bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of soil microbial communities for promoting sustainability in agriculture and a global carbon fix
Authors: Johnson David , Ellington Joe , Eaton Wesley 
Published: January 2018

The goals of this research were to explore alternative agriculture management practices in both greenhouse and field trials that do not require the use of synthetic and/or inorganic nutrient amendments but instead would emulate mechanisms operating in natural ecosystems, between plant and Soil Microbial Communities (SMC), for plant nutrient acquisition and growth.
Greenhouse plant-growth trials, implementing a progression of soil conditions with increasing soil carbon (C) (C= 0.14% to 5.3%) and associated SMC population with increasing Fungal to Bacterial ratios (F:B) ( from 0.04 to 3.68), promoted a) increased C partitioning into plant shoot and plant fruit partitions (m=4.41, r2=0.99), b) significant quantities of plant photosynthate, 49%-97% of Total System New C (CTSN), partitioned towards increasing soil C c) four times reduction in soil C respiration (CR) as F:B ratios increased, starting with 44% of initial treatment soil C content respired in bacterial-dominant soils (low F:B), to 11% of soil C content respired in higher fertility fungal-dominant soils (Power Regression, r2=0.90; p=0.003).
Plant growth trials in fields managed for increased soil C content and enhanced SMC population and structure (increased F:B) demonstrated: a) dry aboveground biomass production rates (g m-2) of ~1,980 g in soils initiating SMC enhancement (soil C=0.87, F:B= 0.80) with observed potentials of 8,450 g in advanced soils (soil C=7.6%, F:B=4.3) b) a 25-times increase in active soil fungal biomass and a ~7.5 times increase in F:B over a 19 month application period to enhance SMC and c) reduced soil C respiration rates, from 1.25 g C m-2 day-1 in low fertility soils (soil C= 0.6%, F:B= 0.25) with only a doubling of respiration rates to 2.5 g C m-2 day-1 in a high-fertility soil with an enhanced SMC (F:B= 4.3) and >7 times more soil C content (soil C= 7.6%).
Enhancing SMC population and F:B structure in a 4.5 year agricultural field study promoted annual average capture and storage of 10.27 metric tons soil C ha-1 year -1 while increasing soil macro-, meso- and micro-nutrient availability offering a robust, cost-effective carbon sequestration mechanism within a more productive and long-term sustainable agriculture management approach.
spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Authors: Vitting-Seerup Kristoffer , Porse Bo T , Sandelin Albin , Waage Johannes E 
Published: January 2018

Background: With the increasing depth and decreasing costs of RNA-sequencing researchers are now able to profile the transcriptome with unprecedented detail. These advances not only allow for precise approximation of gene expression levels, but also for the characterization of alternative transcript usage/switching between conditions. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.
Results: spliceR uses the full-length transcripts output from RNA-seq assemblers, to detect single- and multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements facilitating downstream sequence analysis. Furthermore, isoform fraction values are calculated for effective post-filtering, i.e. identification of transcript switching between conditions. Lastly spliceR predicts the coding potential, as well as the potential nonsense mediated decay (NMD) sensitivity of each transcript.
Conclusions: spliceR is a easy-to-use tool that allows detection of alternative splicing, transcript switching and NMD sensitivity from RNA-seq data, extending the usability of RNA-seq and assembly technologies. spliceR is implemented as an R package and is freely available from the Bioconductor repository (http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html).
The effects of reduced impact logging and logging intensity on stand damage, biomass loss and tree species richness in tropical forests: a meta-analysis
Authors: Martin Philip A , Newton Adrian , Pfeifer Marion , Khoo MinSheng , Bullock James 
Published: January 2018

