bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural circuitry of abdominal pain‐related fear learning and reinstatement in irritable bowel syndrome
Authors: Icenhour A. , Langhorst J. , Benson S. , Schlamann M. , Hampel S. , Engler H. , Forsting M. , Elsenbruch S. 
Published: December 2014

AbstractBackgroundAltered pain anticipation likely contributes to disturbed central pain processing in chronic pain conditions like irritable bowel syndrome (IBS), but the learning processes shaping the expectation of pain remain poorly understood. We assessed the neural circuitry mediating the formation, extinction, and reactivation of abdominal pain‐related memories in IBS patients compared to healthy controls (HC) in a differential fear conditioning paradigm.MethodsDuring fear acquisition, predictive visual cues (CS+) were paired with rectal distensions (US), while control cues (CS−) were presented unpaired. During extinction, only CSs were presented. Subsequently, memory reactivation was assessed with a reinstatement procedure involving unexpected USs. Using functional magnetic resonance imaging, group differences in neural activation to CS+ vs CS− were analyzed, along with skin conductance responses (SCR), CS valence, CS‐US contingency, state anxiety, salivary cortisol, and alpha‐amylase activity. The contribution of anxiety symptoms was addressed in covariance analyses.Key ResultsFear acquisition was altered in IBS, as indicated by more accurate contingency awareness, greater CS‐related valence change, and enhanced CS+‐induced differential activation of prefrontal cortex and amygdala. IBS patients further revealed enhanced differential cingulate activation during extinction and greater differential hippocampal activation during reinstatement. Anxiety affected neural responses during memory formation and reinstatement.Conclusions & InferencesAbdominal pain‐related fear learning and memory processes are altered in IBS, mediated by amygdala, cingulate cortex, prefrontal areas, and hippocampus. Enhanced reinstatement may contribute to hypervigilance and central pain amplification, especially in anxious patients. Preventing a ‘relapse’ of learned fear utilizing extinction‐based interventions may be a promising treatment goal in IBS.
GLABROUS INFLORESCENCE STEMS3 (GIS3) regulates trichome initiation and development in Arabidopsis
Authors: Sun Lili , Zhang Aidong , Zhou Zhongjing , Zhao Yongqin , Yan An , Bao Shengjie , Yu Hao , Gan Yinbo 
Published: December 2014

Summary

Arabidopsis trichome formation is an excellent model for studying various aspects of plant cell development and cell differentiation. Our previous works have demonstrated that several C2H2 zinc finger proteins, including GIS, GIS2, ZFP5, ZFP6 and ZFP8, control trichome cell development through GA and cytokinin signalling in Arabidopsis.

We identified a novel C2H2 zinc finger protein, GLABROUS INFLORESCENCE STEMS 3 (GIS3), which is a key factor in regulating trichome development in Arabidopsis.

In comparison with wild‐type plants, loss‐of‐function of GIS3 mutants exhibited a significantly decreased number of trichomes in cauline leaves, lateral branches, sepals of flowers, and main stems. Overexpression of GIS3 resulted in increased trichome densities in sepal, cauline leaves, lateral branches, main inflorescence stems and in the appearance of ectopic trichomes on carpels.

The molecular and genetic analyses show that GIS3 acts upstream of GIS, GIS2, ZFP8 and the key trichome initiation factors, GL1 and GL3. Steroid‐inducible gene expression analyses and chromatin immunoprecipitation (ChIP) experiments suggest that GIS and GIS2 are the direct target genes of GIS3.
Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development
Authors: Martínez‐García Laura B. , Richardson Sarah J. , Tylianakis Jason M. , Peltzer Duane A. , Dickie Ian A. 
Published: December 2014

