Al-InSnZnO TFTs with field-effect mobility higher than 30 cm2/Vs, which enable isolation between pixels, by employing industry-friendly process methods. The fingerprint sensors are designed to reduce parasitic resistance and capacitance in terms of the entire system. The excellent uniformity and low leakage current (<10−12) of the oxide TFTs allow successful capture of a fingerprint image.
Epidemiological characteristics of nasopharyngeal Streptococcus pneumoniae strains among children with pneumonia in Chongqing, China
Authors: Yu Yi-Yi , Xie Xiao-Hong , Ren Luo , Deng Yu , Gao Yu , Zhang Yao , Li Hui , Luo Jian , Luo Zheng-Xiu , Liu En-Mei
Published: March 2019

Streptococcus pneumoniae (pneumococcus) is the most common respiratory pathogen worldwide. Nasopharyngeal carriage with S. pneumoniae is the major source of lower respiratory tract infection and horizontal spread among children. Investigating nasopharyngeal S. pneumoniae is crucial for clinicians to control pneumococcus disease. Here, we retrospectively analyzed clinical information of 5,960 hospitalized children, focusing on pneumonia children less than five years with positive nasopharyngeal pneumococcal cultures. Nasopharyngeal aspirates (NPAs) were collected between June 2009 and December 2016, which were outside the pneumococcal conjugate vaccine(PCV) period. NPAs were subjected to common bacterial culture and antibiotic susceptibility tests, and serotypes were identified by both multiplex PCR and DNA sequencing. Results clearly revealed that clinical manifestations of the children whose NPAs were S. pneumoniae culture positive were serious, especially in those less than twelve months old. Fifteen different serotypes of nasopharyngeal S. pneumoniae were detected, the most common ones being 19F (35.2%), 6A/B (23.8%), 19A (11.4%), 15B/C (9.3%) and 23F (7.8%). Eight serotypes, accounting for 85.5% of the isolates, corresponded to the PCV13 serotypes. Approximately one-third of all S. pneumoniae strains were susceptible to penicillin. Overall, we consider nasopharyngeal S. pneumoniae culture is beneficial in assessing the situations of pneumonia children. Moreover, PCV13 could be useful in preventing pneumococcal disease in Chongqing, China.
Transportan 10 improves the pharmacokinetics and pharmacodynamics of vancomycin
Authors: Ruczyński Jarosław , Rusiecka Izabela , Turecka Katarzyna , Kozłowska Agnieszka , Alenowicz Magdalena , Gągało Iwona , Kawiak Anna , Rekowski Piotr , Waleron Krzysztof , Kocić Ivan
Published: March 2019

In the presented study, transportan 10 (TP10), an amphipathic cell penetrating peptide (CPP) with high translocation activity, was conjugated with vancomycin (Van), which is known for poor access to the intracellular bacteria and the brain. The antibacterial activity of the conjugates was tested on selected clinical strains of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus sp. It turned out that all of them had superior antimicrobial activity in comparison to that of free Van, which became visible particularly against clinical MRSA strains. Furthermore, one of the conjugates was tested against MRSA - infected human cells. With respect to them, this compound showed high bactericidal activity. Next, the same conjugate was screened for its capacity to cross the blood brain barrier (BBB). Therefore, qualitative and quantitative analyses of the conjugate’s presence in the mouse brain slices were carried out after its iv administration. They indicated the conjugate’s presence in the brain in amount >200 times bigger than that of Van. The conjugates were safe with respect to erythrocyte toxicity (erythrocyte lysis assay). Van in the form of a conjugate with TP10 acquires superior pharmacodynamic and pharmacokinetic.
Rapid analysis of intraperitoneally administered morphine in mouse plasma and brain by microchip electrophoresis-electrochemical detection
Authors: Ollikainen Elisa , Aitta-aho Teemu , Koburg Michaela , Kostiainen Risto , Sikanen Tiina
Published: March 2019

