bluuebunny/crossref_metadata_2025_split huggingface dataset:
InxGa1−xSe mixed crystals grown from an In flux by the traveling heater method for THz wave generation
Authors: Sato Yohei , Tang Chao , Watanabe Katsuya , Ohsaki Junya , Yamamoto Takuya , Tanabe Tadao , Oyama Yutaka 
Published: June 2020

Abstract
The growth rate of crystalline GaSe from solution was increased by using indium as a solvent. The solubility and concentration gradient of Se were measured using differential scanning calorimetry (DSC). The Se solubility and the temperature coefficient of the solubility were respectively 15 times and 2.2 times greater in crystals grown from an In flux with GaSe at saturation compared with the case of Se dissolved in a Ga flux. In this study, we succeeded in growing InxGa1−xSe ingots from an In flux without the need for a seed crystal, and in increasing the growth rate of GaSe from solution. In addition, we used difference frequency generation to generate THz waves (with a frequency of 9.7 THz) in an InxGa1−xSe mixed crystal and investigated the relationship between the output energy of the THz radiation and the interaction length of the excitation light. The conversion efficiency of THz wave (9.7 THz) from the InxGa1−xSe mixed crystal with thickness of 860 μm was 26 times greater than that of GaSe crystal with thickness 100 μm grown from Ga solvent.
Drainage reduces the resilience of a boreal peatland
Authors: Harris Lorna I , Roulet Nigel T , Moore Tim R 
Published: June 2020

Abstract
Drier conditions caused by drainage for infrastructure development, or associated with global climate warming, may test the resilience of carbon-rich northern peatlands. Feedbacks among biological and hydrological processes maintain the long-term stability of peatlands, but if hydrological thresholds are passed, these feedbacks may be weakened, causing a shift in ecosystem state and potentially large losses of carbon (C). To determine peatland response to hydrological change, we examined the structure (vegetation composition and hydrology) and biogeochemical function (carbon dioxide exchange) of a pristine bog and a bog subject to ∼7 years localised drainage (caused by regional groundwater drawdown due to mine dewatering) in the Hudson Bay Lowland, Canada. Water tables at the drained bog were ∼1 m below the hummock surface at the time of study compared to ∼0.3 m at the pristine bog. For hummocks and intermediate microforms at the drained bog, plant production was significantly less than at the pristine bog, most likely due to small changes in vegetation structure (reduced Sphagnum cover and smaller shrub leaf:stem ratios) caused by deeper water tables and significantly reduced moisture content of surface peat. Despite these changes in vegetation and hydrology, net ecosystem production (NEP) remained positive (C sink) for these microforms at the drained bog. Dry pools with mostly bare peat at the drained bog had negative NEP (C source to atmosphere), in stark contrast to Sphagnum- and sedge-dominated pools at the pristine bog with small but positive NEP. Our study shows that dry pools now occupy an unstable state, but the hydrological thresholds for a shift in ecosystem state have not yet been reached for hummocks and intermediate microforms at the drained bog. However, weak or no relationships between water table depth, peat surface moisture content, and plant production for these microforms at the drained bog, suggest that drainage has weakened the hydrological feedbacks regulating peat production, causing peat accumulation to slow. If drier conditions prevail, this reduced resilience increases the potential for a shift in ecosystem state and raises the risk of large C loss due to continued decomposition of deeper peat in oxic conditions, and wildfire.
Randomized CP tensor decomposition
Authors: Erichson N Benjamin , Manohar Krithika , Brunton Steven L , Kutz J Nathan 
Published: June 2020

Abstract
The CANDECOMP/PARAFAC (CP) tensor decomposition is a popular dimensionality-reduction method for multiway data. Dimensionality reduction is often sought after since many high-dimensional tensors have low intrinsic rank relative to the dimension of the ambient measurement space. However, the emergence of ‘big data’ poses significant computational challenges for computing this fundamental tensor decomposition. By leveraging modern randomized algorithms, we demonstrate that coherent structures can be learned from a smaller representation of the tensor in a fraction of the time. Thus, this simple but powerful algorithm enables one to compute the approximate CP decomposition even for massive tensors. The approximation error can thereby be controlled via oversampling and the computation of power iterations. In addition to theoretical results, several empirical results demonstrate the performance of the proposed algorithm.
The influence of sorbitol doping on aggregation and electronic properties of PEDOT:PSS: a theoretical study
Authors: Friederich Pascal , León Salvador , Perea José Darío , Roch Loïc M , Aspuru-Guzik Alán 
Published: June 2020

