Miracle-dz/UniFAR-FTUs huggingface dataset:
MULTICORE PARALLELIZATION OF MESHLESS PDE SOLUTION BY OPENMP

The application of the local meshless numerical method (LRBFCM) in solving partial di erential equations (PDE) is explored with the respect to a parallel implementation on multicore computers. The numerical approach is tested on the natural convection problem governed by the uid ow and energy transport. To solve such kind of problems a pressure-velocity coupling is required, which in general pose a global problem and therefore introduces global communication and consequently smaller e ciency of the parallel implementation. The coupling is performed iteratively, with a local pressure correction, predicted from the violation of the mass continuity. The analysis of OpenMP based parallelization of the proposed numerical approach is presented. The meshless local approach is evaluated through various tests, which are gradually complicated from the simplest independent calculations to the solution of a coupled system of PDEs describing the unsteady natural convection problem. The results show superlinear speedup for larger problem domains and smaller number of cores with gradually decreasing e ciency for larger number of cores.
An Intelligent Database System Using Natural Language Processing

Enormous amount of data are being processed and exchanged in our daily life, and database, which is used to organize data has been an active research topic for a long time. Database plays a major role in many computer systems and there is always a demand from technical and nontechnical people to ease the process of accessing data on database. Using Natural Language to directly interact with a database is a nice and user friendly solution. In order to achieve this type of communication between the computer (In particular, database) and human we have to make the computer understand what the human asks, and then, be able to respond with the right answer that was expected to be extracted from the database. In this paper we present an intelligent system for converting Natural Language queries into equivalent database Structured Query Language (SQL). Our system also allows processing complex Natural Language queries. We call this Intelligent Agent based Natural Language Interface to Database (INLIDB). The query results from the INLIDB is presented in an attractive succinctly viewable format. We have obtained encouraging results from INLIDB.
An MPI-Based Python Framework for Distributed Training with Keras

We present a lightweight Python framework for distributed training of neural networks on multiple GPUs or CPUs. The framework is built on the popular Keras machine learning library. The Message Passing Interface (MPI) protocol is used to coordinate the training process, and the system is well suited for job submission at supercomputing sites. We detail the software's features, describe its use, and demonstrate its performance on systems of varying sizes on a benchmark problem drawn from high-energy physics research.
Psoriasis occurring during anti-TNF-α therapy: causal effect or unrelated?

The introduction of biologic agents, such as tumor necrosis factor (TNF) inhibitors, has transformed our therapeutic approach to rheumatic diseases in recent years. Anti-TNF-α therapy has shown a significant reduction in disease activity in a variety of inflammatory joint conditions, such as rheumatoid arthritis, ankylosing spondylitis, juvenile idiopathic arthritis and psoriatic arthritis [1–3]. In addition, TNF-α antagonists have been effectively used for the treatment of other inflammatory conditions, such as Crohn’s disease, Adamantiades-Behcet’s syndrome and refractory plaque-type psoriasis [4–6]. At present, there are three TNF-blocking agents that are used in rheumatology: two monoclonal anti-TNF-α antibodies (infliximab and adalimumab) and one soluble TNF-α receptor (etanercept). With the expanded use of these agents in clinical practice, outside the setting of randomized clinical trials, an increasing number of cutaneous adverse reactions have been observed [7,8]. Severe cutaneous reactions, such as urticaria, erythema multiforme, cutaneous lupus erythematosus, necrotizing vasculitis, dermatomyositis and lymphomatoid papulosis-like and bullous skin lesions have been described, either in anecdotal case reports or in larger prospective studies [7–10]. One of the most striking reactions has been the development of psoriatic or psoriasiform eruptions in patients without a previous history of psoriasis following the administration of TNF-α inhibitors [11–19]. This contradicts the documented efficacy of these agents in plaque-type psoriasis by virtue of their role in decreasing the activity of proinflammatory mediators in psoriatic inflammation [101]. Although there is an open debate as to whether the development of these psoriasiform lesions is triggered by anti-TNF-α treatment or whether it is a coincidental manifestation of a previously ‘latent’ psoriasis, the accumulating evidence in the literature suggests that psoriasis can occur with TNF-α inhibition and that its early recognition and treatment can spare the patient from substantial morbidity, without necessarily discontinuing a beneficial treatment for the underlying inflammatory condition.
Endocrinology and paracrinology Effect of gonadotrophin on cell and matrix retention and expression of metalloproteinases and their inhibitor in cultured human granulosa cells modelling corpus luteum function

