bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer vision and machine learning for robust phenotyping in genome-wide studies
Authors: Zhang Jiaoping , Naik Hsiang Sing , Assefa Teshale , Sarkar Soumik , Reddy R. V. Chowda , Singh Arti , Ganapathysubramanian Baskar , Singh Asheesh K. 
Published: March 2017

AbstractTraditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems.
Individual Movement Strategies Revealed through Novel Clustering of Emergent Movement Patterns
Authors: Valle Denis , Cvetojevic Sreten , Robertson Ellen P. , Reichert Brian E. , Hochmair Hartwig H. , Fletcher Robert J. 
Published: March 2017

AbstractUnderstanding movement is critical in several disciplines but analysis methods often neglect key information by adopting each location as sampling unit, rather than each individual. We introduce a novel statistical method that, by focusing on individuals, enables better identification of temporal dynamics of connectivity, traits of individuals that explain emergent movement patterns, and sites that play a critical role in connecting subpopulations. We apply this method to two examples that span movement networks that vary considerably in size and questions: movements of an endangered raptor, the snail kite (Rostrhamus sociabilis plumbeus), and human movement in Florida inferred from Twitter. For snail kites, our method reveals substantial differences in movement strategies for different bird cohorts and temporal changes in connectivity driven by the invasion of an exotic food resource, illustrating the challenge of identifying critical connectivity sites for conservation in the presence of global change. For human movement, our method is able to reliably determine the origin of Florida visitors and identify distinct movement patterns within Florida for visitors from different places, providing near real-time information on the spatial and temporal patterns of tourists. These results emphasize the need to integrate individual variation to generate new insights when modeling movement data.
CNT Enabled Co-braided Smart Fabrics: A New Route for Non-invasive, Highly Sensitive & Large-area Monitoring of Composites
Authors: Luo Sida , Wang Yong , Wang Guantao , Wang Kan , Wang Zhibin , Zhang Chuck , Wang Ben , Luo Yun , Li Liuhe , Liu Tao 
Published: March 2017

AbstractThe next-generation of hierarchical composites needs to have built-in functionality to continually monitor and diagnose their own health states. This paper includes a novel strategy forin-situmonitoring the processing stages of composites by co-braiding CNT-enabled fiber sensors into the reinforcing fiber fabrics. This would present a tremendous improvement over the present methods that excessively focus on detecting mechanical deformations and cracks. The CNT enabled smart fabrics, fabricated by a cost-effective and scalable method, are highly sensitive to monitor and quantify various events of composite processing including resin infusion, onset of crosslinking, gel time, degree and rate of curing. By varying curing temperature and resin formulation, the clear trends derived from the systematic study confirm the reliability and accuracy of the method, which is further verified by rheological and DSC tests. More importantly, upon wisely configuring the smart fabrics with a scalable sensor network, localized processing information of composites can be achieved in real time. In addition, the smart fabrics that are readily and non-invasively integrated into composites can provide life-long structural health monitoring of the composites, including detection of deformations and cracks.
Sound Insulation in a Hollow Pipe with Subwavelength Thickness
Authors: Zhang Hai-Long , Zhu Yi-Fan , Liang Bin , Yang Jing , Yang Jun , Cheng Jian-Chun 
Published: March 2017

AbstractSuppression of the transmission of undesired sound in ducts is a fundamental issue with wide applications in a great variety of scenarios. Yet the conventional ways of duct noise control have to rely on mismatched impedance or viscous dissipation, leading the ducts to have ventilation capability weakened by inserted absorbers or a thick shell to accommodate bulky resonators. Here we present a mechanism for insulating sound transmission in a hollow pipe with subwavelength thickness, by directly reversing its propagating direction via anomalous reflection at the flat inner boundary with well-designed phase profile. A metamaterial-based implementation is demonstrated both in simulation and in experiment, verifying the theoretical prediction on high-efficient sound insulation at the desired frequencies by the resulting device, which has a shell as thin as 1/8 wavelength and an entirely open passage that maintains the continuity of the background medium. We have also investigated the potential of our scheme to work in broadband by simply cascading different metamaterial unit cells. Without the defects of blocked path and bulky size of existing sound insulators, we envision our design will open new route to sound insulation in ducts and have deep implication in practical applications such as designs of ventilation fans and vehicle silencers.
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY
Authors: Shi Jade , Nobrega R. Paul , Schwantes Christian , Kathuria Sagar V. , Bilsel Osman , Matthews C. Robert , Lane T. J. , Pande Vijay S. 
Published: March 2017