Animal studies remain an essential part of drug discovery sincein vitromodels are not capable of describing the complete living organism. We developed and qualified a microchip electrophoresis-electrochemical detection (MCE-EC) method for rapid analysis of morphine in mouse plasma using a commercial MCE-EC device. Following liquid-liquid extraction (LLE), we achieved within-run precision of 3.7 and 4.5% (coefficient of variation, CV, n = 6) and accuracy of 106.9% and 100.7% at biologically relevant morphine concentrations of 5 and 20 µM in plasma, respectively. The same method was further challenged by morphine detection in mouse brain homogenates with equally good within-run precision (7.8% CV, n = 5) at 1 µM concentration. The qualified method was applied to analyze a set of plasma and brain homogenate samples derived from a behavioral animal study. After intraperitoneal administration of 20 mg/kg morphine hydrochloride, the detected morphine concentrations in plasma were between 6.7 and 17 µM. As expected, the morphine concentrations in the brain were significantly lower,ca. 80–125 nM (280–410 pg morphine/mg dissected brain), and could only be detected after preconcentration achieved during LLE. In all, the microchip-based separation system is proven feasible for rapid analysis of morphine to provide supplementary chemical information to behavioral animal studies.
Comparing the effects of non-homogenous mixing patterns on epidemiological outcomes in equine populations: A mathematical modelling study
Authors: Milwid Rachael M. , O’Sullivan Terri L. , Poljak Zvonimir , Laskowski Marek , Greer Amy L.
Published: March 2019

Disease transmission models often assume homogenous mixing. This assumption, however, has the potential to misrepresent the disease dynamics for populations in which contact patterns are non-random. A disease transmission model with an SEIR structure was used to compare the effect of weighted and unweighted empirical equine contact networks to weighted and unweighted theoretical networks generated using random mixing. Equine influenza was used as a case study. Incidence curves generated with the unweighted empirical networks were similar in epidemic duration (5–8 days) and peak incidence (30.8–46.4%). In contrast, the weighted empirical networks resulted in a more pronounced difference between the networks in terms of the epidemic duration (8–15 days) and the peak incidence (5–25%). The incidence curves for the empirical networks were bimodal, while the incidence curves for the theoretical networks were unimodal. The incorporation of vaccination and isolation in the model caused a decrease in the cumulative incidence for each network, however, this effect was only seen at high levels of vaccination and isolation for the complete network. This study highlights the importance of using empirical networks to describe contact patterns within populations that are unlikely to exhibit random mixing such as equine populations.
Giant proximity effect in single-crystalline MgB2 bilayers
Authors: Jung Soon-Gil , Pham Duong , Park Tae-Ho , Choi Han-Yong , Seo Jin Won , Kang Won Nam , Park Tuson
Published: March 2019

Although giant proximity effect (GPE) can shed important information on understanding superconducting pairing mechanisms and superconducting electronics, reports on the GPE are few because the fabrication of the junctions with GPE is technologically difficult. Here, we report a GPE in the single-crystalline MgB2bilayers (S′/S), where theS′ is the damaged MgB2layer by cobalt (Co)-ion irradiation and theSis the undamaged MgB2layer. Superconducting properties of theS′ is remarkably degraded by the irradiation, whereas those of theSis uninfluenced by the irradiation. The degraded superconductivity in theS′ is fully recovered by increasing the thickness of undamaged MgB2layerSdespite almost ten times larger thickness ~ 95 nm ofS′ than the superconducting coherence lengthξab(0) ~ 8.5 nm of theS, indicating a presence of GPE in theS′/SMgB2bilayers. A diffusion of electrons in theS′ into theScan reduce a pair breaking scattering in theS′, and the similar electronic structures ofS′ andSlayers and a finite attractive electron-electron interaction in theS′ are thought to be origins of unpredicted GPE between the same superconducting materials. Both upper critical field (μ0Hc2) and in-field critical current density (Jc) ofS′/Sbilayers show a significant enhancement, representing a strong correlation betweenS′ andS. These discoveries provide the blue print to the design of the superconducting multilayers for fundamental researches on the mechanism of the GPE as well as their technological applications.
Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli
Authors: Oldenkott Bastian , Yang Yingying , Lesch Elena , Knoop Volker , Schallenberg-Rüdinger Mareike
Published: March 2019

