bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-harmonic generation in amorphous solids
Authors: You Yong Sing , Yin Yanchun , Wu Yi , Chew Andrew , Ren Xiaoming , Zhuang Fengjiang , Gholam-Mirzaei Shima , Chini Michael , Chang Zenghu , Ghimire Shambhu 
Published: September 2017

AbstractHigh-harmonic generation in isolated atoms and molecules has been widely utilized in extreme ultraviolet photonics and attosecond pulse metrology. Recently, high-harmonic generation has been observed in solids, which could lead to important applications such as all-optical methods to image valance charge density and reconstruct electronic band structures, as well as compact extreme ultraviolet light sources. So far these studies are confined to crystalline solids; therefore, decoupling the respective roles of long-range periodicity and high density has been challenging. Here we report the observation of high-harmonic generation from amorphous fused silica. We decouple the role of long-range periodicity by comparing harmonics generated from fused silica and crystalline quartz, which contain the same atomic constituents but differ in long-range periodicity. Our results advance current understanding of the strong-field processes leading to high-harmonic generation in solids with implications for the development of robust and compact extreme ultraviolet light sources.
Chemically intuited, large-scale screening of MOFs by machine learning techniques
Authors: Borboudakis Giorgos , Stergiannakos Taxiarchis , Frysali Maria , Klontzas Emmanuel , Tsamardinos Ioannis , Froudakis George E. 
Published: September 2017

AbstractA novel computational methodology for large-scale screening of MOFs is applied to gas storage with the use of machine learning technologies. This approach is a promising trade-off between the accuracy of ab initio methods and the speed of classical approaches, strategically combined with chemical intuition. The results demonstrate that the chemical properties of MOFs are indeed predictable (stochastically, not deterministically) using machine learning methods and automated analysis protocols, with the accuracy of predictions increasing with sample size. Our initial results indicate that this methodology is promising to apply not only to gas storage in MOFs but in many other material science projects.
Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas
Authors: Madubata Chioma J , Roshan-Ghias Alireza , Chu Timothy , Resnick Samuel , Zhao Junfei , Arnes Luis , Wang Jiguang , Rabadan Raul 
Published: September 2017

AbstractCancer is caused by germline and somatic mutations, which can share biological features such as amino acid change. However, integrated germline and somatic analysis remains uncommon. We present a framework that uses machine learning to learn features of recurrent somatic mutations to (1) predict somatic variants from tumor-only samples and (2) identify somatic-like germline variants for integrated analysis of tumor-normal DNA. Using data from 1769 patients from seven cancer types (bladder, glioblastoma, low-grade glioma, lung, melanoma, stomach, and pediatric glioma), we show that “somatic-like” germline variants are enriched for autosomal-dominant cancer-predisposition genes (p < 4.35 × 10−15), including TP53. Our framework identifies germline and somatic nonsense variants in BRCA2 and other Fanconi anemia genes in 11% (11/100) of bladder cancer cases, suggesting a potential genetic predisposition in these patients. The bladder carcinoma patients with Fanconi anemia nonsense variants display a BRCA-deficiency somatic mutation signature, suggesting treatment targeted to DNA repair.
Buckling analysis in stretchable electronics
Authors: Wang Bo , Bao Siyuan , Vinnikova Sandra , Ghanta Pravarsha , Wang Shuodao 
Published: September 2017

