bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prolonged sleep restriction induces changes in pathways involved in cholesterol metabolism and inflammatory responses
Authors: Aho Vilma , Ollila Hanna M. , Kronholm Erkki , Bondia-Pons Isabel , Soininen Pasi , Kangas Antti J. , Hilvo Mika , Seppälä Ilkka , Kettunen Johannes , Oikonen Mervi , Raitoharju Emma , Hyötyläinen Tuulia , Kähönen Mika , Viikari Jorma S.A. , Härmä Mikko , Sallinen Mikael , Olkkonen Vesa M. , Alenius Harri , Jauhiainen Matti , Paunio Tiina , Lehtimäki Terho , Salomaa Veikko , Orešič Matej , Raitakari Olli T. , Ala-Korpela Mika , Porkka-Heiskanen Tarja 
Published: April 2016

AbstractSleep loss and insufficient sleep are risk factors for cardiometabolic diseases, but data on how insufficient sleep contributes to these diseases are scarce. These questions were addressed using two approaches: an experimental, partial sleep restriction study (14 cases and 7 control subjects) with objective verification of sleep amount, and two independent epidemiological cohorts (altogether 2739 individuals) with questions of sleep insufficiency. In both approaches, blood transcriptome and serum metabolome were analysed. Sleep loss decreased the expression of genes encoding cholesterol transporters and increased expression in pathways involved in inflammatory responses in both paradigms. Metabolomic analyses revealed lower circulating large HDL in the population cohorts among subjects reporting insufficient sleep, while circulating LDL decreased in the experimental sleep restriction study. These findings suggest that prolonged sleep deprivation modifies inflammatory and cholesterol pathways at the level of gene expression and serum lipoproteins, inducing changes toward potentially higher risk for cardiometabolic diseases.
Exact comprehensive equations for the photon management properties of silicon nanowire
Authors: Li Yingfeng , Li Meicheng , Li Ruike , Fu Pengfei , Wang Tai , Luo Younan , Mbengue Joseph Michel , Trevor Mwenya 
Published: April 2016

AbstractUnique photon management (PM) properties of silicon nanowire (SiNW) make it an attractive building block for a host of nanowire photonic devices including photodetectors, chemical and gas sensors, waveguides, optical switches, solar cells, and lasers. However, the lack of efficient equations for the quantitative estimation of the SiNW’s PM properties limits the rational design of such devices. Herein, we establish comprehensive equations to evaluate several important performance features for the PM properties of SiNW, based on theoretical simulations. Firstly, the relationships between the resonant wavelengths (RW), where SiNW can harvest light most effectively, and the size of SiNW are formulized. Then, equations for the light-harvesting efficiency at RW, which determines the single-frequency performance limit of SiNW-based photonic devices, are established. Finally, equations for the light-harvesting efficiency of SiNW in full-spectrum, which are of great significance in photovoltaics, are established. Furthermore, using these equations, we have derived four extra formulas to estimate the optimal size of SiNW in light-harvesting. These equations can reproduce majority of the reported experimental and theoretical results with only ~5% error deviations. Our study fills up a gap in quantitatively predicting the SiNW’s PM properties, which will contribute significantly to its practical applications.
Soluble VEGF receptor 1 (sFLT1) induces non-apoptotic death in ovarian and colorectal cancer cells
Authors: Miyake Tatsuya , Kumasawa Keiichi , Sato Noriko , Takiuchi Tsuyoshi , Nakamura Hitomi , Kimura Tadashi 
Published: April 2016

AbstractSoluble Vascular Endothelial Growth Factor Receptor 1 (sVEGFR1/sFLT1) is an angiogenesis inhibitor that competes with angiogenic factors such as VEGF and Placental Growth Factor (PlGF). Imbalances of VEGF and sFLT1 levels can cause pathological conditions such as tumour growth or preeclampsia. We observed direct damage caused by sFLT1 in tumour cells. We exposed several kinds of cells derived from ovarian and colorectal cancers as well as HEK293T cells to sFLT1 in two ways, transfection and exogenous application. The cell morphology and an LDH assay revealed cytotoxicity. Additional experiments were performed to clarify how sFLT1 injured cells. In this study, non-apoptotic cell damage was found to be induced by sFLT1. Moreover, sFLT1 showed an anti-tumour effect in a mouse model of ovarian cancer. Our results suggest that sFLT1 has potential as a cancer therapeutic candidate.
Response of tomato wilt pathogen Ralstonia solanacearum to the volatile organic compounds produced by a biocontrol strain Bacillus amyloliquefaciens SQR-9
Authors: Raza Waseem , Ling Ning , Yang Liudong , Huang Qiwei , Shen Qirong 
Published: April 2016

