Miracle-dz/UniFAR-FTUs huggingface dataset:
Human methylenetetrahydrofolate reductase pharmacogenomics: gene resequencing and functional genomics

5,10-Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme in the folate metabolic pathway. Common genetic polymorphisms in the human MTHFR gene are associated with individual variation in the efficacy and toxicity of chemotherapeutic agents, such as methotrexate and 5-fluorouracil. However, the full range of polymorphisms and intragene haplotypes in the human MTHFR gene remains unclear. Furthermore, cellular mechanisms by which common, naturally occurring nonsynonymous coding single nucleotide polymorphisms (cSNPs) might alter the function of this enzyme have not been defined. The present study focused on the systematic identification and investigation of common polymorphisms and haplotypes in the MTHFR gene using a genotype-to-phenotype strategy, followed by functional genomic studies. Specifically, we resequenced exons, splice junctions and portions of the 5′-flanking region (5′-FR) of the human MTHFR gene using 240 DNA samples from four ethnic groups. A total of 65 polymorphisms were observed, 11 of which were nonsynonymous cSNPs. We then performed functional genomic studies with constructs for wild-type and 15 variant allozymes (some with multiple alterations in amino acid sequence) using a mammalian expression system. Activity for the variant allozymes ranged from 13% to 149% of wild-type activity. Levels of immunoreactive protein for the allozymes ranged from 31% to 120% of wild-type and were significantly correlated with enzyme activity (Rp=0.85, P<0.0001), suggesting that a major mechanism by which nonsynonymous cSNPs influence the function of this gene is by alteration in the quantity of protein. These observations represent steps towards an understanding of molecular genetic mechanisms responsible for variation in MTHFR function that may contribute to individual differences in drug efficacy and toxicity, as well as disease risk.
A novel image alignment and a fast efficient localized euclidean distance minutia matching algorithm for fingerprint recognition system

A fingerprint recognition system involves several steps. In such recognition systems, the matching of unequal number of minutia features is the most important and challenging step in fingerprint based bio-metrics recognition systems. In this paper, we used clustering based fingerprint image rotation algorithm, to improve the performance of the fingerprint recognition system and proposed a Localized Euclidean Distance Minutia Matching (LEDMM) algorithm for matching, which will give better results while comparing minutia sets of different sizes as well as in slightly different orientation during the matching process. The experimental results on the fingerprint image database demonstrate that the proposed methods can achieve much better minutia detection as well as better matching with improved performance in terms of accuracy.
One-Step Transpapillary Balloon Dilation under Cap-Fitted Endoscopy without a Preceding Sphincterotomy for the Removal of Bile Duct Stones in Billroth II Gastrectomy

Background/Aims Endoscopic sphincterotomy may be limited in Billroth II gastrectomy because of difficulty in orientating the duodenoscope and sphincterotome as a result of altered anatomy. This study was planned to investigate the efficacy and safety of endoscopic transpapillary large balloon dilation (EPBD) without preceding sphincterotomy for removal of large CBD stones in Billroth II gastrectomy. Methods Between March 2010 and February 2011, one-step EPBD under cap-fitted forward-viewing endoscopy was performed in patients who had undergone Billroth II gastrectomy at two tertiary referral centers. Main outcome measurements were successful duct clearance and EPBD-related complications. Results Successful access to major duodenal papilla was performed in 13 patients, but successful selective CBD cannulation was achieved in 12 patients (92.3%). Median maximum transverse stone size was 11.5 mm (10 to 14 mm). The mean number of stones was 2 (1-5). The median CBD diameter was 15 mm (12 to 19 mm). Mean procedure time from successful biliary access to complete stone removal was 17.8 min. Complete duct clearance was achieved in all patients. Four patients (33.3%) needed one more session of ERCP for removal of remnant stones. Asymptomatic hyperamylasemia in two patients and minor bleeding in another occurred. Conclusions Without preceding sphincterotomy, one-step EPBD (≥10 mm) under cap-fitted forward-viewing endoscopy may be safe and effective for the removal of large stones (≥10 mm) with CBD dilatation in Billroth II gastrectomy.
Effect of contact lens material on cytotoxicity potential of multipurpose solutions using human corneal epithelial cells

