Miracle-dz/UniFAR-FTUs huggingface dataset:
The Protective Role of the −735C/T and the −1306C/T Polymorphisms of the MMP-2 Gene in the Development of Primary Open-angle Glaucoma

Abstract Background: It has been suggested that the matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) are involved in the degradation of extracellular matrix components, resulting in ocular tissue damage. The −735C/T and −1306C/T polymorphisms recognized in the promoter region of the MMP-2 gene resulting in its expression level were investigated in association with the development of primary open-angle glaucoma (POAG) in a Polish population. Methods: DNA samples collected from 271 patients with POAG and 281 healthy controls were used in this study. Polymorphisms were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Clinical parameters of the rim area (RA) and retinal neuron fiber layer (RNFL) were also analyzed. Results: We found that the −735C/T and −1306C/T polymorphisms of MMP-2 were not associated with a risk of POAG. However, both the −735T/T (OR = 0.18 (0.04–0.92) p = 0.03) and the −1306T/T (OR = 0.14 (0.03–0.67) p = 0.007) genotypes of MMP-2 were significantly associated with the rim area factor in early stage of POAG suggesting its protective role in the disease progression. Conclusion: Finally, our data suggest that gene polymorphisms of MMP-2 may have a protective role in the progression of primary open-angle glaucoma in a Polish population.
Dune-CurvilinearGrid: Parallel Dune Grid Manager for Unstructured Tetrahedral Curvilinear Meshes

We introduce the dune-curvilineargrid module. The module provides the self-contained, parallel grid manager, as well as the underlying elementary curvilinear geometry module dune-curvilineargeometry. This work is motivated by the need for reliable and scalable electromagnetic design of nanooptical devices. Curvilinear geometries improve both the accuracy of modeling smooth material boundaries, and the h/p-convergence rate of PDE solutions, reducing the necessary computational effort. dune-curvilineargrid provides a large spectrum of features for scalable parallel implementations of Finite Element and Boundary Integral methods over curvilinear tetrahedral geometries, including symbolic polynomial mappings and operations, recursive integration, sparse and dense grid communication, parallel timing and memory footprint diagnostics utilities. It is written in templated C++ using MPI for parallelization and ParMETIS for grid partitioning, and is provided as a module for the DUNE interface. The dune-curvilineargrid grid manager is continuously developed and improved, and so is this documentation. For the most recent version of the documentation, as well as the source code, please refer to the provided repositories and our website.
Saving space in fast string-matching

The string-matching problem is to find all instances (as contiguous substrings) of a “pattern” character string x in a longer “text" string ”. The naive algorithm, trying the pattern from scratch starting at each successive text position, requires only a fixed number of auxiliary storage locations but time proportional to $|x|\cdot|Y|$ (worst case). On the other hand, the fast algorithm of Knuth, Morris, and Pratt requires only time proportional to $|Y|$ but extra space proportional to $|x|$ (every case). Algorithms described in this paper reduce the extra space used by the Knuth–Morris–Pratt algorithm down to $O(\log |x|)$, and the time for the naive algorithm down to $O(|x|^\varepsilon |y|)$ for any fixed $\varepsilon > 0$. Also described are implementations on two-way multihead finite automata and multitape Turing machines.
Simple Optimization Algorithm for MOS-Based Resource Assignment

A novel algorithm is proposed to calculate a solution for cross-layer optimization (CLO) between application (APP) layer and medium access control (MAC) layer. The CLO problem is analyzed mathematically and for a related similar optimization problem an explicit solution is found. Based on this solution a deterministic iterative algorithm is deducted, which can approximate the solution of the original problem with little complexity in an upper bounded number of steps. There is an easy way to adapt the algorithm to different objectives, e.g., to maximize the sum of the users' mean opinion scores (MOS) or to limit the outage of users. Multiple examples are given and simulation results are provided.
A Region-Based Scheme Using RKLT and Predictive Classified Vector Quantization

This paper proposes a compression scheme for face profile images based on three stages, modelling, transformation, and the partially predictive classified vector quantization (CVQ) stage. The modelling stage employs deformable templates in the localisation of salient features of face images and in the normalization of the image content. The second stage uses a dictionary of feature-bases trained for profile face images to diagonalize the image blocks. At this stage, all normalized training and test images are spatially clustered (objectively) into four subregions according to their energy content, and the residuals of the most important clusters are further clustered (subjectively) in the spectral domain, to exploit spectral redundancies. The feature-basis functions are established with the region-based Karhunen? Loeve transform (RKLT) of clustered image blocks. Each image block is matched with a representative of near-best basis functions. A predictive approach is employed for mid-energy clusters, in both stages of search for a basis and for a codeword from the range of its cluster. The proposed scheme employs one stage of a cascaded region-based KLT-SVD and CVQ complex, followed by residual VQ stages for subjectively important regions. The first dictionary of feature-bases is dedicated to the main content of the image and the second is dedicated to the residuals. The proposed scheme is experimented in a set of human face images.
GAGM-AAM: A genetic optimization with Gaussian mixtures for Active Appearance Models

