bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of a molecular subtyping system associated with the prognosis of Asian hepatocellular carcinoma patients receiving liver resection
Authors: Ma Xiaohua , Gu Jingxian , Wang Kun , Zhang Xing , Bai Juan , Zhang Jingyao , Liu Chang , Qiu Qiang , Qu Kai
Published: May 2019

Hepatocellular carcinoma (HCC) remains a severe health issue worldwide, especially in Asia. To date, molecular classifications proposed for the overall survival (OS) or recurrence-free survival (RFS) prediction of Asian HCC patients after hepatectomy are quite few and limited in clinical practice. Here, we established a molecular subtyping system for Asian HCC to facilitate prognosis evaluation. Firstly, differentially expressed genes (DEGs) (FDR [false discovery rate] <0.05) between different types of liver cancer and non-tumor tissue were screened. Among the DEGs solely between HCC and non-tumor samples, 185 genes simultaneously significantly associated with the OS and RFS were identified as HCC-characteristic genes. The molecular subtypes were developed based on the expression profiles of the 185 genes in the training dataset (TCGA [The Cancer Genome Atlas] dataset) using non-negative matrix factorization (NMF) clustering method. Patients were then classified into Subtype1 and Subtype2 groups denoting unfavorable and favorable clinical outcome respectively. The robustness and effectiveness of the molecular subtype was confirmed in another independent dataset (GSE14520) by the same clustering approach and Kaplan-Meier analyses. Moreover, functional prediction analysis revealed that the identified molecular signature was involved in chemotaxis, apoptosis and cell development associated pathways. Besides, the molecular signature was closely related to the clinical characteristics including TNM stage, preoperative alpha-fetoprotein (AFP) level and TP53 mutation. Furthermore, integration of the molecular subtype and TNM stage was demonstrated to improve risk stratification. Taken together, our molecular subtyping system exhibited great utility and potential in prognosis prediction and therapeutic decision making of Asian HCC patients.
SLTChemDB: A database of chemical compounds present in Smokeless tobacco products
Authors: Kaur Jasmine , Sharma Arun , Kumar Amit , Bhartiya Deeksha , Sinha Dhirendra Narain , Kumari Suchitra , Gupta Ruchika , Mehrotra Ravi , Singh Harpreet
Published: May 2019

Smokeless tobacco (SLT), a cause of potentially preventable diseases, has a diverse chemical composition encompassing toxicants as well as potent carcinogens. Though the chemical profile of SLT products has been analyzed earlier, this information is not available in a comprehensive and easily accessible format. Hence, there is an imperative felt need to develop a one-stop information source providing inclusive information on SLT products. SLTChemDB is the first such database that makes available detailed information on various properties of chemical compounds identified across different brands of SLT products. The primary information for the database was extracted through extensive literature search, which was further curated from popular chemical web servers and databases. At present, SLTChemDB contains comprehensive information on 233 unique chemical compounds and 82 SLT products. The database has been made user-friendly with facility for systematic search and filters. SLTChemDB would provide the initial data on chemical compounds in SLT products to various tobacco testing laboratories. The database also highlights research gaps and thus, would be a guide for researchers interested in chemistry and toxicology of SLT products. With regular update of information in the database, it shall be a valuable evidence base for policymakers to formulate stringent policies for SLT control.
Protective effect of calcitriol on rhabdomyolysis-induced acute kidney injury in rats
Authors: Reis Natany Garcia , Francescato Heloísa Della Coletta , de Almeida Lucas Ferreira , Silva Cleonice Giovanini Alves da , Costa Roberto Silva , Coimbra Terezila Machado
Published: May 2019

Glycerol injection in rats can lead to rhabdomyolysis, with the release of the intracellular muscle content to the extracellular compartment and acute kidney injury (AKI). Oxidative stress and the inflammatory processes contribute to the disturbances in renal function and structure observed in this model. This study evaluated the effect of calcitriol administration in AKI induced by rhabdomyolysis and its relationship with oxidative damage and inflammatory process. Male Wistar Hannover rats were treated with calcitriol (6 ng/day) or vehicle (0.9% NaCl) for 7 days and were injected with 50% glycerol or saline 3 days after the beginning of calcitriol or saline administration. Four days after glycerol or saline injection, urine, plasma and renal tissue samples were collected for renal function and structural analysis. The oxidative stress and the inflammatory processes were also evaluated. Glycerol-injected rats presented increased sodium fractional excretion and decreased glomerular filtration rates. These alterations were associated with tubular injury in the renal cortex. These animals also presented increased oxidative damage, apoptosis, inflammation, higher urinary excretion of vitamin D-binding protein and decreased cubilin expression in renal tissue. All these alterations were less intense in calcitriol-treated animals. This effect was associated with decreases in oxidative damage and inflammation.
Endogenous APOBEC3B Overexpression Constitutively Generates DNA Substitutions and Deletions in Myeloma Cells
Authors: Yamazaki Hiroyuki , Shirakawa Kotaro , Matsumoto Tadahiko , Hirabayashi Shigeki , Murakawa Yasuhiro , Kobayashi Masayuki , Sarca Anamaria Daniela , Kazuma Yasuhiro , Matsui Hiroyuki , Maruyama Wataru , Fukuda Hirofumi , Shirakawa Ryutaro , Shindo Keisuke , Ri Masaki , Iida Shinsuke , Takaori-Kondo Akifumi
Published: May 2019

Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) DNA cytosine deaminases have emerged as potential genomic mutators in various cancers. Multiple myeloma accumulates APOBEC signature mutations as it progresses; however, the mechanisms underlying APOBEC signature acquisition and its consequences remain elusive. In this study, we examined the significance and clinical impact of APOBEC3B (A3B) activity in multiple myeloma. Among APOBECs, only highly expressed A3B was associated with poor prognosis in myeloma patients, independent of other known poor prognostic factors. Quantitative PCR revealed that CD138-positive primary myeloma cells and myeloma cell lines exhibited remarkably high A3B expression levels. Interestingly, lentiviral A3B knockdown prevented the generation of deletion and loss-of-function mutations in exogenous DNA, whereas in control cells, these mutations accumulated with time. A3B knockdown also decreased the basal levels of γ-H2AX foci, suggesting that A3B promotes constitutive DNA double-strand breaks in myeloma cells. Importantly, among control shRNA-transduced cells, we observed the generation of clones that harboured diverse mutations in exogenous genes and several endogenous genes frequently mutated in myeloma, including TP53. Taken together, the results suggest that A3B constitutively mutates the tumour genome beyond the protection of the DNA repair system, which may lead to clonal evolution and genomic instability in myeloma.
First observation of electronic trap levels in freestanding GaN crystals extracted from Si substrates by hydride vapour phase epitaxy
Authors: Lee Moonsang , Ahn Chang Wan , Vu Thi Kim Oanh , Lee Hyun Uk , Kim Eun Kyu , Park Sungsoo
Published: May 2019

The electronic deep level states of defects embedded in freestanding GaN crystals exfoliated from Si substrates by hydride vapour phase epitaxy (HVPE) is investigated for the first time, using deep level transient spectroscopy (DLTS). The electron traps are positioned 0.24 eV (E1) and 1.06 eV (E2) below the conduction band edge, respectively. The capture cross sections of E1 and E2 are evaluated to be 1.65 × 10−17 cm2 and 1.76 × 10−14 cm2 and the corresponding trap densities are 1.07 × 1014 cm−3 and 2.19 × 1015 cm−3, respectively. The DLTS signal and concentration of the electronic deep levels are independent of the filling pulse width, and the depth toward the bottom of the sample, evidenced by the fact that they are correlated to noninteracting point defects. Furthermore, Photoluminescence (PL) measurement shows green luminescence, suggesting that unidentified point defects or complex, which affect the optical characterisitics, exhibit. Despite the Si-based materials, the freestanding GaN exhibits deep level characteristics comparable to those of conventional freestanding GaN, suggesting that it is a desirable material for use in the next generation optoelectronic devices with the large-scalibilityand low production costs.
Association between Sleep Duration and Chronic Rhinosinusitis among the Korean General Adult Population: Korea National Health and Nutrition Examination Survey
Authors: Kim Jeong-Whun , Jung Hahn Jin , Choi Hyo Geun , Rhee Chae-Seo , Wee Jee Hye
Published: May 2019

An association between sleep duration and a wide spectrum of diseases has been reported, but little is known about its relationship with chronic rhinosinusitis (CRS). The present study aimed to investigate whether sleep duration was associated with CRS after adjusting for potential confounding factors in Korean adults. We analyzed data from the Korea National Health and Nutrition Examination Survey 2005–2009 and enrolled 24,658 participants aged ≥20 years. Data regarding sociodemographic characteristics, self-reported sleep duration, CRS, and other medical diseases were collected from questionnaires. Multiple logistic regression analyses were used to identify the relationship between sleep duration and CRS. The overall prevalence of CRS was 4.4%. Subjects with sleep duration ≤5 hours showed a highest prevalence for CRS (6.1%), compared to subjects with longer sleep duration (p = 0.02). After adjusting for covariates (age, sex, household income, residency, dwelling type, education, depression, alcohol, allergic rhinitis, chronic otitis media, angina or myocardial infarction, asthma, chronic obstructive pulmonary disease, bronchiectasis, and gastric ulcer), the sleep duration of ≤5 hours was significantly associated with CRS (OR = 1.502; 95% CI = 1.164–1.938). Only in older subgroup (≥50 years old), shorter sleep duration (≤5 hours) showed higher odds for CRS. These results suggested that sleep duration may be negatively associated with CRS in older Korean adults.
Thermal expansion behavior of thin films expanding freely on water surface
Authors: Kim Jae-Han , Jang Kyung-Lim , Ahn Kwangho , Yoon Taeshik , Lee Tae-Ik , Kim Taek-Soo
Published: May 2019

Coefficient of thermal expansion (CTE) for thin film has been measured only from change in thickness because thin film has to be constrained on a solid substrate. However, thin film CTE shows different values depending on the supporting solid substrate. Here, a novel measurement method is suggested to quantitatively measure the in-plane thermal expansion of thin films floating on a water surface. In-plane thermal expansion of thin films on water surface is achieved by heating the water. The CTE is measured through a digital image correlation (DIC) technique. The DIC tracks displacement marks deposited on the film surface, and the in-plane thermal strain is defined as the change in distance between the patterns. The method can be applied to measure the CTE of polymer, metal, and graphene with a thickness ranging from a micrometer to one-atom-thickness. The in-plane thermal expansion of the polystyrene (PS) thin film decreased as the film thickness decreased. The negative CTE of graphene is also successfully explored without any substrate effects or complicated calculations. The CTE measurement method can provide understanding of the intrinsic thermal expansion behavior of thin films including emerging two-dimensional materials.
Attempted Arm and Hand Movements can be Decoded from Low-Frequency EEG from Persons with Spinal Cord Injury
Authors: Ofner Patrick , Schwarz Andreas , Pereira Joana , Wyss Daniela , Wildburger Renate , Müller-Putz Gernot R.
Published: May 2019

