Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data

Accumulating evidence indicates that the intestinal microbiota regulates our physiology and metabolism. Bacteria marketed as probiotics confer health benefits that may arise from their ability to affect the microbiota. Here high-throughput screening of the intestinal microbiota was carried out and integrated with serum lipidomic profiling data to study the impact of probiotic intervention on the intestinal ecosystem, and to explore the associations between the intestinal bacteria and serum lipids. We performed a comprehensive intestinal microbiota analysis using a phylogenetic microarray before and after Lactobacillus rhamnosus GG intervention. While a specific increase in the L. rhamnosus-related bacteria was observed during the intervention, no other changes in the composition or stability of the microbiota were detected. After the intervention, lactobacilli returned to their initial levels. As previously reported, also the serum lipid profiles remained unaltered during the intervention. Based on a high-resolution microbiota analysis, intake of L. rhamnosus GG did not modify the composition of the intestinal ecosystem in healthy adults, indicating that probiotics confer their health effects by other mechanisms. The most prevailing association between the gut microbiota and lipid profiles was a strong positive correlation between uncultured phylotypes of Ruminococcus gnavus-group and polyunsaturated serum triglycerides of dietary origin. Moreover, a positive correlation was detected between serum cholesterol and Collinsella (Coriobacteriaceae). These associations identified with the spectrometric lipidome profiling were corroborated by enzymatically determined cholesterol and triglyceride levels. Actinomycetaceae correlated negatively with triglycerides of highly unsaturated fatty acids while a set of Proteobacteria showed negative correlation with ether phosphatidylcholines. Our results suggest that several members of the Firmicutes, Actinobacteria and Proteobacteria may be involved in the metabolism of dietary and endogenous lipids, and provide a scientific rationale for further human studies to explore the role of intestinal microbes in host lipid metabolism.
Silencing of uncoupling protein 2 by small interfering RNA aggravates mitochondrial dysfunction in cardiomyocytes under septic conditions

Uncoupling protein 2 (UCP2) regulates the production of mitochondrial reactive oxygen species (ROS) and cellular energy transduction under physiological or pathological conditions. In this study, we aimed to determine whether mitochondrial UCP2 plays a protective role in cardiomyocytes under septic conditions. In order to mimic the septic condition, rat embryonic cardiomyoblast-derived H9C2 cells were cultured in the presence of lipopolysaccharide (LPS) plus peptidoglycan G (PepG) and small interfering RNA (siRNA) against UCP2 (siUCP2) was used to suppress UCP2 expression. Reverse transcription quantitative-polymerase chain reaction (RT-qPCR), western blot analysis, transmission electron microscopy (TEM), confocal microscopy and flow cytometry (FCM) were used to detect the mRNA levels, protein levels, mitochondrial morphology and mitochondrial membrane potential (MMP or ΔΨm) in qualitative and quantitative analyses, respectively. Indicators of cell damage [lactate dehydrogenase (LDH), creatine kinase (CK), interleukin (IL)-6 and tumor necrosis factor (TNF)-α in the culture supernatant] and mitochondrial function [ROS, adenosine triphosphate (ATP) and mitochondrial DNA (mtDNA)] were detected. Sepsis enhanced the mRNA and protein expression of UCP2 in the H9C2 cells, damaged the mitochondrial ultrastructure, increased the forward scatter (FSC)/side scatter (SSC) ratio, increased the CK, LDH, TNF-α and IL-6 levels, and lead to the dissipation of MMP, as well as the overproduction of ROS; in addition, the induction of sepsis led to a decrease in ATP levels and the deletion of mtDNA. The silencing of UCP2 aggravated H9C2 cell damage and mitochondrial dysfunction. In conclusion, our data demonstrate that mitochondrial morphology and funtion are damaged in cardiomyocytes under septic conditions, while the silencing of UCP2 using siRNA aggravated this process, indicating that UCP2 may play a protective role in cardiomyocytes under septic conditions.
The Intricate Beauty of Sphagnum mosses: a Finnish Guide to Identification