Granulosa cells were prepared from follicular aspirates obtained at oocyte collection for in-vitro fertilization (IVF) and maintained in culture. Substantial loss of cells from the culture surface occurred in the absence of gonadotrophin when cells were maintained on a thin layer of extracellular matrix (ECM) using a defined, serum-free medium. This cell loss was clearly and significantly reduced in the presence of human chorionic gonadotrophin (HCG) by days 4-6 of culture, and occurred in conjunction with loss of ECM. Analysis of culture medium by zymography using gelatin as substrate demonstrated the presence of metalloproteinases (MMP), MMP-9 (gelatinase B) appearing as the predominant band. Measurement of overall gelatinase activity in culture media revealed a progressive fall in gelatinase expressed on a per cell basis in media from HCG-treated cultures and this was less marked in controls. This suppression of gelatinase activity was consistent with an observed increase in production of tissue inhibitor of metalloproteinase-1 (TIMP-1) by HCG-treated cells, which was significant by days 6-8 of culture. We speculate that stabilization of the ECM may be an important aspect of HCG action in the corpus luteum.
Colonization and Inflammation Deficiencies in Mongolian Gerbils Infected by Helicobacter pylori Chemotaxis Mutants

ABSTRACT Helicobacter pylori causes disease in the human stomach and in mouse and gerbil stomach models. Previous results have shown that motility is critical for H. pylori to colonize mice, gerbils, and other animal models. The role of chemotaxis, however, in colonization and disease is less well understood. Two genes in the H. pylori chemotaxis pathway, cheY and tlpB, which encode the chemotaxis response regulator and a methyl-accepting chemoreceptor, respectively, were disrupted. The cheY mutation was complemented with a wild-type copy of cheY inserted into the chromosomal rdxA gene. The cheY mutant lost chemotaxis but retained motility, while all other strains were motile and chemotactic in vitro. These strains were inoculated into gerbils either alone or in combination with the wild-type strain, and colonization and inflammation were assessed. While the cheY mutant completely failed to colonize gerbil stomachs, the tlpB mutant colonized at levels similar to those of the wild type. With the tlpB mutant, there was a substantial decrease in inflammation in the gerbil stomach compared to that with the wild type. Furthermore, there were differences in the numbers of each immune cell in the tlpB-mutant-infected stomach: the ratio of lymphocytes to neutrophils was about 8 to 1 in the wild type but only about 1 to 1 in the mutant. These results suggest that the TlpB chemoreceptor plays an important role in the inflammatory response while the CheY chemotaxis regulator plays a critical role in initial colonization. Chemotaxis mutants may provide new insights into the steps involved in H. pylori pathogenesis.
Estrogen regulates bcl-x expression in rat hippocampus

In this study, we examined whether experimental alterations of circulating estrogen levels are associated with changes in the expression of bcl-x, an inhibitor of apoptosis. We report that bcl-x mRNA expression in rat hippocampus significantly decreases after reduction of estrogen levels resulting from ovariectomy. Exposure of ovariectomized rats to 17β-estradiol for either 5 or 28 days restored bcl-x mRNA expression to levels at or above those observed in sham-ovariectomized control animals. These data demonstrate that physiological levels of estrogen regulate hippocampal expression of bcl-x, an important modulator of neuronal apoptosis. Estrogen-mediated regulation of bcl-x may be relevant to the maintenance of neuronal viability and may contribute to the mechanism of estrogen neuroprotection.
Abnormal development of embryonic and extraembryonic cell lineages in parthenogenetic mouse embryos