AbstractIn the last decade, stretchable electronics evolved as a class of novel systems that have electronic performances equal to established semiconductor technologies, but can be stretched, compressed, and twisted like a rubber band. The compliance and stretchability of these electronics allow them to conform and mount to soft, elastic biological organs and tissues, thereby providing attractive opportunities in health care and bio-sensing. Majority of stretchable electronic systems use an elastomeric substrate to carry an ultrathin circuit mesh that consists of sparsely distributed stiff, thin-film electronic components interconnected by various forms of stretchable metal strips or low-dimension materials. During the fabrication processes and application of stretchable electronics, the thin-film components or nanomaterials undergo different kinds of in-plane deformation that often leads to out-of-plane or lateral buckling, in-surface buckling, or a combination of all. A lot of creative concepts and ideas have been developed to control and harness buckling behaviors, commonly regarded as pervasive occurrences in structural designs, to facilitate fabrication of stretchable structures, or to enhance stretchability. This paper provides a brief review of recent progresses on buckling analysis in stretchable electronics. Detailed buckling mechanics reveals important correlations between the geometric/material properties and system performance (e.g., mechanical robustness, deformability, structural architecture, and control). These mechanics models and analysis provide insights to design and optimize stretchable electronics for a wide range of important applications.
Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest
Authors: Cheng Tingcai , Wu Jiaqi , Wu Yuqian , Chilukuri Rajendra V. , Huang Lihua , Yamamoto Kohji , Feng Li , Li Wanshun , Chen Zhiwei , Guo Huizhen , Liu Jianqiu , Li Shenglong , Wang Xiaoxiao , Peng Li , Liu Duolian , Guo Youbing , Fu Bohua , Li Zhiqing , Liu Chun , Chen Yuhui , Tomar Archana , Hilliou Frederique , Montagné Nicolas , Jacquin-Joly Emmanuelle , d’Alençon Emmanuelle , Seth Rakesh K. , Bhatnagar Raj K. , Jouraku Akiya , Shiotsuki Takahiro , Kadono-Okuda Keiko , Promboon Amornrat , Smagghe Guy , Arunkumar Kallare P. , Kishino Hirohisa , Goldsmith Marian R. , Feng Qili , Xia Qingyou , Mita Kazuei 
Published: September 2017

AbstractThe tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect’s natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India–South China–Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.
Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans
Authors: Attwood Misty M. , Krishnan Arunkumar , Almén Markus Sällman , Schiöth Helgi B. 
Published: September 2017

AbstractThe dramatic increase in membrane proteome complexity is arguably one of the most pivotal evolutionary events that underpins the origin of multicellular animals. However, the origin of a significant number of membrane families involved in metazoan development has not been clarified. In this study, we have manually curated the membrane proteomes of 22 metazoan and 2 unicellular holozoan species. We identify 123,014 membrane proteins in these 24 eukaryotic species and classify 86% of the dataset. We determine 604 functional clusters that are present from the last holozoan common ancestor (LHCA) through many metazoan species. Intriguingly, we show that more than 70% of the metazoan membrane protein families have a premetazoan origin. The data show that enzymes are more highly represented in the LHCA and expand less than threefold throughout metazoan species; in contrast to receptors that are relatively few in the LHCA but expand nearly eight fold within metazoans. Expansions related to cell adhesion, communication, immune defence, and developmental processes are shown in conjunction with emerging biological systems, such as neuronal development, cytoskeleton organization, and the adaptive immune response. This study defines the possible LHCA membrane proteome and describes the fundamental functional clusters that underlie metazoan diversity and innovation.
The Quasi-Coarse-Grained Dynamics Method to Unravel the Mesoscale Evolution of Defects/Damage during Shock Loading and Spall Failure of Polycrystalline Al Microstructures
Authors: Agarwal Garvit , Valisetty Ramakrishna R. , Namburu Raju R. , Rajendran Arunachalam M. , Dongare Avinash M. 
Published: September 2017

AbstractA long-standing problem in modeling of shock response of metals is the ability to model defect nucleation and evolution mechanisms during plastic deformation and failure at the mesoscales. This paper demonstrates the capability of the “quasi-coarse-grained dynamics” (QCGD) simulation method to unravel microstructural evolution of polycrystalline Al microstructures at the mesoscales. The various QCGD simulations discussed here investigate the shock response of Al microstructures comprising of grain sizes ranging from 50 nm to 3.20 µm and correspond to system sizes ranging from 150 nm to 9.6 µm, respectively. The QCGD simulations are validated by demonstrating the capability to retain atomistic characteristics of the wave propagation behavior, plastic deformation mechanisms (dislocation nucleation, dissociation/recombination behavior, dislocation interactions/reactions), evolution of damage (voids), and evolution of temperature during shock loading. The capability to unravel the mesoscale evolution of microstructure is demonstrated by investigating the effect of grain size, shock pulse and system size on the shock response and spall failure of the metal. The computed values of spall strengths predicted using the QCGD simulations agree very well with the trend predicted by MD simulations and a strain rate dependence of the spall strength is proposed that fits the experimentally available values in the literature.
IRS1 DNA promoter methylation and expression in human adipose tissue are related to fat distribution and metabolic traits
Authors: Rohde Kerstin , Klös Matthias , Hopp Lydia , Liu Xuanshi , Keller Maria , Stumvoll Michael , Dietrich Arne , Schön Michael R. , Gärtner Daniel , Lohmann Tobias , Dreßler Miriam , Kovacs Peter , Binder Hans , Blüher Matthias , Böttcher Yvonne 
Published: September 2017

