bluuebunny/crossref_metadata_2025 huggingface dataset:
Peripheral blood gene expression profiles linked to monoamine metabolite levels in cerebrospinal fluid
Authors: Luykx J J , Olde Loohuis L M , Neeleman M , Strengman E , Bakker S C , Lentjes E , Borgdorff P , van Dongen E P A , Bruins P , Kahn R S , Horvath S , de Jong S , Ophoff R A
Published: December 2016

The blood–brain barrier separates circulating blood from the central nervous system (CNS). The scope of this barrier is not fully understood which limits our ability to relate biological measurements from peripheral to central phenotypes. For example, it is unknown to what extent gene expression levels in peripheral blood are reflective of CNS metabolism. In this study, we examine links between central monoamine metabolite levels and whole-blood gene expression to better understand the connection between peripheral systems and the CNS. To that end, we correlated the prime monoamine metabolites in cerebrospinal fluid (CSF) with whole-genome gene expression microarray data from blood (N=240 human subjects). We additionally applied gene-enrichment analysis and weighted gene co-expression network analyses (WGCNA) to identify modules of co-expressed genes in blood that may be involved with monoamine metabolite levels in CSF. Transcript levels of two genes were significantly associated with CSF serotonin metabolite levels after Bonferroni correction for multiple testing: THAP7 (P=2.8 × 10−8, β=0.08) and DDX6 (P=2.9 × 10−7, β=0.07). Differentially expressed genes were significantly enriched for genes expressed in the brain tissue (P=6.0 × 10−52). WGCNA revealed significant correlations between serotonin metabolism and hub genes with known functions in serotonin metabolism, for example, HTR2A and COMT. We conclude that gene expression levels in whole blood are associated with monoamine metabolite levels in the human CSF. Our results, including the strong enrichment of brain-expressed genes, illustrate that gene expression profiles in peripheral blood can be relevant for quantitative metabolic phenotypes in the CNS.
Implication of NOTCH1 gene in susceptibility to anxiety and depression among sexual abuse victims
Authors: Steine I M , Zayats T , Stansberg C , Pallesen S , Mrdalj J , Håvik B , Soulé J , Haavik J , Milde A M , Skrede S , Murison R , Krystal J , Grønli J
Published: December 2016

Sexual abuse contributes to the development of multiple forms of psychopathology, including anxiety and depression, but the extent to which genetics contributes to these disorders among sexual abuse victims remains unclear. In this translational study, we first examined gene expression in the brains of rodents exposed to different early-life conditions (long, brief or no maternal separation). Hypothesizing that genes revealing changes in expression may have relevance for psychiatric symptoms later in life, we examined possible association of those genes with symptoms of anxiety and depression in a human sample of sexual abuse victims. Changes in rodent brain gene expression were evaluated by means of correspondence and significance analyses of microarrays by comparing brains of rodents exposed to different early-life conditions. Tag single-nucleotide polymorphisms (SNPs) of resulting candidate genes were genotyped and tested for their association with symptoms of anxiety and depression (Hospital Anxiety and Depression Scale) in a sample of 361 sexual abuse victims, using multinomial logistic regression. False discovery rate was applied to account for multiple testing in the genetic association study, withq-value of 0.05 accepted as significant. We identified four genes showing differential expression among animals subjected to different early-life conditions as well as having potential relevance to neural development or disorders: Notch1, Gabrr1, Plk5 and Zfp644. In the human sample, significant associations were observed for twoNOTCH1tag SNPs: rs11145770 (OR=2.21,q=0.043) and rs3013302 (OR=2.15,q=0.043). Our overall findings provide preliminary evidence thatNOTCH1may be implicated in the susceptibility to anxiety and depression among sexual abuse victims. The study also underscores the potential importance of animal models for future studies on the health consequences of early-life stress and the mechanisms underlying increased risk for psychiatric disorders.
Single-unit-cell thick Co9S8nanosheets from preassembled Co14nanoclusters
Authors: Wu Zhennan , Zou Haoyang , Li Tingting , Cheng Ziyi , Liu Huiwen , Liu Yi , Zhang Hao , Yang Bai
Published: December 2016

Single-unit-cell thick Co9S8nanosheets are prepared from preassembled Co14nanoclusters by combining the advantages of a self-assembly technique with solid-phase material sulfurization at elevated temperature.
Chemistry at the square nanometer: reactivity at liquid/solid interfaces revealed with an STM
Authors: Münninghoff Joris A. W. , Elemans Johannes A. A. W.
Published: December 2016

An overview is given of single molecule reactivity at a liquid/solid interface employing a scanning tunneling microscope.
Carborane–stilbene dyads: the influence of substituents and cluster isomers on photoluminescence properties
Authors: Ferrer-Ugalde A. , Cabrera-González J. , Juárez-Pérez E. J. , Teixidor F. , Pérez-Inestrosa E. , Montenegro J. M. , Sillanpää R. , Haukka M. , Núñez R.
Published: December 2016

A family of stilbene-containing meta- and ortho-carborane derivatives substitute at the second carbon cluster atom are synthesised and their photophysical properties evaluated.
Pursuing the active species in an aluminium-based Lewis acid system for catalytic Diels–Alder cycloadditions
Authors: Liu Zhizhou , Ganguly Rakesh , Vidović Dragoslav
Published: December 2016