AbstractIt is important to study the response of plant pathogens to the antibiosis traits of biocontrol microbes to design the efficient biocontrol strategies. In this study, we evaluated the role of volatile organic compounds (VOCs) produced by a biocontrol strain Bacillus amyloliquefaciens SQR-9 on the growth and virulence traits of tomato wilt pathogen Ralstonia solanacearum (RS). The VOCs of SQR-9 significantly inhibited the growth of RS on agar medium and in soil. In addition, the VOCs significantly inhibited the motility traits, production of antioxidant enzymes and exopolysaccharides, biofilm formation and tomato root colonization by RS. The strain SQR-9 produced 22 VOCs, but only nine VOCs showed 1–11% antibacterial activity against RS in their corresponding amounts; however, the consortium of all VOCs showed 70% growth inhibition of RS. The proteomics analysis showed that the VOCs of SQR-9 downregulated RS proteins related to the antioxidant activity, virulence, carbohydrate and amino acid metabolism, protein folding and translation, while the proteins involved in the ABC transporter system, amino acid synthesis, detoxification of aldehydes and ketones, methylation, protein translation and folding, and energy transfer were upregulated. This study describes the significance and effectiveness of VOCs produced by a biocontrol strain against tomato wilt pathogen.
Microwave-assisted Facile and Ultrafast Growth of ZnO Nanostructures and Proposition of Alternative Microwave-assisted Methods to Address Growth Stoppage
Authors: Rana Abu ul Hassan Sarwar , Kang Mingi , Kim Hyun-Seok 
Published: April 2016

AbstractThe time constraint in the growth of ZnO nanostructures when using a hydrothermal method is of paramount importance in contemporary research, where a long fabrication time rots the very essence of the research on ZnO nanostructures. In this study, we present the facile and ultrafast growth of ZnO nanostructures in a domestic microwave oven within a pressurized environment in just a few minutes. This method is preferred for the conventional solution-based method because of the ultrafast supersaturation of zinc salts and the fabrication of high-quality nanostructures. The study of the effect of seed layer density, growth time, and the solution’s molar concentration on the morphology, alignment, density, and aspect ratio of ZnO nanorods (ZNRs) is explored. It is found in a microwave-assisted direct growth method that ~5 mins is the optimum time beyond which homogeneous nucleation supersedes heterogeneous nucleation, which results in the growth stoppage of ZNRs. To deal with this issue, we propound different methods such as microwave-assisted solution-replacement, preheating, and PEI-based growth methods, where growth stoppage is addressed and ZNRs with a high aspect ratio can be grown. Furthermore, high-quality ZnO nanoflowers and ZnO nanowalls are fabricated via ammonium hydroxide treatment in a very short time.
Negative incidental emotions augment fairness sensitivity
Authors: Liu Cuizhen , Chai Jing Wen , Yu Rongjun 
Published: April 2016

AbstractPrevious studies have shown that task-unrelated emotions induced incidentally exert carryover effects on individuals’ subsequent decisions in financial negotiations. However, the specificity of these emotion effects are not clear. In three experiments, we systematically investigated the role of seven transiently induced basic emotions (disgust, sadness, anger, fear, happiness, surprise and neutral) on rejection of unfair offers using the ultimatum game. We found that all negative emotions (disgust, sadness, anger and fear), but not happiness or surprise, significantly increased rejection rates, suggesting that the effect of incidental negative emotions on fairness is not specific to the type of negative emotion. Our findings highlight the role of fleeting emotions in biasing decision-making processes and suggest that all incidental negative emotions exert similar effects on fairness sensitivity, possibly by potentiating attention towards negative aspects of the situation.
The sporulation of the green alga Ulva prolifera is controlled by changes in photosynthetic electron transport chain
Authors: Wang Hui , Lin Apeng , Gu Wenhui , Huan Li , Gao Shan , Wang Guangce 
Published: April 2016