We show that persons with spinal cord injury (SCI) retain decodable neural correlates of attempted arm and hand movements. We investigated hand open, palmar grasp, lateral grasp, pronation, and supination in 10 persons with cervical SCI. Discriminative movement information was provided by the time-domain of low-frequency electroencephalography (EEG) signals. Based on these signals, we obtained a maximum average classification accuracy of 45% (chance level was 20%) with respect to the five investigated classes. Pattern analysis indicates central motor areas as the origin of the discriminative signals. Furthermore, we introduce a proof-of-concept to classify movement attempts online in a closed loop, and tested it on a person with cervical SCI. We achieved here a modest classification performance of 68.4% with respect to palmar grasp vs hand open (chance level 50%).
Bowel preparation for colonoscopy may decrease the levels of testosterone in Korean men
Authors: Lee Soo-Hyun , Park Seung Geon , Kim Moon-Jong , Chun Hyejin , Cho Doo-Yeoun , Hong Doohee , Kim Young-Sang
Published: May 2019

Although colonoscopy is commonly conducted for medical check-ups in Korea, investigations for the influence of bowel preparation on various health conditions are insufficient. This cross-sectional study investigated whether bowel preparation has an influence on serum levels of testosterone. A total of 1114 men were divided into the bowel preparation group and control groups. The median total and free testosterone levels were significantly lower in the bowel preparation group (14.89 and 0.26 nmol/L, respectively) than in the control groups (15.72 and 0.28 nmol/L, respectively). The level of total testosterone significantly increased with age in the bowel preparation group (r = 0.103). The differences in the levels of total and free testosterone between the 2 groups were more prominent in younger men than in older men. In multivariate regression models, bowel preparation was independently associated with the levels of total and free testosterone. In these models, the interaction between age and bowel preparation was significant for the levels of total and free testosterone. In conclusion, bowel preparation may independently decrease the serum levels of total and free testosterone. The decline in testosterone was more evident in younger men than in older men.
Optofluidic variable optical path modulator
Authors: Wang Qiong-Hua , Xiao Liang , Liu Chao , Li Lei
Published: May 2019

The optofluidic devices including optofluidic lens, optical switch and liquid prism have found widespread applications in imaging, optical communication and lighting. Here, we report a novel optofluidic device called optofluidic variable optical path modulator. Our proposed modulator consists of two main chambers. The two chambers are connected by two tubes to form a closed-loop fluidic system. Two immiscible liquids are filled into the two chambers and form two L-L interfaces. A transparent sheet is placed between one L-L interface to get flat interface. When a voltage is applied on the device, the flat interface can move up and down. Thus, variable optical path can be obtained by applying a voltage. To prove the concept, we fabricate an optofluidic device whose largest movable distance of L-L interface is ~7.5 mm and the optical path length change is ~1.15 mm. The proposed optofluidic device has potential applications in imaging, adaptive optics, optical detection and so on.
Lasy-Seq: a high-throughput library preparation method for RNA-Seq and its application in the analysis of plant responses to fluctuating temperatures
Authors: Kamitani Mari , Kashima Makoto , Tezuka Ayumi , Nagano Atsushi J.
Published: May 2019

RNA-Seq is a whole-transcriptome analysis method used to research biological mechanisms and functions but its use in large-scale experiments is limited by its high cost and labour requirements. In this study, we have established a high-throughput and cost-effective RNA-Seq library preparation method that does not require mRNA enrichment. The method adds unique index sequences to samples during reverse transcription (RT) that is conducted at a higher temperature (≥62 °C) to suppress RT of A-rich sequences in rRNA, and then pools all samples into a single tube. Both single-read and paired-end sequencing of libraries is enabled. We found that the pooled RT products contained large amounts of RNA, mainly rRNA, causing over-estimations of the quantity of DNA and unstable tagmentation results. Degradation of RNA before tagmentation was found to be necessary for the stable preparation of libraries. We named this protocol low-cost and easy RNA-Seq (Lasy-Seq) and used it to investigate temperature responses in Arabidopsis thaliana. We analysed how sub-ambient temperatures (10–30 °C) affected the plant transcriptomes using time-courses of RNA-Seq from plants grown in randomly fluctuating temperature conditions. Our results suggest that there are diverse mechanisms behind plant temperature responses at different time scales.
Origin of arc magmatic signature: A temperature-dependent process for trace element (re)-mobilization in subduction zones
Authors: Gamal El Dien Hamed , Li Zheng-Xiang , Kil Youngwoo , Abu-Alam Tamer
Published: May 2019

Serpentinite is a major carrier of fluid-mobile elements in subduction zones, which influences the geochemical signature of arc magmatism (e.g. high abundances of Li, Ba, Sr, B, As, Mo and Pb). Based on results from Neoproterozoic serpentinites in the Arabian-Nubian Shield, we herein report the role of antigorite in the transportation of fluid-mobile elements (FME) and light rare earth elements (LREE) from the subducted slab to arc-related magma during subduction. The serpentinites contain two generations of antigorites: the older generation is coarse-grained, formed at a temperature range of 165–250 °C and is enriched in Li, Rb, Ba and Cs, whereas the younger generation is finer-grained, formed at higher temperature conditions (425–475 °C) and has high concentrations of B, As, Sb, Mo, Pb, Sr and LREE. Magnesite, on the other hand, remains stable at sub-arc depths beyond the stability field of both antigorites, and represents a potential reservoir of FME and LREE for deeper mantle melts. Magnesite has high FME and LREE absorbing capacity (over 50–60%) higher than serpentine phases. Temperature is the main controlling factor for stability of these minerals and therefore the release of these elements from subducted slabs into arc magmatism. As the liberation of these elements varies along the length of the slab, the resulting cross-arc geochemical variation trend can help to determine the subduction polarity of ancient arcs.
Ultra-processed food consumption by Brazilian adolescents in cafeterias and school meals
Authors: Noll Priscilla Rayanne e Silva , Noll Matias , de Abreu Luiz Carlos , Baracat Edmund Chada , Silveira Erika Aparecida , Sorpreso Isabel Cristina Esposito
Published: May 2019