SummaryLittle is known about the response of arbuscular mycorrhizal fungal communities to ecosystem development. We use a long‐term soil chronosequence that includes ecosystem progression and retrogression to quantify the importance of host plant identity as a factor driving fungal community composition during ecosystem development.We identified arbuscular mycorrhizal fungi and plant species from 50 individual roots from each of 10 sites spanning 5–120 000 yr of ecosystem age using terminal restriction fragment length polymorphism (T‐RFLP), Sanger sequencing and pyrosequencing.Arbuscular mycorrhizal fungal communities were highly structured by ecosystem age. There was strong niche differentiation, with different groups of operational taxonomic units (OTUs) being characteristic of early succession, ecosystem progression and ecosystem retrogression. Fungal alpha diversity decreased with ecosystem age, whereas beta diversity was high at early stages and lower in subsequent stages. A total of 39% of the variance in fungal communities was explained by host plant and site age, 29% of which was attributed to host and the interaction between host and site (24% and 5%, respectively).The strong response of arbuscular mycorrhizal fungi to ecosystem development appears to be largely driven by plant host identity, supporting the concept that plant and fungal communities are tightly coupled rather than independently responding to habitat.
Reconciling functions and evolution of isoprene emission in higher plants
Authors: Loreto Francesco , Fineschi Silvia 
Published: December 2014

SummaryCompilation and analysis of existing inventories reveal that isoprene is emitted by c. 20% of the perennial vegetation of tropical and temperate regions of the world. Isoprene emitters are found across different plant families without any clear phylogenetic thread. However, by critically appraising information in inventories, several ecological patterns of isoprene emission can be highlighted, including absence of emission from C4 and annual plants, and widespread emission from perennial and deciduous plants of temperate environments. Based on this analysis, and on available information on biochemistry, ecology and functional roles of isoprene, it is suggested that isoprene may not have evolved to help plants face heavy or prolonged stresses, but rather assists C3 plants to run efficient photosynthesis and to overcome transient and mild stresses, especially during periods of active plant growth in warm seasons. When the stress status persists, or when evergreen leaves cope with multiple and repeated stresses, isoprene biosynthesis is replaced by the synthesis of less volatile secondary compounds, in part produced by the same biochemical pathway, thus indicating causal determinism in the evolution of isoprene‐emitting plants in response to the environment.

Contents

Summary
578

I.
Introduction
578

II.
Isoprene emission has clear biological and ecological patterns
579

III.
Reconciling ecological patterns of isoprene emission with possible evolutionary and functional threads
580

Acknowledgements
581

References
581
Durable Purchases over the Later Life Cycle
Authors: Browning Martin , Crossley Thomas F. , Lührmann Melanie 
Published: December 2014

AbstractWe investigate life‐cycle patterns of demand for services from household durables using UK panel data. We take careful account of prices, demographics, labour supply and health. Demand for consumer electronics rises with age, while the demand for household appliances is flat. These findings contrast with the well documented decline in non‐durable consumption at older ages, and suggest that studies that estimate the overall discount rate from nondurable consumption may underestimate consumer patience and the savings required to fund retirement. We also find important non‐separabilities between the demand for durables, labour supply and health status.
Estimating and evaluating Value‐at‐Risk forecasts based on realized variance: empirical evidence from ICE Brent Crude oil futures
Authors: Haugom Erik , Veka Steinar , Lien Gudbrand , Westgaard Sjur 
Published: December 2014

AbstractThis paper is the first to use the concept of realized volatility to forecast Value‐at‐Risk (VaR) for ICE Brent Crude oil futures. We examine sensitivities in the VaR forecasts across intra‐daily sampling frequency used to calculate realized volatility. We evaluate the VaR forecasts using Christoffersen's test for conditional coverage on quantiles of particular interest. Additionally, we examine a percentile–percentile plot of the VaR forecasts for all percentiles. The main empirical results show that very good VaR forecasts can be obtained using Gaussian critical values in combination with volatility forecasts based on realized volatility. An examination of the sampling frequency suggests that the most accurate VaR forecasts are obtained with a sampling frequency of between 1 and 10 min. This has important implications for practitioners operating in the financial oil sector.
Determinants of economic growth in OPEC: an extreme bounds analysis
Authors: Zarra‐Nezhad Mansour , Hosseinpour Fatimah 
Published: December 2014