AbstractThe dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.
An Innovative Approach for Enhancing Bone Defect Healing Using PLGA Scaffolds Seeded with Extracorporeal-shock-wave-treated Bone Marrow Mesenchymal Stem Cells (BMSCs)
Authors: Chen Youbin , Xu Jiankun , Huang Zhonglian , Yu Menglei , Zhang Yuantao , Chen Hongjiang , Ma Zebin , Liao Haojie , Hu Jun 
Published: March 2017

AbstractAlthough great efforts are being made using growth factors and gene therapy, the repair of bone defects remains a major challenge in modern medicine that has resulted in an increased burden on both healthcare and the economy. Emerging tissue engineering techniques that use of combination of biodegradable poly-lactic-co-glycolic acid (PLGA) and mesenchymal stem cells have shed light on improving bone defect healing; however, additional growth factors are also required with these methods. Therefore, the development of novel and cost-effective approaches is of great importance. Our in vitro results demonstrated that ESW treatment (10 kV, 500 pulses) has a stimulatory effect on the proliferation and osteogenic differentiation of bone marrow-derived MSCs (BMSCs). Histological and micro-CT results showed that PLGA scaffolds seeded with ESW-treated BMSCs produced more bone-like tissue with commitment to the osteogenic lineage when subcutaneously implanted in vivo, as compared to control group. Significantly greater bone formation with a faster mineral apposition rate inside the defect site was observed in the ESW group compared to control group. Biomechanical parameters, including ultimate load and stress at failure, improved over time and were superior to those of the control group. Taken together, this innovative approach shows significant potential in bone tissue regeneration.
Colour-crafted phosphor-free white light emitters via in-situ nanostructure engineering
Authors: Min Daehong , Park Donghwy , Lee Kyuseung , Nam Okhyun 
Published: March 2017

AbstractColour-temperature (Tc) is a crucial specification of white light-emitting diodes (WLEDs) used in a variety of smart-lighting applications. Commonly, Tc is controlled by distributing various phosphors on top of the blue or ultra violet LED chip in conventional phosphor-conversion WLEDs (PC-WLEDs). Unfortunately, the high cost of phosphors, additional packaging processes required, and phosphor degradation by internal thermal damage must be resolved to obtain higher-quality PC-WLEDs. Here, we suggest a practical in-situ nanostructure engineering strategy for fabricating Tc-controlled phosphor-free white light-emitting diodes (PF-WLEDs) using metal-organic chemical vapour deposition. The dimension controls of in-situ nanofacets on gallium nitride nanostructures, and the growth temperature of quantum wells on these materials, were key factors for Tc control. Warm, true, and cold white emissions were successfully demonstrated in this study without any external processing.
Fluorescence and Magnetic Resonance Dual-Modality Imaging-Guided Photothermal and Photodynamic Dual-Therapy with Magnetic Porphyrin-Metal Organic Framework Nanocomposites
Authors: Zhang Hui , Li Yu-Hao , Chen Yang , Wang Man-Man , Wang Xue-Sheng , Yin Xue-Bo 
Published: March 2017