Purpose Multipurpose solutions (MPS) are used daily to clean and disinfect silicone hydrogel (SiHy) contact lenses. This in vitro study was undertaken to identify the potential for interaction between MPS, SiHy surface treatments, and lens materials, which may lead to changes in the response of human corneal epithelial cells (HCEC) to MPS-soaked lenses. Methods The MPS tested were renu fresh (formerly known as ReNu MultiPlus; ReNu), OptiFree Express (OFX), OptiFree RepleniSH, SoloCare Aqua, and Complete Moisture Plus. The SiHy materials evaluated were lotrafilcon A, lotrafilcon B, comfilcon A, galyfilcon A, and balafilcon A (BA). MPS-soaked lenses were placed on top of adherent HCEC. The effect of MPS dilutions (0.1 to 10% final concentration in medium) was also characterized. Cell viability, adhesion phenotype and caspase activation were studied after 24-h cell exposure. OFX released from lenses was determined using UV absorbance. Results A significant reduction in viability (between 30 to 50%) was observed with cells exposed to lenses soaked in ReNu and OFX. A significant downregulation of α3 and β1 integrins, with integrin expression ranging from 60% to 75% of control (cells with no lens), was also observed with OFX and ReNu-soaked lenses. With the exception of BA, all other lenses soaked in OFX resulted in significant caspase activation, whereby over 18% of cells stained positive for caspases. Minimal caspase activation was observed in cells exposed to ReNu and Solo soaked lenses. For both OFX and ReNu, exposing cells to at least a 5% dilution had a significant effect on viability and integrin expression. While Complete and Solo did not lead to reduction in viability, cells exposed to a 10% dilution showed reduced integrin expression down to less than 70% of control value. Comparing cell response to diluted MPS solutions and various MPS-soaked lenses showed that it is not possible to reliably use cell response to MPS dilution alone to assess MPS biocompatibility. Conclusions Our results demonstrate that the reaction of HCEC to MPS are affected by the type of lenses the MPS is released from and may potentially be influenced by the surface treatment (or lack of it) of SiHy materials.
Randomized Distributed MIMO with Limited Feedback in Dynamic Relay Networks

In this paper, a cooperative spatial multiplexing scheme is considered for dynamic relay networks. We assume that each relay node is equipped with a single antenna. To obtain spatial multiplexing gains, the distributed multiple-input multiple-output (MIMO) scheme, in which cooperating nodes act as elements of a multiantenna system, has been proposed in many papers. Since the nodes need to know their specific stream and pilot index, either internode communication or a central control unit is required. Our design objective is to obtain spatial multiplexing gains while eliminating the need for stream and pilot allocation. We introduce a novel randomized strategy that decentralize the transmission of multistreams from a set of distributed relay nodes. We analyze the constraints on the random scheme, and propose a limited feedback scheme to further improve its performance.
Urine-based enzyme-linked immunosorbent assay for the detection of Helicobacter pylori infection in children.