AbstractThe aim of this study is to identify robust determinants of economic growth in Organization of Petroleum Exporting Countries (OPEC). To examine the robustness of 101 potential determinants of economic growth in OPEC about 11 million regressions are estimated. The results of extreme bounds analysis with the unbalanced panel data of 21 years shows that variety of trade policy measures are robust and support export‐led growth hypothesis. Proxies of export passed very strict test of Levine and Renelt, while oil export is not robust. The results also support conditional‐convergence hypothesis.
Biological heterogeneity of obsessive–compulsive disorder: A voxel‐based morphometric study based on dimensional assessment
Authors: Okada Kayo , Nakao Tomohiro , Sanematsu Hirokuni , Murayama Keitaro , Honda Shinichi , Tomita Mayumi , Togao Osamu , Yoshiura Takashi , Kanba Shigenobu 
Published: December 2014

AimAlthough many neuroimaging studies of obsessive–compulsive disorder (OCD) have reported broad abnormalities in gray matter (GM), their results remain inconsistent. One reason for this inconsistency could be the heterogeneity of OCD. In the present study, we aimed to classify alterations in brain anatomy by OCD subtype.MethodsMagnetic resonance imaging examinations of 37 OCD patients and 37 matched healthy controls were conducted using a 3.0‐Tesla scanner. In the voxel‐based morphometric procedure, preprocessed GM structural images were used to compare the two groups, and multiple regression analysis was used to investigate the correlation between regional GM volume in OCD patients and the OCD symptom dimension type assessed by using the Dimensional Yale–Brown Obsessive–Compulsive Scale.ResultsWe found significant reductions in GM volume in broad areas of the left prefrontal, right orbitofrontal, right parietal, right temporal, and right posterior cingulate cortex in the OCD patients compared to healthy controls. In addition, we found specific negative correlations between symptomatic dimension scores and regional GM volumes, mainly as decreased right cerebellum in ‘aggression/checking’ and decreased right insula in ‘contamination/washing’.ConclusionThe pathophysiology of OCD may involve widely distributed neural systems. Moreover, there are distinct correlations among symptomatic dimensions and structural abnormalities.
Short‐term hybridisation activates Tnt1 and Tto1 Copia retrotransposons in wild tuber‐bearing Solanum species
Authors: Paz R. C. , Rendina González A. P. , Ferrer M. S. , Masuelli R. W. 
Published: December 2014

AbstractInterspecific hybridisation in tuber‐bearing species of Solanum is a common phenomenon and represents an important source of variability, crucial for adaptation and speciation of potato species. In this regard, the effects of interspecific hybridisation on retrotransposon families present in the genomes, and their consequent effects on generation of genetic variability in wild tuber‐bearing Solanum species, are poorly characterised. The aim of this study was to analyse the activity of retrotransposons in inter‐ and intraspecific hybrids between S. kurtzianum and S. microdontum, obtained by controlled crosses, and the effects on morphological, genetic and epigenetic variability. For genetic and epigenetic analysis, S‐SAP (sequence‐specific amplification polymorphism) and TMD (transposon methylation display) techniques were used, respectively, with specific primers for Tnt1 and Tto1 retrotransposon families (Order LTR, Superfamily Copia). The results indicate that at morphological level, interspecific hybrid genotypes differ from their parental species, whereas derived intraspecific hybrids do not. In both cases, we observed significant reductions in pollen grain viability, and a negative correlation with Tnt1 mobility. Both retrotransposons, Tto1 and Tnt1, were mobilised in the genotypes analysed, with mobility ranging from 0 to 7.8%. Furthermore, at the epigenetic level, demethylation was detected in the vicinity of Tnt1 and Tto1 in the hybrids compared with the parental genotypes. These patterns were positively correlated with the activity of the retrotransposons. The results suggest a possible mechanism through which hybridisation events generate genetic variability in tuber‐bearing species of Solanum through retrotranposon activation.
Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae
Authors: Smith Lisa M. , Burbano Hernán A. , Wang Xi , Fitz Joffrey , Wang George , Ural‐Blimke Yonca , Weigel Detlef 
Published: December 2014

