bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Targeted Next-Generation Sequencing for Detection of Bovine Pathogens in Clinical Samples
Authors: Anis Eman , Hawkins Ian K. , Ilha Marcia R. S. , Woldemeskel Moges W. , Saliki Jeremiah T. , Wilkes Rebecca P. 
Published: April 2018

ABSTRACT

The laboratory diagnosis of infectious diseases, especially those caused by mixed infections, is challenging. Routinely, it requires submission of multiple samples to separate laboratories. Advances in next-generation sequencing (NGS) have provided the opportunity for development of a comprehensive method to identify infectious agents. This study describes the use of target-specific primers for PCR-mediated amplification with the NGS technology in which pathogen genomic regions of interest are enriched and selectively sequenced from clinical samples. In the study, 198 primers were designed to target 43 common bovine and small-ruminant bacterial, fungal, viral, and parasitic pathogens, and a bioinformatics tool was specifically constructed for the detection of targeted pathogens. The primers were confirmed to detect the intended pathogens by testing reference strains and isolates. The method was then validated using 60 clinical samples (including tissues, feces, and milk) that were also tested with other routine diagnostic techniques. The detection limits of the targeted NGS method were evaluated using 10 representative pathogens that were also tested by quantitative PCR (qPCR), and the NGS method was able to detect the organisms from samples with qPCR threshold cycle (

C
T

) values in the 30s. The method was successful for the detection of multiple pathogens in the clinical samples, including some additional pathogens missed by the routine techniques because the specific tests needed for the particular organisms were not performed. The results demonstrate the feasibility of the approach and indicate that it is possible to incorporate NGS as a diagnostic tool in a cost-effective manner into a veterinary diagnostic laboratory.
Approach to Diagnosis of Cardiovascular Implantable-Electronic-Device Infection
Authors: DeSimone Daniel C. , Sohail M. Rizwan 
Published: April 2018

ABSTRACT
Device infection remains a significant challenge as clinical indications for cardiovascular implantable electronic device (CIED) therapy continue to expand beyond the prevention and treatment of cardiac arrhythmias. Patients receiving CIED therapy are now older and have significant comorbidities, placing them at higher risk of complications, including infection. CIED infection warrants complete device removal, as retention is associated with an unacceptably high risk of relapse and increased mortality. However, accurate diagnosis of CIED infections remains a significant challenge that is based on a combination of findings on physical examination, microbiological and laboratory testing, and advanced imaging, such as transesophageal echocardiography or positron emission tomography. Isolating a causative pathogen and performing susceptibility testing are crucial for appropriate choice, route, and duration of antimicrobial therapy. In this review, we present an evidence-based approach to diagnosis of CIED infection.
Converse magnetoelectric effect in Ni(Terfenol-D)/Pb(Zr,Ti)O3 bilayer-laminated composite
Authors: Ge X. H. , Ji H. , Li Y. , Chen J. K. , Wang Y. G. , Pan F. M. 
Published: April 2018

In this study, we propose a new bilayer-laminated magnetoelectric (ME) composite consisting of magnetostrictive Ni and Tb[Formula: see text]Dy[Formula: see text]Fe2 (Terfenol-D) plates and piezoelectric Pb(Zr,Ti)O3 (PZT) plate. The Ni–Terfenol–D-Ni/PZT composite is constructed and compared with the traditional Terfenol-D/PZT composite. The bias magnetic field and the electric field frequency dependences of the converse ME (CME) coefficient were investigated. It is shown that the Ni–Terfenol-D–Ni/PZT exhibits a large CME coefficient of 6.2 × 10[Formula: see text] s/m at the electric field frequency of 42 kHz under a low bias magnetic field of 230 Oe, which results from the highly concentrated flux induced by Ni and the stress-interaction between Ni and magnetostrictive Terfenol-D.
Immunotherapy for Glioblastoma: Playing Chess, Not Checkers
Authors: Jackson Christopher M. , Lim Michael 
Published: April 2018

Abstract
Patients with glioblastoma (GBM) exhibit a complex state of immune dysfunction involving multiple mechanisms of local, regional, and systemic immunosuppression and tolerance. These pathways are now being identified and their relative contributions explored. Delineating how these pathways are interrelated is paramount to effectively implementing immunotherapy for GBM. Clin Cancer Res; 24(17); 4059–61. ©2018 AACR.
See related articles by Woroniecka et al., p. 4175 and Mohme et al., p. 4187
Preliminary Results from the Air Mass Transformation Experiment (AMTEX)
Authors: Lenschow D. H. , Agee E. M. 
Published: April 2018

