Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences

Although the gut microflora is thought to be an essential factor in the development of ulcerative colitis (UC), the entire gut microflora occurring in UC remains unknown. Most studies use feces to represent the microflora distribution; however, here we analyzed the bacterial diversity in colonic mucus from UC patients receiving colectomy surgery and control patients. The diversity of microflora was investigated using a combination of terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of the 16S rRNA gene sequences. In the T-RFLP analysis, the number of terminal restriction fragments (T-RFs) decreased significantly in UC patients when compared to control samples. Also in the clone library analysis, the number of operational taxonomic units (OTU) and the Shannon diversity index were reduced significantly in UC patients. These molecular analyses reveal an overall dysbiosis in UC patients. No specific pathogen was found, and a strong negative correlation in relative abundance of bacterial populations was observed between the phyla Bacteroidetes and Firmicutes in the UC patients. This is the first report showing a significant correlation between these two phyla, which may be important characteristics in the pathogenesis of UC.
Maternal Dietary Patterns Are Associated with Pre-Pregnancy Body Mass Index and Gestational Weight Gain: Results from the “Mamma & Bambino” Cohort

The present study investigated the association of maternal dietary patterns with pre-pregnancy body mass index (BMI) and total gestational weight gain (GWG), using data of 232 women from the “Mamma & Bambino” cohort. Dietary patterns were derived by a food frequency questionnaire and principal component analysis. Self-reported pre-pregnancy BMI and GWG were calculated according to the World Health Organization and Institute of Medicine guidelines, respectively. The adherence to the “Western” dietary pattern—characterized by high intake of red meat, fries, dipping sauces, salty snacks and alcoholic drinks—was associated with increased GWG (β = 1.217; standard error [SE] = 0.487; p = 0.013), especially among obese women (β = 7.363; SE = 1.808; p = 0.005). In contrast, the adherence to the “prudent” dietary pattern—characterized by high intake of boiled potatoes, cooked vegetables, legumes, pizza and soup—was associated with reduced pre-pregnancy BMI (β = −0.631; SE = 0.318; p-trend = 0.038). Interestingly, the adherence to this pattern was positively associated with GWG among underweight (β = 4.127; SE = 1.722; p = 0.048), and negatively among overweight and obese individuals (β = −4.209; SE = 1.635; p = 0.016 and β = −7.356; SE = 2.304; p = 0.031, respectively). Our findings point out that the promotion of a healthy diet might represent a potential preventive strategy against inadequate weight gain, even during the periconceptional period.
Dual Listings on International Exchanges: The Case of Emerging Markets' Stocks

This paper examines the effects on stock returns of dual-listing on an international exchange. My sample consists of 70 firms from 10 emerging markets that dual-listed on the NYSE, NASDAQ and SEAQ-I over the period 1991-1995. The theoretical motivation for this paper lies in the context of the segmentation of international capital markets. When a firm dual-lists, it makes its shares available to a broader investor base resulting in better risk sharing. In the particular case of emerging markets, where barriers to investment are more severe in the sense that international investment is, in the limit, precluded by regulatory and ownership barriers, we expect those effects to be more pronounced. Previous literature has looked at the effects of foreign listings and has found support for investoris awareness and liquidity arguments but is inconclusive regarding the capital markets segmentation explanation. In this paper, I re-examine that issue: I evaluate whether an international dual-listing has any significant effect on returns and I proceed to investigate whether there is evidence to support an International Asset Pricing based explanation. In addition I compare the impact of US and London SEAQ-I listings. My results show that firms experience significant positive abnormal returns before listing and a significant decline in returns following listing and this effect is more pronounced for emerging markets firms. Moreover, for these firms, the valuation impact is similar across exchanges.
The Potential Role of Genomic Medicine in the Therapeutic Management of Rheumatoid Arthritis

During the last decade, important advances have occurred regarding understanding of the pathogenesis and treatment of rheumatoid arthritis (RA). Nevertheless, response to treatment is not universal, and choosing among different therapies is currently based on a trial and error approach. The specific patient’s genetic background influences the response to therapy for many drugs: In this sense, genomic studies on RA have produced promising insights that could help us find an effective therapy for each patient. On the other hand, despite the great knowledge generated regarding the genetics of RA, most of the investigations performed to date have focused on identifying common variants associated with RA, which cannot explain the complete heritability of the disease. In this regard, rare variants could also contribute to this missing heritability as well as act as biomarkers that help in choosing the right therapy. In the present article, different aspects of genetics in the pathogenesis and treatment of RA are reviewed, from large-scale genomic studies to specific rare variant analyses. We also discuss the shared genetic architecture existing among autoimmune diseases and its implications for RA therapy, such as drug repositioning.
Global ensemble projections reveal trophic amplification of ocean biomass declines with climate change