Abstract
Many organic electronics applications such as organic solar cells or thermoelectric generators rely on PEDOT:PSS as a conductive polymer that is printable and transparent. It was found that doping PEDOT:PSS with sorbitol enhances the conductivity through morphological changes. However, the microscopic mechanism is not well understood. In this work, we combine computational tools with machine learning to investigate changes in morphological and electronic properties of PEDOT:PSS when doped with sorbitol. We find that sorbitol improves the alignment of PEDOT oligomers, leading to a reduction of energy disorder and an increase in electronic couplings between PEDOT chains. The high accuracy (r
2 > 0.9) and speed up of energy level predictions of neural networks compared to density functional theory enables us to analyze HOMO energies of PEDOT oligomers as a function of time. We find a surprisingly low degree of static energy disorder compared to other organic semiconductors. This finding might help to better understand the microscopic origin of the high charge carrier mobility of PEDOT:PSS in general and potentially help to design new conductive polymers.
Leaf traits and performance vary with plant age and water availability in Artemisia californica
Authors: Funk Jennifer L , Larson Julie E , Vose Gregory 
Published: June 2020

Abstract

Background and Aims
Leaf functional traits are strongly tied to growth strategies and ecological processes across species, but few efforts have linked intraspecific trait variation to performance across ontogenetic and environmental gradients. Plants are believed to shift towards more resource-conservative traits in stressful environments and as they age. However, uncertainty as to how intraspecific trait variation aligns with plant age and performance in the context of environmental variation may limit our ability to use traits to infer ecological processes at larger scales.

Methods
We measured leaf physiological and morphological traits, canopy volume and flowering effort for Artemisia californica (California sagebrush), a dominant shrub species in the coastal sage scrub community, under conditions of 50, 100 and 150 % ambient precipitation for 3 years.

Key Results
Plant age was a stronger driver of variation in traits and performance than water availability. Older plants demonstrated trait values consistent with a more conservative resource-use strategy, and trait values were less sensitive to drought. Several trait correlations were consistent across years and treatments; for example, plants with high photosynthetic rates tended to have high stomatal conductance, leaf nitrogen concentration and light-use efficiency. However, the trade-off between leaf construction and leaf nitrogen evident in older plants was absent for first-year plants. While few traits correlated with plant growth and flowering effort, we observed a positive correlation between leaf mass per area and performance in some groups of older plants.

Conclusions
Overall, our results suggest that trait sensitivity to the environment is most visible during earlier stages of development, after which intraspecific trait variation and relationships may stabilize. While plant age plays a major role in intraspecific trait variation and sensitivity (and thus trait-based inferences), the direct influence of environment on growth and fecundity is just as critical to predicting plant performance in a changing environment.
Below-ground competition alters attractiveness of an insect-pollinated plant to pollinators
Authors: Flacher Floriane , Raynaud Xavier , Hansart Amandine , Geslin Benoît , Motard Eric , Verstraet Séléné , Bataille Manon , Dajoz Isabelle 
Published: June 2020