RNA editing converting cytidines into uridines is a hallmark of gene expression in land plant chloroplasts and mitochondria. Pentatricopeptide repeat (PPR) proteins have a key role in target recognition, but the functional editosome in the plant organelles has remained elusive. Here we show that individual Physcomitrella patens DYW-type PPR proteins alone can perform efficient C-to-U editing in Escherichia coli reproducing the moss mitochondrial editing. Single amino acid exchanges in the DYW domain abolish RNA editing, confirming it as the functional cytidine deaminase. The modification of RNA targets and the identification of numerous off-targets in the E. coli transcriptome reveal nucleotide identities critical for RNA recognition and cytidine conversion. The straightforward amenability of the new E. coli setup will accelerate future studies on RNA target recognition through PPRs, on the C-to-U editing deamination machinery and towards future establishment of transcript editing in other genetic systems.
Murine osteoclasts secrete serine protease HtrA1 capable of degrading osteoprotegerin in the bone microenvironment
Authors: Ochiai Nagahiro , Nakachi Yutaka , Yokoo Tomotaka , Ichihara Takahiro , Eriksson Tore , Yonemoto Yuki , Kato Takehiko , Ogata Hitoshi , Fujimoto Natsuko , Kobayashi Yasuhiro , Udagawa Nobuyuki , Kaku Shinsuke , Ueki Tomokazu , Okazaki Yasushi , Takahashi Naoyuki , Suda Tatsuo
Published: March 2019

Osteoclasts are multinucleated cells responsible for bone resorption. The differentiation of osteoclasts from bone marrow macrophages (BMMs) is induced by receptor activator of NF-κB ligand (RANKL). Osteoprotegerin (OPG), a decoy receptor of RANKL, inhibits osteoclastogenesis by blocking RANKL signaling. Here we investigated the degradation of OPG in vitro. Osteoclasts, but not BMMs, secreted OPG-degrading enzymes. Using mass spectrometry and RNA-sequencing analysis, we identified high-temperature requirement A serine peptidase 1 (HtrA1) as an OPG-degrading enzyme. HtrA1 did not degrade OPG pre-reduced by dithiothreitol, suggesting that HtrA1 recognizes the three-dimensional structure of OPG. HtrA1 initially cleaved the amide bond between leucine 90 and glutamine 91 of OPG, then degraded OPG into small fragments. Inhibitory activity of OPG on RANKL-induced osteoclastogenesis was suppressed by adding HtrA1 in RAW 264.7 cell cultures. These results suggest that osteoclasts potentially prepare a microenvironment suitable for osteoclastogenesis. HtrA1 may be a novel drug target for osteoporosis.
Topological Larkin-Ovchinnikov phase and Majorana zero mode chain in bilayer superconducting topological insulator films
Authors: Hu Lun-Hui , Liu Chao-Xing , Zhang Fu-Chun
Published: March 2019

Topological superconductors possess a bulk superconducting gap and boundary gapless excitations, known as “Majorana fermion”. Search for new systems with topological superconductivity is of fundamental and application importance due to the potential application of Majorana fermions in topological quantum computation. Here we show that the Larkin-Ovchinnikov superconducting phase with a finite momentum pairing can emerge in a model of bilayer superconducting topological insulator films, in which superconductivity appears for both the top and bottom surface states, and can be topologically non-trivial. This “topological Larkin-Ovchinnikov phase” is induced by an in-plane magnetic field and possesses a Majorana mode chain along the edge perpendicular to the in-plane magnetic field direction due to its non-trivial $${\Bbb Z}_2$$

Z

2

topological nature. Our theoretical model can be naturally realized in superconductor/topological insulator sandwich structure or in Fe(Te, Se) film, a topological material with superconductivity, and thus provides a route to explore unconventional superconductivity in existing systems.
An integrated urea and halogen bond donor based receptor for superior and selective sensing of phosphates
Authors: Ghosh Tamal Kanti , Mondal Sahidul , Bej Somnath , Nandi Mandira , Ghosh Pradyut
Published: March 2019

