Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement of glycine in healthy and tumorous brain by triple‐refocusing MRS at 3 T in vivo

Glycine (Gly) has been implicated in several neurological disorders, including malignant brain tumors. The precise measurement of Gly is challenging largely as a result of the spectral overlap with myo‐inositol (mI). We report a new triple‐refocusing sequence for the reliable co‐detection of Gly and mI at 3 T and for the evaluation of Gly in healthy and tumorous brain. The sequence parameters were optimized with density‐matrix simulations and phantom validation. With a total TE of 134 ms, the sequence gave complete suppression of the mI signal between 3.5 and 3.6 ppm and, consequently, well‐defined Gly (3.55 ppm) and mI (3.64 ppm) peaks. In vivo 1H magnetic resonance spectroscopy (MRS) data were acquired from the gray matter (GM)‐dominant medial occipital and white matter (WM)‐dominant left parietal regions in six healthy subjects, and analyzed with LCModel using in‐house‐calculated basis spectra. Tissue segmentation was performed to obtain the GM and WM contents within the MRS voxels. Metabolites were quantified with reference to GM‐rich medial occipital total creatine at 8 mM. The Gly and mI concentrations were estimated to be 0.63 ± 0.05 and 8.6 ± 0.6 mM for the medial occipital and 0.34 ± 0.05 and 5.3 ± 0.8 mM for the left parietal regions, respectively. From linear regression of the metabolite estimates versus fractional GM content, the concentration ratios between pure GM and pure WM were estimated to be 2.6 and 2.1 for Gly and mI, respectively. Clinical application of the optimized sequence was performed in four subjects with brain tumor. The Gly levels in tumors were higher than those of healthy brain. Gly elevation was more extensive in a post‐contrast enhancing region than in a non‐enhancing region. The data indicate that the optimized triple‐refocusing sequence may provide reliable co‐detection of Gly and mI, and alterations of Gly in brain tumors can be precisely evaluated.
Riemannian coding and dictionary learning: Kernels to the rescue

While sparse coding on non-flat Riemannian manifolds has recently become increasingly popular, existing solutions either are dedicated to specific manifolds, or rely on optimization problems that are difficult to solve, especially when it comes to dictionary learning. In this paper, we propose to make use of kernels to perform coding and dictionary learning on Riemannian manifolds. To this end, we introduce a general Riemannian coding framework with its kernel-based counterpart. This lets us (i) generalize beyond the special case of sparse coding; (ii) introduce efficient solutions to two coding schemes; (iii) learn the kernel parameters; (iv) perform unsupervised and supervised dictionary learning in a much simpler manner than previous Riemannian coding methods. We demonstrate the effectiveness of our approach on three different types of non-flat manifolds, and illustrate its generality by applying it to Euclidean spaces, which also are Riemannian manifolds.
On some errors related to the graduation of measuring instruments

The error on a real quantity Y due to the graduation of the measuring in- strument may be approximately represented, when the graduation is regular and fines down, by a Dirichlet form on R whose square field operator does not depend on the probability law of Y as soon as this law possesses a continuous density. This feature is related to the "arbitrary functions principle" (Poincare, Hopf). We give extensions of this property to R d and to the Wiener space for some approximations of the Brownian motion. We use a Girsanov theorem for Dirichlet forms which has its own interest. Connections are given with the discretization of stochastic differential equations.
Morphology of GABAergic neurons in the inferior colliculus of the cat

The goal of the present study was to provide a comprehensive and quantitative description of neurons immunoreactive for γ‐aminobutyric acid (GABA) in the inferior colliculus (IC) of the cat. Neurons were investigated with two different antisera and two different incubation methods. Free‐floating frozen or vibratome‐cut sections were incubated either with an antiserum to glutamic acid decarboxylase (GAD) or to GABA conjugated to protein with glutaraldehyde. Additional 1.5‐μm‐thick sections were incubated with the GABA antiserum after embedding and removal of the plastic. Quantitative data were obtained from much of this material. Despite the use of these different antisera and reaction methods, the results obtained were remarkably similar.
Erythropoietin Restores Long-Term Neurocognitive Function Involving Mechanisms of Neuronal Plasticity in a Model of Hyperoxia-Induced Preterm Brain Injury

