bluuebunny/crossref_metadata_2025_split huggingface dataset:
A competitive photoelectrochemical immunosensor based on a CdS-induced signal amplification strategy for the ultrasensitive detection of dexamethasone
Authors: Wang Xueping , Yan Tao , Li Yan , Liu Yixin , Du Bin , Ma Hongmin , Wei Qin 
Published: December 2015

AbstractA novel photoelectrochemical immunosensor based on the competitive strategy is proposed for the specific detection of dexamethasone (DXM). Graphitic carbon nitride coupled with bismuth sulfide are used as the sensing matrix for the immobilization of BSA-DXM on the electrode surface, while cadmium sulfide functionalized titanium dioxide (TiO2@CdS) is used as the photoelectric active labels of anti-DXM. Due to the perfect matching of energy levels between TiO2 and CdS, the in situ prepared composite labels show excellent photocurrent response under visible lights. The competitive binding of DXM in sample solutions and BSA-DXM on the electrode surface reduces the specific attachment of labels to the electrode, resulting in a decrease of the photocurrent intensity. Greatly enhanced sensitivity is achieved after the optimization of the detection conditions. Under the optimal detection condition, the well-designed immunosensor for DXM exhibits a low detection limit of 2 pg∙mL−1. Additionally, the proposed immunoassay system shows high specificity, good reproducibility and acceptable stability, which is also expected to become a promising platform for the detection of other small molecules.
Deep sequencing of hepatitis B virus basal core promoter and precore mutants in HBeAg-positive chronic hepatitis B patients
Authors: Yan Linlin , Zhang Henghui , Ma Hui , Liu Di , Li Wei , Kang Yulin , Yang Ruifeng , Wang Jianghua , He Gaixia , Xie Xingwang , Wang Hao , Wei Lai , Lu Zuhong , Shao Qixiang , Chen Hongsong 
Published: December 2015

AbstractMutants in the basal core promoter (BCP) and precore (PC) regions of hepatitis B virus (HBV) genome are associated with the progression of chronic hepatitis B (CHB) infection. However, quasispecies characteristics of naturally occurring mutants in those regions in HBeAg-positive CHB patients has not been well described, partly limited by quantitative assay. This study aimed to develop an Ion Torrent deep sequencing assay to determine BCP and PC mutant percentages in HBeAg-positive CHB patients who were treatment naïve and correlate them with different viral and host factors. Our results showed that Ion Torrent deep sequencing could achieve high accuracy (R2>0.99) within a dynamic range between 1% and 100%. Twelve hotspots with prevalence of greater than 20% were observed in EnhII/BCP/PC regions. G1719T, T1753V, A1762T and G1764A were genotype C related. BCP A1762T/G1764A double mutants were generally accompanied with PC 1896 wild type or lower PC G1896A mutant percentage. Lower serum HBeAg and HBsAg levels were associated with higher BCP A1762T/G1764A mutant percentages (≥50%). ALT levels were higher in patients with PC G1896A mutant percentage greater than 10%. In conclusion, deep sequencing such as Ion Torrent sequencing could accurately quantify HBV mutants for providing clinical relevant information during HBV infection.
Monomeric Garnet, a far-red fluorescent protein for live-cell STED imaging
Authors: Hense Anika , Prunsche Benedikt , Gao Peng , Ishitsuka Yuji , Nienhaus Karin , Ulrich Nienhaus G. 
Published: December 2015

AbstractThe advancement of far-red emitting variants of the green fluorescent protein (GFP) is crucially important for imaging live cells, tissues and organisms. Despite notable efforts, far-red marker proteins still need further optimization to match the performance of their green counterparts. Here we present mGarnet, a robust monomeric marker protein with far-red fluorescence peaking at 670 nm. Thanks to its large extinction coefficient of 95,000 M−1cm−1, mGarnet can be efficiently excited with 640-nm light on the red edge of its 598-nm excitation band. A large Stokes shift allows essentially the entire fluorescence emission to be collected even with 640-nm excitation, counterbalancing the lower fluorescence quantum yield of mGarnet, 9.1%, that is typical of far-red FPs. We demonstrate an excellent performance as a live-cell fusion marker in STED microscopy, using 640 nm excitation and 780 nm depletion wavelengths.
Emission color-tuned light-emitting diode microarrays of nonpolar InxGa1–xN/GaN multishell nanotube heterostructures
Authors: Hong Young Joon , Lee Chul-Ho , Yoo Jinkyoung , Kim Yong-Jin , Jeong Junseok , Kim Miyoung , Yi Gyu-Chul 
Published: December 2015