Significance Climate change can affect the distribution and abundance of marine life, with consequences for goods and services provided to people. Because different models can lead to divergent conclusions about marine futures, we present an integrated global ocean assessment of climate change impacts using an ensemble of multiple climate and ecosystem models. It reveals that global marine animal biomass will decline under all emission scenarios, driven by increasing temperature and decreasing primary production. Notably, climate change impacts are amplified at higher food web levels compared with phytoplankton. Our ensemble projections provide the most comprehensive outlook on potential climate-driven ecological changes in the global ocean to date and can inform adaptive management and conservation of marine resources under climate change. While the physical dimensions of climate change are now routinely assessed through multimodel intercomparisons, projected impacts on the global ocean ecosystem generally rely on individual models with a specific set of assumptions. To address these single-model limitations, we present standardized ensemble projections from six global marine ecosystem models forced with two Earth system models and four emission scenarios with and without fishing. We derive average biomass trends and associated uncertainties across the marine food web. Without fishing, mean global animal biomass decreased by 5% (±4% SD) under low emissions and 17% (±11% SD) under high emissions by 2100, with an average 5% decline for every 1 °C of warming. Projected biomass declines were primarily driven by increasing temperature and decreasing primary production, and were more pronounced at higher trophic levels, a process known as trophic amplification. Fishing did not substantially alter the effects of climate change. Considerable regional variation featured strong biomass increases at high latitudes and decreases at middle to low latitudes, with good model agreement on the direction of change but variable magnitude. Uncertainties due to variations in marine ecosystem and Earth system models were similar. Ensemble projections performed well compared with empirical data, emphasizing the benefits of multimodel inference to project future outcomes. Our results indicate that global ocean animal biomass consistently declines with climate change, and that these impacts are amplified at higher trophic levels. Next steps for model development include dynamic scenarios of fishing, cumulative human impacts, and the effects of management measures on future ocean biomass trends.
Decreased collagen VI in the tunica media of pulmonary vessels during exposure to hypoxia: a novel step in pulmonary arterial remodeling

The development of hypoxic pulmonary hypertension is characterized by the structural remodeling of pulmonary arteries. However, the relationship between changes of arterial cells and the extracellular matrix remains unclear. We focused on the evaluation of the non-fibrillar collagen changes in tunica media induced by a four-day exposure to hypoxia and the correlation of these changes with the pulmonary arterial wall structure modifications. We used 20 adult male Wistar rats. The amount and localization of collagen VI, collagen IV, matrix metalloproteinase (MMP) 2, and MMP9 were tested in pulmonary arteries immunohistochemically. Two-dimensional electrophoresis and messenger RNA (mRNA) expression were used for the subsequent comparison of protein changes in arterial tunica media cells (normoxia/hypoxia). Collagen VI was significantly reduced strictly in the tunica media of conduit arteries of hypoxia-exposed rats; however, its mRNA increased. The amount of collagen IV and its mRNA were not altered. We detected a significant increase of MMP9 strictly in the tunica media. In addition, a significantly increased number of MMP9-positive cells surrounded the arteries. MMP2 and the expression of its mRNA were decreased in tunica media. We conclude that the loss of collagen VI is an important step characterizing the remodeling of pulmonary arteries. It could influence the phenotypic status and behavior of smooth muscle cells and modify their proliferation and migration.
The response of five intestinal cell lines to anoxic conditions in vitro

In vivo oxygen levels in tissues range from 1% to 15%, while mechanistic cell culture studies employ an atmospheric oxygen level of 21% to grow cells. These oxygen concentrations are therefore not representative for conditions where the cell response is dependent on oxygen partial pressure. In pathological situation, such as (colon) cancer or chronic inflammation, tissue oxygenation is severely affected, and even under physiological conditions a steep oxygen gradient is present in the large intestine, where epithelial cells co‐exist with microbial species, resulting in almost anoxia at the midpoint of the lumen. In these situations, a better characterisation of the essential cellular behaviour under hypoxia or anoxia is required.
FPGA Side Channel Attacks without Physical Access

As FPGA use becomes more diverse, the shared use of these devices becomes a security concern. Multi-tenant FPGAs that contain circuits from multiple independent sources or users will soon be prevalent in cloud and embedded computing environments. The recent discovery of a new attack vector using neighboring long wires in Xilinx SRAM FPGAs presents the possibility of covert information leakage from an unsuspecting user's circuit. The work described in this paper makes two contributions that dramatically extend this finding. First, we rigorously evaluate several Intel SRAM FPGAs and confirm that long wire information leakage is also prevalent in these devices. Second, we present the first successful attack on an unsuspecting circuit in an FPGA using information passively obtained from neighboring long-lines. Information obtained from a single AES S-box input wire combined with analysis of encrypted output is used to rapidly expose an AES key. This attack is performed remotely without modifying the victim circuit, using electromagnetic probes or power measurements, or modifying the FPGA in any way. We show that our approach is effective for three different FPGA devices. Our results demonstrate that the attack can recover encryption keys from AES circuits running at 10MHz, and has the capability to scale to much higher frequencies.
Soil water stable isotopes reveal evaporation dynamics at the soil–plant–atmosphere interface of the critical zone