Detailed characterization of the catalytically active aluminium species supported by a bis(imino)aryl ligand has been reported.
Computational study of An–X bonding (An = Th, U; X = p-block-based ligands) in pyrrolic macrocycle-supported complexes from the quantum theory of atoms in molecules and bond energy decomposition analysis
Authors: O'Brien Kieran T. P. , Kaltsoyannis Nikolas
Published: December 2016

Good correlations are found between QTAIM BCP and EDA data for a range of Th(iv)- and Th(iii)-p element bonds.
Macroporous resin purification and characterization of flavonoids from Platycladus orientalis (L.) Franco and their effects on macrophage inflammatory response
Authors: Ren Jiaoyan , Zheng Yamei , Lin Zehua , Han Xin , Liao Wenzhen
Published: December 2016

LPS-induced macrophage cells as a model of inflammatory response to investigate the anti-inflammatory mechanism of the purifiedPlatycladus orientalis(L.) Franco flavonoids.
Structure of the Fe and Ni L X-ray spectra
Authors: Sepúlveda A. , Rodríguez T. , Pérez P. D. , Bertol A. P. L. , Carreras A. C. , Trincavelli J. , Vasconcellos M. A. Z. , Hinrichs R. , Castellano G.
Published: December 2016

Diagram and satellite line parameters were obtained from Fe-L and Ni-L X-ray spectra induced by electron impact.
Superior performance of an active electrolyte enhanced supercapacitor based on a toughened porous network gel polymer
Authors: Feng Enke , Ma Guofu , Sun Kanjun , Ran Feitian , Peng Hui , Lei Ziqiang
Published: December 2016

A primary challenge of gel electrolytes in the development of flexible and wearable devices is their weak mechanical strength and poor electrochemical performances.
Studies on neptunium complexation with CMPO- and diglycolamide-functionalized ionic liquids: experimental and computational studies
Authors: Sengupta Arijit , Mohapatra Prasanta Kumar , Pathak Priyanath , Ghanty Tapan Kumar , Verboom Willem
Published: December 2016

A CMPO-functionalized task-specific ionic liquid provided significantly greater extraction of Np4+than of NpO22+, which is of interest for radioactive waste treatment.
Systematic synthetic and biophysical development of mixed sequence DNA binding agents
Authors: Paul Ananya , Kumar Arvind , Nanjunda Rupesh , Farahat Abdelbasset A. , Boykin David W. , Wilson W. David
Published: December 2016

Development of heterocyclic diamidines as programmable molecules for sequence-specific DNA recognition.
Tuning the hybridization properties of modified oligonucleotides: from flexible to conformationally constrained phosphonate internucleotide linkages
Authors: Páv Ondřej , Barvík Ivan , Liboska Radek , Petrová Magdalena , Šimák Ondřej , Rosenbergová Šárka , Novák Pavel , Buděšínský Miloš , Rosenberg Ivan
Published: December 2016

We utilized the concept of conformational restriction to prepare a set of constrained oligonucleotides derived from 1,4-dioxane and 1,3-dioxolane-locked nucleoside phosphonates and evaluated their hybridization abilities.
A rapid and highly enantioselective C–11C bond formation of l-[11C]phenylalanine via chiral phase-transfer catalysis
Authors: Pekošak Aleksandra , Filp Ulrike , Škrinjar Janja , Poot Alex J. , Windhorst Albert D.
Published: December 2016

Multistep asymmetric phase-transfer catalyzed carbon-11 benzylation for the enantioselective radiolabeling of l- and d-[11C]phenylalanine.
Aerobic oxidative decyanation–amidation of arylacetonitriles with urea as a nitrogen source
Authors: Xu Xuezhao , Li Bingnan , Zhao Yingwei , Song Qiuling
Published: December 2016

An iron-catalyzed aerobic oxidative amidation of aryl acetonitriles to afford amides is achieved using urea as a convenient nitrogen source.
Argumentation to foster pre-service science teachers’ knowledge, competency, and attitude on the domains of chemical literacy of acids and bases
Authors: Cigdemoglu C. , Arslan H. O. , Cam A.
Published: December 2016

Argumentative practices have the potential to contribute to scientific literacy. However, these practices are not widely incorporated in science classrooms and so their effect on the domains of literacy is still not revealed. Therefore, this study proposes to reveal the effect of argumentation on the three domains of chemical literacy related to the concepts of acids and bases. The study participants comprised 29 freshman pre-service science teachers’ enrolled in a General Chemistry-II course. Argumentation practices were implemented over six weeks. Open-ended contextual chemical literacy items were developed to assess the differences in the chemical literacy domains and the items were administered before and right after the intervention. The responses to the chemical literacy items were scored with a rubric and three scores were calculated: knowledge, competency, and attitudes. Paired samplet-tests were used to compare the mean scores. All the intervention sessions were video recorded, and three of them were analyzed according to three criteria: the presence of arguments, the frequency of arguments, and the levels of the arguments. The findings revealed that the argumentation practices contributed to the pre-service teachers’ chemical literacy skills, mostly to their knowledge and competencies when compared to their attitudes. Moreover, distinct differences in the quality of argumentation levels were observed over the six weeks.
Correction: Ligand design for Rh(iii)-catalyzed C–H activation: an unsymmetrical cyclopentadienyl group enables a regioselective synthesis of dihydroisoquinolones
Authors: Hyster Todd K. , Dalton Derek M. , Rovis Tomislav
Published: December 2016