SummaryMicroRNAs (miRNAs) are short RNAs involved in gene regulation through translational inhibition and transcript cleavage. After processing from imperfect fold‐back structures, miRNAs are incorporated into RNA‐induced silencing complexes (RISCs) before targeting transcripts with varying degrees of complementarity. Some miRNAs are evolutionarily deep‐rooted, and sequence complementarity with their targets is maintained through purifying selection. Both Arabidopsis and Capsella belong to the tribe Camelineae in the Brassicaceae, with Capsella rubella serving as an outgroup to the genus Arabidopsis. The genome sequence of C. rubella has recently been released, which allows characterization of its miRNA complement in comparison with Arabidopsis thaliana and Arabidopsis lyrata. Through next‐generation sequencing, we identify high‐confidence miRNA candidates specific to the C. rubella lineage. Only a few lineage‐specific miRNAs have been studied for evolutionary constraints, and there have been no systematic studies of miRNA target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in miRNAs and their targets within A. thaliana, and between A. thaliana, A. lyrata and C. rubella. We document a surprising amount of small‐scale variation in miRNA–target pairs, where many miRNAs are predicted to have species‐specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many miRNA–target pairs can be observed even on a relatively short evolutionary time‐scale, with non‐random occurrences of differences in miRNAs and their complements in the miRNA precursors, the miRNA* sequences.
Calcium signalling in developing cardiomyocytes: implications for model systems and disease
Authors: Louch William E. , Koivumäki Jussi T. , Tavi Pasi 
Published: December 2014

AbstractAdult cardiomyocytes exhibit complex Ca2+ homeostasis, enabling tight control of contraction and relaxation. This intricate regulatory system develops gradually, with progressive maturation of specialized structures and increasing capacity of Ca2+ sources and sinks. In this review, we outline current understanding of these developmental processes, and draw parallels to pathophysiological conditions where cardiomyocytes exhibit a striking regression to an immature state of Ca2+ homeostasis. We further highlight the importance of understanding developmental physiology when employing immature cardiomyocyte models such as cultured neonatal cells and stem cells.
Effect of deformable registration on the dose calculated in radiation therapy planning CT scans of lung cancer patients a)
Authors: Cunliffe Alexandra R. , Contee Clay , Armato Samuel G. , White Bradley , Justusson Julia , Malik Renuka , Al‐Hallaq Hania A. 
Published: December 2014

Purpose:To characterize the effects of deformable image registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan.Methods:Eighteen patients who received curative doses (≥60 Gy, 2 Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic‐quality pretherapy (4–75 days) CT scan and a treatment planning scan with an associated dose map were collected. To establish correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pretherapy scans then were coregistered with planning scans (and associated dose maps) using the demons deformable registration algorithm and two variants of the Fraunhofer MEVIS algorithm (“Fast” and “EMPIRE10”). Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from each of the three algorithms. The Euclidean distance between manually and automatically mapped landmark points (dE) and the absolute difference in planned dose (|ΔD|) were calculated. Using regression modeling, |ΔD| was modeled as a function of dE, dose (D), dose standard deviation (SDdose) in an eight‐pixel neighborhood, and the registration algorithm used.Results:Over 1400 landmark point pairs were identified, with 58–93 (median: 84) points identified per patient. Average |ΔD| across patients was 3.5 Gy (range: 0.9–10.6 Gy). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, with an average dE across patients of 5.2 mm (compared with >7 mm for the other two algorithms). Consequently, average |ΔD| was also lowest using the Fraunhofer MEVIS EMPIRE10 algorithm. |ΔD| increased significantly as a function of dE (0.42 Gy/mm), D (0.05 Gy/Gy), SDdose (1.4 Gy/Gy), and the algorithm used (≤1 Gy).Conclusions:An average error of <4 Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration, with the majority of points yielding dose‐mapping error <2 Gy (approximately 3% of the total prescribed dose). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, resulting in the smallest errors in mapped dose. Dose differences following registration increased significantly with increasing spatial registration errors, dose, and dose gradient (i.e., SDdose). This model provides a measurement of the uncertainty in the radiation dose when points are mapped between serial CT scans through deformable registration.
HDR 192Ir source speed measurements using a high speed video camera
Authors: Fonseca Gabriel P. , Viana Rodrigo S. S. , Podesta Mark , Rubo Rodrigo A. , de Sales Camila P. , Reniers Brigitte , Yoriyaz Hélio , Verhaegen Frank 
Published: December 2014