Abstract. Understanding the influence of vegetation on water storage and flux in the upper soil is crucial in assessing the consequences of climate and land use change. We sampled the upper 20 cm of podzolic soils at 5 cm intervals in four sites differing in their vegetation (Scots Pine (Pinus sylvestris) and heather (Calluna sp. and Erica Sp)) and aspect. The sites were located within the Bruntland Burn long-term experimental catchment in the Scottish Highlands, a low energy, wet environment. Sampling took place on 11 occasions between September 2015 and September 2016 to capture seasonal variability in isotope dynamics. The pore waters of soil samples were analyzed for their isotopic composition (δ2H and δ18O) with the direct-equilibration method. Our results show that the soil waters in the top soil are, despite the low potential evaporation rates in such northern latitudes, kinetically fractionated compared to the precipitation input throughout the year. This fractionation signal decreases within the upper 15 cm resulting in the top 5 cm being isotopically differentiated to the soil at 15–20 cm soil depth. There are significant differences in the fractionation signal between soils beneath heather and soils beneath Scots pine, with the latter being more pronounced. But again, this difference diminishes within the upper 15 cm of soil. The enrichment in heavy isotopes in the topsoil follows a seasonal hysteresis pattern, indicating a lag time between the fractionation signal in the soil and the increase/decrease of soil evaporation in spring/autumn. Based on the kinetic enrichment of the soil water isotopes, we estimated the soil evaporation losses to be about 5 and 10 % of the infiltrating water for soils beneath heather and Scots pine, respectively. The high sampling frequency in time (monthly) and depth (5 cm intervals) revealed high temporal and spatial variability of the isotopic composition of soil waters, which can be critical, when using stable isotopes as tracers to assess plant water uptake patterns within the critical zone or applying them to calibrate tracer-aided hydrological models either at the plot to the catchment scale.
History of tRNA research in strasbourg

The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl‐tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two‐way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health‐focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1066–1087, 2019
Differences in Clinical Profile and Outcomes of Low Iron Storage vs Defective Iron Utilization in Patients With Heart Failure: Results From the DEFINE-HF and BIOSTAT-CHF Studies.

Importance Iron deficiency is present in half of patients with heart failure (HF) and is associated with increased morbidity and an impaired prognosis. Iron deficiency due to low iron storage (LIS) and defective iron utilization (DIU) are not entirely the same clinical problem, although they generally receive the same treatment. Objective To define and describe similarities and differences between LIS and DIU in patients with HF. Design, Setting, and Participants This analysis included data from 2 prospective observational studies: the Definition of Iron Deficiency in Chronic Heart Failure (DEFINE-HF) study, a single-center study conducted from 2013 to 2015 including 42 patients with a reduced left ventricular ejection fraction of 45% or less scheduled for coronary artery bypass graft surgery, and the A Systems Biology Study to Tailored Treatment in Chronic Heart Failure (BIOSTAT-CHF) study, a multinational study conducted from 2010 to 2014 including 2357 patients with worsening HF from 69 centers in 11 countries. The median (interquartile range) follow-up time was 1.8 (1.3-2.3) years. Data were analyzed from January 2018 to January 2019. Main Outcomes and Measures The DEFINE-HF cohort was set up to derive a definition for different etiologies of iron deficiency using bone marrow iron staining as the criterion standard. This definition was applied to the BIOSTAT-CHF cohort to assess its association with clinical profile, biomarkers, and the primary composite end point of all-cause mortality or HF hospitalizations. Results Among the 42 patients in the DEFINE-HF study, 10 (24%) were women, and the mean (SD) age was 68.0 (9.5) years. Low iron storage was defined as a bone marrow-validated combination of transferrin saturation less than 20% and a serum ferritin concentration of 128 ng/mL or less; DIU was defined as transferrin saturation less than 20% and a serum ferritin concentration greater than 128 ng/mL. These criteria were applied to 2356 patients with worsening HF in the BIOSTAT-CHF study; 1074 (45.6%) were women, and the mean (SD) age was 68.9 (12.0) years. A total of 1453 patients with worsening HF (61.6%) had iron deficiency, of whom 960 (66.1%) had LIS and 493 (33.9%) had DIU. Low iron storage was characterized by a higher proportion of anemia and a poorer quality of life, while DIU was characterized by higher levels of various inflammatory markers. Both LIS and DIU were associated with an impaired 6-minute walking test. Low iron storage was independently associated with the composite end point of all-cause mortality or HF hospitalizations (hazard ratio, 1.47; 95% CI, 1.26-1.71; P < .001), while DIU was not (hazard ratio, 1.05; 95% CI, 0.87-1.26; P = .64). Conclusions and Relevance In this study, both LIS and DIU were prevalent in patients with HF and had a distinct clinical profile. Only LIS was independently associated with increased rates of morality and HF hospitalizations, while DIU was not.
Some Developments of the Equilibrium Particle Simulation Method for the Direct Simulation of Compressible Flows