AbstractCompetitive interactions between plants can affect patterns of allocation to reproductive structures through modulation of resource availability. As floral traits involved in plant attractiveness to pollinators can be sensitive to these resources, competition with any neighbouring species may influence the attractiveness of insect-pollinated plants. While pollination research has primarily focused on above-ground interactions, this study aims at investigating if the presence of a competitor plant can modulate neighbouring insect-pollinated plant attractiveness to pollinators and resulting fecundity, especially through below-ground competitive interactions for soil resources. We set up a plot experiment in which we grew an insect-pollinated plant, Sinapis alba (Brassicaceae), in a mixture dominated by a wind-pollinated plant, Holcus lanatus (Poaceae). Individuals of S. alba were either subjected to or isolated from (with buried tubes in the soil) below-ground competition. Across the flowering season, floral traits involved in attractiveness of S. alba and pollinator visitation were followed at the plot and plant level to investigate different scales of attractiveness. At the end of the experiment, seeds were harvested to assess plant fecundity. Competition had a significant negative effect on plot and plant floral display size as well as flower size while nectar traits were not affected. When plants of S. alba were in competition, the time to first visit was altered: the proportion of plots that received a visit was smaller for a given time; in other words, it took more time for a given proportion of plots to be visited and some plots were even never visited. Moreover, pollinators made fewer visits per plots. The proportion of viable seeds produced by S. alba in competition was lower and probably linked to the competition itself rather than changes in pollinator visitation. This study suggests that competitive interactions between plants can modulate pollination interactions even when competing plant species are not insect-pollinated.
Deferiprone Stimulates Aged Dermal Fibroblasts via HIF-1α Modulation
Authors: Pagani Andrea , Kirsch B Manuela , Hopfner Ursula , Aitzetmueller Matthias M , Brett Elizabeth A , Thor Dominik , Mela Petra , Machens Hans-Guenther , Duscher Dominik 
Published: June 2020

Abstract

Background
Hypoxia-inducible factor 1α (HIF-1α), a transcription factor responsible for tissue homeostasis and regeneration, presents reduced functionality in advanced age. In addition to absence of oxygen, sequestration of iron also stimulates HIF-1α. Therefore, we analyzed the efficacy of the iron-chelator deferiprone (DFP) at stimulating dermal fibroblasts.

Objectives
The main objective of this study was to quantify the DFP concentrations capable of stimulating dermal fibroblasts in vitro and to correlate the effective DFP concentrations with the ability of DFP to penetrate the epidermis, reach the dermis, and activate HIF-1α in vivo.

Methods
We measured cell proliferation, metabolic activity, HIF-1α expression, and lactate dehydrogenase levels of both young and aged fibroblasts after a 24-hour in vitro preconditioning with DFP. In addition, we evaluated cell survival rates and morphology with different cellular stainings. Finally, we performed a transdermal permeation study with a 1% DFP topical formulation to quantify the concentration required to reach the dermis.

Results
In vitro administration of iron-chelation therapy (156-312.5 µg/mL DFP ) on aged fibroblasts resulted in activation of various antiaging processes. The concentration required to reach the dermis within 24 hours was 1.5% (0.15 mg/mL), which corresponds well with the effective doses of our laboratory analyses.

Conclusions
The activation of HIF-1α by DFP enhances cell metabolism, proliferation, and survival of fibroblasts while reducing lactate dehydrogenase levels. Modulation of HIF-1α is linked to activation of key regeneration enzymes and proteins, and by proxy, antiaging. Therefore, the antiaging properties of DFP and its satisfactory dermal penetration make it a promising regenerative agent.
Neighborhood bully: no difference in territorial response toward neighbors or strangers in marmots
Authors: Ferrandiz-Rovira Mariona , Zidat Timothée , Dupont Pierre , Berger Vérane , Rézouki Célia , Cohas Aurélie 
Published: June 2020

Abstract
Territorial animals are expected to adjust their response to intruders according to the perceived threat level. One of the factors that drives threat level is the identity of the intruder. The dear enemy phenomenon theory postulates that individuals should respond with lower intensity to neighbors, already possessing a territory, than to strangers that may fight to evict them. In social species, the hierarchical status of the intruder might also mediate this response. Such behavioral adjustments presuppose a capacity to discriminate between individuals posing different threat levels. Here, we tested the behavioral response of Alpine marmots to territorial intrusions in a wild population. We compared both dominant females’ and males’ responses to scents from neighbor and stranger dominant males (dear enemy phenomenon) and to dominant and subordinate stranger males (social status-specific response). In addition, we tested for any covariance between male scents and social status. We showed that female and male dominant marmots do not adjust the intensity of their behavioral responses to whether the intruder’s territory is bordering or not (neighbors or strangers) or to the intruder’s social status, even though dominant and subordinate males are thought to pose different threats and social status is encoded in scents. Thus, we did not find support for the dear enemy phenomenon and conclude instead that, in dominant Alpine marmots, no intruder should enter a foreign territory. Research taking a more holistic approach of the evolution and maintenance of territoriality is required to understand the flexibility of responses to intruders in group-living species.
Predicting microRNA–disease associations from lncRNA–microRNA interactions via Multiview Multitask Learning
Authors: Huang Yu-An , Chan Keith C C , You Zhu-Hong , Hu Pengwei , Wang Lei , Huang Zhi-An 
Published: June 2020