Cerebral white and grey matter injury is the leading cause of an adverse neurodevelopmental outcome in prematurely born infants. High oxygen concentrations have been shown to contribute to the pathogenesis of neonatal brain damage. Here, we focused on motor-cognitive outcome up to the adolescent and adult age in an experimental model of preterm brain injury. In search of the putative mechanisms of action we evaluated oligodendrocyte degeneration, myelination, and modulation of synaptic plasticity-related molecules. A single dose of erythropoietin (20,000 IU/kg) at the onset of hyperoxia (24 hours, 80% oxygen) in 6-day-old Wistar rats improved long-lasting neurocognitive development up to the adolescent and adult stage. Analysis of white matter structures revealed a reduction of acute oligodendrocyte degeneration. However, erythropoietin did not influence hypomyelination occurring a few days after injury or long-term microstructural white matter abnormalities detected in adult animals. Erythropoietin administration reverted hyperoxia-induced reduction of neuronal plasticity-related mRNA expression up to four months after injury. Thus, our findings highlight the importance of erythropoietin as a neuroregenerative treatment option in neonatal brain injury, leading to improved memory function in adolescent and adult rats which may be linked to increased neuronal network connectivity.
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference

MOTIVATION Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external interventions such as RNA interference or gene knock-outs come into play. Even if the expression of the signaling genes is not changed, secondary effects in downstream genes shed light on the pathway, and allow partial reconstruction of its topology. RESULTS We introduce an algorithm to infer non-transcriptional pathway features based on differential gene expression in silencing assays. We demonstrate the power of our algorithm in the controlled setting of simulation studies, and explain its practical use in the context of an RNA interference dataset investigating the response to microbial challenge in Drosophila melanogaster.
Information Overload and its Consequences in the Context of Online Consumer Reviews

An online consumer review is the information including experiences, evaluations and opinions on products from the consumer perspective. An online consumer review plays two roles - informant and recommender. Considering two factors of review structure (the number of reviews and review type), this study analyzes the effect of online consumer reviews on consumers’ information processing depending on their levels of involvement. Generally, more positive reviews seem better from the perspective of online consumer reviews as recommenders. However, from the perspective of online consumer reviews as information providers, consumers may be confronted with too much information when a large number of reviews are offered, which results in information overload. We investigate when information overload occurs in the context of online consumer reviews, what strategies against the information overload consumers use depending on their levels of involvement, and how the product attitude and purchasing intention are changed. Our findings have implications for online sellers in terms of how to manage online consumer reviews contents.
Serum thyrotropin response to thyrotropin-releasing hormone in psychiatric patients: a review.

: In 1972 it was reported that in some euthyroid depressed patients the serum thyrotropin (TSH) response to thyrotropin-releasing hormone (TRH) was deficient. Since then, 41 reports describing 917 depressed patients have confirmed this finding. Although it is useful to report differences between mean response values of patient populations, it is necessary to identify those individuals in whom the fault occurs so that sensitivity, specificity, state-trait distribution, and clinical correlates can be determined. Present data allow some tentative conclusions: 1) the fault usually reflects a defect in central regulation of the pituitary-thyroid axis, 2) in some patients the fault may be a trait marker, and 3) it may represent a biological bridge between some depressed patients and some patients with other mental disorders.
Effects of Two Years of Teriparatide, Denosumab, or Both on Bone Microarchitecture and Strength (DATA-HRpQCT study).