AbstractSporulation and spore release are essential phases of the life cycle in algae and land plants. Ulva prolifera, which is an ideal organism for studying sporulation and spore release, was used as the experimental material in the present study. The determination of photosynthetic parameters, combined with microscopic observation, treatment with photosynthetic inhibitors, limitation of carbon acquisition, and protein mass spectrometry, was employed in this experiment. Cycle electron transport (CEF) was found enhanced at the onset of sporangia formation. The inhibition effect of dibromothymoquinone (DBMIB) towards sporulation was always strong during the sporulation process whereas the inhibition effect of 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea (DCMU) was continuously declined accompanied with the progress of sporulation. The changes of photosynthesis resulted from the limitation of CO2 acquisition could stimulate sporulation onset. Quantitative protein analysis showed that enzymes involved in carbon fixation, including RUBISCO and pyruvate orthophosphate dikinase, declined during sporogenesis, while proteins involved in sporulation, including tubulin and centrin, increased. These results suggest that enhanced cyclic electron flow (CEF) and oxidation of the plastoquinone pool are essential for sporangia formation onset, and changes in photosynthetic electron transport chain have significant impacts on sporulation of the green algae.
Dietary proanthocyanidins boost hepatic NAD+ metabolism and SIRT1 expression and activity in a dose-dependent manner in healthy rats
Authors: Aragonès Gerard , Suárez Manuel , Ardid-Ruiz Andrea , Vinaixa Maria , Rodríguez Miguel A. , Correig Xavier , Arola Lluís , Bladé Cinta 
Published: April 2016

AbstractProanthocyanidins (PACs) have been reported to modulate multiple targets by simultaneously controlling many pivotal metabolic pathways in the liver. However, the precise mechanism of PAC action on the regulation of the genes that control hepatic metabolism remains to be clarified. Accordingly, we used a metabolomic approach combining both nuclear magnetic resonance and mass spectrometry analysis to evaluate the changes induced by different doses of grape-seed PACs in the liver of healthy rats. Here, we report that PACs significantly increased the hepatic nicotinamide adenine dinucleotide (NAD+) content in a dose-dependent manner by specifically modulating the hepatic concentrations of the major NAD+ precursors as well as the mRNA levels of the genes that encode the enzymes involved in the cellular metabolism of NAD+. Notably, Sirtuin 1 (Sirt1) gene expression was also significantly up-regulated in a dose-response pattern. The increase in both the NAD+ availability and Sirt1 mRNA levels, in turn, resulted in the hepatic activation of SIRT1, which was significantly associated with improved protection against hepatic triglyceride accumulation. Our data clearly indicates that PAC consumption could be a valid tool to enhance hepatic SIRT1 activity through the modulation of NAD+ levels.
Spinal Compression Fracture Management
Authors: Genev Ivo K. , Tobin Matthew K. , Zaidi Saher P. , Khan Sajeel R. , Amirouche Farid M. L. , Mehta Ankit I. 
Published: April 2016

Study Design Narrative review. Objective Despite the numerous treatment options for vertebral compression fractures, a consensus opinion for the management of patients with these factures has not been established. This review is meant to provide an up-to-date overview of the most common treatment strategies for compression fractures and to suggest possible routes for the development of clearer treatment guidelines. Methods A comprehensive database search of PubMed was performed. All results from the past 30 years were obtained and evaluated based on title and abstract. The full length of relevant studies was analyzed for level of evidence, and the strongest studies were used in this review. Results The major treatment strategies for patients with compression fractures are conservative pain management and vertebral augmentation. Despite potential adverse effects, medical management, including nonsteroidal anti-inflammatory drugs, calcitonin, teriparatide, and bisphosphonates, remains the first-line therapy for patients. Evidence suggests that vertebral augmentation, especially some of the newer procedures, have the potential to dramatically reduce pain and improve quality of life. At this time, balloon-assisted kyphoplasty is the procedure with the most evidence of support. Conclusions Based on current literature, it is evident that there is a lack of standard of care for patients with vertebral compression fractures, which is either due to lack of evidence that a procedure is successful or due to serious adverse effects encountered with prolonged treatment. For a consensus to be reached, prospective clinical trials need to be formulated with potential new biomarkers to assess efficacy of treatment strategies.
Inanspruchnahme zentraler Notaufnahmen: Qualitative Erhebung der Motivation von Patientinnen und Patienten mit nichtdringlichem Behandlungsbedarf
Authors: Schmiedhofer M. , Searle J. , Slagman A. , Möckel M. 
Published: April 2016