This cross-sectional study utilized the National School Health Survey 2015 database to assess the association between school cafeterias; the meals offered by the Brazilian School Food Program (PNAE); and the consumption of industrialized/ultra-processed salty foods, sweets, and soft drinks among Brazilian adolescents. A sample of 102,072 adolescents, aged 11–19 years, who were enrolled in the 9th grade completed the survey. The evaluated outcome was the consumption of industrialized/ultra-processed salty foods, sweets, and soft drinks. A Poisson regression model-based multivariate analysis was performed. The effect measure was the prevalence ratio (PR) with its respective 95% confidence intervals (CIs). The results indicated that Brazilian adolescents who attended schools without meals offered through the PNAE had a higher probability of regularly (≥5 times/week) consuming ultra-processed salty foods [PR = 1.06, CI = 1.01–1.11] and soft drinks [PR = 1.08, CI = 1.03–1.14] compared to those who attended schools that offered PNAE meals. Moreover, the presence of a school cafeteria was associated with a higher probability to consume industrialized/ultra-processed salty foods [PR = 1.05, CI = 1.02–1.08], sweets [PR = 1.09, CI = 1.07–1.11], and soft drinks [PR = 1.10, CI = 1.07–1.13]. School meals appear to be associated with the consumption of ultra-processed foods by Brazilian adolescents, indicating areas for health promotion programs.
Improvement in creativity after transcranial random noise stimulation (tRNS) over the left dorsolateral prefrontal cortex
Authors: Peña Javier , Sampedro Agurne , Ibarretxe-Bilbao Naroa , Zubiaurre-Elorza Leire , Ojeda Natalia
Published: May 2019

Creativity has previously been shown to improve after the application of direct and alternating current transcranial stimulation over the dorsolateral prefrontal cortex (DLPFC). However, previous studies have not tested whether transcranial random noise stimulation (tRNS) was efficient for this purpose. The aim of this randomized, double-blind, placebo-controlled study was to investigate the effect of tRNS on both verbal convergent and (verbal and visual) divergent thinking during left DLPFC tRNS stimulation. Thirty healthy participants were randomly allocated to either a tRNS active group or a sham group. Each session lasted 20 min and the current was set to 1.5 mA (100–500 Hz). Participants’ verbal convergent thinking was assessed with the Remote Associates Test (RAT). Verbal and visual divergent thinking were respectively measured by using the Unusual Uses and Picture Completion subtests from the Torrance Tests of Creative Thinking. Bootstrapped analysis of variance showed significant differences in the mean change scores between the active tRNS group and the sham group in RAT scores (d = 1.68); unusual uses: fluency (d = 2.29) and originality (d = 1.43); and general creativity (d = 1.45). Visual divergent thinking, in contrast, did not show any significant improvement. Our results suggested that tRNS over the left DLPFC is effective for increasing verbal divergent and convergent thinking.
Gait training using a robotic hip exoskeleton improves metabolic gait efficiency in the elderly
Authors: Martini Elena , Crea Simona , Parri Andrea , Bastiani Luca , Faraguna Ugo , McKinney Zach , Molino-Lova Raffaello , Pratali Lorenza , Vitiello Nicola
Published: May 2019

Robotic exoskeletons are regarded as promising technologies for neurological gait rehabilitation but have been investigated comparatively little as training aides to facilitate active aging in the elderly. This study investigated the feasibility of an exoskeletal Active Pelvis Orthosis (APO) for cardiopulmonary gait training in the elderly. Ten healthy elderly volunteers exhibited a decreased (−26.6 ± 16.1%) Metabolic Cost of Transport (MCoT) during treadmill walking following a 4-week APO-assisted training program, while no significant changes were observed for a randomly assigned control group (n = 10) performing traditional self-paced overground walking. Moreover, robot-assisted locomotion was found to require 4.24 ± 2.57% less oxygen consumption than free treadmill walking at the same speed. These findings support the adoption of exoskeletal devices for the training of frail individuals, thus opening new possibilities for sustainable strategies for healthy aging.
Histone H2A insufficiency causes chromosomal segregation defects due to anaphase chromosome bridge formation at rDNA repeats in fission yeast
Authors: Yamamoto Takaharu G. , Ding Da-Qiao , Nagahama Yuki , Chikashige Yuji , Haraguchi Tokuko , Hiraoka Yasushi
Published: May 2019