AbstractThe SNP variant rs2943650 near IRS1 gene locus was previously associated with decreased body fat and IRS1 gene expression as well as an adverse metabolic profile in humans. Here, we hypothesize that these effects may be mediated by an interplay with epigenetic alterations. We measured IRS1 promoter DNA methylation and mRNA expression in paired human subcutaneous and omental visceral adipose tissue samples (SAT and OVAT) from 146 and 41 individuals, respectively. Genotyping of rs2943650 was performed in all individuals (N = 146). We observed a significantly higher IRS1 promoter DNA methylation in OVAT compared to SAT (N = 146, P = 8.0 × 10−6), while expression levels show the opposite effect direction (N = 41, P = 0.011). OVAT and SAT methylation correlated negatively with IRS1 gene expression in obese subjects (N = 16, P = 0.007 and P = 0.010). The major T-allele is related to increased DNA methylation in OVAT (N = 146, P = 0.019). Finally, DNA methylation and gene expression in OVAT correlated with anthropometric traits (waist- circumference waist-to-hip ratio) and parameters of glucose metabolism in obese individuals. Our data suggest that the association between rs2943650 near the IRS1 gene locus with clinically relevant variables may at least be modulated by changes in DNA methylation that translates into altered IRS1 gene expression.
Discriminative Scale Learning (DiScrn): Applications to Prostate Cancer Detection from MRI and Needle Biopsies
Authors: Wang Haibo , Viswanath Satish , Madabhushi Anant 
Published: September 2017

AbstractThere has been recent substantial interest in extracting sub-visual features from medical images for improved disease characterization compared to what might be achievable via visual inspection alone. Features such as Haralick and Gabor can provide a multi-scale representation of the original image by extracting measurements across differently sized neighborhoods. While these multi-scale features are effective, on large-scale digital pathological images, the process of extracting these features is computationally expensive. Moreover for different problems, different scales and neighborhood sizes may be more or less important and thus a large number of features extracted might end up being redundant. In this paper, we present a Discriminative Scale learning (DiScrn) approach that attempts to automatically identify the distinctive scales at which features are able to best separate cancerous from non-cancerous regions on both radiologic and digital pathology tissue images. To evaluate the efficacy of our approach, our approach was employed to detect presence and extent of prostate cancer on a total of 60 MRI and digitized histopathology images. Compared to a multi-scale feature analysis approach invoking features across all scales, DiScrn achieved 66% computational efficiency while also achieving comparable or even better classifier performance.
The Role of Ubiquitination and Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate in the Degradation of the Adrenomedullin Type I Receptor
Authors: Roux Benoît T. , Bauer Claudia C. , McNeish Alister J. , Ward Stephen G. , Cottrell Graeme S. 
Published: September 2017