Background. At least a fifth of tropical forests have been logged in the recent past. This practice is an important source of timber but there are concerns about its long-sustainability and impacts on biodiversity and carbon storage. However, there is wide variation in the impacts of logging, making generalisation, and thus policy implementation, difficult. Recent syntheses of animal biodiversity have indicated that differences in logging intensity – the volume of wood removed per hectare – may help explain some of these differences. In addition there have been suggestions that reduced impact logging (RIL) may reduce some of the negative effects of logging.
Methods. We aimed to test these hypotheses using meta-analyses to explore differences in the impacts of logging on (1) residual tree damage, (2) aboveground biomass and (3) tree species richness. To do this we used a mixture of unweighted mixed models and weighted meta-regression
Results. Our results indicate that RIL may reduce residual tree damage when compared to conventional methods, but that at higher logging intensities this effect is negated. Changes in aboveground biomass were negatively related to logging intensity, but any effect of RIL was obscured by it being carried out at relatively low intensities. Tree richness appeared to initially increase at low intensities but was reduced at higher intensities.
Discussion. Our results give only weak support to the hypothesis that RIL reduces the negative impacts of logging on tree damage, and do not support suggestions that RIL reduces loss of biomass or species richness. However, we do not think this is because there is no difference between the impacts of RIL and conventional logging but rather that better evidence is needed to assess these differences. We suggest that studies that take account of plot-level differences in logging intensity are likely to provide a solution to this knowledge gap.
Pulmonary anatomy in the Trionychia and its bearing on cryptodiran evolution
Authors: Lambertz Markus , Perry Steven F 
Published: January 2018

Background. The relationships among cryptodiran turtles often appear controversial depending on the approach followed (morphology vs. molecules). One controversy concerns the placement of the Trionychia (Carettochelys insculpta Ramsay, 1886 + Trionychidae), which usually is treated as sister taxon of Kinosternidae and thereby nested well within Cryptodira (morphology), or as sister taxon of all remaining cryptodirans (molecules). The aim of the present study is to introduce new data on the respiratory apparatus to this discussion.
Methods. Lungs and associated structures (extrapulmonary airways, coelomic integration, respiratory musculature), of C. insculpta and that of several Trionychidae were examined macroscopically. The excised lungs were dried, opened and photographed, or imaged using a µCT device.
Results. The lungs show a characteristic separation from the viscera by the post-pulmonary septum (PPS), which varies in its extent from highly incomplete to complete. The primary respiratory musculature is composed of the musculus transversus thoracis, m. t. abdominis and m. obliquus abdominis. The lungs of C. insculpta superficially resemble that of the Trionychidae, but differ markedly from them and all other turtles studied so far in that they exhibit a medially located, almost sac-like and elongated, huge additional chamber. The right extrapulmonary bronchi of all trionychians examined are shorter than the left ones, causing a dislocation of the trachea to the right side of the cervical region.
Discussion. The principal coelomic compartmentalization by the PPS agrees with previous studies on turtles, but indicates the convergent development of a completely separated pleural cavity in Trionychidae. The presence and anatomy of the respiratory musculature is in agreement with that recently inferred for turtles as a whole. Our data confirm the evolutionary distinctiveness of the taxon Carettochelyidae with its sole extant member C. insculpta based on their pulmonary autapomorphy. The monophyly of the Trionychia, as defined above, is supported by several potential synapomorphies of the respiratory system. Most important, however, is that our data, especially on the extrapulmonary airways, provide morphological support for the predominantly molecular-based hypothesis of an early split of the Cryptodira into the Trionychia and the remaining lineages. The displacement of the trachea to the right side contrasts with the situation found in all remaining cryptodirans, in which the trachea lies to the left of the esophagus (or an extreme reduction of tracheal length as in Testudinidae). This anatomical dichotomy could be related to the evolution of the specialized mechanism of neck retraction in cryptodirans. Our study points up the importance of so-called soft-tissue characters in inferring the evolutionary relationships of organisms in general, and of turtles in particular.
A diagnostic model for minimal change disease based on biological parameters
Authors: Zhu Hanyu , Han Qiuxia , Zhang Dong , Wang Yong , Gao Jing , Geng Wenjia , Yang Xiaoli , Chen Xiangmei 
Published: January 2018

Background
Minimal change disease (MCD) is a kind of nephrotic syndrome (NS). In this study, we aimed to establish a mathematical diagnostic model based on biological parameters to classify MCD.

Methods
A total of 798 NS patients were divided into MCD group and control group. The comparison of biological indicators between two groups were performed with t-tests. Logistic regression was used to establish the diagnostic model, and the diagnostic value of the model was estimated using receiver operating characteristic (ROC) analysis.