The field phases of AMTEX, a GARP subprogram on air-sea interaction implemented by Japan, were conducted over the East China Sea in the environs of Okinawa, Japan, during the last two weeks of February in 1974 and 1975. Investigators from Australia, Canada, and the United States also participated in this experiment. The weather was generally very favorable for this study of air mass transformation processes in 1975 because of an extensive cold air outbreak during most of the experimental period. A basic synoptic data set was obtained from 6 h soundings from an array of aerological stations centered at Okinawa. In addition, satellite, hourly surface and surface marine, oceanographic, boundary layer, radiation, radar, cloud physics, and aircraft data were obtained and have been or will be available in published data reports or on magnetic tape.
Preliminary results from 1974 and 1975 reported at the Fourth AMTEX Study Conference and joint United States–Japan Cooperative Science Program Seminar, “Air Mass Transformation Processes over the Kuroshio in Winter,” held in Tokyo, 26–30 September 1975, are presented and discussed.
Interannual Variations and Trends in Remotely Sensed and Modeled Soil Moisture in China
Authors: Jia Binghao , Liu Jianguo , Xie Zhenghui , Shi Chunxiang 
Published: April 2018

Abstract
In this study, a microwave-based multisatellite merged product released from the European Space Agency’s Climate Change Initiative (ESA CCI) and two model-based simulations from the Community Land Model 4.5 (CLM4.5) and Global Land Data Assimilation System (GLDAS) were used to investigate interannual variations and trends of soil moisture in China between 1979 and 2010. They were also evaluated using in situ observations from the nationwide agrometeorological network. These three datasets show consistent drying trends for surface soil moisture in northeastern and central China, as well the eastern portion of Inner Mongolia, and wetting trends in the Tibetan Plateau, which are also identified by in situ observations. Trends in the root-zone soil moisture are in line with those of surface soil moisture seen in the CLM4.5 and GLDAS simulations obtained from most areas in China (78%–88%), except for northwestern China and southwest of the Tibetan Plateau. Moreover, the drying trend intensifies with increasing soil depth. Taking the in situ measurements as reference, it is found that ESA CCI has better accuracy in identifying the significant drying trends while CLM4.5 and GLDAS capture wetting trends better. Compared to temperature, precipitation is the primary factor responsible for these trends, which controls the direction of soil moisture changes, while increasing temperatures can also enhance soil drying during periods of decreased precipitation.
Basin-Scale Prediction of Sea Surface Temperature with Artificial Neural Networks
Authors: Patil Kalpesh , Deo M. C. 
Published: April 2018

AbstractThe prediction of sea surface temperature (SST) on the basis of artificial neural networks (ANNs) can be viewed as complementary to numerical SST predictions, and it has fairly sustained in the recent past. However, one of its limitations is that such ANNs are site specific and do not provide simultaneous spatial information similar to the numerical schemes. In this work we have addressed this issue by presenting basin-scale SST predictions based on the operation of a very large number of individual ANNs simultaneously. The study area belongs to the basin of the tropical Indian Ocean (TIO) having coordinates of 30°N–30°S, 30°–120°E. The network training and testing are done on the basis of HadISST data of the past 140 yr. Monthly SST anomalies are predicted at 3813 nodes in the basin and over nine time steps into the future with more than 20 million ANN models. The network testing indicated that the prediction skill of ANNs is attractive up to certain lead times depending on the subbasin. The ANN models performed well over both the western Indian Ocean (WIO) and eastern Indian Ocean (EIO) regions up to 5 and 4 months lead time, respectively, as judged by the error statistics of the correlation coefficient and the normalized root-mean-square error. The prediction skill of the ANN models for the TIO region is found to be better than the physics-based coupled atmosphere–ocean models. It is also observed that the ANNs are capable of providing an advanced warning of the Indian Ocean dipole as well as abnormal basin warming.
Surgical Treatment With Closing-Wedge Distal Femoral Osteotomy for Recurrent Patellar Dislocation With Genu Valgum
Authors: Nha Kyung Wook , Ha Yoonwon , Oh Seungmin , Nikumbha Vivek P. , Kwon Sae Kwang , Shin Woo-Jin , Lee Byung Hoon , Hong Keun Bae 
Published: April 2018