This paper proposes an optimization technique of genetic algorithm (GA) combined with Gaussian mixtures (GAGM) to make a robust, efficient and real time face alignment application for embedded systems. It uses 2.5D Active Appearance Model (AAM) for the face search, the model is generated by taking 3D landmarks and 2D texture of the face image. 3D face alignment requires to optimize 6 DOF (Degrees of Freedom) pose and appearance parameters of AAM. These parameters span in a huge face search space. In order to optimize them GA (due to its exploration property) is taken as an optimization technique, but unfortunately it suffers from massive computations. Thanks to the clustering of appearance parameters by Gaussian Mixture, GA optimization becomes time efficient and accurate. We compare it with other technique of simplex, which is found to be more efficient than classical AAM.
Inactivation of Avian Influenza Viruses by Chemical Agents and Physical Conditions: A Review

The recent outbreaks of avian influenza (AI) worldwide have highlighted the difficulties in controlling this disease both in developed and in developing countries. Biosecurity is considered the most important tool to prevent and control AI. In certain areas of the world, AI has become endemic and the recent outbreaks in Europe and Africa show that the epidemiological situation is evolving in an unprecedented way. The consequences of this situation are economic losses to the poultry industry, food security issues in developing countries and a serious threat to human health, due to the direct consequences of AI infection in humans, and more alarmingly due to the risk of the generation of a new pandemic virus from the animal reservoir. In this paper, the physical and chemical methods of inactivating AI viruses are reviewed, with particular emphasis on the practicalities of using such methods in the poultry industry.
Double Fortified Salt Intervention Improved Iron Intake But Not Energy and Other Nutrient Intakes in Female Tea Plantation Workers From West Bengal, India

Background: Iron deficiency is a global public health concern and has implications on the health status of women in reproductive age. Objective: We hypothesized that improving iron intake with double fortified salt would improve food intake, resulting in higher energy, nutrient intakes, and weight indicators of female tea plantation workers. Methods: In this randomized double-masked study, the participants (n = 245) were assigned to receive salt double fortified with iron and iodine (DFS; treatment) or salt fortified with iodine (control) and followed for 7.5 to 9 months. Dietary intakes were measured at three time points, baseline, midpoint, and end line using (1) food frequency questionnaire, (2) 24-hour recall, and (3) weighed lunch intake. Anthropometric measures of height (cm), weight (kg), and mid-upper arm circumference (cm) were also recorded at three time points. Mixed-model repeated-measures approach was used to detect group differences across time. Results: Double fortified salt improved dietary iron intake in the treatment group compared to the control group (P < .001). No other dietary or anthropometric differences could be attributed to treatment. Significant effect of time was observed in the intake frequency of major food groups and calcium, vitamin A and C (P <.001 for all), suggesting an equal effect of seasonality in both the groups. Conclusion: Addition of DFS in the diet improved dietary iron intake but did not affect the intake of energy, other nutrients, or nutritional status indicators. The improvement observed in the dietary iron intake demonstrates that fortification is an effective strategy to address iron deficiency in at-risk populations.
Extracting Adverse Drug Reactions from Forum Posts and Linking them to Drugs

in medical data mining is growing rapidly as more health- related data becomes available online. We propose methods for extracting Adverse Drug Reactions (ADRs) from forum posts and linking extracted ADRs to the drugs that users claim are responsible for them. We evaluate our methodology using a corpus of annotated forum posts. We find that our ADR extraction method outperforms a strong baseline in terms of precision at the expense of a similar decrease in recall. When used in conjunction with a strong baseline, our method is able to increase recall by 7% without harming precision.
The regulated expression of chimeric tyrosine hydroxylase–insulin transcripts during early development

Biological complexity does not appear to be simply correlated with gene number but rather other mechanisms contribute to the morphological and functional diversity across phyla. Such mechanisms regulate different transcriptional, translational and post-translational processes and include the recently identified transcription induced chimerism (TIC). We have found two novel chimeric transcripts in the chick and quail that result from the fusion of tyrosine hydroxylase (TH) and insulin into a single mature transcript. The th and insulin genes are located in tandem and they are generally transcribed independently. However, it appears that two chimeric transcripts containing exons from both the genes can also be produced in a regulated manner. The TH–INS1 and TH–INS2 chimeras differ in their insulin gene content, and they encode two novel isoforms of the TH protein with markedly reduced functionality when compared with the canonical TH. In addition, the TH–INS1 chimeric mRNA generates a small amount of insulin. We propose that TIC is an additional mechanism that can be employed to further regulate TH and insulin expression according to the specific needs of developing vertebrates.
A Formal Specification of the Memorization Process