The nucleosome, composed of DNA and a histone core, is the basic structural unit of chromatin. The fission yeast Schizosaccharomyces pombe has two genes of histone H2A, hta1+ and hta2+; these genes encode two protein species of histone H2A (H2Aα and H2Aβ, respectively), which differ in three amino acid residues, and only hta2+ is upregulated during meiosis. However, it is unknown whether S. pombe H2Aα and H2Aβ have functional differences. Therefore, in this study, we examined the possible functional differences between H2Aα and H2Aβ during meiosis in S. pombe. We found that deletion of hta2+, but not hta1+, causes defects in chromosome segregation and spore formation during meiosis. Meiotic defects in hta2+ deletion cells were rescued by expressing additional copies of hta1+ or by expressing hta1+ from the hta2 promoter. This indicated that the defects were caused by insufficient amounts of histone H2A, and not by the amino acid residue differences between H2Aα and H2Aβ. Microscopic observation attributed the chromosome segregation defects to anaphase bridge formation in a chromosomal region at the repeats of ribosomal RNA genes (rDNA repeats). These results suggest that histone H2A insufficiency affects the chromatin structures of rDNA repeats, leading to chromosome missegregation in S. pombe.
Non-invasive obstetric anal sphincter injury diagnostics using impedance spectroscopy
Authors: Borycka-Kiciak Katarzyna , Młyńczak Marcel , Kiciak Adam , Pietrzak Piotr , Dziki Adam
Published: May 2019

Obstetric anal sphincter injuries are the most common cause of fecal incontinence in women yet remain under-diagnosed. The aim of this study was to assess the suitability of impedance spectroscopy for diagnosing sphincter injuries arising during delivery. This was a prospective single-center study. 22 female patients were included: 10 with symptoms of sphincter dysfunction, in the early postpartum period, and 12 unaffected, in the distant period of more than 2 years after natural delivery. The presence, extent and severity of anal sphincters injury was assessed by measuring the sphincter parameters in physical examination, the degree of sphincter damage in endoanal ultrasound imaging and the sphincters function parameters in anorectal manometry. All measurements were used as references and compared with the outcomes from the impedance spectroscopy models. Impedance spectroscopy showed the highest precision (with mean accuracy of 83.9%) in relation to transanal ultrasonography. 74.1% of its results corresponded to the results of rectal physical examination and 76.7% - to those of anorectal manometry. The method showed the highest accuracy in the assessment of the sphincter’s parameters, both anatomically and functionally. New impedance spectroscopy techniques hold promise for detecting obstetric anal sphincter injuries.
Spectral dependence of THz emission from InN and InGaN layers
Authors: Norkus Ričardas , Aleksiejūnas Ramūnas , Kadys Arūnas , Kolenda Marek , Tamulaitis Gintautas , Krotkus Arūnas
Published: May 2019

Spectral dependence of terahertz emission is a sensitive tool to analyze the structure of conduction band of semiconductors. In this work, we investigate the excitation spectra of THz pulses emitted from MOCVD-grown InN and InGaN epitaxial layers with indium content of 16%, 68%, and 80%. In InN and indium-rich InGaN layers we observe a gradual saturation of THz emission efficiency with increasing photon energy. This is in stark contrast to other III-V semiconductors where an abrupt drop of THz efficiency occurs at certain photon energy due to inter-valley electron scattering. From these results, we set a lower limit of the intervalley energy separation in the conduction band of InN as 2.4 eV. In terms of THz emission efficiency, the largest optical-to-THz energy conversion rate was obtained in 75 nm thick In0.16Ga0.84N layer, while lower THz emission efficiency was observed from InN and indium-rich InGaN layers due to the screening of built-in field by a high-density electron gas in these materials.
Uncommon mutational profiles of metastatic colorectal cancer detected during routine genotyping using next generation sequencing
Authors: Franczak Claire , Kandathil Shaun M. , Gilson Pauline , Husson Marie , Rouyer Marie , Demange Jessica , Leroux Agnès , Merlin Jean-Louis , Harlé Alexandre
Published: May 2019

RAS genotyping is mandatory to predict anti-EGFR monoclonal antibodies (mAbs) therapy resistance and BRAF genotyping is a relevant prognosis marker in patients with metastatic colorectal cancer. Although the role of hotspot mutations is well defined, the impact of uncommon mutations is still unknown. In this study, we aimed to discuss the potential utility of detecting uncommon RAS and BRAF mutation profiles with next-generation sequencing. A total of 779 FFPE samples from patients with metastatic colorectal cancer with valid NGS results were screened and 22 uncommon mutational profiles of KRAS, NRAS and BRAF genes were selected. In silico prediction of mutation impact was then assessed by 2 predictive scores and a structural protein modelling. Three samples carry a single KRAS non-hotspot mutation, one a single NRAS non-hotspot mutation, four a single BRAF non-hotspot mutation and fourteen carry several mutations. This in silico study shows that some non-hotspot RAS mutations seem to behave like hotspot mutations and warrant further examination to assess whether they should confer a resistance to anti-EGFR mAbs therapy for patients bearing these non-hotspot RAS mutations. For BRAF gene, non-V600E mutations may characterise a novel subtype of mCRC with better prognosis, potentially implying a modification of therapeutic strategy.
Further characterization of the zebrafish model of acrylamide acute neurotoxicity: gait abnormalities and oxidative stress
Authors: Faria Melissa , Valls Arnau , Prats Eva , Bedrossiantz Juliette , Orozco Manuel , Porta Josep M. , Gómez-Oliván Leobardo Manuel , Raldúa Demetrio
Published: May 2019