Correction for ‘Ligand design for Rh(iii)-catalyzed C–H activation: an unsymmetrical cyclopentadienyl group enables a regioselective synthesis of dihydroisoquinolones’ by Todd K. Hyster et al., Chem. Sci., 2015, 6, 254–258.
Recent progress in layered transition metal carbides and/or nitrides (MXenes) and their composites: synthesis and applications
Authors: Hong Ng Vincent Ming , Huang Hui , Zhou Kun , Lee Pooi See , Que Wenxiu , Xu Jason Zhichuan , Kong Ling Bing
Published: December 2016

Beyond the inaugural synthesis of multi-layered Ti3C2Txby etching Ti3AlC2with hydrofluoric acid (HF), novel routes with a myriad of reducing agents, etchants and intercalants have since been explored and have added many new members to the two-dimensional (2D) material constellation.
Redox-triggered controlled release systems-based bi-layered nanocomposite coating with synergistic self-healing property
Authors: Wang Ting , Tan LingHua , Ding ChenDi , Wang MingDong , Xu JianHua , Fu JiaJun
Published: December 2016

Redox-triggered smart nanocontainers, RTSNs 1, assembled by installing supramolecular switches onto the exterior surface of mesoporous silica nanoparticles, were successfully synthesized.
Visual Context Enhanced: The Joint Contribution of Iconic Gestures and Visible Speech to Degraded Speech Comprehension
Authors: Drijvers Linda , Özyürek Asli
Published: December 2016

Purpose

This study investigated whether and to what extent iconic co-speech gestures contribute to information from visible speech to enhance degraded speech comprehension at different levels of noise-vocoding. Previous studies of the contributions of these 2 visual articulators to speech comprehension have only been performed separately.

Method

Twenty participants watched videos of an actress uttering an action verb and completed a free-recall task. The videos were presented in 3 speech conditions (2-band noise-vocoding, 6-band noise-vocoding, clear), 3 multimodal conditions (speech + lips blurred, speech + visible speech, speech + visible speech + gesture), and 2 visual-only conditions (visible speech, visible speech + gesture).

Results

Accuracy levels were higher when both visual articulators were present compared with 1 or none. The enhancement effects of (a) visible speech, (b) gestural information on top of visible speech, and (c) both visible speech and iconic gestures were larger in 6-band than 2-band noise-vocoding or visual-only conditions. Gestural enhancement in 2-band noise-vocoding did not differ from gestural enhancement in visual-only conditions.

Conclusions

When perceiving degraded speech in a visual context, listeners benefit more from having both visual articulators present compared with 1. This benefit was larger at 6-band than 2-band noise-vocoding, where listeners can benefit from both phonological cues from visible speech and semantic cues from iconic gestures to disambiguate speech.
Estimating Subglottal Pressure From Neck-Surface Acceleration During Normal Voice Production
Authors: Fryd Amanda S. , Van Stan Jarrad H. , Hillman Robert E. , Mehta Daryush D.
Published: December 2016

Purpose

The purpose of this study was to evaluate the potential for estimating subglottal air pressure using a neck-surface accelerometer and to compare the accuracy of predicting subglottal air pressure relative to predicting acoustic sound pressure level (SPL).

Method

Indirect estimates of subglottal pressure (P
sg
′) were obtained from 10 vocally healthy speakers during loud-to-soft repetitions of 3 different /p/–vowel gestures (/pa/, /pi/, /pu/) at 3 pitch levels in the modal register. Intraoral air pressure, neck-surface acceleration, and radiated acoustic pressure were recorded, and the root-mean-square amplitude of the acceleration signal was correlated with P
sg
′ and SPL.

Results

The coefficient of determination between accelerometer level and P
sg
′ was high when data were pooled from all vowel and pitch contexts for each participant (
r
2
= .68–.93). These relationships were stronger than corresponding relationships between accelerometer level and SPL (
r
2
= .46–.81). The average 95% prediction interval for estimating P
sg
′ using accelerometer level was ±2.53 cm H
2
O, ranging from ±1.70 to ±3.74 cm H
2
O across participants.

Conclusions

Accelerometer signal amplitude correlated more strongly with P
sg
′ than with SPL. Future work is warranted to investigate the robustness of the relationship in nonmodal voice qualities, individuals with voice disorders, and accelerometer-based ambulatory monitoring of subglottal pressure.
Preparing Our Future Helping Professionals to Become Critical Thinkers: A Tutorial
Authors: Finn Patrick , Brundage Shelley B. , DiLollo Anthony
Published: December 2016

Critical thinking is increasingly recognized as an essential knowledge and skill for the helping professions. Yet, our pedagogical literature has provided infrequent guidance on how instructors can help students to understand what “critical thinking” means or how it might contribute to their professional lives. Therefore, the purpose of this tutorial is to provide guidelines on how instructors might teach future practitioners to become critical thinkers. The main topics address an instructional definition of critical thinking, the basic knowledge and skills that comprise critical thinking, a broad view of instructional approaches, and a summary of developmental milestones of adult critical thinkers. Specific teaching strategies from instructors who have hands-on experience with guiding their students to become critical thinkers are included.
Pedestal substrate integrated waveguide resonators and filters
Authors: Nassar Shamim O. , Meyer Petrie
Published: December 2016