Purpose:The dose delivered with a HDR 192Ir afterloader can be separated into a dwell component, and a transit component resulting from the source movement. The transit component is directly dependent on the source speed profile and it is the goal of this study to measure accurate source speed profiles.Methods:A high speed video camera was used to record the movement of a 192Ir source (Nucletron, an Elekta company, Stockholm, Sweden) for interdwell distances of 0.25–5 cm with dwell times of 0.1, 1, and 2 s. Transit dose distributions were calculated using a Monte Carlo code simulating the source movement.Results:The source stops at each dwell position oscillating around the desired position for a duration up to (0.026 ± 0.005) s. The source speed profile shows variations between 0 and 81 cm/s with average speed of ∼33 cm/s for most of the interdwell distances. The source stops for up to (0.005 ± 0.001) s at nonprogrammed positions in between two programmed dwell positions. The dwell time correction applied by the manufacturer compensates the transit dose between the dwell positions leading to a maximum overdose of 41 mGy for the considered cases and assuming an air‐kerma strength of 48 000 U. The transit dose component is not uniformly distributed leading to over and underdoses, which is within 1.4% for commonly prescribed doses (3–10 Gy).Conclusions:The source maintains its speed even for the short interdwell distances. Dose variations due to the transit dose component are much lower than the prescribed treatment doses for brachytherapy, although transit dose component should be evaluated individually for clinical cases.
CRISPR-Cas9-Mediated Single-Gene and Gene Family Disruption in Trypanosoma cruzi
Authors: Peng Duo , Kurup Samarchith P. , Yao Phil Y. , Minning Todd A. , Tarleton Rick L. 
Published: December 2014

ABSTRACT

Trypanosoma cruzi
is a protozoan parasite of humans and animals, affecting 10 to 20 million people and innumerable animals, primarily in the Americas. Despite being the largest cause of infection-induced heart disease worldwide, even among the neglected tropical diseases (NTDs)
T. cruzi
is considered one of the least well understood and understudied. The genetic complexity of
T. cruzi
as well as the limited set of efficient techniques for genome engineering contribute significantly to the relative lack of progress in and understanding of this pathogen. Here, we adapted the CRISPR-Cas9 system for the genetic engineering of
T. cruzi
, demonstrating rapid and efficient knockout of multiple endogenous genes, including essential genes. We observed that in the absence of a template, repair of the Cas9-induced double-stranded breaks (DSBs) in
T. cruzi
occurs exclusively by microhomology-mediated end joining (MMEJ) with various-sized deletions. When a template for DNA repair is provided, DSB repair by homologous recombination is achieved at an efficiency several orders of magnitude higher than that in the absence of CRISPR-Cas9-induced DSBs. We also demonstrate the high multiplexing capacity of CRISPR-Cas9 in
T. cruzi
by knocking down expression of an enzyme gene family consisting of 65 members, resulting in a significant reduction of enzymatic product with no apparent off-target mutations. Lastly, we show that Cas9 can mediate disruption of its own coding sequence, rescuing a growth defect in stable Cas9-expressing parasites. These results establish a powerful new tool for the analysis of gene functions in
T. cruzi
, enabling the study of essential genes and their functions and analysis of the many large families of related genes that occupy a substantial portion of the
T. cruzi
genome.

IMPORTANCE
Trypanosoma cruzi
, the causative agent of human Chagas disease, is the leading worldwide cause of infectious myocarditis. Diagnostics for the infection are relatively poor, treatment options are limited and of variable effectiveness, and suitable vaccines are nonexistent. The
T. cruzi
genome is replete with genes of unknown function and greatly expanded gene families with hundreds of members. The absence of facile genetic engineering tools, including RNA interference, for
T. cruzi
has prevented elucidation of gene and gene family function and the development of better infection prevention and control measures. In this study, we demonstrate that the CRISPR-Cas9 system is a versatile and powerful tool for genome manipulations in
T. cruzi
, bringing new opportunities for unraveling the functions of previously uncharacterized genes and how this human pathogen engages its large families of genes encoding surface proteins to interact with human and animal hosts.