Occupational, accidental, or suicidal exposure to acrylamide (ACR) may result in a neurotoxic syndrome. Development of animal models of acrylamide neurotoxicity is necessary for increasing our mechanistic understanding of this syndrome and developing more effective therapies. A new model for acute ACR neurotoxicity has been recently developed in adult zebrafish. Whereas the results of the initial characterization were really promising, a further characterization is needed for testing the construct validity of the model. In this study, the presence of gait abnormalities has been investigated by usingZebraGait, software specifically designed to analyze the kinematics of fish swimming in a water tunnel. The results of the kinematic analyses demonstrated that the model exhibits mild-to-moderate gait abnormalities. Moreover, the model exhibited negative scototaxis, a result confirming a phenotype of anxiety comorbid with depression phenotype. Interestingly, depletion of the reduced glutathione levels was found in the brain without a concomitant increase in oxidative stress. Finally, hypolocomotion and positive geotaxis exhibited by this model were fully recovered 5 days after transferring the fish to clean fish-water. All this data support the validity of the ACR acute neurotoxicity model developed in adult zebrafish.
New Insight about Biocompatibility and Biodegradability of Iron Oxide Magnetic Nanoparticles: Stereological and In Vivo MRI Monitor
Authors: Nosrati Hamed , Salehiabar Marziyeh , Fridoni Mohammadjavad , Abdollahifar Mohammad-Amin , Kheiri Manjili Hamidreza , Davaran Soodabeh , Danafar Hossein
Published: May 2019

Iron oxide magnetic nanoparticles (IONPs) have attracted enormous attention because of their extensive medicinal and industrial applicability. PEGylated L-arginine modified iron oxide magnetic nanoparticles (PEG-Arg@IONPs) were synthesized and functioned in the present research as MRI contrast agents considered in vivo BALB/c model. The Synthesized PEG-Arg@IONPs were tracked in certain time intervals by MRI. The intensity of MR imaging of kidneys increased after administration of PEG-Arg@IONPs, which could confirm the emission of these nanoparticles by kidneys shortly after administration. Although PEG-Arg@IONPs were uptake by liver within 2 hours after injection, whereas, the signal change intensity of spleen, heart and kidneys confirmed that PEG-Arg@IONPs existed in other organs. The results illustrated that IONPs coated with PEGylated natural amino acid thin layers had a long circulation time and could be served as T2 contrast agents for diagnosis purpose. Notably, to the best of our knowledge, it was the first time the biocompatibility and biodegradability of IONPs was studied and evaluated by stereological and MRI technique.
Evaluating maize and soybean grain dry-down in the field with predictive algorithms and genotype-by-environment analysis
Authors: Martinez-Feria Rafael A. , Licht Mark A. , Ordóñez Raziel A. , Hatfield Jerry L. , Coulter Jeffrey A. , Archontoulis Sotirios V.
Published: May 2019

A delayed harvest of maize and soybean crops is associated with yield or revenue losses, whereas a premature harvest requires additional costs for artificial grain drying. Accurately predicting the ideal harvest date can increase profitability of US Midwest farms, but today’s predictive capacity is low. To fill this gap, we collected and analyzed time-series grain moisture datasets from field experiments in Iowa, Minnesota and North Dakota, US with various maize (n = 102) and soybean (n = 36) genotype-by-environment treatments. Our goal was to examine factors driving the post-maturity grain drying process, and develop scalable algorithms for decision-making. The algorithms evaluated are driven by changes in the grain equilibrium moisture content (function of air relative humidity and temperature) and require three input parameters: moisture content at physiological maturity, a drying coefficient and a power constant. Across independent genotypes and environments, the calibrated algorithms accurately predicted grain dry-down of maize (r2 = 0.79; root mean square error, RMSE = 1.8% grain moisture) and soybean field crops (r2 = 0.72; RMSE = 6.7% grain moisture). Evaluation of variance components and treatment effects revealed that genotypes, weather-years, and planting dates had little influence on the post-maturity drying coefficient, but significantly influenced grain moisture content at physiological maturity. Therefore, accurate implementation of the algorithms across environments would require estimating the initial grain moisture content, via modeling approaches or in-field measurements. Our work contributes new insights to understand the post-maturity grain dry-down and provides a robust and scalable predictive algorithm to forecast grain dry-down and ideal harvest dates across environments in the US Corn Belt.
Sampling Techniques on Collecting Fine Carbon Nanotube Fibers for Exposure Assessment
Authors: Khattak Jared , Theisen Daniel , Tsai Candace S. J.
Published: May 2019

Carbon nanotube (CNT) sampling using an open-faced 25 mm cassette fiber sampling method and a newly developed direct sampling device was evaluated for the size fractioned analysis of collected airborne CNT fibers to improve the sampling and analytical methods. The open-faced 25 mm cassette fiber sampling method primarily collected large agglomerates, with the majority of collected particles being larger than two micrometer in size. Most of CNT structures collected by the new direct sampling device were individual fibers and clusters smaller than one micrometer with a high particle number concentration discrepancy compared to the open-faced 25 mm cassette method raising the concern of this sampling method to representatively characterize the respirable size fraction of CNT aerosols. This work demonstrates that a specialized technique is needed for collecting small fibers to provide a more representative estimate of exposure. It is recommended that an additional sampler be used to directly collect and analyze small fibers in addition to the widely accepted sampling method which utilizes an open-faced 25 mm cassette.
Detection of smoking status from retinal images; a Convolutional Neural Network study
Authors: Vaghefi Ehsan , Yang Song , Hill Sophie , Humphrey Gayl , Walker Natalie , Squirrell David
Published: May 2019

