bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing generalized coherent states for a free particle
Authors: Maamache Mustapha , Khatir Abderrezak , Lakehal Halim , Choi Jeong Ryeol 
Published: August 2016

AbstractDespite the didactic importance of a free particle in quantum mechanics, its coherent state analysis has long been untouched. It is only recently that it has been noticed and studied in the semiclassical domain. While the previously known solutions, reported by Bagrov et al. for a free particle, are described using the linear non-Hermitian invariant operator, we show in this work that the general solution of the Schrödinger equation can also be naturally derived using a simpler method based on an Hermitian linear invariant operator. According to this, an exact Gaussian wave function that corresponds to a coherent state solution is obtained. An interpretation for such general quantum solution designated within the Lewis-Riesenfeld framework is provided and, further, quantum-classical correspondence principle for the system is reexamined.
Immediate and delayed signal of slab breakoff in Oligo/Miocene Molasse deposits from the European Alps
Authors: Schlunegger Fritz , Castelltort Sébastien 
Published: August 2016

AbstractHigh-resolution 32–20 Ma-old stratigraphic records from the Molasse foreland basin situated north of the Alps and Gonfolite Lombarda conglomerates deposited on the southern Alpine margin, document two consecutive sedimentary responses - an immediate and delayed response - to slab breakoff beneath the central Alps c. 32–30 Ma ago. The first signal, which occurred due to rebound and surface uplift in the Alps, was a regional and simultaneous switch from basin underfill to overfill at 30 Ma paired with shifts to coarse-grained depositional environments in the foreland basin. The second signal, however, arrived several million years after slab breakoff and was marked by larger contributions of crystalline clasts in the conglomerates, larger clast sizes, larger sediment fluxes and shifts to more proximal facies. We propose that this secondary pulse reflects a delayed whiplash-type erosional response to surface uplift, where erosion and sediment flux became amplified through positive feedbacks once larger erosional thresholds of crystalline bedrock were exceeded.
Mesenchymal Stem Cells Enhance Nerve Regeneration in a Rat Sciatic Nerve Repair and Hindlimb Transplant Model
Authors: Cooney Damon S. , Wimmers Eric G. , Ibrahim Zuhaib , Grahammer Johanna , Christensen Joani M. , Brat Gabriel A. , Wu Lehao W. , Sarhane Karim A. , Lopez Joseph , Wallner Christoph , Furtmüller Georg J. , Yuan Nance , Pang John , Sarkar Kakali , Lee W. P. Andrew , Brandacher Gerald 
Published: August 2016

AbstractThis study investigates the efficacy of local and intravenous mesenchymal stem cell (MSC) administration to augment neuroregeneration in both a sciatic nerve cut-and-repair and rat hindlimb transplant model. Bone marrow-derived MSCs were harvested and purified from Brown-Norway (BN) rats. Sciatic nerve transections and repairs were performed in three groups of Lewis (LEW) rats: negative controls (n = 4), local MSCs (epineural) injection (n = 4), and systemic MSCs (intravenous) injection (n = 4). Syngeneic (LEW-LEW) (n = 4) and allogeneic (BN-LEW) (n = 4) hindlimb transplants were performed and assessed for neuroregeneration after local or systemic MSC treatment. Rats undergoing sciatic nerve cut-and-repair and treated with either local or systemic injection of MSCs had significant improvement in the speed of recovery of compound muscle action potential amplitudes and axon counts when compared with negative controls. Similarly, rats undergoing allogeneic hindlimb transplants treated with local injection of MSCs exhibited significantly increased axon counts. Similarly, systemic MSC treatment resulted in improved nerve regeneration following allogeneic hindlimb transplants. Systemic administration had a more pronounced effect on electromotor recovery while local injection was more effective at increasing fiber counts, suggesting different targets of action. Local and systemic MSC injections significantly improve the pace and degree of nerve regeneration after nerve injury and hindlimb transplantation.
Effects of T592 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 can not explain the retroviral restriction defect
Authors: Bhattacharya Akash , Wang Zhonghua , White Tommy , Buffone Cindy , Nguyen Laura A. , Shepard Caitlin N. , Kim Baek , Demeler Borries , Diaz-Griffero Felipe , Ivanov Dmitri N. 
Published: August 2016