CONTEXT In postmenopausal osteoporosis, combining denosumab and teriparatide increases hip and spine bone mineral density more than either monotherapy. OBJECTIVE The objective of the study was to determine the effects of 2 years of combination therapy on bone microarchitecture and estimated strength. DESIGN This was an open-label, randomized controlled trial. PARTICIPANTS AND METHODS We performed high-resolution peripheral quantitative computed tomography at the distal tibia and radius in 94 postmenopausal osteoporotic women randomized to 2 years of teriparatide 20 μg sc daily, denosumab 60 mg sc every 6 months, or both. RESULTS Total volumetric bone mineral density (vBMD) at the radius and tibia, trabecular vBMD at the radius, and cortical vBMD at the tibia all increased more in the combination group than both monotherapy groups (P < .002 for all comparisons with combination). Cortical thickness at the tibia also increased more in the combination group (8.1% ± 4.3%) than both other groups (P < .001). Cortical porosity at both the radius and tibia increased progressively over the 24-month treatment period in the teriparatide group but was stable in both other groups (P < .001 teriparatide vs both other groups). Trabecular vBMD at the tibia increased similarly in all groups, whereas radius trabecular vBMD increased more in the combination group than the other groups (P < .01 for both comparisons). Finite element analysis-estimated strength improved or was maintained by all treatments at both the radius and tibia. CONCLUSIONS Two years of combined teriparatide and denosumab improves bone microarchitecture and estimated strength more than the individual treatments, particularly in cortical bone. These findings suggest that this regimen may be beneficial in postmenopausal osteoporosis.
Synaptic adhesion molecules

Synopsis The chemical synapse is a specialized asymmetric adhesion site between the axon of a neuron and its target cell. Synapse formation is a multi-step process involving target recognition followed by reciprocal inductive interactions that result in recruitment of proteins, such as receptors, and organelles, such as synaptic vesicles, to both the presynaptic and postsynaptic compartments. Synaptic cell adhesion molecules are believed to mediate initial inductive interactions, stabilize connections, and function as nucleation sites for signaling events that promote synapse development and regulate synaptic activity.
Phase I and pharmacokinetic study of ABI-007, a Cremophor-free, protein-stabilized, nanoparticle formulation of paclitaxel.

PURPOSE ABI-007 is a novel Cremophor-free, protein-stabilized, nanoparticle formulation of paclitaxel. The absence of Cremophor EL may permit ABI-007 to be administered without the premedications used routinely for the prevention of hypersensitivity reactions. Furthermore, this novel formulation permits a higher paclitaxel concentration in solution and, thus, a decreased infusion volume and time. This Phase I study examines the toxicity profile, maximum tolerated dose (MTD), and pharmacokinetics of ABI-007. EXPERIMENTAL DESIGN ABI-007 was administered in the outpatient setting, as a 30-min infusion without premedications. Doses of ABI-007 ranged from 135 (level 0) to 375 mg/m2 (level 3). Sixteen patients participated in pharmacokinetic studies. RESULTS Nineteen patients were treated. No acute hypersensitivity reactions were observed during the infusion period. Hematological toxicity was mild and not cumulative. Dose-limiting toxicity, which occurred in 3 of 6 patients treated at level 3 (375 mg/m2), consisted of sensory neuropathy (3 patients), stomatitis (2 patients), and superficial keratopathy (2 patients). The MTD was thus determined to be 300 mg/m2 (level 2). Pharmacokinetic analyses revealed paclitaxel C(max) and area under the curve(inf) values to increase linearly over the ABI-007 dose range of 135-300 mg/m2. C(max) and area under the curve(inf) values for individual patients correlated well with toxicity. CONCLUSIONS ABI-007 offers several features of clinical interest, including rapid infusion rate, absence of requirement for premedication, and a high paclitaxel MTD. Our results provide support for Phase II trials to determine the antitumor activity of this drug.
Sectoral labor supply, choice restrictions and functionalform

In this paper we discuss a general framework for analyzing labor supply behavior in the presence of complicated budget- and quantity constraints of which some are unobserved. The individual’s labor supply decision is viewed as a choice from a set of discrete alternatives (jobs). These jobs are characterized by attributes such as hours of work, sector specific wages and other sector specific aspects of the jobs. We focus in particular on the theoretical justification of functional form assumptions and properties of the random components of the model.The labor supply model for married women is estimated on Norwegian data. Wage elasticities and the outcome of a tax reform analysis show that overall labor supply is moderately elastic, but these modest overall responses shadow for much stronger inter-sectoral changes. Our structural model, with a detailed specification of job opportunities, is compared empirically with a model in which the utility is approximated with a series expansion. It turns out that the performance of our model is at least as good as the labor supply model with flexible preferences.
Influence of air temperature on the first flowering date of Prunus yedoensis Matsum