Cardiovascular diseases are directly linked to smoking habits, which has both physiological and anatomical effects on the systemic and retinal circulations, and these changes can be detected with fundus photographs. Here, we aimed to 1- design a Convolutional Neural Network (CNN), using retinal photographs, to differentiate between smokers and non-smokers; and 2- use the attention maps to better understand the physiological changes that occur in the retina in smokers. 165,104 retinal images were obtained from a diabetes screening programme, labelled with self-reported “smoking” or “non-smoking” status. The images were pre-processed in one of two ways, either “contrast-enhanced” or “skeletonized”. Experiments were run on an Intel Xeon Gold 6128 CPU @ 3.40 GHz with 16 GB of RAM memory and a NVIDIA GeForce TiTan V VOLTA 12 GB, for 20 epochs. The dataset was split 80/20 for training and testing sets, respectively. The overall validation outcomes for the contrast-enhanced model were accuracy 88.88%, specificity 93.87%. In contrast, the outcomes of the skeletonized model were accuracy 63.63%, specificity 65.60%. The “attention maps” that were generated of the contrast-enhanced model highlighted the retinal vasculature, perivascular region and the fovea most prominently. We trained a customized CNN to accurately determine smoking status. The retinal vasculature, the perivascular region and the fovea appear to be important predictive features in the determination of smoking status. Despite a high degree of accuracy, the sensitivity of our CNN was low. Further research is required to establish whether the frequency, duration, and dosage (quantity) of smoking would improve the sensitivity of the CNN.
Towards minimally-invasive, quantitative assessment of chronic kidney disease using optical spectroscopy
Authors: Belghasem Mostafa E. , A’amar Ousama , Roth Daniel , Walker Joshua , Arinze Nkiruka , Richards Sean M. , Francis Jean M. , Salant David J. , Chitalia Vipul C. , Bigio Irving J.
Published: May 2019

The universal pathologic features implicated in the progression of chronic kidney disease (CKD) are interstitial fibrosis and tubular atrophy (IFTA). Current methods of estimating IFTA are slow, labor-intensive and fraught with variability and sampling error, and are not quantitative. As such, there is pressing clinical need for a less-invasive and faster method that can quantitatively assess the degree of IFTA. We propose a minimally-invasive optical method to assess the macro-architecture of kidney tissue, as an objective, quantitative assessment of IFTA, as an indicator of the degree of kidney disease. The method of elastic-scattering spectroscopy (ESS) measures backscattered light over the spectral range 320–900 nm and is highly sensitive to micromorphological changes in tissues. Using two discrete mouse models of CKD, we observed spectral trends of increased scattering intensity in the near-UV to short-visible region (350–450 nm), relative to longer wavelengths, for fibrotic kidneys compared to normal kidney, with a quasi-linear correlation between the ESS changes and the histopathology-determined degree of IFTA. These results suggest the potential of ESS as an objective, quantitative and faster assessment of IFTA for the management of CKD patients and in the allocation of organs for kidney transplantation.
De novo aggregation of Alzheimer’s Aβ25-35 peptides in a lipid bilayer
Authors: Smith Amy K. , Klimov Dmitri K.
Published: May 2019

A potential mechanism of cytotoxicity attributed to Alzheimer’s Aβ peptides postulates that their aggregation disrupts membrane structure causing uncontrollable permeation of Ca2+ ions. To gain molecular insights into these processes, we have performed all-atom explicit solvent replica exchange with solute tempering molecular dynamics simulations probing aggregation of the naturally occurring Aβ fragment Aβ25-35 within the DMPC lipid bilayer. To compare the impact produced on the bilayer by Aβ25-35 oligomers and monomers, we used as a control our previous simulations, which explored binding of Aβ25-35 monomers to the same bilayer. We found that compared to monomeric species aggregation results in much deeper insertion of Aβ25-35 peptides into the bilayer hydrophobic core causing more pronounced disruption in its structure. Aβ25-35 peptides aggregate by incorporating monomer-like structures with stable C-terminal helix. As a result the Aβ25-35 dimer features unusual helix head-to-tail topology supported by a parallel off-registry interface. Such topology affords further growth of an aggregate by recruiting additional peptides. Free energy landscape reveals that inserted dimers represent the dominant equilibrium state augmented by two metastable states associated with surface bound dimers and inserted monomers. Using the free energy landscape we propose the pathway of Aβ25-35 binding, aggregation, and insertion into the lipid bilayer.
Giant beaver palaeoecology inferred from stable isotopes
Authors: Plint Tessa , Longstaffe Fred J. , Zazula Grant
Published: May 2019

This is a multi-individual (n = 11), stable carbon and nitrogen isotope study of bone collagen (δ13Ccolandδ15Ncol) from the giant beaver (genusCastoroides). The now-extinct giant beaver was once one of the most widespread Pleistocene megafauna in North America. We confirm thatCastoroidesconsumed a diet of predominantly submerged aquatic macrophytes. These dietary preferences rendered the giant beaver highly dependent on wetland habitat for survival.Castoroides’δ13Ccolandδ15Ncoldo not support the hypothesis that the giant beaver consumed trees or woody plants, which suggests that it did not share the same behaviours asCastor(i.e., tree-cutting and harvesting). The onset of warmer, more arid conditions likely contributed to the extinction ofCastoroides. Six new radiocarbon dates help establish the chronology of the northward dispersal of the giant beaver in Beringia, indicating a correlation with ice sheet retreat.
Author Correction: Long non-coding RNA expression patterns in lung tissues of chronic cigarette smoke induced COPD mouse model
Authors: Zhang Haiyun , Sun Dejun , Li Defu , Zheng Zeguang , Xu Jingyi , Liang Xue , Zhang Chenting , Wang Sheng , Wang Jian , Lu Wenju
Published: May 2019