AbstractSAMHD1, a dNTP triphosphohydrolase, contributes to interferon signaling and restriction of retroviral replication. SAMHD1-mediated retroviral restriction is thought to result from the depletion of cellular dNTP pools, but it remains controversial whether the dNTPase activity of SAMHD1 is sufficient for restriction. The restriction ability of SAMHD1 is regulated in cells by phosphorylation on T592. Phosphomimetic mutations of T592 are not restriction competent, but appear intact in their ability to deplete cellular dNTPs. Here we use analytical ultracentrifugation, fluorescence polarization and NMR-based enzymatic assays to investigate the impact of phosphomimetic mutations on SAMHD1 tetramerization and dNTPase activity in vitro. We find that phosphomimetic mutations affect kinetics of tetramer assembly and disassembly, but their effects on tetramerization equilibrium and dNTPase activity are insignificant. In contrast, the Y146S/Y154S dimerization-defective mutant displays a severe dNTPase defect in vitro, but is indistinguishable from WT in its ability to deplete cellular dNTP pools and to restrict HIV replication. Our data suggest that the effect of T592 phosphorylation on SAMHD1 tetramerization is not likely to explain the retroviral restriction defect and we hypothesize that enzymatic activity of SAMHD1 is subject to additional cellular regulatory mechanisms that have not yet been recapitulated in vitro.
Physiological and pathological clinical conditions and light scattering in brain
Authors: Kurata Tsuyoshi , Iwata Sachiko , Tsuda Kennosuke , Kinoshita Masahiro , Saikusa Mamoru , Hara Naoko , Oda Motoki , Ohmae Etsuko , Araki Yuko , Sugioka Takashi , Takashima Sachio , Iwata Osuke 
Published: August 2016

AbstractMRI of preterm infants at term commonly reveals subtle brain lesions such as diffuse white matter injury, which are linked with later cognitive impairments. The timing and mechanism of such injury remains unclear. The reduced scattering coefficient of near-infrared light (μs’) has been shown to correlate linearly with gestational age in neonates. To identify clinical variables associated with brain μs’, 60 preterm and full-term infants were studied within 7 days of birth. Dependence of μs’ obtained from the frontal head on clinical variables was assessed. In the univariate analysis, smaller μs’ was associated with antenatal glucocorticoid, emergency Caesarean section, requirement for mechanical ventilation, smaller gestational age, smaller body sizes, low 1- and 5-minute Apgar scores, higher cord blood pH and PO2, and higher blood HCO3− at the time of study. Multivariate analysis revealed that smaller gestational age, requirement for mechanical ventilation, and higher HCO3− at the time of study were correlated with smaller μs’. Brain μs’ depended on variables associated with physiological maturation and pathological conditions of the brain. Further longitudinal studies may help identify pathological events and clinical conditions responsible for subtle brain injury and subsequent cognitive impairments following preterm birth.
Divergent habitat filtering of root and soil fungal communities in temperate beech forests
Authors: Goldmann Kezia , Schröter Kristina , Pena Rodica , Schöning Ingo , Schrumpf Marion , Buscot François , Polle Andrea , Wubet Tesfaye 
Published: August 2016