Climate change is expected to have a significant effect on the first flowering date (FFD) in plants flowering in early spring. Prunus yedoensis Matsum is a good model plant for analyzing this effect. In this study, we used a degree day model to analyze the effect of air temperatures on the FFDs of P. yedoensis at Wuhan University from a long-time series from 1951 to 2012. First, the starting date (=7 February) is determined according to the lowest correlation coefficient between the FFD and the daily average accumulated degree days (ADD). Second, the base temperature (=−1.2°C) is determined according to the lowest root mean square error (RMSE) between the observed and predicted FFDs based on the mean of 62-year ADDs. Finally, based on this combination of starting date and base temperature, the daily average ADD of every year was calculated. Performing a linear fit of the daily average ADD to year, we find that there is an increasing trend that indicates climate warming from a biological climatic indicator. In addition, we find that the minimum annual temperature also has a significant effect on the FFD of P. yedoensis using the generalized additive model. This study provides a method for analyzing the climate change on the FFD in plants' flowering in early spring.
International Journal of Molecular Sciences Quantitative Proteomics to Characterize Specific Histone H2a Proteolysis in Chronic Lymphocytic Leukemia and the Myeloid Thp-1 Cell Line

Proteome studies on hematological malignancies contribute to the understanding of the disease mechanism and to the identification of new biomarker candidates. With the isobaric tag for relative and absolute quantitation (iTRAQ) method we analyzed the protein expression between B-cells of healthy people and chronic lymphocytic leukemia (CLL) B-cells. CLL is the most common lymphoid cancer of the blood and is characterized by a variable clinical course. By comparing samples of patients with an aggressive vs. indolent disease, we identified a limited list of differentially regulated proteins. The enhanced sensitivity attributed to the iTRAQ labels led to the discovery of a previously reported but still not clarified proteolytic product of histone H2A (cH2A) which we further investigated OPEN ACCESS Int. 9408 in light of the suggested functional properties of this modification. In the exploratory proteome study the Histone H2A peptide was up-regulated in CLL samples but a more specific and sensitive screening of a larger patient cohort indicated that cH2A is of myeloid origin. Our subsequent quantitative analysis led to a more profound characterization of the clipping in acute monocytic leukemia THP-1 cells subjected to induced differentiation.
Distinct Cell Death Programs in Monocytes Regulate Innate Responses Following Challenge with Common Causes of Invasive Bacterial Disease

Peripheral blood monocytes represent the rapid response component of mononuclear phagocyte host defense, generating vigorous but finite antibacterial responses. We investigated the fate of highly purified primary human monocytes following phagocytosis of different bacteria. Exposure to high bacterial loads resulted in rapid loss of cell viability and decreased functional competence. Cell death typically involved classical apoptosis. Exposure to high numbers of Escherichia coli and Klebsiella pneumoniae induced nonapoptotic death with loss of cell membrane integrity, marked disruption of phagolysosomes, and caspase-1 activation, while a subset of cells also released caspase-1–regulated extracellular traps. Classical apoptosis increased if extracellular bacterial replication was reduced and decreased if intracellular ATP levels were reduced during these infections. Both classical apoptosis and the alternative forms of cell death allowed monocytes, whose functional competence was exhausted, to downregulate reactive oxygen species and proinflammatory cytokine responses. In contrast, sustained stimulation of glycolytic metabolism and mitochondrial oxidative phosphorylation, with associated hypoxia inducible factor-1α upregulation, maintained intracellular ATP levels and prolonged monocyte functional longevity, as assessed by maintenance of phagocytosis, reactive oxygen species production, and proinflammatory cytokine generation. Monocyte innate responses to bacteria are short-lived and are limited by an intrinsic program of apoptosis, a response that is subverted by overwhelming infection with E. coli and K. pneumoniae or bacterial stimulation of cell metabolism. In this regard, the fate of monocytes following bacterial challenge more closely resembles neutrophils than macrophages.
Denitrification Activity of a Remarkably Diverse Fen Denitrifier Community in Finnish Lapland Is N-Oxide Limited