Background: Closing-wedge distal femoral osteotomy (CWDFO)—combined with medial reefing and lateral release, if necessary— has been used to treat recurrent patellar dislocation (RPD) with genu valgum. Purpose: To evaluate the clinical and radiologic outcomes of surgical treatment with CWDFO for treatment of RPD with genu valgum. Study Design: Case series; Level of evidence, 4. Methods: Fourteen consecutive patients (23 knees) with RPD and genu valgum were treated with CWDFO. Patients with a minimum 2-year follow-up period were eligible for this study. Patients with prior failed surgery were also eligible. Radiographic evaluation was performed with mechanical femorotibial and lateral distal femoral angle. The radiographic parameters presenting patellar positions and pathologic abnormalities associated with RPD were evaluated. Chondral lesion changes in second-look arthroscopic examination were examined, and clinical outcomes (eg, occurrence of redislocation, range of motion, and clinical scores) were assessed pre- and postoperatively at a minimum of 2 years. Results: At a mean follow-up of 30.7 months (range, 25-62 months), the mean mechanical femorotibial and mechanical lateral distal femoral angles changed significantly from valgus 5° (range, 2°-11°) to varus 3° (2°-11°; P < .001) and from 83° (range, 78°-86°) to 89° (84°-92°; P < .001), respectively. The mean patellar congruence angle improved from 40° lateral (range, 20°-53° lateral) to 4° medial (23° medial to 21° lateral; P < .001), as did the lateral patellofemoral angle from 26° (range, 8°-62°) to 9° (0°-15°; P < .001). Computed tomography scans showed that the mean distance of patellar lateral shift decreased from 13.5 mm (range, 4-22 mm) to 2.0 mm (–4 to 5 mm; P < .001). The mean tibial tubercle to trochlear groove distance significantly decreased from 20.4 to 13.5 mm ( P < .001), while the Caton-Deschamps ratio did not change significantly after surgery ( P = .984). Chondral lesions of the patella and trochlear groove significantly improved or were maintained. None of the patients experienced subluxation or redislocation after surgery. Patellar instability symptoms also improved, as validated by radiographic and other clinical outcomes. Conclusion: CWDFO combined with medial reefing and lateral release successfully treated RPD with genu valgum for a minimum follow-up of 2 years, with improved patellar alignment and stability.
Efficacy, Safety, and Regulatory Approval of Food and Drug Administration–Designated Breakthrough and Nonbreakthrough Cancer Medicines
Authors: Hwang Thomas J. , Franklin Jessica M. , Chen Christopher T. , Lauffenburger Julie C. , Gyawali Bishal , Kesselheim Aaron S. , Darrow Jonathan J. 
Published: April 2018

Purpose The breakthrough therapy program was established in 2012 to expedite the development and review of new medicines. We evaluated the times to approval, efficacy, and safety of breakthrough-designated versus non–breakthrough-designated cancer drugs approved by the US Food and Drug Administration (FDA). Methods We studied all new cancer drugs approved by the FDA between January 2012 and December 2017. Regulatory and therapeutic characteristics (time to FDA approval, pivotal trial efficacy end point, novelty of mechanism of action) were compared between breakthrough-designated and non–breakthrough-designated cancer drugs. Random-effects meta-regression was used to assess the association between breakthrough therapy designation and hazard ratios for progression-free survival (PFS), response rates (RRs) for solid tumors, serious adverse events, and deaths not attributed to disease progression. Results Between 2012 and 2017, the FDA approved 58 new cancer drugs, 25 (43%) of which received breakthrough therapy designation. The median time to first FDA approval was 5.2 years for breakthrough-designated drugs versus 7.1 years for non–breakthrough-designated drugs (difference, 1.9 years; P = .01). There were no statistically significant differences between breakthrough-designated and non–breakthrough-designated drugs in median PFS gains (8.6 v 4.0 months; P = .11), hazard ratios for PFS (0.43 v 0.51; P = .28), or RRs for solid tumors (37% v 39%; P = .74). Breakthrough therapy–designated drugs were not more likely to act via a novel mechanism of action (36% v 39%; P = 1.00). Rates of deaths (6% v 4%; P = .99) and serious adverse events (38% v 36%; P = 0.93) were also similar in breakthrough-designated and non–breakthrough-designated drugs. Conclusion Breakthrough-designated cancer drugs were associated with faster times to approval, but there was no evidence that these drugs provide improvements in safety or novelty; nor was there a statistically significant efficacy advantage when compared with non–breakthrough-designated drugs.
Successive duplication-divergence mechanisms at the RCO locus contributed to leaf shape diversity in the Brassicaceae
Authors: Streubel Susanna , Fritz Michael André , Teltow Melanie , Kappel Christian , Sicard Adrien 
Published: April 2018