An integrated urea and halogen bond donor based receptor is utilized for selective and superior sensing of phosphates.
Production of 5α-androstene-3,17-dione from phytosterols by co-expression of 5α-reductase and glucose-6-phosphate dehydrogenase in engineered Mycobacterium neoaurum
Authors: Zhao Yunqiu , Shen Yanbing , Ma Sai , Luo Jianmei , Ouyang Wei , Zhou Haijie , Tang Rui , Wang Min
Published: March 2019

5α-Androstene-3,17-dione (5α-AD), an important intermediate in the synthesis of steroid drugs, is mainly synthesized by chemical methods in industry.
Characterization and utilization of aqueous products from hydrothermal conversion of biomass for bio-oil and hydro-char production: a review
Authors: Usman Muhammad , Chen Huihui , Chen Kaifei , Ren Shuang , Clark James H. , Fan Jiajun , Luo Gang , Zhang Shicheng
Published: March 2019

Hydrothermal conversion (HTC), including hydrothermal liquefaction and hydrothermal carbonization, is a promising thermochemical technology for biomass utilization.
Detection of specific DNA sequences in Maize (Zea mays L.) based on phosphorescent quantum-dot exciton energy transfer
Authors: Lv Jinzhi , Miao Yanming , Yan Guiqin
Published: March 2019

The complementary sequence of genetically-modified marker sequence cauliflower mosaic virus 35S promoter (Ca MV 35S) DNA was trimmed and designed into sequences S1 and S2, which were separately modified onto the surfaces of room-temperature phosphorescent (RTP) quantum dots (QDs), forming QDs-S1 (P1) and QDs-S2 (P2), respectively.
Longitudinal eigenvibration of multilayer colloidal crystals and the effect of nanoscale contact bridges
Authors: Abi Ghanem Maroun , Khanolkar Amey , Wallen Samuel P. , Helwig Mary , Hiraiwa Morgan , Maznev Alexei A. , Vogel Nicolas , Boechler Nicholas
Published: March 2019

Longitudinal contact-based vibrations of colloidal crystals with a controlled layer thickness are studied.
Exciton–dipole coupling in two-dimensional rubrene assembly sensors
Authors: Guan Ying-Shi , Hu Feng , Li Changning , Ren Shenqiang
Published: March 2019

Here, we present exciton–dipole coupling in the two-dimensional (2D) assembly of molecular rubrene excitonic crystals to selectively detect molecules.
Novel defect-fluorite pyrochlore sodium niobate nanoparticles: solution-phase synthesis and radiation tolerance analysis
Authors: Ali Rana Faryad , Ovens Jeffrey S. , Starosta Krzysztof , Gates Byron D.
Published: March 2019

Nanoparticles of defect-fluorite pyrochlore of sodium niobate were synthesized and characterized for their thermal stability and tolerance to neutron irradiation.
Non-isothermal crystallization, yellowing resistance and mechanical properties of heat-resistant nylon 10T/66/titania dioxide/glass fibre composites
Authors: Liu Bingxiao , Hu Guosheng , Zhang Jingting , Yan Wen
Published: March 2019

Herein, we report novel heat-resistant nylon 10T/66/titania dioxide/glass fibre (nylon 10T/66/TiO2/GF) composites based on as-synthesised nylon 10T/66, which is a copolymer of poly(decamethylene terephthalamide) (nylon 10T).
Corrosion inhibition of carboxylate inhibitors with different alkylene chain lengths on carbon steel in an alkaline solution
Authors: Lin Bing , Zuo Yu
Published: March 2019

The inhibition effects of carboxylate compounds with different alkylene chain lengths on Q235 steel in simulated carbonation concrete pore solution were studied using quantum chemical calculations, electrochemical measurement and surface analysis.
Selection of cost-effective yet chemically diverse pathways from the networks of computer-generated retrosynthetic plans
Authors: Badowski Tomasz , Molga Karol , Grzybowski Bartosz A.
Published: March 2019