Zusammenfassung
Einleitung: Die steigende Inanspruchnahme von Zentralen Notaufnahmen (ZNA) durch Patientinnen und Patienten mit akut-, aber nicht notfallmedizinischem Versorgungsbedarf trägt zur Überfüllung der Notaufnahmen bei. Ziel dieser Arbeit ist die Exploration der subjektiven Motive zum Aufsuchen der ZNA durch Menschen mit nichtdringlichem Behandlungsbedarf.
Methode: In einer qualitativen Studie wurden 40 leitfadengestützte Interviews mit ambulanten Patientinnen und Patienten ohne dringlichen Handlungsbedarf an 2 ZNA der Charité Berlin durchgeführt und mit der Qualitativen Inhaltsanalyse ausgewertet.
Ergebnis: Neben der Substitution nicht oder spät verfügbarer Haus- oder Facharzttermine gaben die Befragten als Hauptmotive Zeitautonomie, den Qualitätsstandard eines universitären Krankenhauses sowie die Möglichkeit multidisziplinärer Untersuchungen während eines Termins an. Die Bemühungen um eine Terminfindung im ambulanten Bereich erschienen durch die allzeitige Verfügbarkeit der ZNA teilweise wenig konsequent.
Schlussfolgerung: Die Interviewdaten zeigen eine eigenständige Funktion der ZNA für ambulante Behandlungen auf. Es ist anzunehmen, dass auch eine konsequentere Wahrnehmung des Sicherstellungsauftrages der KV die Anforderungen an die ZNA nicht auf die Versorgung medizinischer Notfälle zurückführen könnte. Zur dauerhaften Sicherstellung der medizinischen Qualität für Patientinnen und Patienten aller Dringlichkeitsstufen ist eine den Anforderungen entsprechende Ausstattung der ZNA erforderlich.
ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction
Authors: Sahoo Sudhakar , Świtnicki Michał P. , Pedersen Jakob Skou 
Published: April 2016

Abstract
Motivation: Recently, new RNA secondary structure probing techniques have been developed, including Next Generation Sequencing based methods capable of probing transcriptome-wide. These techniques hold great promise for improving structure prediction accuracy. However, each new data type comes with its own signal properties and biases, which may even be experiment specific. There is therefore a growing need for RNA structure prediction methods that can be automatically trained on new data types and readily extended to integrate and fully exploit multiple types of data.
Results: Here, we develop and explore a modular probabilistic approach for integrating probing data in RNA structure prediction. It can be automatically trained given a set of known structures with probing data. The approach is demonstrated on SHAPE datasets, where we evaluate and selectively model specific correlations. The approach often makes superior use of the probing data signal compared to other methods. We illustrate the use of ProbFold on multiple data types using both simulations and a small set of structures with both SHAPE, DMS and CMCT data. Technically, the approach combines stochastic context-free grammars (SCFGs) with probabilistic graphical models. This approach allows rapid adaptation and integration of new probing data types.
Availability and Implementation: ProbFold is implemented in C ++. Models are specified using simple textual formats. Data reformatting is done using separate C ++ programs. Source code, statically compiled binaries for x86 Linux machines, C ++ programs, example datasets and a tutorial is available from http://moma.ki.au.dk/prj/probfold/ .
Contact : jakob.skou@clin.au.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
Optimizing transmit interval and logging range while avoiding aliased seabed echoes
Authors: Renfree Josiah S. , Demer David A. 
Published: April 2016