AbstractIntegration of nanostructure lighting source arrays with well-defined emission wavelengths is of great importance for optoelectronic integrated monolithic circuitry. We report on the fabrication and optical properties of GaN-based p–n junction multishell nanotube microarrays with composition-modulated nonpolar m-plane InxGa1–xN/GaN multiple quantum wells (MQWs) integrated on c-sapphire or Si substrates. The emission wavelengths were controlled in the visible spectral range of green to violet by varying the indium mole fraction of the InxGa1–xN MQWs in the range 0.13 ≤ x ≤ 0.36. Homogeneous emission from the entire area of the nanotube LED arrays was achieved via the formation of MQWs with uniform QW widths and composition by heteroepitaxy on the well-ordered nanotube arrays. Importantly, the wavelength-invariant electroluminescence emission was observed above a turn-on of 3.0 V because both the quantum-confinement Stark effect and band filling were suppressed due to the lack of spontaneous inherent electric field in the m-plane nanotube nonpolar MQWs. The method of fabricating the multishell nanotube LED microarrays with controlled emission colors has potential applications in monolithic nonpolar photonic and optoelectronic devices on commonly used c-sapphire and Si substrates.
Design and implementation of contactless power track system with Y‐shaped inductive pickup
Authors: Lee Jia‐You , Shen Hung‐Yu , Chang Hua‐Jing 
Published: December 2015

This study investigated an inductive power transfer technique to construct a new inductive pickup for contactless power track systems. Several three‐phase symmetrical shapes of the core material were simulated for the inductive pickup. The process to design the proposed pickup including a development of the core shape is discussed in this study. A feature of the proposed pickup is its three‐phase symmetrical shape, which enables sharing the flux path and achieving low reluctance. To evaluate the coupling ability of the proposed pickup, a magnetic equivalent circuit with air gap was established. The finite element method and experiments on the contactless power track prototype were analysed to validate the proposed inductive pickup and its magnetic equivalent circuit. A complete Y‐shaped inductive pickup was implemented and tested on a 1.2 kW laboratory‐scale prototype. Fundamental experiments were carried out, and the overall system efficiency and pickup performance were subsequently demonstrated to verify the feasibility and capability of the proposed contactless power track system.
Saccade direction encoding in the primate entorhinal cortex during visual exploration
Authors: Killian Nathaniel J. , Potter Steve M. , Buffalo Elizabeth A. 
Published: December 2015

Significance
Characterizing the dynamic encoding of body orientation and eye movements in the brain is central to understanding spatial representation. Studies in rodents have revealed an allocentric heading representation system known as the head-direction network. Visual information is presumed to be critical to rodent head-direction encoding; however, differences in the primate and rodent visual systems along with differences in exploratory behaviors across species have made it difficult to directly extend the findings from rodents to primates. This study describes a previously unidentified functional cell type in the primate entorhinal cortex that shows selectivity for the direction of saccadic eye movements. Future research avenues critical to increasing our understanding of spatial representation in the brain are suggested.
Origins of stereoselectivity in evolved ketoreductases
Authors: Noey Elizabeth L. , Tibrewal Nidhi , Jiménez-Osés Gonzalo , Osuna Sílvia , Park Jiyong , Bond Carly M. , Cascio Duilio , Liang Jack , Zhang Xiyun , Huisman Gjalt W. , Tang Yi , Houk Kendall N. 
Published: December 2015

Significance
Ketoreductases are the most commonly used enzymes in industrial pharmaceutical synthesis. We investigated the nature of enantioselectivity in closely related mutant ketoreductases that reduce almost-symmetrical 3-oxacyclopentanone and 3-thiacyclopentanone, which are difficult to reduce enantioselectively by other means. We present the efficiencies of select variants and their crystallographic structures. Our experimental and theoretical studies reveal how mutations modulate the stereoselectivity of the reduction. Molecular dynamics simulations of the Michaelis–Menten and transition state-bound complexes were used to rationalize the observed stereochemical outcomes. We discovered that the closed conformation of the flexible substrate binding loop is likely the catalytically active one imparting the stereochemical preferences. Our molecular dynamics approach reveals how each enzyme stabilizes the diastereomeric transition structures by altering the active site size.
Nitrogen regulator GlnR controls uptake and utilization of non-phosphotransferase-system carbon sources in actinomycetes
Authors: Liao Cheng-Heng , Yao Lili , Xu Ya , Liu Wei-Bing , Zhou Ying , Ye Bang-Ce 
Published: December 2015