AbstractCalcitonin receptor-like receptor (CLR) and the receptor activity-modifying protein 2 (RAMP2) comprise a receptor for adrenomedullin (AM). Although it is known that AM induces internalization of CLR•RAMP2, little is known about the molecular mechanisms that regulate the trafficking of CLR•RAMP2. Using HEK and HMEC-1 cells, we observed that AM-induced activation of CLR•RAMP2 promoted ubiquitination of CLR. A mutant (CLRΔ9KR), lacking all intracellular lysine residues was functional and trafficked similar to the wild-type receptor, but was not ubiquitinated. Degradation of CLR•RAMP2 and CLRΔ9KR•RAMP2 was not dependent on the duration of AM stimulation or ubiquitination and occurred via a mechanism that was partially prevented by peptidase inhibitors. Degradation of CLR•RAMP2 was sensitive to overexpression of hepatocyte growth factor-regulated tyrosine kinase substrate (HRS), but not to HRS knockdown, whereas CLRΔ9KR•RAMP2 degradation was unaffected. Overexpression, but not knockdown of HRS, promoted hyperubiquitination of CLR under basal conditions. Thus, we propose a role for ubiquitin and HRS in the regulation of AM-induced degradation of CLR•RAMP2.
Synergistic effect of a drug loaded electrospun patch and systemic chemotherapy in pancreatic cancer xenograft
Authors: Jun Eunsung , Kim Song Cheol , Lee Chan Mi , Oh Juyun , Lee Song , Shim In Kyong 
Published: September 2017

AbstractPancreatic cancer has a high rate of local recurrence and poor prognosis even with adjuvant chemotherapy after curative resection. The aim of this study was to investigate if local drug delivery combined with low dose systemic chemotherapy can increase the therapeutic effect of chemotherapy while reducing systemic toxicities. Poly-L-lactic acid-based 5-FU releasing patch was fabricated by electrospinning, and its tumour killing effects were first confirmed in vitro. The 5-FU patch directly adhered to the tumour in subcutaneous and orthotopic murine models, and induced a significant decrease in tumour size. Systemic gemcitabine treatment group, 5-FU drug releasing patch group, and systemic gemcitabine plus 5-FU patch group were compared by tumour size measurement, non-invasive bio-imaging, and histology in subcutaneous models. Combination of local drug patch and systemic chemotherapy led to increased tumour suppression effects that lasted longer, as well as increased survival rate. Histology revealed higher degree of apoptosis in the combined group. Systemic toxicity was recovered within 7 days after the treatment in all mice. Conclusively, local drug delivery using biocompatible polymer patch significantly inhibited tumour growth, and combination with systemic chemotherapy was more effective than single systemic chemotherapy.
Ageing affects chondroitin sulfates and their synthetic enzymes in the intervertebral disc
Authors: Collin Estelle C , Carroll Oliver , Kilcoyne Michelle , Peroglio Marianna , See Eugene , Hendig Doris , Alini Mauro , Grad Sibylle , Pandit Abhay 
Published: September 2017

AbstractThe depletion of chondroitin sulfates (CSs) within the intervertebral disc (IVD) during degenerative disc disease (DDD) results in a decrease in tissue hydration, a loss of fluid movement, cell apoptosis, a loss of nerve growth inhibition and ultimately, the loss of disc function. To date, little is known with regards to the structure and content of chondroitin sulfates (CSs) during IVD ageing. The behavior of glycosaminoglycans (GAGs), specifically CSs, as well as xylosyltransferase I (XT-I) and glucuronyltransferase I (GT-I), two key enzymes involved in CS synthesis as a primer of glycosaminoglycan (GAG) chain elongation and GAG synthesis in the nucleus pulposus (NP), respectively, were evaluated in a bovine ageing IVD model. Here, we showed significant changes in the composition of GAGs during the disc ageing process (6-month-old, 2-year-old and 8-year-old IVDs representing the immature to mature skeleton). The CS quantity and composition of annulus fibrosus (AF) and NP were determined. The expression of both XT-I and GT-I was detected using immunohistochemistry. A significant decrease in GAGs was observed during the ageing process. CSs are affected at both the structural and quantitative levels with important changes in sulfation observed upon maturity, which correlated with a decrease in the expression of both XT-I and GT-I. A progressive switch of the sulfation profile was noted in both NP and AF tissues from 6 months to 8 years. These changes give an appreciation of the potential impact of CSs on the disc biology and the development of therapeutic approaches for disc regeneration and repair.
Impact of TNF -308 G&gt;A (rs1800629) gene polymorphism in modulation of leprosy risk: a reappraise meta-analysis of 14 case–control studies
Authors: Areeshi Mohammed Y. , Mandal Raju K. , Dar Sajad A. , Jawed Arshad , Wahid Mohd , Lohani Mohtashim , Panda Aditya K. , Mishra Bhartendu N. , Akhter Naseem , Haque Shafiul 
Published: September 2017