Abstract
Echosounder surveys of fish and zooplankton are typically conducted using fixed values of the echosounder transmit-pulse (“ping”) interval and data-logging range. The transmit-pulse interval must be long enough to sample to the range of the farthest (deepest) species under study, potentially causing undersampling of closer (shallower) species. We present an algorithm to dynamically minimize both the logging range and transmit-pulse interval while ensuring that the logging range equals or exceeds the range to the seabed up to a chosen maximum data-logging range. The algorithm also allows avoidance of aliased seabed echoes (“false bottoms”) by adjusting the minimized transmit interval such that seabed reverberation from a previous transmission is not present in the data logged for an ensuing transmission. Additionally, periodic measures of ambient noise allow evaluations of signal quality and useful range. This optimization scheme (“adaptive logging”) effectively increases the horizontal resolution and signal-to-noise ratio of the data, and may reduce the total data volume and storage-space requirement. The efficacy of the adaptive logging algorithm is quantified using simulations. Furthermore, an example implementation of the algorithm is demonstrated for a commonly used scientific echosounder (Simrad EK60).
Fine Configuration of Thoracic Type II Meningeal Cysts
Authors: Thorpe Lowis Casper G. , Zhang Ming , Amin Nahid F. 
Published: April 2016

Study Design.
A cadaveric study

Objective.
The aim of this study was to analyze the in situ macro- and microscopic configuration of the type II cyst and its anatomic relationship with surrounding structures.

Summary of Background Data.
The lack of consensus of surgical strategy to manage symptomatic type II meningeal cysts (Tarlov cysts) is because our knowledge of type II cyst anatomy remains incomplete. It has been assumed that the cyst communicates with the subarachnoid space via microconnections. Till date, however, no direct evidence demonstrates the existence of the microconnections, although delayed contrast filling of type II cysts is commonly observed in CT myelography.

Methods.
Three type II meningeal cysts analyzed in this study were incidentally found in one of 16 plastinated spines. The spine was from an 89-year-old female cadaver and plastinated as a set of 164 transverse sections with a thickness of 2.5 mm. The sections were examined under a stereomicroscope.

Results.
Three type II cysts were in the thoracic spine and had a common feature that a clearly identifiable cyst neck connected the cyst body to the subarachnoid space. The dorsal root of the spinal nerve was centered in the cyst neck but spread over the cyst body or traversed the cyst cavity. The meningeal opening of the cyst was located above the inferior border of the vertebral pedicle, thus, the cyst neck hugged around the pedicle and sharply turned inferolaterally into the intervertebral foramen. The cyst body was halted by the dorsal ganglion.

Conclusion.
This study reveals in situ macro- and microscopic configuration of the type II cyst and its relationship with the structures and suggests that it may be feasible to localize and ligate the cyst neck for surgical management of type II cysts.

Level of Evidence: 3
Clinical Features and Prognostic Factors of Patients With Nerve Sheath Tumors in the Cervical Spine
Authors: Li Bo , Yin Huabin , Meng Tong , Zhou Pingting , Han Zhitao , Jia Qi , Cai Weiluo , Han Shuai , Wang Ting , Chen Tianrui , Zhou Wang , Xiao Jianru 
Published: April 2016

Study Design.
A retrospective study was performed.

Objective.
The aim of the study was to illustrate the long-term follow-up results and discuss the possible factors that may affect outcomes of patients with cervical spinal nerve sheath tumors (CSNSTs).

Summary of Background Data.
Nerve sheath tumors are the most common neoplasms in the spine, but minimal information was published in the literature, especially when regarding to prognostic factors due to the benign nature. The objective of our study was to present long-term follow-up results and discuss the possible factors that may affect outcomes of patients with CSNSTs.

Methods.
A retrospective analysis of patients with CSNSTs was performed by survival analysis. The local relapse-free survival (LRFS) and overall survival (OS) rates were estimated using the Kaplan-Meier method to identify potential prognostic factors. Factors with P values ≤0.1 were subjected to multivariate analysis by Cox regression analysis. P values ≤0.05 were considered statistically significant.

Results.
A total of 169 patients with CSNSTs were included in the study. All patients received surgical treatment. The mean follow-up period was 72.1 months (median 62.0, range 1–158). Local recurrence was detected in 14 patients after surgery in our center, whereas death occurred in 9 patients with a mean follow-up of 27.2 months (median 24, range 1–84). The statistical analyses suggested that resection mode and pathology type were independent prognostic factors for LRFS and OS. In addition, postoperative recurrence was an adverse independent factor to OS.

Conclusion.
Total resection could significantly improve the LRFS and OS for patients with CSNSTs, whereas malignant CSNST was associated with worse prognosis. Moreover, postoperative recurrence was an adverse independent factor to OS.

Level of Evidence: 4