A new substrate integrated waveguide resonator in the form of a square‐ or cross‐shaped pedestal is proposed. The structure is developed from T‐shaped ridge waveguides, and utilises the mode separation characteristics of this type of guide to achieve wider spacing between the first two resonances, as well as miniaturisation of the resonator. Two fourth‐order X‐band filters, one with cross‐coupling, are designed using, respectively, square‐ and cross‐shaped pedestal resonators, and validated by simulation and measurement.
A numerical solution to Monge’s problem with a Finsler distance as cost
Authors: Benamou Jean-David , Carlier Guillaume , Hatchi Roméo
Published: December 2016

Monge’s problem with a Finsler cost is intimately related to an optimal ow problem. Discretization of this problem and its dual leads to a well-posed finite-dimensional saddle-point problem which can be solved numerically relatively easily by an augmented Lagrangian approach in the same spirit as the Benamou–Brenier method for the optimal transport problem with quadratic cost. Numerical results validate the method. We also emphasize that the algorithm only requires elementary operations and in particular never involves evaluation of the Finsler distance or of geodesics.
An MRI Evaluation of Patients Who Underwent Treatment with a Cell-Mediated Gene Therapy for Degenerative Knee Arthritis: A Phase IIa Clinical Trial
Authors: Cho Jung , Totterman Saara , Elmallah Randa , Kim Tae , Lee Bumsup , Mont Michael
Published: December 2016

Multiple therapies have been developed to slow down the progression of knee osteoarthritis (OA), with the aim of avoiding or delaying TKA. One such potential method is cell-mediated gene therapy, which utilizes allogeneic human chondrocytes modified to express transforming growth factor-β1. Using magnetic resonance imaging (MRI), we evaluated patients who underwent treatment with this injection in a Phase II study and assessed structural changes in: (1) bone marrow edema lesions, (2) cartilage defect depth and surface area, (3) articular bone surface and osteophytes, and (4) meniscus structure and signal, as well as changes in (5) joint fluid, (6) periarticular inflammation, and (7) synovial inflammation. Twenty-seven patients (6 men and 21 women) who had late-stage OA were randomized 1:1 to receive a 3:1 mixture of nontransduced chondrocytes and genetically engineered chondrocytes, at doses of 6 × 106 cells (group 1) or 1.8 × 107 cells (group 2). MRI was performed at baseline (preinjection), and at 6 and 12 months postinjection. The whole-organ MRI score system was used to assess the aforementioned changes. Treatment was considered to be successful if patients experienced an improvement in or no change in their scores, indicating that the disease had not progressed. All patients in both cohorts individually demonstrated an improvement or no change in one or more of the assessment parameters. At 6 months, the low-dose cohort demonstrated worsening in mean scores in one parameter (bone surface and osteophytes), while the high-dose cohort demonstrated no worsening in mean scores. At 12 months, the low-dose cohort had worsening in the mean score in a subset of one parameter (cartilage signal intensity), and the high-dose cohort demonstrated worsening in mean scores in two parameters (bone surface osteophytes and periarticular inflammation). This is the first study to evaluate MRI changes in patients treated with this injection. These findings provide an impetus for further research on this topic, as well as a starting point for Phase III testing.
Scientific assessments to facilitate deliberative policy learning
Authors: Kowarsch Martin , Garard Jennifer , Riousset Pauline , Lenzi Dominic , Dorsch Marcel J. , Knopf Brigitte , Harrs Jan-Albrecht , Edenhofer Ottmar
Published: December 2016

Putting the recently adopted global Sustainable Development Goals or the Paris Agreement on international climate policy into action will require careful policy choices. Appropriately informing decision-makers about longer-term, wicked policy issues remains a considerable challenge for the scientific community. Typically, these vital policy issues are highly uncertain, value-laden and disputed, and affect multiple temporal and spatial scales, governance levels, policy fields, and socioeconomic contexts simultaneously. In light of this, science-policy interfaces should help facilitate learning processes and open deliberation among all actors involved about potentially acceptable policy pathways. For this purpose, science-policy interfaces must strive to foster some enabling conditions: (1) “representation” in terms of engaging with diverse stakeholders (including experts) and acknowledging divergent viewpoints; (2) “empowerment” of underrepresented societal groups by co-developing and integrating policy scenarios that reflect their specific knowledge systems and worldviews; (3) “capacity building” regarding methods and skills for integration and synthesis, as well as through the provision of knowledge synthesis about the policy solution space; and (4) “spaces for deliberation”, facilitating direct interaction between different stakeholders, including governments and scientists. We argue that integrated, multi-stakeholder, scientific assessment processes—particularly the collaborative assessments of policy alternatives and their various implications—offer potential advantages in this regard, compared with alternatives for bridging scientific expertise and public policy. This article is part of a collection on scientific advice to governments.
Crystal Structure of a Heterometallic Luminophore: The RuII Complex of a Ferrocenyl-Terpyridine with a Flexible Linkage
Authors: Lee Young Hoon , Shin Jong Won , Sekimoto Yusuke , Hayami Shinya , Harrowfield Jack , Kim Yang
Published: December 2016

Crystal structure determination on the mixed ligand complex [Ru(tpy)(L1)](ClO4)2 (tpy = 2,2′:6′,2″-terpyridine; L1 = 4′-(ferrocenylmethylaminomethylphenyl)terpyridine) shows the ferrocenyl group to be located as remotely as possible from the RuII centre. This may explain the fact that emission from the RuII centre is detectable even at room temperature in solution.
On-site determination of bisphenol A in river water by a novel solid-state electrochemiluminescence quenching sensor
Authors: Wang Xiaoying , Wang Yijie , Jiang Meng , Shan Yanqun , Wang Xiaobing
Published: December 2016