ABSTRACT
Gene duplication is a major driver for the increase of biological complexity. The divergence of newly duplicated paralogs may allow novel functions to evolve, while maintaining the ancestral one. Alternatively, partitioning the ancestral function among paralogs may allow parts of that role to follow independent evolutionary trajectories. We studied the REDUCED COMPLEXITY (RCO) locus, which contains three paralogs that have evolved through two independent events of gene duplication, and which underlies repeated events of leaf shape evolution within the Brassicaceae. In particular, we took advantage of the presence of three potentially functional paralogs in Capsella to investigate the extent of functional divergence among them. We demonstrate that the RCO copies control growth in different areas of the leaf. Consequently, the copies that are retained active in the different Brassicaceae lineages contribute to define the leaf dissection pattern. Our results further illustrate how successive gene duplication events and subsequent functional divergence can increase trait evolvability by providing independent evolutionary trajectories to specialized functions that have an additive effect on a given trait.
Plant cell surface receptor-mediated signaling – a common theme amid diversity
Authors: He Yunxia , Zhou Jinggeng , Shan Libo , Meng Xiangzong 
Published: April 2018

ABSTRACT
Sessile plants employ a diverse array of plasma membrane-bound receptors to perceive endogenous and exogenous signals for regulation of plant growth, development and immunity. These cell surface receptors include receptor-like kinases (RLKs) and receptor-like proteins (RLPs) that harbor different extracellular domains for perception of distinct ligands. Several RLK and RLP signaling pathways converge at the somatic embryogenesis receptor kinases (SERKs), which function as shared co-receptors. A repertoire of receptor-like cytoplasmic kinases (RLCKs) associate with the receptor complexes to relay intracellular signaling. Downstream of the receptor complexes, mitogen-activated protein kinase (MAPK) cascades are among the key signaling modules at which the signals converge, and these cascades regulate diverse cellular and physiological responses through phosphorylation of different downstream substrates. In this Review, we summarize the emerging common theme that underlies cell surface receptor-mediated signaling pathways in Arabidopsis thaliana: the dynamic association of RLKs and RLPs with specific co-receptors and RLCKs for signal transduction. We further discuss how signaling specificities are maintained through modules at which signals converge, with a focus on SERK-mediated receptor signaling.
Actin-mediated movement of chloroplasts
Authors: Wada Masamitsu , Kong Sam-Geun 
Published: April 2018

ABSTRACT
Plants are sessile and require diverse strategies to adapt to fluctuations in the surrounding light conditions. Consequently, the photorelocation movement of chloroplasts is essential to prevent damages that are induced by intense light (avoidance response) and to ensure efficient photosynthetic activities under weak light conditions (accumulation response). The mechanisms that underlie chloroplast movements have been revealed through analysis of the behavior of individual chloroplasts and it has been found that these organelles can move in any direction without turning. This implies that any part of the chloroplast periphery can function as the leading or trailing edge during movement. This ability is mediated by a special structure, which consists of short actin filaments that are polymerized at the leading edge of moving chloroplasts and are specifically localized in the space between the chloroplast and the plasma membrane, and is called chloroplast-actin. In addition, several of the genes that encode proteins that are involved in chloroplast-actin polymerization or maintenance have been identified. In this Review, we discuss the mechanisms that regulate chloroplast movements through polymerization of the chloroplast-actin and propose a model for actin-driven chloroplast photorelocation movement.
A Wide Array of Photoinduced Motions in Molecular and Macromolecular Assemblies at Interfaces
Authors: Seki Takahiro 
Published: April 2018