Purpose: Earlier studies have shown that tumor necrosis factor (TNF) -308 G&gt;A (rs1800629) gene polymorphism is implicated in the susceptibility to leprosy, but results were inconsistent.
Methods: A meta-analysis of 14 studies involving 3327 leprosy cases and 3203 controls was performed to appraise the association of TNF -308 G&gt;A polymorphism with leprosy using MEDLINE (PUBMED), EMBASE, and Google Scholar web databases.
Results: Overall, no significant association was observed in allelic (A vs. G: P=0.068; OR = 0.836, 95% CI = 0.689–1.013), homozygous (AA vs. GG: P=0.394; OR = 0.810, 95% CI = 0.499–1.315), heterozygous (GA vs. GG: P=0.059; OR = 0.780, 95% CI = 0.603–1.010), dominant (AA + GA vs. GG: P=0.067; OR = 0.797, 95% CI = 0.625–1.016), and recessive (AA vs. GG + GA: P=0.594; OR = 0.877, 95% CI = 0.542– 1.420) genetic models. Subgroup analysis showed no association in Asians. Whereas, reduced risk was found in allelic contrast (A vs. G: P=0.014; OR = 0.832, 95% CI = 0.718–0.963) and dominant models (AA + GA vs. GG: P=0.004; OR = 0.790, 95% CI = 0.673–0.928) of the mixed population.
Conclusions: TNF -308 G&gt;A polymorphism is not associated with leprosy risk in the overall population. However, subgroup analysis demonstrated protective effect of the said polymorphism in leprosy risk in the Latin American population, but showed no association in the Asians.
Validating a Rapid, Automated Test of Spatial Release From Masking
Authors: Jakien Kasey M. , Kampel Sean D. , Stansell Meghan M. , Gallun Frederick J. 
Published: September 2017

Purpose
To evaluate the test–retest reliability of a headphone-based spatial release from a masking task with two maskers (referred to here as the SR2) and to describe its relationship to the same test done over loudspeakers in an anechoic chamber (the SR2A). We explore what thresholds tell us about certain populations (such as older individuals or individuals with hearing impairment) and discuss how the SR2 might be useful in the clinic.

Method
Fifty-four participants completed speech intelligibility tests in which a target phrase and two masking phrases from the Coordinate Response Measure corpus (Bolia, Nelson, Ericson, & Simpson, 2000) were presented either via earphones using a virtual spatial array or via loudspeakers in an anechoic chamber. For the SR2, the target sentence was always at 0° azimuth angle, and the maskers were either colocated at 0° or positioned at ± 45°. For the SR2A, the target was located at 0°, and the maskers were colocated or located at ± 15°, ± 30°, ± 45°, ± 90°, or ± 135°. Spatial release from masking was determined as the difference between thresholds in the colocated condition and each spatially separated condition. All participants completed the SR2 at least twice, and 29 of the individuals who completed the SR2 at least twice also participated in the SR2A. In a second experiment, 40 participants completed the SR2 8 times, and the changes in performance were evaluated as a function of test repetition.

Results
Mean thresholds were slightly better on the SR2 after the first repetition but were consistent across 8 subsequent testing sessions. Performance was consistent for the SR2A, regardless of the number of times testing was repeated. The SR2, which simulates 45° separations of target and maskers, produced spatially separated thresholds that were similar to thresholds obtained with 30° of separation in the anechoic chamber. Over headphones and in the anechoic chamber, pure-tone average was a strong predictor of spatial release, whereas age only reached significance for colocated conditions.

Conclusions
The SR2 is a reliable and effective method of testing spatial release from masking, suitable for screening abnormal listening abilities and for tracking rehabilitation over time. Future work should focus on developing and validating rapid, automated testing to identify the ability of listeners to benefit from high-frequency amplification, smaller spatial separations, and larger spectral differences among talkers.