Environmental contextBisphenol A is an endocrine disruptor, which may migrate and transfer to the environment where it presents a potential risk to the health of humans and animals. Herein, we demonstrate that electrospun nanofibers could be used to develop a highly efficient solid-state quenching sensor for on-site determination of bisphenol A in river water samples. The strategy has great potential for routine environmental analyses. AbstractA novel solid-state electrochemiluminescence (ECL) quenching sensor based on luminescent composite nanofibres for detection of bisphenol A (BPA) has been designed. Luminescent composite nanofibres of ruthenium(ii) tris(bipyridine) (Ru(bpy)32+)-doped core–shell Cu@Au alloy nanoparticles (Ru/Cu@Au) mixed with nylon 6 (PA6)–amino-functionalised multi-walled carbon nanotubes (MWCNTs), Ru/Cu@Au-MWCNTs-PA6, were successfully fabricated by a one-step electrospinning technique. The Ru/Cu@Au-MWCNTs-PA6 nanofibres, with a unique 3D nanostructure, large specific surface area and double Ru(bpy)32+-ECL signal amplification, exhibited excellent ECL photoelectric behaviours on a glassy carbon electrode. As a solid-state ECL sensor, the Ru/Cu@Au-MWCNTs-PA6 nanofibres can sensitively detect low concentrations of BPA by monitoring the BPA-dependent ECL intensity change. The detection limit for BPA is 10 pM, which is comparable or better than that in the reported assays. The sensor was successfully applied to on-site determination of BPA in river water samples obtained from eight different sampling sites with good recovery, ranging from 97.8 to 103.4%. The solid-state ECL sensor displayed wide-range linearity, high sensitivity and good stability, and has great potential in the field of environmental analyses.
Seed fall, seed predation, twigging and litter fall of Cascabela thevetia (L.) Lippold
Authors: Bebawi Faiz F. , Campbell Shane D. , Mayer Robert J.
Published: December 2016

Cascabela thevetia (L.) Lippold is a garden ornamental in northern Australia and two biotypes, the peach and the yellow, are recognised. In some areas it has naturalised and now has environmental and economic effects. As part of a broader research program into the ecology of C. thevetia, a field study was undertaken in northern Queensland to quantify seed fall and seed predation (by avian wildlife) of the peach biotype. The amount of twigging caused by birds while they fed on the seeds and the level of litter production were also recorded. Seed fall, seed predation, twigging and litter production occurred in all months of the year. Seed fall increased slowly over late spring and summer before peaking in mid- to late autumn (April–May) and then declining until October. Mean (± s.e.m.) estimated total annual seed fall was 19140 ± 2880 and 17030 ± 2930 seeds ha–1 in the first and second years respectively. Seed predation by birds was substantial, with 57% of all seeds predated. Birds also chewed an average of 600 twigs ha–1 year–1. Litter production varied from 430 to 950 kg dry weight (DW) ha–1 month–1. In total, 7900 ± 640 and 7390 ± 1420 kg (DW) litter was produced during the first and second years respectively. Although seed production of C. thevetia is less than a lot of other rangeland weeds, seed predation by birds further reduces the number of seeds entering the soil seed bank. The stem damage that occurred in conjunction with seed predation contributed to overall litter production and warrants further investigation in terms of its effect on plant growth.
Soil respiration simulation based on soil temperature and water content in artificial smooth brome grassland
Authors: Wu Juying , Pang Zhuo , Sun Tiejun , Kan Haiming , Hu Wei , Li Xiaona
Published: December 2016

Correctly quantifying the relationships between soil respiration and environmental factors and their sources of variability is essential to predict future carbon fluxes and climate feedback. Soil water conditions and soil temperature strongly affect soil respiration and the dynamics of soil organic matter. Despite this, simulation of soil respiration (Rs) based on soil temperature (Ts) and soil volumetric water content (θ) must still be improved, as demonstrated by its discrepant model performance among different seasons. With the objective of gaining a further understanding of the relationships of Rs with Ts and θ and providing an improved model to simulate Rs variations, we measured hourly Rs, Ts and θ using the chamber technique in artificial smooth brome grassland for analysis. We began by dividing the four seasons of a year according to the daily mean air temperature, followed by representing the seasonal variation of Rs, Ts and θ. We found that Rs correlated significantly with Ts in an exponential relationship and with θ in a parabolic relationship seasonally, where the determination coefficient of the Rs-θ relationship was significantly larger than that of the Rs-Ts relationship. We also discovered that the shape of the Rs-θ relationship was seasonally dependent because the optimal θ and the width of the peak Rs around the optimal θ were seasonally specific. Finally, by considering seasonality, the combinational simulation model explained more variation of soil respiration. Thus, seasonality should be considered for more reliable model simulations of soil respiration. These findings are relevant for more accurate predictions and modelling of soil respiration, particularly in temperate artificial grasslands with a continental monsoon climate, where the ‘Birch effect’ strengthens seasonality, and these findings further our understanding of changes in the rates of soil carbon losses as artificial grassland is established.
Greening trend in grassland of the Lhasa River Region on the Qinghai-Tibetan Plateau from 1982 to 2013
Authors: Luo Han , Tang Ya , Zhu Xuan , Di Baofeng , Xu Yuhui
Published: December 2016