Significance
Actinomycetes abundantly generate beneficial metabolic products. The efficient coutilization of heterogeneous carbon sources remains a major technical challenge for the industrial-scale production of drugs, chemicals, materials, and fuels by actinomycetes. Here, we present insights into the regulatory mechanisms of uptake and utilization of multiple carbohydrates in actinomycetes. GlnR (central regulator of nitrogen metabolism) was shown to regulate the control of ATP-binding cassette transport systems for secondary, non-phosphotransferase-system carbon sources. By integrating nitrogen signals to modulate the uptake and utilization of multiple carbon sources, GlnR mediates the interplay between nitrogen and carbon metabolism. These findings highlight the potential of actinomycetes in carbon utilization (especially cofermentation of biomass-derived sugars) for biorefinery applications. To our knowledge, our data represent the first systematic description of GlnR-mediated regulation of carbohydrate metabolism in actinomycetes.
Laser refrigeration of hydrothermal nanocrystals in physiological media
Authors: Roder Paden B. , Smith Bennett E. , Zhou Xuezhe , Crane Matthew J. , Pauzauskie Peter J. 
Published: December 2015

SignificanceAlthough the laser refrigeration of bulk crystals has recently shown to cool below cryogenic temperatures (∼90 K) in vacuum, to date the laser refrigeration of physiological media has not been reported. In this work, a low-cost hydrothermal synthetic approach is used to prepare nanocrystals that are capable of locally refrigerating physiological buffers (PBS, DMEM) upon near-infrared illumination. Optical tweezers are used in tandem with cold Brownian motion analysis to observe the refrigeration of individual (Yb3+)-doped nanocrystals >10 °C below ambient conditions. The ability to optically generate local refrigeration fields around individual nanocrystals promises to enable precise optical temperature control within integrated electronic/photonic/microfluidic circuits, and also thermal modulation of basic biomolecular processes, including the dynamics of motor proteins.
The precise temporal calibration of dinosaur origins
Authors: Marsicano Claudia A. , Irmis Randall B. , Mancuso Adriana C. , Mundil Roland , Chemale Farid 
Published: December 2015

Significance
Many hypotheses have been put forth to explain the origin and early radiation of dinosaurs, but poor age constraints for constituent fossil assemblages make these scenarios difficult to test. Using precise radioisotopic ages, we demonstrate that the temporal gap between assemblages containing only dinosaur precursors and those with the first dinosaurs was 5–10 million years shorter than previously thought. Thus, these data suggest that the origin of dinosaurs was a relatively rapid evolutionary event. Combined with our synthesis of paleoecological data, we demonstrate there was little compositional difference between the dinosaur precursor assemblages and the earliest dinosaur assemblages, and thus, the initial appearance of dinosaurs was not associated with a fundamental shift in ecosystem composition, as classically stated.
The ancestral gene repertoire of animal stem cells
Authors: Alié Alexandre , Hayashi Tetsutaro , Sugimura Itsuro , Manuel Michaël , Sugano Wakana , Mano Akira , Satoh Nori , Agata Kiyokazu , Funayama Noriko 
Published: December 2015

Significance
This work reveals the deeply conserved gene repertoire of animal stem cells, from sponges to mammals. This repertoire mostly contains ancient (premetazoan) genes and few novel (metazoan-specific) genes, but the latter point to the importance of genome protection in the origin of stem cells. Additionally, regulators of DNA transcription are only marginally represented among conserved stem-cell genes, whereas genes directly acting upon RNA predominate, including orthologues of RNA-binding proteins that control mammalian embryonic stem cells. Thus posttranscriptional regulation of gene expression has been crucial in animal stem-cell biology across hundreds of millions of years of animal evolution.
CREB pathway links PGE2 signaling with macrophage polarization
Authors: Luan Bing , Yoon Young-Sil , Le Lay John , Kaestner Klaus H. , Hedrick Susan , Montminy Marc 
Published: December 2015

Significance
The second messenger cAMP exerts potent immunosuppressive effects on the innate immune system, in part by activating class IIa histone deacetylases, and thereby inhibiting NF-κB–dependent transcription. We found that cAMP also promotes M2 macrophage polarization by stimulating the cyclic AMP-responsive element binding (CREB)/cAMP-regulated transcriptional coactivators TORC1 pathway. In the setting of acute overnutrition, macrophage CREB inhibits the production of inflammatory mediators and contributes to the maintenance of insulin sensitivity.
Tropical nighttime warming as a dominant driver of variability in the terrestrial carbon sink
Authors: Anderegg William R. L. , Ballantyne Ashley P. , Smith W. Kolby , Majkut Joseph , Rabin Sam , Beaulieu Claudie , Birdsey Richard , Dunne John P. , Houghton Richard A. , Myneni Ranga B. , Pan Yude , Sarmiento Jorge L. , Serota Nathan , Shevliakova Elena , Tans Pieter , Pacala Stephen W. 
Published: December 2015