AbstractDistance decay, the general reduction in similarity of community composition with increasing geographical distance, is known as predictor of spatial variation and distribution patterns of organisms. However, changes in fungal communities along environmental gradients are little known. Here we show that distance decays of soil-inhabiting and root-associated fungal assemblages differ and identify explanatory environmental variables. High-throughput sequencing analysis of fungal communities of beech-dominated forests at three study sites across Germany shows that root-associated fungi are recruited from the soil fungal community. However, distance decay is substantially weaker in the root-associated than in the soil community. Variance partitioning of factors contributing to the observed distance decay patterns support the hypothesis that host trees stabilize the composition of root-associated fungi communities, relative to soil communities. Thus, they not only have selective impacts on associated communities, but also buffer effects of changes in microclimatic and environmental variables that directly influence fungal community composition.
Inhibition of CDK9 as a therapeutic strategy for inflammatory arthritis
Authors: Hellvard Annelie , Zeitlmann Lutz , Heiser Ulrich , Kehlen Astrid , Niestroj André , Demuth Hans-Ulrich , Koziel Joanna , Delaleu Nicolas , Jan Potempa  , Mydel Piotr 
Published: August 2016

AbstractRheumatoid arthritis is characterised by synovial inflammation and proliferation of fibroblast-like synoviocytes. The induction of apoptosis has long been proposed as a target for proliferative autoimmune diseases and has further been shown to act as a successful treatment of experimental models of arthritis, such as collagen-induced arthritis. Here we examined the effects of specific oral small-molecule inhibitors of the transcription regulating cyclin-dependent kinase 9 on the development and progression of collagen-induced arthritis. DBA/1 mice were immunised with bovine collagen type II and treated orally with specific CDK9 inhibitors. The effects of CDK9 inhibition on RNA levels and protein expression, apoptosis induction, caspase activation and lymphocyte phenotype were further analysed. Mice showed a significant delay in disease onset and a reduction in disease severity following treatment with CDK9 inhibitors. Inhibiting CDK9 activity in peripheral blood mononuclear cells resulted in the loss of Mcl-1 expression at both the protein and RNA levels, along with a subsequent increase in apoptosis. CDK9 specific inhibitors may be a potential alternative treatment not only of cancer, but also for autoimmune- and inflammatory diseases. Taken together, these results show that transient inhibition of CDK9 induces apoptosis in leukocyte subsets and modulates the immune response.
Evidence of salt accumulation in beach intertidal zone due to evaporation
Authors: Geng Xiaolong , Boufadel Michel C. , Jackson Nancy L. 
Published: August 2016

AbstractIn coastal environments, evaporation is an important driver of subsurface salinity gradients in marsh systems. However, it has not been addressed in the intertidal zone of sandy beaches. Here, we used field data on an estuarine beach foreshore with numerical simulations to show that evaporation causes upper intertidal zone pore-water salinity to be double that of seawater. We found the increase in pore-water salinity mainly depends on air temperature and relative humidity and tide and wave actions dilute a fraction of the high salinity plume, resulting in a complex process. This is in contrast to previous studies that consider seawater as the most saline source to a coastal aquifer system, thereby concluding that seawater infiltration always increases pore-water salinity by seawater-groundwater mixing dynamics. Our results demonstrate the combined effects of evaporation and tide and waves on subsurface salinity distribution on a beach face. We anticipate our quantitative investigation will shed light on the studies of salt-affected biological activities in the intertidal zone. It also impacts our understanding of the impact of global warming; in particular, the increase in temperature does not only shift the saltwater landward, but creates a different salinity distribution that would have implications on intertidal biological zonation.
Risk factors for Clostridium difficile infection in hemato-oncological patients: A case control study in 144 patients
Authors: Fuereder Thorsten , Koni Danjel , Gleiss Andreas , Kundi Michael , Makristathis Athanasios , Zielinski Christoph , Steininger Christoph 
Published: August 2016