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Author Correction: 3D Muography for the Search of Hidden Cavities
Authors: Cimmino Luigi , Baccani Guglielmo , Noli Pasquale , Amato Lucio , Ambrosino Fabio , Bonechi Lorenzo , Bongi Massimo , Ciulli Vitaliano , D’Alessandro Raffaello , D’Errico Mariaelena , Gonzi Sandro , Melon Barbara , Minin Gianluca , Saracino Giulio , Scognamiglio Luca , Strolin Paolo , Viliani Lorenzo
Published: May 2019

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Pressure dependence of direct optical transitions in ReS2 and ReSe2
Authors: Oliva Robert , Laurien Magdalena , Dybala Filip , Kopaczek Jan , Qin Ying , Tongay Sefaattin , Rubel Oleg , Kudrawiec Robert
Published: May 2019

The ReX2 system (X = S, Se) exhibits unique properties that differ from other transition metal dichalcogenides. Remarkably, its reduced crystal symmetry results in a complex electronic band structure that confers this material in-plane anisotropic properties. In addition, multilayered ReX2 presents a strong 2D character even in its bulk form. To fully understand the interlayer interaction in this system, it is necessary to obtain an accurate picture of the electronic band structure. Here, we present an experimental and theoretical study of the electronic band structure of ReS2 and ReSe2 at high-hydrostatic pressures. The experiments are performed by photoreflectance spectroscopy and are analyzed in terms of ab initio calculations within the density functional theory. Experimental pressure coefficients for the two most dominant excitonic transitions are obtained and compared with those predicted by the calculations. We assign the transitions to the Z k-point of the Brillouin zone and other k-points located away from high-symmetry points. The origin of the pressure coefficients of the measured direct transitions is discussed in terms of orbital analysis of the electronic structure and van der Waals interlayer interaction. The anisotropic optical properties are studied at high pressure by means of polarization-resolved photoreflectance measurements.
Publisher Correction: A c-di-AMP riboswitch controlling kdpFABC operon transcription regulates the potassium transporter system in Bacillus thuringiensis
Authors: Wang Xun , Cai Xia , Ma Hongdan , Yin Wen , Zhu Li , Li Xinfeng , Lim Heon M. , Chou Shan-Ho , He Jin
Published: May 2019

In the original published version of the article, the country names for affiliations 1 and 3 were incorrect. The error has been corrected in the HTML and PDF versions of the article.
Oxidation behavior of the TiAlN hard coating in the process of recycling coated hardmetal scrap
Authors: Kuang Hai , Tan Dunqiang , He Wen , Yi Zhiqiang , Yuan Fan , Xu Yukun
Published: May 2019

The final oxide scale was triple-layered, consisting of a WO3-rich outmost layer, Al2O3-concentrated middle layer and TiO2-concentrated inner layer.
Impact of tunable 2-(1H-indol-3-yl)acetonitrile based fluorophores towards optical, thermal and electroluminescence properties
Authors: Muruganantham Subramanian , Velmurugan Gunasekaran , Jesuraj Justin , Hafeez Hassan , Ryu Seung Yoon , Venuvanalingam Ponnambalam , Renganathan Rajalingam
Published: May 2019

Herein, we have synthesized 4,5-diphenyl-1H-imidazole and 2-(1H-indol-3-yl)acetonitrile based donor–π–acceptor fluorophores and studied their optical, thermal, electroluminescence properties.
Antioxidant properties of ALD grown nanoceria films with tunable valency
Authors: Gupta Ankur , Sakthivel Tamil S. , Neal Craig J. , Koul Supriya , Singh Sushant , Kushima Akihiro , Seal Sudipta
Published: May 2019

Precise control of ceria surface chemistry in ALD-grown thin films as a platform for biocompatible coating.
Electrodeposition of pure phase SnSb exhibiting high stability as a sodium-ion battery anode
Authors: Ma Jeffrey , Prieto Amy L.
Published: May 2019

Electrodeposition of pure phase SnSb is reported for the first time.
Fluorinated porous molecular crystals: vapor-triggered on–off switching of luminescence and porosity
Authors: Sasaki Hiroshi , Imoto Hiroaki , Kitao Takashi , Uemura Takashi , Yumura Takashi , Naka Kensuke
Published: May 2019

Fluorinated porous molecular crystals (PMCs) were fabricated from platinum(ii) dihalide complexes with 9-pentafluorophenyl-9-arsafluorene. The diiodide complex formed a PMC exhibiting open–close switching of porosity as well as on–off switching of luminescence.
A painted layer for high-rate and high-capacity solid-state lithium–metal batteries
Authors: Sun Bin , Jin Yang , Lang Jialiang , Liu Kai , Fang Minghao , Wu Hui
Published: May 2019

Based on a garnet solid electrolyte, an electron/ion dual-conductive framework established by a spraying method enabled an alloy anode that realized a high-rate operation.
A DNAzyme-powered cross-catalytic circuit for amplified intracellular imaging
Authors: Zou Lana , Wu Qiong , Zhou Yangjie , Gong Xue , Liu Xiaoqing , Wang Fuan
Published: May 2019

A heterogeneously cross-catalytic CHA–DNAzyme circuit that integrates built-in molecule-recognition and signal-amplification is assembled through a feedback loop.
Structural origins, tunable photoluminescence governed by impurities and white-light irradiation in transparent Pr3+:BaTiO3glass-ceramics
Authors: Xie Wenqing , Li Panpan , Zhu Qijing , Wang Yun , Zhang Yunjie , Cai Yangjian , Xu Shiqing , Zhang Junjie
Published: May 2019

Study for impurity- and irradiation-induced structure evolution in mono Pr3+:BaTiO3glass ceramics notably promotes the active control of fluorescence emission.