In this article we present the formal language STOchastic Process Algebra (STOPA) to specify cognitive systems. In addition to the usual characteristics of these formalisms, this language features the possibility of including stochastic time. This kind of time is useful to represent systems where the delays are not controlled by fix amounts of time, but they are given by probability distribution functions. In order to illustrate the usefulness of our formalism we will formally represent a cognitive model of the memory. Following contemporary theories of memory classification (see Solso, 1999; Squire, Knowlton, & Musen, 1993) we consider sensory buffer, short-term, and long-term memories. Moreover, borrowing from Wang and Wang (2006), we also consider the so-called action buffer memory.
Primary mucinous adenocarcinoma of the vulva, intestinal type

Primary vulva malignancy is a rare gynecologic malignancy. Most of them are squamous cell carcinomas and adenocarcinomas are much less common. Intestinal type is a rare variant of primary adenocarcinoma of the vulva. It histologically resembles mucinous colonic carcinomas. Origin from cloacal remnants has been suggested but remains speculative. A 64-year-old woman was referred to our clinic with a 1-month history of an itching vulva mass. An incisional biopsy was performed at other hospital and disclosed adenocarcinoma of intestinal type. Extensive workups were performed to detect other underlying carcinomas but revealed nothing abnormal. She underwent wide local excision without lymph node dissection for a primary vulva carcinoma. She received no adjuvant therapy and has been free from recurrent disease for 12 months after surgery. The authors report a rare case and review the relevant literature.
Response time for cloud computing providers

Cloud services are becoming popular in terms of distributed technology because they allow cloud users to rent well-specified resources of computing, network, and storage infrastructure. Users pay for their use of services without needing to spend massive amounts for integration, maintenance, or management of the IT infrastructure. This creates the need for a reliable measurement methodology of the scalability for this type of new paradigm of services. In this paper, we develop performance metrics to measure and compare the scalability of the resources of virtualization on the cloud data centres. First, we discuss the need for a reliable method to compare the performance of cloud services among a number of various services being offered. Second, we develop a different type of metrics and propose a suitable methodology to measure the scalability using these types of metrics. We focus on the visualization resources such as CPU, storage disk, and network infrastructure. Finally, we compare well-known cloud providers using the proposed approach and conclude the recommendations. This type of research will help cloud consumers, before signing any official contract to use the desired services, to ascertain the ability and capacity of the cloud providers to deliver a particular service.
A flexible and scalable message broker for sensor network integration

Sensor network technologies have experienced an enormous development with the proliferation of sensor devices, custom communication protocols, and methods to exploit the data gathered on such networks. The actual impact of this technology on the enterprise, however, has been quite limited. This is because the community has focused almost exclusively on the sensor devices themselves, while paying little attention to the means to integrate this novel technology into the current enterprise infrastructure. We argue that facilitating this integration would encourage the adoption of sensor networks. Thus we present a scalable message broker for message-oriented middleware that is able to interact with any sensor network by providing a flexible and extensible communication subsystem. This message broker then provides the link to the messaging middleware used in the enterprise network. We describe the architecture of such a broker's communication subsystem and its implementation in Java#8482;. We present the performance of the broker, demonstrating that it scales to interconnect many sensor networks and is able to cope with potentially very large amounts of data from the sensors' readings. Finally, we present an overview of the sensor protocols we have developed, and how they are integrated into the broker, enabling for end-to-end interaction with external enterprise applications unaware of the sensor technology.
Peripheral Blood Mononuclear Cell &bgr;-Endorphin Concentration Is Decreased in Chronic Fatigue Syndrome and Fibromyalgia but Not in Depression: Preliminary Report

ObjectiveThe aim of this study was to examine the possible role of the immune system in the pathophysiology of chronic fatigue syndrome and fibromyalgia syndrome and in the differential diagnosis of depression by investigating changes in peripheral blood mononuclear cell levels of &bgr;-endorphin, an endogenous opioid known to be involved in regulation of the immune system function. Design&bgr;-Endorphin concentrations were measured by radioimmunoassay in peripheral blood mononuclear cells from healthy controls (n = 8) and patients with chronic fatigue syndrome (n = 17), fibromyalgia syndrome (n = 5), or depression (n = 10). Results&bgr;-Endorphin concentrations were significantly lower in patients with chronic fatigue syndrome or fibromyalgia syndrome than in normal subjects and depressed patients (p <0.001 and p <0.01, respectively). They were significantly higher in depressed patients than in controls (p <0.01). ConclusionsEvaluation of peripheral blood mononuclear cell &bgr;-endorphin concentrations could represent a diagnostic tool for chronic fatigue syndrome and fibromyalgia and help with differential diagnosis of these syndromes versus depression. The results obtained are also consistent with the hypothesis that the immune system is activated in both chronic fatigue syndrome and fibromyalgia syndrome.
100x Evolution of Video Codec Chips