Significance
The future of the terrestrial carbon (C) sink has tremendous consequences for society and the rate of climate change, but is highly uncertain. The sensitivity of interannual variability in the C sink to climate drivers can help elucidate the mechanisms driving the C sink. Here, we test the statistical strength of major climate drivers of the C sink and find that nighttime tropical temperatures are most strongly associated with the global C sink from 1959–2010, likely acting through their effect on respiration. The temperature-mediated sensitivity of the global C sink to respiration highlights that tropical C stores may be vulnerable to robust projected increases in tropical nighttime temperatures.
Moisture distribution and texture of spaghetti rehydrated under different conditions
Authors: Ogawa Takenobu , Adachi Shuji 
Published: December 2015

Abstract
Dried spaghetti was rehydrated to its optimal cooking state, known as al dente, at 60, 80, and 100 °C, in distilled water or 0.1, 1.0, and 2.0 mol/L sodium chloride solutions. Then, the moisture distributions and stress–strain curves were examined to identify the major factors governing the texture of rehydrated spaghetti. The difference in moisture content between the inner and peripheral regions of rehydrated spaghetti and its breaking stress were greater at higher rehydration temperatures; however, rehydration temperature did not affect breaking strain. The sodium chloride concentration of the immersion solution did not affect moisture distribution or breaking stress, while breaking strain was decreased by rehydration at higher sodium chloride concentrations. The results obtained in this study suggest that moisture distribution within spaghetti and its material properties govern its breaking stress and strain, respectively.
Studies on the biosynthesis of ralfuranones in Ralstonia solanacearum
Authors: Kai Kenji , Ohnishi Hideyuki , Kiba Akinori , Ohnishi Kouhei , Hikichi Yasufumi 
Published: December 2015

Abstract
Ralfuranones, aryl-furanone secondary metabolites, are involved in the virulence of Ralstonia solanacearum in solanaceous plants. Ralfuranone I (6) has been suggested as a biosynthetic precursor for other ralfuranones; however, this conversion has not been confirmed. We herein investigate the biosynthesis of ralfuranones using feeding experiments with ralfuranone I (6) and its putative metabolite, ralfuranone B (2). The results obtained demonstrated that the biosynthesis of ralfuranones proceeded in enzymatic and non-enzymatic manners.
Joint detection of copy number variations in parent-offspring trios
Authors: Liu Yongzhuang , Liu Jian , Lu Jianguo , Peng Jiajie , Juan Liran , Zhu Xiaolin , Li Bingshan , Wang Yadong 
Published: December 2015

Abstract
Motivation: Whole genome sequencing (WGS) of parent-offspring trios is a powerful approach for identifying disease-associated genes via detecting copy number variations (CNVs). Existing approaches, which detect CNVs for each individual in a trio independently, usually yield low-detection accuracy. Joint modeling approaches leveraging Mendelian transmission within the parent-offspring trio can be an efficient strategy to improve CNV detection accuracy.
Results: In this study, we developed TrioCNV, a novel approach for jointly detecting CNVs in parent-offspring trios from WGS data. Using negative binomial regression, we modeled the read depth signal while considering both GC content bias and mappability bias. Moreover, we incorporated the family relationship and used a hidden Markov model to jointly infer CNVs for three samples of a parent-offspring trio. Through application to both simulated data and a trio from 1000 Genomes Project, we showed that TrioCNV achieved superior performance than existing approaches.
Availability and implementation: The software TrioCNV implemented using a combination of Java and R is freely available from the website at https://github.com/yongzhuang/TrioCNV.
Contact: ydwang@hit.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Developments in the Orthopaedic Management of Children With Stüve-Wiedemann Syndrome: Use of the Fassier-Duval Telescopic Rod to Maintain Correction of Deformity
Authors: Wright Jonathan , Kazzaz Sarmad , Hill Robert A. 
Published: December 2015

Background:
Stüve-Wiedemann syndrome is a rare inherited condition, which is frequently fatal in infancy. Those patients who survive into childhood demonstrate a complex progressive deformity of the long bones, with high rates of recurrence after initial successful correction. Because of the rarity of the condition there is, at present, limited evidence on the most appropriate treatment.