Results
Thirteen indicators including Anti-phospholipase A2 receptor (anti-PLA2R) (P = 0.000), Total protein (TP) (P = 0.000), Albumin (ALB) (P = 0.000), Direct bilirubin (DB) (P = 0.002), Creatinine (Cr) (P = 0.000), Total cholesterol (CH) (P = 0.000), Lactate dehydrogenase (LDH) (P = 0.007), High density lipoprotein cholesterol (HDL) (P = 0.000), Low density lipoprotein cholesterol (LDL) (P = 0.000), Thrombin time (TT) (P = 0.000), Plasma fibrinogen (FIB) (P = 0.000), Immunoglobulin A (IgA) (P = 0.008) and Complement 3 (C3) (P = 0.019) were significantly correlated with MCD. Furthermore, the area under ROC curves of CH, HDL, LDL, TT and FIB were more than 0.70. Logistic analysis demonstrated that CH and TT were risk factors for MCD. According to the ROC of “CH+TT”, the AUC was 0.827, with the sensitivity of 83.0% and the specificity of 69.8% (P = 0.000).

Conclusion
The established diagnostic model with CH and TT could be used for classified diagnosis of MCD.
Weekend effect in upper gastrointestinal bleeding: a systematic review and meta-analysis
Authors: Shih Pei-Ching , Liu Shu-Jung , Li Sung-Tse , Chiu Ai-Chen , Wang Po-Chuan , Liu Lawrence Yu-Min 
Published: January 2018

AimTo perform a systematic review and meta-analysis of the weekend effect on the mortality of patients with upper gastrointestinal bleeding(UGIB).MethodsThe review protocol has been registered in the PROSPERO International Prospective Register of Systematic Reviews (registration number: CRD42017073313) and was written according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. We conducted a search of the PUBMED, COCHRANE, EMBASE and CINAHL databases from inception to August 2017. All observational studies comparing mortality between UGIB patients with weekend versus weekday admissions were included. Articles that were published only in abstract form or not published in a peer-reviewed journal were excluded. The quality of articles was assessed using the Newcastle-Ottawa Scale. We pooled results from the articles using random-effect models. Heterogeneity was evaluated by the chi-square-basedQ-test andI2test. To address heterogeneity, we performed sensitivity and subgroup analyses. Potential publication bias was assessed via funnel plot.ResultsEighteen observational cohort studies involving 1,232,083 study patients were included. Weekend admission was associated with significantly higher 30-day or in-hospital mortality in all studies (OR = 1.12, 95% CI [1.07–1.17],P < 0.00001). Increased in-hospital mortality was also associated with weekend admission (OR = 1.12, 95% CI [1.08–1.17],P < 0.00001). No significant difference in in-hospital mortality was observed between patients admitted with variceal bleeding during the weekend or on weekdays (OR = 0.99, 95% CI [0.91–1.08],P = 0.82); however, weekend admission was associated with a 15% increase in in-hospital mortality for patients with non-variceal bleeding (OR = 1.15, 95% CI [1.09–1.21],P < 0.00001). The time to endoscopy for weekday admission was significantly less than that obtained for weekend admission (MD = −2.50, 95% CI [−4.08–−0.92],P = 0.002).ConclusionsThe weekend effect is associated with increased mortality of UGIB patients, particularly in non-variceal bleeding. The timing of endoscopic intervention might be a factor that influences mortality of UGIB patients.
New Magnetospheric Substorm Injection Monitor: Image Electron Spectrometer On Board a Chinese Navigation IGSO Satellite
Authors: Zong Qiugang , Wang Yongfu , Zou Hong , Wang Linghua , Rankin Robert , Zhang Xiaoxin 
Published: January 2018