AbstractMotivationIdentifying microRNAs that are associated with different diseases as biomarkers is a problem of great medical significance. Existing computational methods for uncovering such microRNA-diseases associations (MDAs) are mostly developed under the assumption that similar microRNAs tend to associate with similar diseases. Since such an assumption is not always valid, these methods may not always be applicable to all kinds of MDAs. Considering that the relationship between long noncoding RNA (lncRNA) and different diseases and the co-regulation relationships between the biological functions of lncRNA and microRNA have been established, we propose here a multiview multitask method to make use of the known lncRNA–microRNA interaction to predict MDAs on a large scale. The investigation is performed in the absence of complete information of microRNAs and any similarity measurement for it and to the best knowledge, the work represents the first ever attempt to discover MDAs based on lncRNA–microRNA interactions.ResultsIn this paper, we propose to develop a deep learning model called MVMTMDA that can create a multiview representation of microRNAs. The model is trained based on an end-to-end multitasking approach to machine learning so that, based on it, missing data in the side information can be determined automatically. Experimental results show that the proposed model yields an average area under ROC curve of 0.8410+/−0.018, 0.8512+/−0.012 and 0.8521+/−0.008 when k is set to 2, 5 and 10, respectively. In addition, we also propose here a statistical approach to predicting lncRNA-disease associations based on these associations and the MDA discovered using MVMTMDA.AvailabilityPython code and the datasets used in our studies are made available at https://github.com/yahuang1991polyu/MVMTMDA/.
CoMut: visualizing integrated molecular information with comutation plots
Authors: Crowdis Jett , He Meng Xiao , Reardon Brendan , Van Allen Eliezer M 
Published: June 2020

Abstract

Motivation
Large-scale sequencing studies have created a need to succinctly visualize genomic characteristics of patient cohorts linked to widely variable phenotypic information. This is often done by visualizing the co-occurrence of variants with comutation plots. Current tools lack the ability to create highly customizable and publication quality comutation plots from arbitrary user data.

Results
We developed CoMut, a stand-alone, object-oriented Python package that creates comutation plots from arbitrary input data, including categorical data, continuous data, bar graphs, side bar graphs and data that describes relationships between samples.

Availability and implementation
The CoMut package is open source and is available at https://github.com/vanallenlab/comut under the MIT License, along with documentation and examples. A no installation, easy-to-use implementation is available on Google Colab (see GitHub).
Accommodating trait overlap and individual variability in species diagnosis ofIschnosiphon(Marantaceae)
Authors: Buitrago Aristizábal María Alejandra , Oliveira Gouvêa De Figueiredo Fernando , André Thiago 
Published: June 2020

AbstractRecognition and delimitation of taxonomic categories of biological organisms are still challenging and full of controversy. We used Ischnosiphon as a model to unravel the importance of morphometrics as individual-based variables to disentangle the morphological variability of plant species. Ischnosiphon spp. continue to be problematic for users, taxonomists and ecologists, due mainly to the huge morphological variability, the species criteria and circumscription proposed for many taxa and the many habitat and vegetative macro-morphological characters lacking in most currently available exsiccates. Twenty-three morphometric variables were sampled from 228 individuals, belonging to 22 Ischnosiphon spp. Principal components and discriminant multivariate analyses were used to describe and identify patterns of morphological variation in Ischnosiphon. Individual-landmark assessment analysed with multivariate methods captured morphometric intraspecific diversity and morphological variability in Ischnosiphon spp., along with the continuous variation of important morphological traits. By examining the morphology of Ischnosiphon spp. through individual-landmark assessment, we demonstrate that different morphological species concepts used today in the identification of the species are difficult to apply. We propose a replicable and analytical framework to accommodate individual variability in species diagnosis in morphologically diverse plant groups.
Immune Monitoring Using QuantiFERON®-CMV Assay in Congenital Cytomegalovirus Infection: Correlation With Clinical Presentation and CMV DNA Load
Authors: Capretti Maria Grazia , Marsico Concetta , Chiereghin Angela , Gabrielli Liliana , Aceti Arianna , Lazzarotto Tiziana 
Published: June 2020

Abstract

Background
Cytomegalovirus (CMV)-specific CD8 + T-cell responses can be detected early in fetal life, but their role in the manifestations of congenital CMV (cCMV) infection remains largely unknown.