Local residents of the Lhasa River Region (LRR) on the Qinghai-Tibetan Plateau in western China have noticed that the surrounding mountains have appeared conspicuously green since the 1980s. To verify these claims, we investigated trends of grassland activities in the LRR from 1982 to 2013 by using remotely sensed Normalised Difference Vegetation Index (NDVI) data, as a proxy for photosynthetic activity. Due to the limitation of available remote sensing data, we used long-term data with low resolution, GIMMS3 g NDVI, to explore the temporal changes between 1982 and 2012; we used moderate resolution data, MODIS NDVI, to investigate the spatial variations of trends between 2001 and 2013. In addition, we examined the relationship between grassland change and climate change. The results revealed a significant upward trend in the annual mean NDVI of the LRR from 1982 to 2012, corroborating the observations of the local people. The increasing trend was more pronounced during the period of 1982–1999 than during the period of 2000–2012. The seasonal NDVI also exhibited a significant upward trend in spring and summer from 1982 to 1999. From the higher resolution MODIS NDVI data analysis, during 2001–2013, the lower regression slope values were mainly distributed in the river valley (the area of lower elevation), whereas the higher values pixels were located in the northern LRR (the area of higher elevation). In addition, the annual NDVI correlated significantly with temperature and precipitation during the study period. Temperature is a more significant factor influencing grassland change than precipitation in spring and autumn. However, the precipitation with the time lag effect is more significantly correlated with NDVI during the growing season (from May to October). The results of this project will help to monitor regional vegetation changes, understand the impact of climate change, and better manage the economically, environmentally and culturally significant grasslands of the LRR.
Assembly of long error-prone reads using de Bruijn graphs
Authors: Lin Yu , Yuan Jeffrey , Kolmogorov Mikhail , Shen Max W. , Chaisson Mark , Pevzner Pavel A.
Published: December 2016

Significance

When the long reads generated using single-molecule se-quencing (SMS) technology were made available, most researchers were skeptical about the ability of existing algorithms to generate high-quality assemblies from long error-prone reads. Nevertheless, recent algorithmic breakthroughs resulted in many successful SMS sequencing projects. However, as the recent assemblies of important plant pathogens illustrate, the problem of assembling long error-prone reads is far from being resolved even in the case of relatively short bacterial genomes. We propose an algorithmic approach for assembling long error-prone reads and describe the ABruijn assembler, which results in accurate genome reconstructions.
On the role of water density fluctuations in the inhibition of a proton channel
Authors: Gianti Eleonora , Delemotte Lucie , Klein Michael L. , Carnevale Vincenzo
Published: December 2016

Significance

Hv1, a voltage-gated proton channel, is an emerging pharmacological target implicated in many pathological conditions, including cancer and ischemic brain damage. We used the recently published experimental structure of Hv1 to generate structural models of relevant conformational states. Thermodynamic analyses of pore waters shed light on the molecular underpinnings of Hv1 druggability. We exploit this information to suggest possible optimizations of known inhibitors and identify a potential binding site located at the exit of the proton path. The resulting molecular picture paves the way for the discovery of novel Hv1 inhibitors and outlines a general approach for identifying druggable binding sites in ion channels.
Decentralization can help reduce deforestation when user groups engage with local government
Authors: Wright Glenn D. , Andersson Krister P. , Gibson Clark C. , Evans Tom P.
Published: December 2016

Significance

Decentralization is one of the most important innovations in environmental policy during the past 30 years. Despite the pervasiveness and large amounts of resources invested to implement these reforms, little is known about their environmental effects. Given worldwide interest in forest conservation, this lack of knowledge hampers efforts to improve the effectiveness of current policy initiatives. Using quasi-experimental methods, we find that the environmental effects of decentralization reforms depend on how the reforms affect the conditions for user groups to govern their forests. Our findings show that decentralization to general-purpose governments may be most effective in places where forest users take advantage of opportunities to engage with local politicians about forestry issues.
β2-Adrenergic receptor-dependent chemokine receptor 2 expression regulates leukocyte recruitment to the heart following acute injury
Authors: Grisanti Laurel A. , Traynham Christopher J. , Repas Ashley A. , Gao Erhe , Koch Walter J. , Tilley Douglas G.
Published: December 2016

Significance

The sympathetic nervous system influences various immune cell functions, in particular via β2-adrenergic receptor (β2AR) signaling. Although immune cell recruitment is critical for cardiac repair following ischemia, the impact of β2AR on this process is unclear. We describe how immune cell-specific β2AR depletion ablates chemokine receptor 2 (CCR2) expression and leukocyte recruitment to the heart postischemia. Reciprocally, β2AR activation increases CCR2 expression and responsiveness in a β-arrestin–dependent manner, and expression of a β-arrestin–biased β2AR in β2AR-depleted immune cells restores CCR2 levels and leukocyte recruitment to the postischemic heart. These results highlight the potential utility of next-generation β-arrestin–biased β2AR ligands to selectively modulate leukocyte responsiveness, and suggest that β-blockers, used commonly in peri/postischemic patients, may impact leukocyte-mediated repair mechanisms.
Phosphorylation of the Mdm2 oncoprotein by the c-Abl tyrosine kinase regulates p53 tumor suppression and the radiosensitivity of mice
Authors: Carr Michael I. , Roderick Justine E. , Zhang Hong , Woda Bruce A. , Kelliher Michelle A. , Jones Stephen N.
Published: December 2016