AbstractSubstorm injections are one of the most dynamic processes in Earth's magnetosphere and have global consequences and broad implications for space weather modeling. They can be monitored using energetic electron detectors on geosynchronous satellites. The Imaging Electron Spectrometer (IES) on board a Chinese navigation satellite, launched on 16 October 2015 into an inclined geosynchronous satellite orbit (IGSO), provides the first energetic electron measurement in IGSO orbit to the best of our knowledge. The IES was developed by Peking University and is named hereafter as BD‐IES. Using a pin‐hole technique, the BD‐IES instrument measures 50–600 keV incident electrons in eight energy channels from nine directions covering a range of 180° in polar angle. Data collection by the BD‐IES instrument have recently passed the 1 year mark, which reflects a successful milestone for the mission. The innermost and outermost signatures of substorm injection at L ~ 6 and 12 have been observed by the BD‐IES with a high L shell spatial coverage, complementary to the existing missions such as the Van Allen Probes that covers the range below L ~ 6. There are another two BD‐IES instruments to be installed in the coming Chinese Sun‐synchronous and geosynchronous satellites, respectively. Such a configuration will provide a unique opportunity to investigate inward and outward radial propagation of the substorm injection region simultaneously at high and low L shells. It will further elucidate potential mechanisms for the particle energization and transport, two of the most important topics in magnetospheric dynamics.
Biosourced Foam‐Like Activated Carbon Materials as High‐Performance Supercapacitors
Authors: Ba Housseinou , Wang Wei , Pronkin Sergey , Romero Thierry , Baaziz Walid , Nguyen‐Dinh Lam , Chu Wei , Ersen Ovidiu , Pham‐Huu Cuong 
Published: January 2018

AbstractBio‐inspired and cost‐effective development of highly porous foam‐like carbon structure originating from waste fig‐fruit raw materials using chemical activation is described. The as‐synthesized porous sample exhibits a specific surface area higher than 2000 m2 g−1 and relatively high porosity with ultimately interconnected micro‐, meso‐, and macropores. Such sample displays superior specific capacitance in aqueous electrolyte of 340 and 217 F g−1 at current density of 0.5 A and 20 A g−1, respectively, along with a high energy/power density performance compared to that developed in the literature and the commercial supercapacitors up to now. In addition, the sample also exhibits an extremely high stability as a function of cycling tests with more 99% capacitance retention after 10 000 cycles.
Insights into the Failure Mechanisms of Organic Photodetectors
Authors: Kielar Marcin , Daanoune Mehdi , François‐Martin Olivier , Flament Bruno , Dhez Olivier , Pandey Ajay K. , Chambon Sylvain , Clerc Raphaël , Hirsch Lionel 
Published: January 2018

AbstractThis work investigates in detail the reliability of poly(2,7‐carbazole‐alt‐4, 7‐dithienyl‐2,1,3‐benzothiadiazole):phenyl‐C61‐butyric acid methyl ester‐based organic photodiodes (OPDs) under visible light and air exposure. The current–voltage (I–V) characteristics of the state‐of‐the‐art OPDs are measured both at room and low temperature, before, during, and after ageing. While electrodes are only slightly impacted by ageing, the active layer is significantly damaged regardless the absence of UV light, leading to a major decrease in the responsivity. The combination of the thermally stimulated current and the I–V characteristics versus temperature (I–V–T) techniques along with the extensive use of the drift‐diffusion simulations all reveals that the observed degradation is the consequence of the generation of shallow traps (0.2 eV, NT = 1016 cm−3) that significantly reduce the charge carrier mobility. In contrast, deep traps (0.7 eV, NT = 7 × 1015 cm−3) are found to be present on freshly prepared samples and their concentration remains unchanged after ageing.
Semiprobabilistische Dauerhaftigkeitsbemessung von Stahlbetonbauten unter Chlorideinwirkung
Authors: Rahimi Amir , Gehlen Christoph 
Published: January 2018

AbstractDie Dauerhaftigkeit neu zu errichtender Betonbauwerke wird nach derzeitigen Regelwerken deskriptiv maßgeblich durch die Einhaltung von Mindestanforderungen an Betonzusammensetzung, Betondeckung und Nachbehandlung geregelt. Eine leistungsbezogene Bewertung nach dem Performance‐Konzept, wie bei der Tragwerksbemessung, wird in der Regel nicht vorgenommen. Die in jüngster Zeit entwickelten Bemessungskonzepte auf Basis geprüfter Leistungsfähigkeit (Performance) sind in der Regel aufwendiger und benötigen darüber hinaus gesonderte Fachkenntnisse und spezielle Software. In diesem Beitrag wird ein semiprobabilistisches Konzept vorgestellt, das eine Dauerhaftigkeitsbemessung hinsichtlich chloridinduzierter Betonstahlkorrosion für neu zu errichtende Bauteile wesentlich leichter, auch ohne spezielle Software, ermöglicht.
Influence of External Forces during Supercooling on Dispersion Stability during Melt Emulsification
Authors: Abramov Serghei , Ahammou Abdeljaouad , Karbstein Heike Petra 
Published: January 2018