Methods
CMV-specific CD8 + T-cell responses were assessed in neonates with cCMV using QuantiFERON®-CMV assay, within day 14 of life (T0) and during the second month of life (T1). Detection and quantification of CMV DNA in whole blood and urine samples were performed at both time points. QuantiFERON®-CMV results were evaluated in relation to timing of maternal infection, clinical manifestations of cCMV and CMV DNA levels.

Results
Thirty neonates were enrolled (10/30 [33%] symptomatic; 20/30 [67%] asymptomatic). At T0 16/30 (53%) subjects had a reactive QuantiFERON®-CMV result and 16/16 (100%) were asymptomatic, whereas 14/30 (47%) had a nonreactive or indeterminate QuantiFERON®-CMV result and 4/14 (29%) were asymptomatic. At T1, 17/29 (59%) subjects had a reactive QuantiFERON®-CMV result, and 17/17 (100%) were asymptomatic, whereas 12/29 (41%) had a nonreactive or indeterminate result and 3/12 (25%) were asymptomatic. At both T0 and T1 reactive QuantiFERON®-CMV results correlated with lack of symptoms (P = .0001). At T1 median CMV DNAemia was lower in subjects with reactive QuantiFERON®-CMV results as compared with subjects with nonreactive or indeterminate results (1.82 log IU/mL [1.82–2.89] vs 2.55 log IU/mL [1.82–4.42], P = .009). No correlation was found between QuantiFERON®-CMV results and gestational age at maternal infection nor with urine CMV DNA levels.

Conclusions
A detectable CMV-specific CD8 + T-cell response, evaluated using the QuantiFERON®-CMV assay, correlates with the lack of CMV-related symptoms and the control of CMV DNAemia.
Proton pump inhibitors do not increase the risk of dementia: a systematic review and meta-analysis of prospective studies
Authors: Desai Madhav , Nutalapati Venkat , Srinivasan Sachin , Fathallah Jihan , Dasari Chandra , Chandrasekhar Viveksandeep Thoguluva , Mohammad Bilal , Kohli Divyanshoo , Vaezi Michael , Katz Philip O , Sharma Prateek 
Published: June 2020

SUMMARY
Published studies have reported variable results on the association between duration of proton pump inhibitor (PPI) use and the risk of dementia. An extensive literature search was performed in PubMed, Embase, Google Scholar, and Cochrane for studies examining the risk of cognitive decline and dementia among PPI users versus non-PPI users in prospective studies. Retrospective database linkage studies, case reports, case series, editorials, uncontrolled cohort studies, cross-sectional studies, and review articles were excluded. Primary outcome was pooled hazard rate (HR) of any dementia among PPI users compared with non-PPI users. Secondary outcomes were pooled HR of Alzheimer’s dementia (AD) and risk with long-term PPI follow-up (more than 5 years) studies. Meta-analysis outcomes, heterogeneity (I2), and meta-regression (for the effect of covariates) were derived by statistical software R and Open meta-analyst. A total of six studies (one RCT and five prospective) with 308249 subjects, average age of 75.8 ± 5.2 years, and follow-up of 5 (range 1.5–11) years were included in the analysis. Pooled HR of any dementia was 1.16 (n = 6, 95% confidence interval (CI) = 0.86–1.47). Results remained unchanged when only studies with long-term PPI use (more than 5 years) were analyzed (n = 4, pooled HR 1.10, 95% CI 0.66–1.53). Finally, the pooled HR for AD was 1.06 (n = 3, 95% CI 0.70–1.41). There was substantial heterogeneity among inclusion studies (I2 = 93%). Meta-regression did not demonstrate a significant role of age at study start (P = 0.1) or duration of PPI use (P = 0.62) to incident dementia. The results of this systematic review and meta-analysis do not show a significant relationship between PPI use and dementia in prospective studies with at least a 5-year follow-up.