Abstract
Molecular and macromolecular assemblies have good “chemistry” with light. In the research of photochromic molecules and systems, the number of papers in the most recent 10 years exceeds the half of the whole past century. Photochromic molecules have been studied for their characteristic color changes. Although the importance in this line has not dimmed, other powerful areas have emerged in the last two or three decades. Much more attention has been drawn to light induced motions triggered by photoreactions utilizing molecular and polymer assemblies. Probably, this field is one of the most developing areas in advanced soft material research. This review article mainly deals with azobenzene and diarylethene as the photochroms, and systematically introduces light triggered dynamic processes taking place at interfaces. In terms of the feature size, the systems at interfaces, mesoscopic and microscopic level materials are particularly highlighted. Molecular design and understanding of interfaces are the key to realize smart motility properties in molecular and polymer assemblies.
Hydrologic Evaluation of Residential Rain Gardens Using a Stormwater Runoff Simulator
Authors: Anderson Andrew R. , Franti Thomas G. , Shelton David P. 
Published: April 2018

Abstract. Engineered bioretention cells with underdrains have shown water quality and hydrologic benefits for abating urban stormwater problems. Less is known about the hydrologic performance of residential rain gardens that rely on soil infiltration as the primary mechanism of volume control. Eleven residential rain gardens in Lincoln, Nebraska, were evaluated using a variable-rate stormwater runoff simulator. A volume-based water quality volume (WQV) design storm of 3.0 cm was applied to each rain garden as an SCS Type II runoff hydrograph until the system began overflowing to test the rain gardens for surface and subsurface storage capacity, drawdown rate, ponding depth, and overflow characteristics. Every rain garden tested drained in 30 h or less, with six gardens draining in less than 1 h. Rain garden surface storage capacity was poor, retaining on average only 16% of the WQV. On average, the rain gardens studied could store and infiltrate only 40% of the WQV, with only two gardens able to store and infiltrate greater than 90% of the WQV. On average, 59% of the runoff was captured as subsurface storage. Results of this study indicate that these 2- to 4-year-old rain gardens are limited not by drain times and rates, which often met or exceeded common design recommendations, but rather by inadequate surface storage characteristics. Extrapolating measured surface storage volumes to hypothetical systems with evenly graded depths of 15.2 cm, a minimum local depth recommendation, resulted in only one garden with enough storage to contain the WQV. On average, the extrapolated storage held only 65% of the WQV. It was shown that subsurface storage can make up for a lack of surface storage; the systems studied herein had an average of 2.7 times more subsurface storage than surface storage as a percentage of inflow volume before overflow began. Keywords: Best management practice, Low-impact development, Rain garden, Runoff simulator, Stormwater.
Deep Feature Representation with Stacked Sparse Auto-Encoder and Convolutional Neural Network for Hyperspectral Imaging-Based Detection of Cucumber Defects
Authors: Liu Ziyi , He Yong , Cen Haiyan , Lu Renfu 
Published: April 2018

Abstract. It is challenging to achieve rapid and accurate processing of large amounts of hyperspectral image data. This research was aimed to develop a novel classification method by employing deep feature representation with the stacked sparse auto-encoder (SSAE) and the SSAE combined with convolutional neural network (CNN-SSAE) learning for hyperspectral imaging-based defect detection of pickling cucumbers. Hyperspectral images of normal and defective pickling cucumbers were acquired using a hyperspectral imaging system running at two conveyor speeds of 85 and 165 mm s-1. An SSAE model was developed to learn the feature representation from the preprocessed data and to perform five-class (normal, watery, split/hollow, shrivel, and surface defect) classification. To deal with a more complicated task for different types of surface defects (i.e., dirt/sand and gouge/rot classes) in six-class classification, a CNN-SSAE system was developed. The results showed that the CNN-SSAE system improved the classification performance, compared with the SSAE, with overall accuracies of 91.1% and 88.3% for six-class classification at the two conveyor speeds. Additionally, the average running time of the CNN-SSAE system for each sample was less than 14 ms, showing considerable potential for application in an automated on-line inspection system for cucumber sorting and grading. Keywords: Convolutional neural network, Defect detection, Hyperspectral imaging, Pickling cucumber, Representation learning, Stacked sparse auto-encoder.