Parthenogetically activated, diploid mouse oocytes can develop to midgestation stages in utero. However, even these advanced parthenogenones appear to die because of much reduced trophoblast and yolk sac development. Previous studies have compared the general features of parthenogenetic and androgenetic development and determined the fate of uniparental cells in chimeras with normal embryos. These studies led to the concept of genomic imprinting as the cause for developmental failure when either the maternal or the paternal genome is duplicated, with the corresponding deficiency of the other. Genomic imprinting appears to arise during gametogenesis and to act through dosage effects in a set of imprinted genes, whose expression depends on their parental origin. In this study we undertook a more detailed morphological analysis of parthenogenetic development in the mouse and established a classification system to quantify the developmental extent of parthenogenones. We found that the failure of parthenogenones occurred at different times during early postimplantation development, generating a spectrum of concepti which had developed to different extents, with only a small fraction of the embryos reaching advanced somite stages. In all parthenogenones differentiation and proliferation of the trophectoderm and primitive endoderm lineages (both extraembryonic) was abnormal, and in all, even the best‐developed parthenogenones, we observed similar deficiencies in the embryonic lineages, especially the mesoderm. Common to all abnormally developed lineages was that the proportion of undifferentiated precursor cells was much reduced, while their differentiated descendants were relatively abundant. We propose, therefore, that the failure of parthenogenones to develop to term is due to abnormal regulation of differentiation and proliferation in both embryonic and extraembryonic lineages. In this hypothesis, the apparent tissue specific defects observed in parthenogenones arise as a consequence of the functional importance of certain tissues (like the trophoblast) early in development. The spectrum of parthenogenones thus appears to reflect critical events in early development, whose regulation are affected by genomic imprinting. © 1994 Wiley‐Liss, Inc.
Performance Modelling of Hardware Transactional Memory

Transactional Memory (TM) is a recent alternative to traditional lock based synchronization mechanisms for parallel programming. Our analysis of existing literature in these areas highlights the existence of a relevant gap, which we aim to fill with this dissertation: the lack of performance models for hardware-based implementations of TM, also known as Hardware Transactional Memory (HTM). In order to monetize all the available transistors in a modern processor, HTM is usually built on top of the existing cache coherency protocols, whose dynamics we capture in the presented simulative and analytical models. Moreover, the simulation model is tested regarding Intel’s implementation of HTM and predicts, with little discrepancies, probability of abort and throughput. Subsequently, the analytical model is validated against this simulation, with an average error of 1.69% and 4.07% regarding probability of abort and throughput, respectively.
malaria gametocytocidal assay using oxidoreduction indicator , alamarBlue

Efforts to move from malaria control to eradication will require new approaches to block malaria transmission, such as the development of anti-malarial drugs with gametocytocidal activity. Here fluorescent oxidoreduction indicator alamarBlue is used to develop a screen for gametocyte viability. The fluorescent ccepted 3 February 2011 vailable online 18 February 2011
Topo‐climatic microrefugia explain the persistence of a rare endemic plant in the Alps during the last 21 millennia