AbstractPhototherapy shows some unique advantages in clinical application, such as remote controllability, improved selectivity, and low bio-toxicity, than chemotherapy. In order to improve the safety and therapeutic efficacy, imaging-guided therapy seems particularly important because it integrates visible information to speculate the distribution and metabolism of the probe. Here we prepare biocompatible core-shell nanocomposites for dual-modality imaging-guided photothermal and photodynamic dual-therapy by the in situ growth of porphyrin-metal organic framework (PMOF) on Fe3O4@C core. Fe3O4@C core was used as T2-weighted magnetic resonance (MR) imaging and photothermal therapy (PTT) agent. The optical properties of porphyrin were well remained in PMOF, and PMOF was therefore selected for photodynamic therapy (PDT) and fluorescence imaging. Fluorescence and MR dual-modality imaging-guided PTT and PDT dual-therapy was confirmed with tumour-bearing mice as model. The high tumour accumulation of Fe3O4@C@PMOF and controllable light excitation at the tumour site achieved efficient cancer therapy, but low toxicity was observed to the normal tissues. The results demonstrated that Fe3O4@C@PMOF was a promising dual-imaging guided PTT and PDT dual-therapy platform for tumour diagnosis and treatment with low cytotoxicity and negligible in vivo toxicity.
The effect of diurnal distribution of carbohydrates and fat on glycaemic control in humans: a randomized controlled trial
Authors: Kessler Katharina , Hornemann Silke , Petzke Klaus J. , Kemper Margrit , Kramer Achim , Pfeiffer Andreas F. H. , Pivovarova Olga , Rudovich Natalia 
Published: March 2017

AbstractDiurnal carbohydrate and fat distribution modulates glycaemic control in rodents. In humans, the optimal timing of both macronutrients and its effects on glycaemic control after prolonged consumption are not studied in detail. In this cross-over trial, 29 non-obese men were randomized to two four-week diets: (1) carbohydrate-rich meals until 13.30 and fat-rich meals between 16.30 and 22.00 (HC/HF) versus (2) inverse sequence of meals (HF/HC). After each trial period two meal tolerance tests were performed, at 09.00 and 15.40, respectively, according to the previous intervention. On the HF/HC diet, whole-day glucose level was increased by 7.9% (p = 0.026) in subjects with impaired fasting glucose and/or impaired glucose tolerance (IFG/IGT, n = 11), and GLP-1 by 10.2% (p = 0.041) in normal glucose-tolerant subjects (NGT, n = 18). Diet effects on fasting GLP-1 (p = 0.009) and PYY (p = 0.034) levels were observed in IFG/IGT, but not in NGT. Afternoon decline of glucose tolerance was more pronounced in IFG/IGT and associated with a stronger decrease of postprandial GLP-1 and PYY levels, but not with changes of cortisol rhythm. In conclusion, the HF/HC diet shows an unfavourable effect on glycaemic control in IFG/IGT, but not in NGT subjects. Consequently, large, carbohydrate-rich dinners should be avoided, primarily by subjects with impaired glucose metabolism.
PD-1 inhibitors increase the incidence and risk of pneumonitis in cancer patients in a dose-independent manner: a meta-analysis
Authors: Wu Jiaying , Hong Dongsheng , Zhang Xiangnan , Lu Xiaoyang , Miao Jing 
Published: March 2017

AbstractTherapies that targeted PD-1 have shown remarkable rates of durable clinical responses in patients with various tumor types. However, the extent and knowledge of pulmonary toxicities associated with PD-1 blockade, mainly manifested as pneumonitis, remains obscure. In this study, a total of 6360 subjects from 16 phase II/III clinical trials were pooled for meta-analysis to evaluate the overall incidence and risk of PD-1 inhibitors-related pneumonitis in cancer patients. The incidence of pneumonitis during anti-PD-1 immunotherapy was 2.92% (95%CI: 2.18–3.90%) for all-grade and 1.53% (95%CI: 1.15–2.04%) for high-grade pneumonitis. Compared with routine chemotherapy, PD-1 inhibitors were associated with a significant increased risk of pneumonitis. Moreover, among the types of tumor treated with PD-1 inhibitors, the melanoma patients have the lowest incidence of pneumonitis, while the non-small cell lung cancer (NSCLC) and renal cell carcinoma (RCC) patients have the highest. Furthermore, no significant differences were detected in the incidences of all- and high-grade pneumonitis between high-dose and low-dose groups of PD-1 inhibitors. In conclusion, PD-1 inhibitors were probably associated with an increased risk of pneumonitis in a dose-independent manner, compared with routine chemotherapeutic agents. The frequency and severity of treatment-mediated pneumonitis was quite different in patients with various tumor types.
EMI and ground leakage current reduction in single‐phase grid‐connected power converter
Authors: Hedayati Mohammad Hassan , John Vinod 
Published: March 2017