Methods:
We describe our experience in the management of 4 patients, who underwent correction of deformity and fixation with Fassier-Duval telescopic rods.

Results:
In this series we have seen good correction of deformity and maintenance of alignment, with improvement in the walking ability of children treated with this technique.

Conclusion:
Fassier-Duval rodding has a role in the prevention of recurrence of deformity and should be considered as a means to reduce the number of operative procedures required.

Level of Evidence:
Level IV—therapeutic.
Echography of the Portal Vein in a Patient With Shock
Authors: Piton Gaël , Capellier Gilles , Delabrousse Eric 
Published: December 2015

Objectives:
To report the utility of abdominal ultrasonography to identify portal venous gas in patients with shock, as an indicator of acute mesenteric ischemia, and to illustrate the aspect of portal venous gas on ultrasonography.

Data Sources:
Clinical observation of a patient, images of abdominal ultrasonography and abdominal computed tomography, and video of portal venous gas.

Study Selection:
Not applicable.

Data Extraction:
Relevant information contained in the medical observation of the patient and selection of image and video of ultrasonography performed in the patient.

Data Synthesis:
We report a case of nonocclusive mesenteric ischemia in a 76-year-old patient following cardiac surgery. The diagnosis of acute mesenteric ischemia was proposed based on evidence of portal venous gas on abdominal ultrasonography and then confirmed by abdominal computed tomography showing transverse colonic ischemia, the presence of gas in the mesenteric veins but not in the portal vein. Urgent laparotomy confirmed extensive nonocclusive mesenteric ischemia, and the patient rapidly died of multiple organ failure.

Conclusions:
Intensive care physicians should be aware of the ultrasound characteristics of portal venous gas. In patients with shock, in addition to cardiac and thoracic echography, investigation of portal venous gas using bedside ultrasonography may help the clinician to identify patients in whom acute mesenteric ischemia develops.
Among Unstable Angina and Non–ST-Elevation Myocardial Infarction Patients, Transient Myocardial Ischemia and Early Invasive Treatment Are Predictors of Major In-hospital Complications
Authors: Pelter Michele M. , Loranger Denise L. , Kozik Teri M. , Kedia Anita , Ganchan Richard P. , Ganchan Deborah , Hu Xiao , Carey Mary G. 
Published: December 2015

Background:
Treatment for unstable angina (UA) or non–ST-elevation myocardial infarction (NSTEMI) is aimed at plaque stabilization to prevent infarction. Two treatment strategies are (1) invasive (ie, cardiac catheterization laboratory <24 hours after admission) or (2) selectively invasive (ie, medications with cardiac catheterization laboratory >24 hours for recurrent symptoms). However, it is not known if the frequency of transient myocardial ischemia (TMI) or complications during hospitalization varies by treatment.

Purpose:
We aimed to (1) examine occurrence of TMI in UA/NSTEMI, (2) compare frequency of TMI by treatment pathway, and (3) determine predictors of in-hospital complications (ie, death, myocardial infarction [MI], pulmonary edema, shock, dysrhythmia with intervention).

Methods:
Hospitalized patients with coronary artery disease (ie, history of MI, percutaneous coronary intervention/stent, coronary artery bypass graft, >50% lesion via angiogram, or positive troponin) were recruited, and 12-lead electrocardiogram Holter initiated. Clinicians, blinded to Holter data, decided treatment strategy; offline analysis was done after discharge. Transient myocardial ischemia was defined as more than 1-mm ST segment ↑ or ↓, in more than 1 electrocardiographic lead, more than 1 minute.

Results:
Of 291 patients, 91% were white, 66% were male, 44% had prior MI, and 59% had prior percutaneous coronary intervention/stent or coronary artery bypass graft. Treatment pathway was early in 123 (42%) and selective in 168 (58%). Forty-nine (17%) had TMI: 19 (15%) early invasive, 30 (18%) selective (P = .637). Acute MI after admission was higher in patients with TMI regardless of treatment strategy (early: no TMI 4% vs yes TMI 21%; P = .020; selective: no TMI 1% vs yes TMI 13%; P = .0004). Predictors of major in-hospital complication were TMI (odds ratio, 9.9; 95% confidence interval, 3.84–25.78) and early invasive treatment (odds ratio 3.5; 95% confidence interval, 1.23–10.20).

Conclusions:
In UA/NSTEMI patients treated with contemporary therapies, TMI is not uncommon. The presence of TMI and early invasive treatment are predictors of major in-hospital complications.