This book serves as a guide for identifying Sphagnum mosses in both field and laboratory. Forty species, typical of more continental parts of Europe, but also commonly found elsewhere in the northern hemisphere, are presented. The primary emphasis is on the illustrations, mainly photographs, depicting both macroscoptic and microscopic characteristics of the species.
Streamlining weaning: protocols and weaning units

Remodelling of the airway smooth muscle layer is not confined to patients with severe CF but occurs also in those with mild to moderate disease Most patients with cystic fibrosis (CF) develop progressive airflow obstruction. A subgroup of these patients also have airway hyperresponsiveness to inhaled bronchoconstricting agents1,2 and reversibility of airflow obstruction in response to bronchodilators.3 Parallels have been drawn between these observations and other airway diseases manifesting with airway obstruction and bronchial hyperresponsiveness such as asthma and chronic obstructive pulmonary disease (COPD). This led to speculation that remodelling of the airway smooth muscle (ASM) layer may contribute to bronchial hyperresponsiveness in CF. Studies in the past have been restricted to patients with severe CF. Pathological studies of the lungs of these patients obtained either at necropsy or following transplantation or lobectomy showed an increase in smooth muscle area compared with healthy controls or patients with COPD.4,5 In this issue of Thorax Hays et al 6 have, for the first time, studied the ASM layer in patients with mild to moderate CF using bronchoscopy and design based stereology. They found that the volume of smooth muscle in the airway submucosa in subjects with CF was higher than in normal controls and, furthermore, that this difference was attributable to smooth muscle cell hyperplasia rather than hypertrophy. This study raises several interesting questions. 1. Is this increase in the volume of the smooth muscle layer responsible for the airway hyperresponsiveness seen …
Planning and reporting of quality-of-life outcomes in cancer trials.

BACKGROUND Information about the impact of cancer treatments on patients' quality of life (QoL) is of paramount importance to patients and treating oncologists. Cancer trials that do not specify QoL as an outcome or fail to report collected QoL data, omit crucial information for decision making. To estimate the magnitude of these problems, we investigated how frequently QoL outcomes were specified in protocols of cancer trials and subsequently reported. DESIGN Retrospective cohort study of RCT protocols approved by six research ethics committees in Switzerland, Germany, and Canada between 2000 and 2003. We compared protocols to corresponding publications, which were identified through literature searches and investigator surveys. RESULTS Of the 173 cancer trials, 90 (52%) specified QoL outcomes in their protocol, 2 (1%) as primary and 88 (51%) as secondary outcome. Of the 173 trials, 35 (20%) reported QoL outcomes in a corresponding publication (4 modified from the protocol), 18 (10%) were published but failed to report QoL outcomes in the primary or a secondary publication, and 37 (21%) were not published at all. Of the 83 (48%) trials that did not specify QoL outcomes in their protocol, none subsequently reported QoL outcomes. Failure to report pre-specified QoL outcomes was not associated with industry sponsorship (versus non-industry), sample size, and multicentre (versus single centre) status but possibly with trial discontinuation. CONCLUSIONS About half of cancer trials specified QoL outcomes in their protocols. However, only 20% reported any QoL data in associated publications. Highly relevant information for decision making is often unavailable to patients, oncologists, and health policymakers.
Both a monoclonal antibody and antisera specific for determinants unique to individual cloned helper T cell lines can substitute for antigen and antigen-presenting cells in the activation of T cells