Ongoing rapid climate change is predicted to cause local extinction of plant species in mountain regions. However, some plant species could have persisted during Quaternary climate oscillations without shifting their range, despite the limited evidence from fossils. Here, we tested two candidate mechanisms of persistence by comparing the macrorefugia and microrefugia (MR) hypotheses. We used the rare and endemic Saxifraga florulenta as a model taxon and combined ensembles of species distribution models (SDMs) with a high‐resolution paleoclimatic and topographic dataset to reconstruct its potential current and past distribution since the last glacial maximum. To test the macrorefugia hypothesis, we verified whether the species could have persisted in or shifted to geographic areas defined by its realized niche. We then identified potential MR based on climatic and topographic properties of the landscape and applied refined scenarios of MR dynamics and functions over time. Last, we quantified the number of known occurrences that could be explained by either the macrorefugia or MR model. A consensus of two or three SDM techniques predicted absence between 14–10, 3–4 and 1 ka bp, which did not support the macrorefugia model. In contrast, we showed that S. florulenta could have contracted into MR during periods of absence predicted by the SDMs and later re‐colonized suitable areas according to the macrorefugia model. Assuming a limited and realistic seed dispersal distance for our species, we explained a large number of the current occurrences (61–96%). Additionally, we showed that MR could have facilitated range expansions or shifts of S. florulenta. Finally, we found that the most recent and the most stable MR were the ones closest to current occurrences. Hence, we propose a novel paradigm to explain plant persistence by highlighting the importance of supporting functions of MR when forecasting the fate of plant species under climate change.
A reverse flow-metabolism mismatch pattern on PET is related to multivessel disease in patients with acute myocardial infarction.

UNLABELLED Hypoperfused myocardium with increased uptake of 18F-fluorodeoxyglucose (FDG) is considered to be ischemic but viable myocardium. However, the significance of a more severe defect of FDG than of 13N ammonia (NH3) (i.e., reverse flow-metabolism mismatch) is not well understood. METHODS To study a reverse flow-metabolism mismatch pattern, PET with NH3 and FDG under glucose loading was performed in 35 patients within 2 wk after onset of first acute myocardial infarction (AMI) and in 29 patients with old myocardial infarction (OMI). The left ventricle was divided into nine segments on a bull's eye polar map, and the mean counts of NH3 (%NH3) and FDG (%FDG) were compared for the segment with the least %NH3. RESULTS Ten patients in the AMI group demonstrated a marked reverse flow-metabolism mismatch pattern (greater than 10% difference between %NH3 and %FDG), whereas only 2 patients in the OMI group demonstrated the mismatch pattern (P < 0.05). Sixteen patients with AMI demonstrated %FDG > %NH3 (group 1), and 19 patients with AMI demonstrated %FDG < %NH3 (group 2). There were no significant differences in age, sex, location of infarction, diameter of stenosis of infarct-related artery or left ventricular ejection fraction between groups 1 and 2. Eleven patients in group 2 and only 3 in group 1 had multivessel disease (P < 0.02). There was no significant relationship between the number of diseased vessels and the flow-metabolism pattern in patients with OMI. CONCLUSION The finding of a reverse flow-metabolism mismatch on PET in the subacute phase of myocardial infarction was closely related to multivessel disease.
Skeletal muscle tissue engineering

The reconstruction of skeletal muscle tissue either lost by traumatic injury or tumor ablation or functional damage due to myopathies is hampered by the lack of availability of functional substitution of this native tissue. Until now, only few alternatives exist to provide functional restoration of damaged muscle tissues. Loss of muscle mass and their function can surgically managed in part using a variety of muscle transplantation or transposition techniques. These techniques represent a limited degree of success in attempts to restore the normal functioning, however they are not perfect solutions. A new alternative approach to addresssing difficult tissue reconstruction is to engineer new tissues. Although those tissue engineering techniques attempting regeneration of human tissues and organs have recently entered into clinical practice, the engineering of skletal muscle tissue ist still a scientific challenge. This article reviews some of the recent findings resulting from tissue engineering science related to the attempt of creation and regeneration of functional skeletal muscle tissue.
Effect of substance P, insulin-like growth factor-1 and vasoactive intestinal polypeptide on corneal re-epithelialization in galactosemic rats.