Ground leakage current in a power converter is a major concern, which has stringent limitations due to safety concerns. Presence of high‐frequency pulses, with high dv/dt due to switching actions in common‐mode (CM) voltage, result in injection of current waveforms with large di/dt spikes into the ground and causes high electromagnetic interference (EMI) noise level. In this study, a new method is proposed to make the CM voltage, of a single‐phase grid‐connected inverter, sinusoidal and free of high‐frequency pulses. The proposed method consists of two parallel connected H‐bridge power converters, which uses unipolar pulse width modulation (PWM) with carrier interleaving angle of 180°. The proposed method reduces the ground leakage current by more than an order of magnitude. A novel modification to the LCL filter is proposed which further reduces the leakage current by 48%. It is shown that these modifications make the overall system insensitive to circuit non‐idealities. Experimental results based on ground leakage current measurements on a 7.5 kW parallel single‐phase PWM rectifier are presented. These results validate the effectiveness of the proposed method.
Synthesis of Secosterols as an Arena for C–H Functionalization and C–C Manipulation Tactics
Authors: Heretsch Philipp , Heinze Robert 
Published: March 2017

The chemical synthesis of secosterols is an arena for the application of C–H functionalization methods as well as C–C manipulations. Studies on the innate reactivity of synthetic intermediates to undergo C–C scissions and rearrangements can shed light on biosynthetic pathways, or, provide proof for biosynthetic proposals. Examples of the authors work (synthesis of the 14,15-secosterol strophasterol A), as well as examples from current literature (Tian’s synthetic work on 13,14:14,15-disecosterols glaucogenins C and D, and Baran’s synthesis of 9,10-secosterol cortistatin A) are discussed.1	Introduction2	The Synthesis of Strophasterol A Employing the Concept of Innate Reactivity3	Synthetic Work in the Glaucogenin Family of Natural Products4	The Synthesis of Cortistatin A Using a Radical Ring Expansion5	Conclusion
Is There a Role for Placental Cultures in Cases of Clinical Chorioamnionitis Complicating Preterm Premature Rupture of Membranes?
Authors: Many Ariel , Orbach Rotem , Shapira Udi , Amit Sharon , Grisaru-Soen Galia , Mandel Dror , Shinar Shiri , Fouks Yuval 
Published: March 2017

Objective To assess the role of placental cultures in cases of preterm premature rupture of membranes (PPROM) complicated by chorioamnionitis and to determine the effect of positive cultures on short-term neonatal outcomes.
Design A retrospective single-center study. The medical records of all women with PPROM between January 1, 2011, and December 31, 2015, were reviewed. Cases were divided into placental culture positive (group A) and placental culture negative (group B) groups. Maternal and pregnancy characteristics as well as short-term neonatal outcomes were compared between groups.
Results During the 5-year study period, 61 cases of clinical chorioamnionitis complicating PPROM were diagnosed: 25 cases were culture positive (group A) and 36 were culture negative (group B). Neonatal outcome measures, including Apgar score at 5 minutes (p = 0.028; odds ratio [OR]: 5.27; confidence interval [CI]: 1.19–23.34), respiratory distress syndrome (p = 0.026; OR: 4.11; CI: 1.18–14.25), and neonatal infection (p < 0.0001; OR: 11.59; CI: 3.37–39.87) were significantly more common in group A newborns, regardless of gestational age at delivery as was the composite neonatal outcome (p = 0.017; OR: 7.35: CI: 1.42–37.79). Placental isolates were primarily Streptococci and Escherichia coli.
Conclusion Placental cultures may be an essential predictor of neonatal morbidity in PPROM and may contribute to the modification of neonatal treatment.
Massive increase in visual range preceded the origin of terrestrial vertebrates
Authors: MacIver Malcolm A. , Schmitz Lars , Mugan Ugurcan , Murphey Todd D. , Mobley Curtis D. 
Published: March 2017