Two antisera and a monoclonal antibody raised in BALB.K mice against cloned, major histocompatibility complex (MHC)-restricted, antigen- specific helper T cell lines are described. These antibodies are specific for individual cloned T cell lines and are potent inducers of T cell proliferation. The induction of T cell proliferation by these antibodies requires the presence of an adherent accessory cell. There is no H-2 restriction between this accessory cell and the cloned T cell, nor is this antibody-induced proliferation blocked by a monoclonal anti-Fc receptor antibody. The requirement for an accessory cell, however, is eliminated in the presence of an IL-1- or IL-2-rich supernatant. Thus this system allows the analysis of helper T cell activation with only a single cell type present. Anti-T cell sera also induce T cell-dependent B cell proliferation and immunoglobulin secretion. The induction of T cell-dependent B cell activation by these sera does not require H-2-matched T cells and B cells. The specificity of these antibodies and their ability to stimulate cloned helper T cells in the absence of antigen and antigen-presenting cells strongly suggest that these antibodies are directed against antigen and/or Ia recognition sites on the T cell.
Inhibition of dynamin-dependent endocytosis increases shedding of the amyloid precursor protein ectodomain and reduces generation of amyloid β protein

Background: The amyloid precursor protein (APP) is transported via the secretory pathway to the cell surface, where it may be cleaved within its ectodomain by α-secretase, or internalized within clathrin-coated vesicles. An alternative proteolytic pathway occurs within the endocytic compartment, where the sequential action of βand γ-secretases generates the amyloid β protein (Aβ). In this study, we investigated the effects of modulators of endocytosis on APP processing. Results: Human embryonic kidney cells were transfected with a dominant negative mutant of dynamin I, an important mediator of clathrin-dependent endocytosis, and APP proteolysis was analyzed. Overexpression of the mutant dynamin (dyn I K44A) resulted in increased shedding of the APP ectodomain (sAPPα), accumulation of the C-terminal α-secretase product C83, and a reduction in the release of Aβ. Levels of mature APP on the cell surface were increased in cells expressing dyn I K44A, and internalization of surface-immunolabeled APP, assessed by fluorescence microscopy, was inhibited. Dynamin is a substrate for protein kinase C (PKC), and it was hypothesized that activators of PKC, which are known to stimulate α-secretase-mediated cleavage of APP, might exert their effects by inhibiting dynamin-dependent endocytosis. However, the internalization of surface-biotinylated APP was unaffected by treatment of cells with phorbol 12myristate 13-acetate in the presence of the α-secretase inhibitor TAPI-1. Conclusion: The results indicate that APP is internalized by a dynamin-dependent process, and suggest that alterations in the activity of proteins that mediate endocytosis might lead to significant changes in Aβ production. Background The amyloid precursor protein (APP) is a single-pass transmembrane protein that gives rise to the small peptides (known as Aβ) that form amyloid deposits in the brains of patients with Alzheimer's disease (AD) [1,2]. Aβ peptides are generated by the successive cleavage of APP Published: 11 August 2005 BMC Cell Biology 2005, 6:30 doi:10.1186/1471-2121-6-30 Received: 18 March 2005 Accepted: 11 August 2005 This article is available from: http://www.biomedcentral. com/1471-2121/6/30 © 2005 Carey et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Radiogenic isotope studies of crust-forming processes in the Lofoten-Vesterålen province of north Norway

﻿ The Lofoten-Vesteralen province of North Norway consists almost exclusively of Precambrian granulite-facies rocks. The oldest rocks in the province are monzonitic and dioritic migmatitic gneisses, the protoliths of which were formed at 2.7 Ga. The migmatites are overlain by a series of supracrustal gneisses, from 2.1 Ga, largely volcanogenic in origin, but with interbedded marbles and banded ironstones. The first occurrence of marble in western Lofoten is reported. Deposition in a subsiding back-arc basin or in an Andean- type environment on a thin continental margin is inferred. Both gneiss sequences were intruded by basic rocks at 1.8 Ga. The basic rocks could not have been formed simply by extraction from the mantle at 1.8 Ga. The required contribution from 2.7 Ga migmatites could be as much as 37%, but less if contamination took place via anatectic melts. The first report of eclogitic rocks from the Lofoten-Vesteralen province is made in this study; their formation is associated with shear deformation Both gneiss sequences and the basic rocks were intruded by mangeritic rocks at 1.8 - 1.7 Ga. Their chemical compositions can be explained by fractional crystallization from magmas formed from 2.7 Ga and 2.1 Ga gneisses and 1.8 Ga mantle-derived magmas. Parameters derived from Rb-Sr, Sm-Nd and U-Pb systems to express the relative proportions of crust and mantle contributions to the mangerites mutually correlate, supporting the crust-mantle source model for the mangerites. Mixing calculations suggest that the late Archaean contributes in excess of 50% by mass for almost all mangerites. Anatectic veins present, especially in the Moskenesoy supracrustal gneisses, are inferred to represent partial melts which coalesced to form the mangerites at higher structural levels. Anatexis was caused by basaltic underplating associated with limited crustal extension. Later rock-forming events were the emplacement of dolerite dykes; the 1.65 Ga Lodingen Granite; the Leknes Group metasediments and the Caledonian granite pegmatites.
Regularizing and Optimizing LSTM Language Models