Significance

The p53 transcription factor is stabilized in response to cellular stress and regulates the expression of genes involved in numerous biological activities, thereby suppressing tumorigenesis. DNA damage and other stress signals upregulate p53, in part, by freeing p53 from negative regulation imposed by the Mdm2 and MdmX (Mdm4) oncoproteins. MDM proteins are subject to posttranslational modification, and accumulating evidence indicates that phosphorylation of Mdm2 by different stress-activated kinases such as ATM or c-Abl alters Mdm2-p53 signaling and profoundly affects p53 function. A better understanding of the in vivo effects of Mdm2 phosphorylation may facilitate the development of novel therapeutics capable of stimulating p53 antitumor activity or alleviating p53-dependent toxicities in nonmalignant tissues.
Neutrophils induce proangiogenic T cells with a regulatory phenotype in pregnancy
Authors: Nadkarni Suchita , Smith Joanne , Sferruzzi-Perri Amanda N. , Ledwozyw Agata , Kishore Madhav , Haas Robert , Mauro Claudio , Williams David J. , Farsky Sandra H. P. , Marelli-Berg Federica M. , Perretti Mauro
Published: December 2016

Significance

Neutrophils are typically known as short-lived cells that act as the first line of defense in response to pathogens. However, emerging data indicate that neutrophils have wider implications in the immune system and have a direct influence on the ensuing immune response. Establishment of successful pregnancy requires immune tolerance at the maternal–fetal interface. Aberrations in normal placental development can lead to complications, including preeclampsia. In this study, we examined a role for maternal neutrophils in maintaining normal pregnancy through their interactions with T cells, resulting in a population of T cells that are both regulatory and proangiogenic and are required for normal placental development. Such interactions are absent in patients with preeclampsia, suggesting a potential therapeutic target for pregnancy-related pathologies.
Accomplishing simple, solubility-based separations of rare earth elements with complexes bearing size-sensitive molecular apertures
Authors: Bogart Justin A. , Cole Bren E. , Boreen Michael A. , Lippincott Connor A. , Manor Brian C. , Carroll Patrick J. , Schelter Eric J.
Published: December 2016

Significance

Rare earth metals, La–Lu, Sc, and Y, are essential components of electronic materials and permanent magnets in diverse technologies. But, their mining and separations chemistry are unsustainable and plagued with supply problems. Recycling of consumer materials containing rare earths is a promising new source of these critical materials but similarly requires efficient separations. We report the use of a tripodal hydroxylaminato ligand, TriNOx
3–
, with rare earth cations that enable fast, efficient separations through a simple leaching process. This approach is expected to contribute to a new method for recycling postconsumer materials including lighting phosphors and magnets, to diversify and improve the sustainability of the rare earth metal supply chain.
Mutant p53 promotes tumor progression and metastasis by the endoplasmic reticulum UDPase ENTPD5
Authors: Vogiatzi Fotini , Brandt Dominique T. , Schneikert Jean , Fuchs Jeannette , Grikscheit Katharina , Wanzel Michael , Pavlakis Evangelos , Charles Joël P. , Timofeev Oleg , Nist Andrea , Mernberger Marco , Kantelhardt Eva J. , Siebolts Udo , Bartel Frank , Jacob Ralf , Rath Ariane , Moll Roland , Grosse Robert , Stiewe Thorsten
Published: December 2016

Significance

p53 mutations are the most frequent genetic alteration in cancer and are often indicative of poor patient survival prognosis. The most prevalent missense mutations lead to a “gain of function” (GOF) that actively drives tumor progression, metastasis, and therapy resistance. Our study links the mutant p53 (mutp53) GOF to enhanced N-glycoprotein folding via ectonucleoside triphosphate diphosphohydrolase 5 (ENTPD5) in the calnexin/calreticulin cycle of the endoplasmic reticulum. Mutp53 thus increases expression of prometastatic cell surface proteins, such as receptors and integrins, not only quantitatively but also qualitatively, with respect to N-glycosylation state. Our study reveals N-glycoprotein quality control in the endoplasmic reticulum as an indispensable mechanism underlying the progression of tumors with GOF mutp53 that could provide new possibilities for treating prognostically challenging p53-mutated cancers.
Low-stringency selection of TEM1 for BLIP shows interface plasticity and selection for faster binders
Authors: Cohen-Khait Ruth , Schreiber Gideon
Published: December 2016

Significance

The ability of proteins to interact quickly and specifically is fundamental for most living activities. For a protein interaction to be formed, the corresponding surfaces need a high degree of chemical and structural complementarity. Here we investigated the level of plasticity of composition of a protein–protein interface without affecting the high-affinity binding. Using directed evolution and mild selection, we show that most interface residues can be exchanged without a loss in binding affinity. Conversely, many of the buried residues were highly conserved. Interestingly, the selection process resulted in sequences promoting faster binding kinetics. Selection of faster binders was further promoted by drastically shortening the incubation time, resulting in preequilibrium selection, which provides a path for evolution of fast-binding complexes.
Nogo receptor blockade overcomes remyelination failure after white matter stroke and stimulates functional recovery in aged mice
Authors: Sozmen Elif G. , Rosenzweig Shira , Llorente Irene L. , DiTullio David J. , Machnicki Michal , Vinters Harry V. , Havton Lief A. , Giger Roman J. , Hinman Jason D. , Carmichael S. Thomas
Published: December 2016