PURPOSE The purpose of the study was to examine the effect of topical application of substance P (SP), insulin-like growth factor-1 (IGF-1) and vasoactive intestinal polypeptide (VIP) on corneal re-epithelialization in galactosemic rats. METHODS Experimental galactosemia was induced by feeding a diet containing 30% galactose for 4-6 months. The corneal epithelium was debrided bi-laterally by scraping with a blunted scalpel blade. One eye (control) received only a saline solution whilst the other eye received a solution of SP and/or IGF-1 or VIP. A single drop of control or test solution was administered 4 times daily until wound closure. Corneas were stained with fluorescein and videotaped under ultraviolet illumination at regular time intervals after debridement. After digitizing the video image, the wound area was calculated using an image analysis program (NIH Image). RESULTS Corneal re-epithelialization was significantly delayed in galactosemic compared to normal animals. Rates of healing were 1.3 +/- 0.07 mm2/hour and 1.02 +/- 0.02 mm2/hour for normal and galactosemic animals, respectively. Topical application of SP in concentrations ranging from 25 pg/ml up to 250 microg/ml had no significant effect on the rate of corneal re-epithelialization. Similarly, IGF-1 (1 microg/ml) or VIP (1 microg/ml) when applied alone did not affect re-epithelialization. Furthermore, resurfacing of the debrided area was not affected by co-application of SP (250 microg/ml) and IGF-1 or VIP. CONCLUSIONS Independent or combined topical application of SP, VIP or IGF-1 at the concentrations tested, does not modulate corneal epithelial wound healing in rats with galactosemia induced by 30% galactose.
Pure Erythroid Leukemia: The Sole Acute Erythroid Leukemia

Pure Erythroid Leukemia (PEL) is an aggressive and exceedingly rare form of acute leukemia. In the 2008 WHO classifi cation PEL was one of the subtypes of acute erythroid leukemia the other subtype being erythroleukemia (erythroid/ myeloid). In the 2016 WHO classifi cation update, erythroleukemia was merged into myelodysplastic syndrome and PEL now is the only type of acute erythroid leukemia.106 cases of acute myeloid leukemia were diagnosed in 28 months in children’s hospital Lahore and PEL constituted 0.94%. Diagnosis of PEL is made by the bone marrow morphology showing predominant Immature erythroid precursors (proerythroblastic or undifferentiated), Periodic AcidSchiff staining and immunophenotyping. In PEL no specifi c genetic mutations have been described but complex karyotypes and TP53 mutations are frequently noted. Future collaborative studies to identify the molecular defects will contribute to the development of targeted therapies that might improve the prognosis. Research Article
Recent Trends in the Prevalence of Marijuana Use and Associated Disorders in the United States.

Recent Trends in the Prevalence of Marijuana Use and Associated Disorders in the United States Using data from 2 waves of the National Epidemiologic Survey of Alcohol and Related Conditions (NESARC), Hasin and colleagues1 reported that the past-year prevalence of marijuana use in the United States has more than doubled in a decade (2002-2003 to 2012-2013), along with a comparable increase in the past-year prevalence of marijuana use disorder as defined by the DSM-IV. Because a previous report documented large discrepancies between drug use estimates from the NESARC and those provided by the National Survey on Drug Use and Health (NSDUH),2 we sought to directly compare prevalence estimates and trends in marijuana use and marijuana use disorder from the NSDUH those from the NESARC.
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A

The zinc finger DNA-binding motif occurs in many proteins that regulate eukaryotic gene expression. The crystal structure of a complex containing the three zinc fingers from Zif268 (a mouse immediate early protein) and a consensus DNA-binding site has been determined at 2.1 angstroms resolution and refined to a crystallographic R factor of 18.2 percent. In this complex, the zinc fingers bind in the major groove of B-DNA and wrap part way around the double helix. Each finger has a similar relation to the DNA and makes its primary contacts in a three-base pair subsite. Residues from the amino-terminal portion of an alpha helix contact the bases, and most of the contracts are made with the guanine-rich strand of the DNA. This structure provides a framework for understanding how zinc fingers recognize DNA and suggests that this motif may provide a useful basis for the design of novel DNA-binding proteins.