Recurrent neural networks (RNNs), such as long short-term memory networks (LSTMs), serve as a fundamental building block for many sequence learning tasks, including machine translation, language modeling, and question answering. In this paper, we consider the specific problem of word-level language modeling and investigate strategies for regularizing and optimizing LSTM-based models. We propose the weight-dropped LSTM which uses DropConnect on hidden-to-hidden weights as a form of recurrent regularization. Further, we introduce NT-ASGD, a variant of the averaged stochastic gradient method, wherein the averaging trigger is determined using a non-monotonic condition as opposed to being tuned by the user. Using these and other regularization strategies, we achieve state-of-the-art word level perplexities on two data sets: 57.3 on Penn Treebank and 65.8 on WikiText-2. In exploring the effectiveness of a neural cache in conjunction with our proposed model, we achieve an even lower state-of-the-art perplexity of 52.8 on Penn Treebank and 52.0 on WikiText-2.
High molecular weight hyaluronic acid increases the differentiation potential of the murine chondrocytic ATDC5 cell line

Osteoarthritis (OA) is a group of common, chronic, and painful inflammatory joint diseases. One important finding in OA patients is a remarkable decrease in the molecular weight of hyaluronic acid (HA) in the synovial fluid of affected joints. Therapeutic HA is available to patients in most parts of the world as a viscosupplementation product for the treatment of OA. Previous clinical reports show that high molecular weight HA (HMWHA) more effectively relieves pain than low molecular weight HA (LMWHA). However, the mechanism behind this finding remains unclear. In this study, we investigated whether a LMWHA (Low‐0.9 MDa) and two types of HMWHA (High‐1.9 MDa and 6 MDa) differentially affected chondroregulatory action. We tested this using ATDC5 cell, a murine chondrocytic cell line widely used in culture systems to study chondrogenic differentiation. We found that HMWHA, especially hylan G‐F 20 (High‐6 MDa), significantly induced aggrecan and proteoglycan accumulation, nodule formation, and mRNA expression of chondrogenic differentiation markers in a time‐ and dose‐dependent manner. In addition, we showed that HMWHA prevented TNF‐α induced inhibition of chondrogenic differentiation, with no effect on cell proliferation or viability. These results reveal that HMWHA significantly promotes chondrogenic differentiation of ATDC5 cells in vitro, and suggest that HMWHA plays a significant chondroregulatory role in vivo. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 32:1619–1627, 2014.
Analysis of the semisynchronous carrier sense multiple access on the bus topology

Consider an arbitrary number of stations equally spaced on a channel configured as a bus topology. The stations access the channel according to the nonpersistent CSMA protocol, which may be with or without collision detection. Users are synchronized to the propagation delay between two adjacent users, and are thus semisynchronized. Such a system with single-buffered users and an exponential backoff strategy, is modeled. The system throughput and the mean delay are evaluated, and it is shown how to obtain the distribution of the packet interdeparture time as well as the packet delay. It is shown that the rescheduling strategy has a profound effect on the station performance, and that it can be used to eliminate the difference between the performance of different stations at any given offered load. The model is also used to accommodate finer synchronization steps, as well as arbitrary topologies. >
A virtual machine re-packing approach to the horizontal vs. vertical elasticity trade-off for cloud autoscaling