Significance
Starting 385 million years ago, certain fish slowly evolved into legged animals living on land. We show that eyes tripled in size and shifted from the sides to the top of the head long before fish modified their fins into limbs for land. Before permanent life on land, these animals probably hunted like crocodiles, looking at prey from just above the water line, where the vastly higher transparency of air enabled long-distance vision and selected for larger eyes. The “buena vista” hypothesis that our study forwards is that seeing opportunities far away provided an informational zip line to the bounty of invertebrate prey on land, aiding selection for limbs—first for brief forays onto land and eventually, for life there.
Entanglement of quantum clocks through gravity
Authors: Castro Ruiz Esteban , Giacomini Flaminia , Brukner Časlav 
Published: March 2017

Significance
We find that there exist fundamental limitations to the joint measurability of time along neighboring space–time trajectories, arising from the interplay between quantum mechanics and general relativity. Because any quantum clock must be in a superposition of energy eigenstates, the mass–energy equivalence leads to a trade-off between the possibilities for an observer to define time intervals at the location of the clock and in its vicinity. This effect is fundamental, in the sense that it does not depend on the particular constitution of the clock, and is a necessary consequence of the superposition principle and the mass–energy equivalence. We show how the notion of time in general relativity emerges from this situation in the classical limit.
Phosphoproteins in extracellular vesicles as candidate markers for breast cancer
Authors: Chen I-Hsuan , Xue Liang , Hsu Chuan-Chih , Paez Juan Sebastian Paez , Pan Li , Andaluz Hillary , Wendt Michael K. , Iliuk Anton B. , Zhu Jian-Kang , Tao W. Andy 
Published: March 2017

Significance
Protein phosphorylation is a major regulatory mechanism for many cellular functions, but no phosphoprotein in biofluids has been developed for disease diagnosis because of the presence of active phosphatases. This study presents a general strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs from small volumes of plasma samples and more than 100 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer as compared with healthy controls. This study demonstrates that the development of phosphoproteins in plasma EVs as disease biomarkers is highly feasible and may transform cancer screening and monitoring.
Integrin-β4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells
Authors: Bierie Brian , Pierce Sarah E. , Kroeger Cornelia , Stover Daniel G. , Pattabiraman Diwakar R. , Thiru Prathapan , Liu Donaher Joana , Reinhardt Ferenc , Chaffer Christine L. , Keckesova Zuzana , Weinberg Robert A. 
Published: March 2017

Significance
It is widely appreciated that carcinoma cells exhibiting certain mesenchymal traits are enriched for cancer stem cells (CSCs) and can give rise to tumors with aggressive features. Whereas it has been proposed that mesenchymal carcinoma cell populations are internally heterogeneous, the field has made little progress in resolving the specific subtypes of mesenchymal carcinoma cells that pose the greatest risk for patients. We demonstrate the utility of integrin-β4 (ITGB4) in segregating these cells into distinct subpopulations with differing tumor-initiating abilities and pathological behaviors. In addition, we identified mechanistic links between ZEB1 (zinc finger E-box binding homeobox 1) and TAp63α (tumor protein 63 isoform 1) as regulators of ITGB4 expression and demonstrate that ITGB4 can be used as a marker to determine which patients are more likely to relapse after treatment.