AbstractEvidence on risk factors for Clostridium difficile infection (CDI) in hemato-oncologic patients is conflicting. We studied risk factors for CDI in a large, well-characterized cohort of hemato-oncological patients. 144 hemato-oncological patients were identified in this retrospective, single center study with a microbiologically confirmed CDI-associated diarrhea. Patients were compared with 144 age and sex matched hemato-oncologic patients with CDI negative diarrhea. Risk factors such as prior antimicrobial therapy, type of disease, chemotherapy and survival were evaluated. CDI-positive patients received more frequently any antimicrobial agent and antimicrobial combination therapy than CDI-negative patients (79% vs. 67%; OR = 2.26, p = 0.038 and OR = 2.62, p = 0.003, respectively). CDI positive patients were treated more frequently with antimicrobial agents active against C. difficile than CDI negative ones (25% vs. 13%; OR = 2.2, p = 0.039). The interval between last chemotherapy and onset of diarrhea was significantly shorter in patients without CDI (median, 17 days vs 36 days; p < 0.001). Our study demonstrates that chemotherapy is not a significant risk factor for CDI but for early onset CDI negative diarrhea. The predominant modifiable risk factor for CDI is in hemato-oncological patients antimicrobial treatment. These findings should be taken into account in the daily clinical practice to avoid CDI associated complications and excess health care costs.
Hepatic and serum lipid signatures specific to nonalcoholic steatohepatitis in murine models
Authors: Chiappini Franck , Desterke Christophe , Bertrand-Michel Justine , Guettier Catherine , Le Naour François 
Published: August 2016

AbstractNonalcoholic fatty liver (NAFL) is a precursor of nonalcoholic steatohepatitis (NASH), a condition that may progress to cirrhosis and hepatocellular carcinoma. Markers for diagnosis of NASH are still lacking. We have investigated lipid markers using mouse models that developed NAFL when fed with high fat diet (HFD) or NASH when fed using methionine choline deficient diet (MCDD). We have performed a comprehensive lipidomic analysis on liver tissues as well as on sera from mice fed HFD (n = 5), MCDD (n = 5) or normal diet as controls (n = 10). Machine learning approach based on prediction analysis of microarrays followed by random forests allowed identifying 21 lipids out of 149 in the liver and 14 lipids out of 155 in the serum discriminating mice fed MCDD from HFD or controls. In conclusion, the global approach implemented allowed characterizing lipid signatures specific to NASH in both liver and serum from animal models. This opens new avenue for investigating early and non-invasive lipid markers for diagnosis of NASH in human.
Ubiquitin C-terminal hydrolase L1 (UCH-L1): structure, distribution and roles in brain function and dysfunction
Authors: Bishop Paul , Rocca Dan , Henley Jeremy M. 
Published: August 2016

Ubiquitin C-terminal hydrolase L1 (UCH-L1) is an extremely abundant protein in the brain where, remarkably, it is estimated to make up 1–5% of total neuronal protein. Although it comprises only 223 amino acids it has one of the most complicated 3D knotted structures yet discovered. Beyond its expression in neurons UCH-L1 has only very limited expression in other healthy tissues but it is highly expressed in several forms of cancer. Although UCH-L1 is classed as a deubiquitinating enzyme (DUB) the direct functions of UCH-L1 remain enigmatic and a wide array of alternative functions has been proposed. UCH-L1 is not essential for neuronal development but it is absolutely required for the maintenance of axonal integrity and UCH-L1 dysfunction is implicated in neurodegenerative disease. Here we review the properties of UCH-L1, and how understanding its complex structure can provide new insights into its roles in neuronal function and pathology.
Acute Effects of Synthetic Cannabinoids: Update 2015
Authors: Tournebize Juliana , Gibaja Valérie , Kahn Jean-Pierre 
Published: August 2016