A family of network algorithms allows the Chematica retrosynthetic platform to plan both cost-effective and chemically diverse syntheses.
High-performance carbon molecular sieve membranes for hydrogen purification and pervaporation dehydration of organic solvents
Authors: Ngamou P. H. Tchoua , Ivanova M. E. , Guillon O. , Meulenberg W. A.
Published: March 2019

Successful synthesis of a ceramic-supported ultrathin carbon membrane with unprecedently high hydrogen permeance and outstanding H2/CO2, H2/N2 and H2/CH4 selectivities at elevated temperatures.
Interface engineering of solution-grown silver nanofiber networks designed as flexible transparent electrodes
Authors: Li Peng , Wang Xiao , Ma Jiangang , Wang Tingfeng , Zhang Wei , Xu Haiyang , Liu Yichun
Published: March 2019

Flexible transparent electrodes were fabricated by chemical plating of Ag on electrospun polymer nanofiber templates. Argon plasma treatment and Joule heat-assisted self-welding were exploited to improve the conductivity of the solution-grown Ag nanofibers network.
A NIR ratiometric fluorescent probe for the ‘naked-eye’ detection of endogenous hypochlorous acid in practical samples
Authors: Xiong Kangming , Huo Fangjun , Zhang Yongbin , Wen Ying , Yin Caixia
Published: March 2019

We designed a near-infrared ratiometric (2.1 to 15.3, I608/I735) fluorescent probe with a quick response (20 s) based on cyanine polyene derivatives. This probe can detect endogenous hypochlorous acid in HepG-2 cells and determine the hypochlorous acid content in 84 disinfectant and other actual samples.
DNA tetrahedron-based nanogels for siRNA delivery and gene silencing
Authors: Xue Han , Ding Fei , Zhang Jiao , Guo Yuanyuan , Gao Xihui , Feng Jing , Zhu Xinyuan , Zhang Chuan
Published: March 2019

DNA tetrahedra are employed as building blocks to construct a novel DNA-based nanogel for intracellular siRNA delivery.
Copper-catalyzed intermolecular oxidative trifluoromethyl-arylation of styrenes with NaSO2CF3 and indoles involving C–H functionalization
Authors: Min Man-Yi , Song Ren-Jie , Ouyang Xuan-Hui , Li Jin-Heng
Published: March 2019

A new copper-catalyzed three-component oxidative 1,2-trifluoromethylarylation of styrenes with NaSO2CF3 and indoles involving aryl C–H bond functionalization is described.
Three-electron reversible redox for a high-energy fluorophosphate cathode: Na3V2O2(PO4)2F
Authors: Peng Manhua , Zhang Dongtang , Wang Xiayan , Xia Dingguo , Sun Yugang , Guo Guangsheng
Published: March 2019

Na3V2O2(PO4)2F crystallising in space group I4/mmm shows three-electron reversible redox behavior.
Fluorine anion-enriched nickel hydroxyl oxide as an efficient oxygen evolution reaction electrocatalyst
Authors: Chen Liming , Chang Jiuli , Zhang Yi , Gao Zhiyong , Wu Dapeng , Xu Fang , Guo Yuming , Jiang Kai
Published: March 2019

F− anions-enriched Ni hydroxyl oxide (F-NHO) mesocrystalline microspheres were prepared by a facile hydrothermal hydrolysis of a Ni precursor mediated by NH4F.
Chiral induction in a pcu-derived network from achiral precursors
Authors: Xue Hui , Zhou Kang , Liu Luyao , Wu Dong , Hong Zixiao , Chen Qihui , Jiang Feilong , Yuan Daqiang , Zhang Jian , Hong Maochun
Published: March 2019

The first chiral network derived from a classic pcu net has been rationally prepared from achiral precursors.
Unusual temperature-promoted carbon dioxide capture in deep-eutectic solvents: the synergistic interactions
Authors: Shukla Shashi Kant , Mikkola Jyri-Pekka
Published: March 2019

Equivalent donor and acceptor tendencies in DESs bring strong synergistic interaction into play and result in high CO2 uptake by lowering the ΔH° and ΔS°.