AbstractA special high‐pressure homogenization process – simultaneous homogenization and mixing (SHM) – was applied to produce hexadecane (C16H34), octadecane (C18H38), eicosane (C20H42), and docosane (C22H46) in water dispersions. Additionally, a high‐shear stress zone (HSSZ) was connected to the SHM unit to investigate the influence of external forces during supercooling on dispersion stability. The HSSZ did not affect the droplet disruption efficiency but induced aggregation behavior of the dispersed phase with increasing alkane chain length and dispersed‐phase content. High‐shear treatment during crystallization led to a change in particle shape, which was more favorable to aggregation.
An Exploration of Induced Supramolecular Chirality Through Association of Chiral Ammonium Ions and Tartrates with the Achiral Host Cucurbit[7]uril
Authors: Wu Wenjing , Cronin Michael P. , Wallace Lynne , Day Anthony I. 
Published: January 2018

AbstractThe chiral amines (R,R and S,S)‐1‐amino‐2‐benzyloxycyclopentane and (R and S)‐α‐methylbenzylamine were converted to ammonium (D and L) hydrogen tartrate salts and induced chiroptic effects were investigated following encapsulation in Q[7]. Significant chiroptic differences were observed in ORD and CD spectra for the two amines. The optical spectra were performed as a precursor study to a potential method for enantiomer separation, utilising Q[7] encapsulation in conjunction with enantio‐pure hydrogen tartrates. An enantiomeric excess was achieved for the two antipodes of 1‐amino‐2‐benzyoxycyclopentane but not for those of α‐methylbenzylamine. However, material differences of crystallinity or the formation of a glass were observed for the latter amine induced by the different antipodes of hydrogen tartrate. 1H NMR spectra of aminobenzyloxycyclopentane showed back‐folding of the two rings with complete encapsulation in Q[7], leading to a secondary helical structure observed in CD spectra.
Responses of Human Large Granular Lymphocytes and Classical T-Cells in Culture to Allogeneic Cells, Lectins, and Soluble Antigen
Authors: Ortaldo John R , Seeley Janet M , Mori Nancy , Bolhuis Reinder L H 
Published: January 2018

Abstract
Subpopulations of human peripheral blood mononuclear lymphocytes, after depletion of B-cells and monocytes (by sequential adherence to plastic and nylon wool columns) were separated by Percoll density gradient centrifugation and tested for their ability to proliferate in response to various mitogens, recall antigens, and alloantigens, and to develop cytolytic reactivity in vitro. The low-density fraction [mostly large-granular lymphocytes (LGL)] contained greater than 95% of the total cytotoxic activity of unfractionated nonadherent lymphocytes, against the natural killer (NK)-susceptible K562 target cell, and against other NK-susceptible targets, whereas the high-density lymphocyte fraction (mostly classical T-lymphocytes) demonstrated little or no cytolytic activity against these targets. Conversely, cytotoxic alloreactivity against the lymphoblasts of the donor used for stimulation developed only in the cultures of high density cells. Autologous cytotoxic reactivity, against autologous phytohemagglutinin (PHA)-stimulated lymphoblasts, was not restricted to either subset but developed by both LGL as well as high-density lymphocytes. LGL and high-density T-lymphocytes demonstrated significant proliferative responses to lectins [PHA, concanavalin A (Con A), pokeweed mitogen], and the responses of the LGL were similar in magnitude to those of peripheral blood mononuclear cells or of high-density T-cells. In contrast, only T-lymphocytes responded to the specific recall antigen, purified protein derivative (PPD). These results indicate that LGL are capable of proliferative responses to various lectins, but have no detectable specific memory responses to a soluble antigen. In addition, a different subset of lymphoid cells was responsible for the development of NK-like and specific alloreactivity. Therefore, NK cells and T-cells, although sharing proliferative responses to mitogens, exhibit different function regarding cytotoxic effectors.