Peatlands cover more than 30% of the Finnish land area and impact N2O fluxes. Denitrifiers release N2O as an intermediate or end product. In situ N2O emissions of a near pH neutral pristine fen soil in Finnish Lapland were marginal during gas chamber measurements. However, nitrate and ammonium fertilization significantly stimulated in situ N2O emissions. Stimulation with nitrate was stronger than with ammonium. N2O was produced and subsequently consumed in gas chambers. In unsupplemented anoxic microcosms, fen soil produced N2O only when acetylene was added to block nitrous oxide reductase, suggesting complete denitrification. Nitrate and nitrite stimulated denitrification in fen soil, and maximal reaction velocities (vmax) of nitrate or nitrite dependent denitrification where 18 and 52 nmol N2O h-1 gDW -1, respectively. N2O was below 30% of total produced N gases in fen soil when concentrations of nitrate and nitrite were <500 μM. vmax for N2O consumption was up to 36 nmol N2O h-1 gDW -1. Denitrifier diversity was assessed by analyses of narG, nirK/nirS, and nosZ (encoding nitrate-, nitrite-, and nitrous oxide reductases, respectively) by barcoded amplicon pyrosequencing. Analyses of ~14,000 quality filtered sequences indicated up to 25 species-level operational taxonomic units (OTUs), and up to 359 OTUs at 97% sequence similarity, suggesting diverse denitrifiers. Phylogenetic analyses revealed clusters distantly related to publicly available sequences, suggesting hitherto unknown denitrifiers. Representatives of species-level OTUs were affiliated with sequences of unknown soil bacteria and Actinobacterial, Alpha-, Beta-, Gamma-, and Delta-Proteobacterial sequences. Comparison of the 4 gene markers at 97% similarity indicated a higher diversity of narG than for the other gene markers based on Shannon indices and observed number of OTUs. The collective data indicate (i) a high denitrification and N2O consumption potential, and (ii) a highly diverse, nitrate limited denitrifier community associated with potential N2O fluxes in a pH-neutral fen soil.
Association of the vitamin D binding protein polymorphisms with the risk of type 2 diabetes mellitus: a meta-analysis

Objective Previous studies on the association between vitamin D binding protein (DBP) polymorphisms and the risk of type 2 diabetes mellitus (T2DM) have produced conflicting results. The purpose of this meta-analysis was to examine whether DBP polymorphisms are associated with the risk of T2DM. Design Systematic review and meta-analysis. Methods All eligible studies were searched and acquired from the Cochrane, Pubmed, ISI, CNKI (Chinese) and Wanfang (Chinese) databases. ORs with corresponding 95% CIs were computed to estimate the association between DBP polymorphisms and T2DM. In addition, heterogeneity test, meta-regression and sensitivity analysis were also conducted. Results Six studies, which included 1191 cases and 882 controls, met the inclusion criteria and were included in the meta-analysis. The results showed that no significant associations were found between codon 416 and codon 420 polymorphisms in the DBP and the risk of T2DM in the overall analyses. In stratified analysis, significant associations between the codon 420 polymorphism and T2DM were found in Asians (allele Lys vs Thr: OR (95% CI) 1.49 (1.19 to 1.85), genotype Lys/Thr versus Thr/Thr: OR (95% CI) 1.80 (1.36 to 2.38), and Lys/Thr+Lys/Lys versus Thr/Thr: OR (95% CI) 1.81 (1.37 to 2.39), respectively) but not in Caucasians. For the codon 416, the significant association with T2DM was also detected in Asians (genotype Glu/Asp+Glu/Glu vs Asp/Asp: OR (95% CI) 1.36 (1.04 to 1.78)) but not in Caucasians. Conclusions This meta-analysis demonstrated that the DBP polymorphism was moderately associated with increased susceptibility to T2DM in Asians, but a similar association was not found in Caucasians. It suggested that ethnicity might be the potential factor associated with heterogeneity.