The direct simulation Monte Carlo (DSMC) method is the established technique for the simulation of rarefied gas flows. In some flows of engineering interest, such as occur for aero-braking spacecraft in the upper atmosphere, DSMC can become prohibitively expensive in CPU time because some regions of the flow, particularly on the windward side of blunt bodies, become collision dominated. As an alternative to using a hybrid DSMC and continuum gas solver (Euler or Navier-Stokes solver) this work is aimed at making the particle simulation method efficient in the high density regions of the flow. A high density, infinite collision rate limit of DSMC, the Equilibrium Particle Simulation method (EPSM) was proposed by Pullin [J. Comput. Phys. v34, p231, 1980]. EPSM is developed here for the flow of a gas consisting of many different species of molecules and is shown to be computationally efficient (compared to DSMC) for high collision rate flows. It thus offers great potential as part of a hybrid DSMC/EPSM code which could handle flows in the transition regime between rarefied gas flows and fully continuum flows. As a first step towards this goal, a pure EPSM code is described. The next step of combining DSMC and EPSM is not attempted here but should be straightforward. EPSM and DSMC are applied to Taylor-Couette flow with Knudsen numbers Kn = 0.02 and 0.0133 and `wall-speed ratio' S_w = 3. Toroidal vortices develop for both methods but some differences are found. EPSM appears to be less sensitive to the sequence of random numbers used in the simulation than is DSMC, and may also be more dissipative. The question of the origin and the magnitude of the dissipation in EPSM is addressed. It is suggested that this analysis is also relevant to DSMC when the usual accuracy requirements on the cell size and the decoupling time step are relaxed in the interests of computational efficiency.
Influence of Climate on Radial Growth of Holm Oaks (Quercus Ilex Subsp. Ballota Desf) from SW Spain

Influence of Climate on Radial Growth of Holm Oaks (Quercus Ilex Subsp. Ballota Desf) from SW Spain A total of 47 trunk sections from Holm Oak (Quercus ilex subsp. ballota Desf) trees growing at two different sites at the Extremadura region (SW Spain) were considered in the computation of a regional tree-ring chronology useful to interpret the tree-ring/Mediterranean climate relationships. This is the first dendroclimatological research of Holm Oaks conducted to reveal its potential use as a climatic proxy. The obtained tree-ring chronologies were compared with climatic parameters based on monthly, seasonal and annual rainfall, and monthly maximum, minimum and average temperature. The best correlations were obtained with maximum temperatures during the period between previous winter and early spring. Influence of rainfall was less relevant. Growth of this species indicates a typical bimodal (spring and autumn) strategy that avoids low winter temperatures and summer drought. Despite some technical difficulties recognizing tree rings in Holm Oaks, its good sensitivity to climate variability and its wide distribution and longevity (~800 years), allow us to consider this species as a good candidate for temperature reconstructions in the Mediterranean Basin.
A randomized control trial of comparing ultrasound-guided ozone (O2-O3) vs corticosteroid injection in patients with shoulder impingement.

INTRODUCTION Ozone has been recently used as a safe alternative treatment in musculoskeletal disorders with fewer side effects than corticosteroids. The aim of this study was to compare the efficacy of a single injection of ozone with that of a corticosteroid in the treatment of shoulder impingement. DESIGN 30 patients with shoulder pain and clinical signs and symptoms of impingement were randomly assigned into two groups: ultrasound-guided injection with ozone or corticosteroid. Patients' symptoms were evaluated by Visual Analog Scale (VAS), Constant score, Shoulder Pain and Disability Scale (SPADI), shoulder range of motion (ROM) and ultra-sonographic measures before treatment, two weeks and two months after injections. RESULTS Patients' VAS, SPADI and Constant score improved significantly in both groups (P<0.001), but the benefits were in favor of corticosteroid group (P<0.001). At intervals between the two follow-ups, an improvement was observed in the VAS score among patients receiving ozone, while during the same interval, patients' pain slightly worsened in the corticosteroid group. The ROM and ultra-sonographic measures did not show statistical differences between the two groups. CONCLUSION Corticosteroid injection improves the pain and disability scores more significantly than a one-time ozone injection. Ozone may serve as an alternative modalities in treating shoulder impingement when the use of steroids is contraindicated.