Background Cannabis is the most widely used illicit drug in the United States and Europe. In recent years, a range of new substances with cannabis-like effects—known as synthetic cannabinoids (SCs)—have suddenly burst on the drug scene. However, there is limited information about the clinical hazards linked to the use of these emerging substances. This review summarizes the literature to date relating the health effects of SCs. Method: A systematic literature review of original case studies was performed using PubMed and Web of Science (January 1980–July 2015). Only articles in which a drug screening was reported were included in this review. Results Forty-six articles meeting the inclusion criteria were included in this review, reporting data on 114 patients who went to hospital emergency departments after exposure to SCs. The majority of patients were adolescent or young adult males (14–25 years; 24.5 ± 10.1 years). The most common route of administration was smoking. The SCs most involved were John William Huffman (JWH) derivatives, followed by XRL-11, ADB-PINACA, AM-2201, MAM-2201, and 5F-PB-22. This analysis showed that the use of these substances may cause minor and moderate side effects similar to those of cannabis intoxication, including tachycardia, nausea, somnolence, hallucinations, paranoia, xerostomia, and injected conjunctivae among others. However, atypical cannabis intoxication effects and worse complications (such as renal injuries, aggressiveness, cerebral ischemia, myocardial infarction, etc.) were also observed, which led to a significant morbidity were also observed. Some SCs were highlighted as being involved in 24 cases of deaths. Conclusions In this review, the nature and frequency of the signs and symptoms of SC poisoning were estimated in order to inform health professionals about the health risks of these new and emerging substances.
Reliability of the two-point measurement of the spatial correlation length from Gaussian-shaped fluctuating signals in fusion-grade plasmas
Authors: Kim Jaewook , Nam Y.U. , Lampert M. , Ghim Y.-C. 
Published: August 2016

Abstract
A statistical method for the estimation of the spatial correlation lengths of Gaussian-shaped fluctuating signals with two measurement points is examined to quantitatively evaluate its reliability (variance) and accuracy (bias error). The standard deviation of the correlation value is analytically derived for randomly distributed Gaussian shaped fluctuations satisfying stationarity and homogeneity, allowing us to evaluate, as a function of fluctuation-to-noise ratios, the sizes of averaging time windows and the ratios of the distance between the two measurement points to the true correlation length, and the goodness of the two-point measurement for estimating the spatial correlation length. Analytic results are confirmed with numerically generated synthetic data and real experimental data obtained with the KSTAR beam emission spectroscopy diagnostic. Our results can be applied to Gaussian-shaped fluctuating signals where a correlation length must be measured with only two measurement points.
Contrasting patterns of genetic variation in core and peripheral populations
of highly outcrossing and wind pollinated forest tree species
Authors: Wójkiewicz Błażej , Litkowiec Monika , Wachowiak Witold 
Published: August 2016

Abstract
Gene flow tends to have a homogenising effect on a species’ background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine—a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species’ putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average F ST  = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management programs.
A two-part mixed-effects model for analyzing longitudinal microbiome compositional data
Authors: Chen Eric Z. , Li Hongzhe 
Published: August 2016

AbstractMotivation: The human microbial communities are associated with many human diseases such as obesity, diabetes and inflammatory bowel disease. High-throughput sequencing technology has been widely used to quantify the microbial composition in order to understand its impacts on human health. Longitudinal measurements of microbial communities are commonly obtained in many microbiome studies. A key question in such microbiome studies is to identify the microbes that are associated with clinical outcomes or environmental factors. However, microbiome compositional data are highly skewed, bounded in [0,1), and often sparse with many zeros. In addition, the observations from repeated measures in longitudinal studies are correlated. A method that takes into account these features is needed for association analysis in longitudinal microbiome data.Results: In this paper, we propose a two-part zero-inflated Beta regression model with random effects (ZIBR) for testing the association between microbial abundance and clinical covariates for longitudinal microbiome data. The model includes a logistic regression component to model presence/absence of a microbe in the samples and a Beta regression component to model non-zero microbial abundance, where each component includes a random effect to account for the correlations among the repeated measurements on the same subject. Both simulation studies and the application to real microbiome data have shown that ZIBR model outperformed the previously used methods. The method provides a useful tool for identifying the relevant taxa based on longitudinal or repeated measures in microbiome research.Availability and Implementation: https://github.com/chvlyl/ZIBRContact: hongzhe@upenn.edu