An automated solution to horizontal vs. vertical elasticity problem is central to make cloud autoscalers truly autonomous. Today's cloud autoscalers are typically varying the capacity allocated by increasing and decreasing the number of virtual machines (VMs) of a predefined size (horizontal elasticity), not taking into account that as load varies it may be advantageous not only to vary the number but also the size of VMs (vertical elasticity). We analyze the price/performance effects achieved by different strategies for selecting VM-sizes for handling increasing load and we propose a cost-benefit based approach to determine when to (partly) replace a current set of VMs with a different set. We evaluate our repacking approach in combination with different auto-scaling strategies. Our results show a range of 7% up to 60% cost saving in total resource utilization cost of our sample applications and workloads.
On a two-dimensional elliptic problem with large exponent in nonlinearity

A semilinear elliptic equation on a bounded domain in R2 with large exponent in the nonlinear term is studied in this paper. We investigate positive solutions obtained by the variational method. It turns put that the con- strained minimizing problem possesses nice asymptotic behavior as the nonlin- ear exponent, serving as a parameter, gets large. We shall prove that cp , the minimum of energy functional with the nonlinear exponent equal to p , is like (&Ke)lf2p~^2 as p tends to infinity. Using this result, we shall prove that the variational solutions remain bound- ed uniformly in p . As p tends to infinity, the solutions develop one or two peaks. Precisely the solutions approach zero except at one or two points where they stay away from zero and bounded from above. Then we consider the problem on a special class of domains. It turns out that the solutions then develop only one peak. For these domains, the solutions enlarged by a suitable quantity behave like a Green's function of -A. In this case we shall also prove that the peaks must appear at a critical point of the Robin function of the domain.
Space-Dimension Models of Spectrum Usage for Cognitive Radio Networks

The dynamic spectrum access (DSA) principle, relying on the cognitive radio (CR) paradigm, allows users to access spectrum over time intervals or spatial areas where it remains unused. Due to the opportunistic nature of DSA/CR, the behavior and performance of DSA/CR networks depends on the perceived spectrum usage pattern. An accurate modeling of spectrum occupancy therefore becomes essential in the context of DSA/CR. In this context, this paper addresses the problem of accurately modeling the spectrum occupancy pattern perceived by DSA/CR users in the spatial domain. A novel spatial modeling approach is introduced to enable a simple yet practical and accurate characterization of spectrum. First, a set of models is proposed to characterize and predict the average level of occupancy perceived by DSA/CR users at various locations based on the knowledge of some simple signal parameters. An extension is then proposed to characterize not only the average occupancy level but the instantaneous channel state perceived simultaneously by DSA/CR users observing the same transmitter from different locations as well. The validity and accuracy of the theoretical models are demonstrated with results from an extensive spectrum measurement campaign. Some illustrative examples of their potential applicability are presented and discussed as well.
Fault gouge dating: history and evolution

ABSTRACT Radiometric dating of fault gouges has become a useful tool for regional tectonics studies and for exploring and understanding fault and earthquake processes. Methods to define the absolute age of faults achieved a solid scientific foundation almost 25 years ago when the development and application of illite age analysis for investigating sedimentary burial and thermal histories found a new potential application – defining the age of fold-and-thrust development. Since then, the methods have benefitted from further development and incorporation of the 40Ar/39Ar micro-encapsulation method and quantitative clay mineral evaluation to distinguish polytypes (Wildfire). These refinements to the methods have improved their application in fold-and-thrust terrains and have opened up applications in normal and strike-slip fault environments. Another important development is the use of absolute dating methods in retrograde clay gouges in which clays in a fault develop from igneous or metamorphic wall rocks that contain no clays. In addition, the method has also been shown to be useful at dating folds in fold-and-thrust belts. We think the method is now an established part of the geological toolkit, look forward to future fault structural and tectonic studies that incorporate fault ages and hope that researchers continue to probe and discover ways that the method can assist fault process studies, including earthquake fault studies.