In the past two decades, there has been tremendous progress in video compression technologies. Meanwhile, the use of these technologies, along with the ever-increasing demand for emerging ultra-high-definition applications greatly challenges the design of video codec chips, with the extensive requirements on both memory (DRAM) bandwidth and computation power. Besides, the high data dependencies of video coding algorithms restrict the degree of efficient hardware parallelism and pipelining. This paper describes the techniques to realize high-performance video codec chips. Firstly, we introduce various optimization techniques to solve the DRAM traffic issue. Furthermore, the techniques to reduce the computational complexity and alleviate data dependencies are described. The proposed techniques have been implemented in several ASIC video codecs. Experiments show that the DRAM traffic and DRAM access time are reduced by 80% and 90% respectively. The performance of the video codec chips can achieve 7680x4320@120fps, which is more than 100x better than previous works.
Gene positioning is regulated by phosphorylation of the nuclear pore complex by Cdk1

In yeast, many genes are targeted to the nuclear periphery through interaction with the Nuclear Pore Complex upon activation. Targeting requires nucleoporin proteins and DNA elements in the promoters of these genes. We have recently found that targeting is regulated through the cell cycle. Immediately following the initiation of DNA replication, active genes lose peripheral localization for ~30 minutes. This regulation is mediated by cyclic phosphorylation of a nucleoporin by Cdk1. Some genes that are targeted to the nuclear periphery upon activation remain at the nuclear periphery after repression, a phenomenon called transcriptional memory. Curiously, the mechanism that regulates localization of active genes to the nuclear periphery does not regulate the localization of the same genes after repression, suggesting that these genes are targeted by two distinct mechanisms. Finally, the localization of other parts of the genome that localize at the nuclear periphery seem to be regulated by a distinct mechanism, suggesting that the spatial organization of the genome is tightly coupled to the progression of the cell cycle.
Boymaw, Overexpressed in Brains with Major Psychiatric Disorders, May Encode a Small Protein to Inhibit Mitochondrial Function and Protein Translation

The t(1,11) chromosome translocation co-segregates with major psychiatric disorders in a large Scottish family. The translocation disrupts the DISC1 and Boymaw (DISC1FP1) genes on chromosomes 1 and 11, respectively. After translocation, two fusion genes are generated. Our recent studies found that the DISC1-Boymaw fusion protein is localized in mitochondria and inhibits oxidoreductase activity, rRNA expression, and protein translation. Mice carrying the DISC1-Boymaw fusion genes display intermediate behavioral phenotypes related to major psychiatric disorders. Here, we report that the Boymaw gene encodes a small protein predominantly localized in mitochondria. The Boymaw protein inhibits oxidoreductase activity, rRNA expression, and protein translation in the same way as the DISC1-Boymaw fusion protein. Interestingly, Boymaw expression is up-regulated by different stressors at RNA and/or protein translational levels. In addition, we found that Boymaw RNA expression is significantly increased in the postmortem brains of patients with major psychiatric disorders. Our studies therefore suggest that the Boymaw gene is a potential susceptibility gene for major psychiatric disorders in both the Scottish t(1,11) family and the general population of patients.
Organization and expression of genes responsible for type 1 piliation in Escherichia coli

The genetic organization of a segment of recombinant DNA conferring the capacity of synthesize E. coli type 1 pili was examined. This 11.2-kilobase (kb) segment of DNA, derived from a clinical isolate, conferred a piliated phenotype (Pil+) on a nonpiliated (Pil-) strain of E. coli K-12 that lacked DNA homologous to the 11.2-kb region. Insertional mutagenesis, deletion mutagenesis, and subcloning of various regions of the 11.2-kb fragment allowed the localization of five genes, each encoding a polypeptide, that were associated with pilus expression. Three gene products, 17, 86, and 30 kilodaltons (kd) in size, were involved in pilus assembly; assembly of the 17-kd structural (pilin) protein into pili was not seen in mutants lacking either the 86- or 30-kd proteins, but pilin synthesis and proteolytic processing were not affected. The fourth polypeptide, 23 kd in size, appeared to be involved in the regulation of pilus expression because mutants lacking this protein exhibited a 40-fold increase in the amount of pilin antigen per cell. The last protein, 14 kd in size, was not associated with piliation by genetic criteria; however, the 14-kd protein was immunoprecipitated with pili, suggesting an association with pili or immunological cross-reactivity with pilin. Immunoprecipitates of minicell transcription translation products revealed that pilus polymerization was taking place in minicells. This may facilitate the study of the molecular steps in pilus biosynthesis and, as a consequence, provide clues to the assembly of supramolecular structures in general.