Significance

White matter stroke is a common clinical problem that leads to widespread cognitive and sensorimotor deficits. The incidence of white matter stroke is sharply age-associated; imaging studies indicate that, over age 80, virtually all of us will have white matter strokes. Little is known of the repair processes after white matter stroke. Here, we report the tissue repair processes after white matter stroke and identify Nogo receptor 1 (NgR1) ligands as inhibitors. We show that white matter repair and functional recovery are indeed possible in aged brains when an engineered NgR1 decoy receptor is systemically administered after white matter stroke, even at chronic periods in this disease.
Brief treatment with a highly selective immunoproteasome inhibitor promotes long-term cardiac allograft acceptance in mice
Authors: Sula Karreci Esilida , Fan Hao , Uehara Mayuko , Mihali Albana B. , Singh Pradeep K. , Kurdi Ahmed T. , Solhjou Zhabiz , Riella Leonardo V. , Ghobrial Irene , Laragione Teresina , Routray Sujit , Assaker Jean Pierre , Wang Rong , Sukenick George , Shi Lei , Barrat Franck J. , Nathan Carl F. , Lin Gang , Azzi Jamil
Published: December 2016

Significance

The potential of proteasome inhibitors to prevent transplant rejection and to treat other immune disorders is hindered by mechanism-based toxicity from inhibition of constitutive proteasomes. Here, we demonstrate that briefly, reversibly, and selectively inhibiting the immunoproteasome prolonged the survival of transplanted hearts in mice and allowed long-term survival when combined with single-dose CTLA4-Ig. Immunoproteasome inhibition noncytotoxically reduced T-cell proliferation and the numbers of effector T cells in the allograft and draining nodes while increasing T-cell expression of exhaustion markers. The immunoproteasome thus appears to play a role in suppressing induction of T-cell exhaustion. Selective inhibition of the immunoproteasome may be a potential treatment option for the management of transplant rejection.
Arabidopsis
male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues
Authors: Hsieh Ping-Hung , He Shengbo , Buttress Toby , Gao Hongbo , Couchman Matthew , Fischer Robert L. , Zilberman Daniel , Feng Xiaoqi
Published: December 2016

Significance

Cytosine methylation is a mechanism of epigenetic inheritance—the transmission across generations of information that does not reside in DNA sequence. This transmission is mediated by enzymes that copy methylation states following DNA replication. Only a small group of plant cells—gametes and their progenitors—participates in inheritance, yet methylation is usually studied in other cell types, in which cytosine methylation within CG dinucleotides appears to be too low for stable maintenance. Here, we examine methylation in the pollen grains of
Arabidopsis thaliana
plants with methyltransferase mutations and show that although methylation is maintained by similar mechanisms in pollen and somatic cells, maintenance of CG methylation is more efficient in pollen, explaining how methylation can be faithfully inherited across generations.
VarMatch: robust matching of small variant datasets using flexible scoring schemes
Authors: Sun Chen , Medvedev Paul
Published: December 2016

Motivation

Small variant calling is an important component of many analyses, and, in many instances, it is important to determine the set of variants which appear in multiple callsets. Variant matching is complicated by variants that have multiple equivalent representations. Normalization and decomposition algorithms have been proposed, but are not robust to different representation of complex variants. Variant matching is also usually done to maximize the number of matches, as opposed to other optimization criteria.

Results

We present the VarMatch algorithm for the variant matching problem. Our algorithm is based on a theoretical result which allows us to partition the input into smaller subproblems without sacrificing accuracy. VarMatch is robust to different representation of complex variants and is particularly effective in low complexity regions or those dense in variants. VarMatch is able to detect more matches than either the normalization or decomposition algorithms on tested datasets. It also implements different optimization criteria, such as edit distance, that can improve robustness to different variant representations. Finally, the VarMatch software provides summary statistics, annotations and visualizations that are useful for understanding callers’ performance.

Availability and Implementation

VarMatch is freely available at: https://github.com/medvedevgroup/varmatch

Supplementary information

Supplementary data are available at Bioinformatics online.
High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE
Authors: Majoros William H , Campbell Michael S , Holt Carson , DeNardo Erin K , Ware Doreen , Allen Andrew S , Yandell Mark , Reddy Timothy E
Published: December 2016

Motivation

The accurate interpretation of genetic variants is critical for characterizing genotype–phenotype associations. Because the effects of genetic variants can depend strongly on their local genomic context, accurate genome annotations are essential. Furthermore, as some variants have the potential to disrupt or alter gene structure, variant interpretation efforts stand to gain from the use of individualized annotations that account for differences in gene structure between individuals or strains.

Results

We describe a suite of software tools for identifying possible functional changes in gene structure that may result from sequence variants. ACE (‘Assessing Changes to Exons’) converts phased genotype calls to a collection of explicit haplotype sequences, maps transcript annotations onto them, detects gene-structure changes and their possible repercussions, and identifies several classes of possible loss of function. Novel transcripts predicted by ACE are commonly supported by spliced RNA-seq reads, and can be used to improve read alignment and transcript quantification when an individual-specific genome sequence is available. Using publicly available RNA-seq data, we show that ACE predictions confirm earlier results regarding the quantitative effects of nonsense-mediated decay, and we show that predicted loss-of-function events are highly concordant with patterns of intolerance to mutations across the human population. ACE can be readily applied to diverse species including animals and plants, making it a broadly useful tool for use in eukaryotic population-based resequencing projects, particularly for assessing the joint impact of all variants at a locus.

Availability and Implementation

ACE is written in open-source C ++ and Perl and is available from geneprediction.org/ACE

Supplementary information

Supplementary information is available at Bioinformatics online.