OBJECTIVE Serology and (13)C-urea breath test have been widely used as noninvasive tests to detect Helicobacter pylori infection. However, easier collection of samples and lower costs are desirable for diagnosis of the individual patient or for use in epidemiologic studies. Our aim was to study the diagnostic accuracy of a recently developed urine-based enzyme-linked immunosorbent assay (ELISA) kit for the detection of H pylori-specific immunoglobulin G (IgG) antibodies in children. STUDY DESIGN Specimens of serum and randomly voided urine were collected from 816 children (0-15 years old) and were analyzed using 2 serum-based ELISA kits and a urine-based ELISA kit, respectively. Based on results of serology, the sensitivity, specificity, and accuracy of the urine-based ELISA kit were evaluated. With regard to false-positive and false-negative results, urinary IgG concentrations and IgG/creatinine levels were studied. RESULTS Both serum-based ELISAs were positive in 41 children and were negative in 666, who were enrolled in this study. The remaining 109 children were excluded because of disagreement between the results of the 2 serum-based ELISAs, including indeterminate values. Overall sensitivity, specificity, and accuracy of urine-based ELISA test compared with serology were 85.4%, 95.5%, and 94.9%, respectively. On positivity rates, the urine-based ELISA was closely coincident with the serum-based ELISA in each age group. There was no correlation between antibody levels detected by urine-based ELISA and each serum-based ELISA. Urinary IgG concentrations and IgG/creatinine levels were significantly higher in false-positives and were lower in false-negatives than in true-positives plus true-negatives for serology. Most of those with false-positive results had trace to moderate proteinuria. CONCLUSIONS The urine-based ELISA is an alternative to serum-based ELISA for diagnosis of H pylori infection in children and should be suitable for large-scale epidemiologic studies concerning the organism. In children with proteinuria, results of the test should be interpreted with caution. It is possible that the urine-based ELISA method would be applicable to diagnosis of other infectious diseases.
Realistic Subsurface Anomaly Discrimination Using Electromagnetic Induction and an SVM Classifier

The environmental research program of the United States military has set up blind tests for detection and discrimination of unexploded ordnance. One such test consists of measurements taken with the EM-63 sensor at Camp Sibert, AL. We review the performance on the test of a procedure that combines a field-potential (HAP) method to locate targets, the normalized surface magnetic source (NSMS) model to characterize them, and a support vector machine (SVM) to classify them. The HAP method infers location from the scattered magnetic field and its associated scalar potential, the latter reconstructed using equivalent sources. NSMS replaces the target with an enclosing spheroid of equivalent radial magnetization whose integral it uses as a discriminator. SVM generalizes from empirical evidence and can be adapted for multiclass discrimination using a voting system. Our method identifies all potentially dangerous targets correctly and has a false-alarm rate of about 5%.
Transplantation of mesenchymal stem cells promotes the functional recovery of the central nervous system following cerebral ischemia by inhibiting myelin-associated inhibitor expression and neural apoptosis

Cerebral ischemia, which may lead to cerebral hypoxia and damage of the brain tissue, is a leading cause of human mortality and adult disability. Mesenchymal stem cells (MSCs) are a class of adult progenitor cells with the ability to differentiate into multiple cell types. The transplantation of bone marrow-derived MSCs is a potential therapeutic strategy for cerebral ischemia. However, the underlying mechanism has yet to be elucidated. In the present study, primary MSCs were isolated from healthy rats, labeled and transplanted into the brains of middle cerebral artery occlusion rat models. The location of the labeled MSCs in the rat brains were determined by fluorescent microscopy, and the neurological functions of the rats were scored. Immunohistochemical analyses demonstrated that the protein expression levels of myelin-associated inhibitors of regeneration, including Nogo-A, oligodendrocyte myelin glycoprotein and myelin-associated glycoprotein, were decreased following transplantation of the bone marrow-derived MSCs. Furthermore, the mRNA expression levels of Capase-3 and B-cell lymphoma 2, as determined by reverse transcription-quantitative polymerase chain reactions, were downregulated and upregulated, respectively, in the MSC-transplanted rats; thus suggesting that neural apoptosis was inhibited. The results of the present study suggested that the transplantation of bone marrow-derived MSCs was able to promote the functional recovery of the central nervous system following cerebral ischemia. Accordingly, inhibitors targeting myelin-associated inhibitors and apoptosis may be of clinical significance for cerebral ischemia in the future.
Hsc70 Rapidly Engages Tau after Microtubule Destabilization*

The microtubule-associated protein Tau plays a crucial role in regulating the dynamic stability of microtubules during neuronal development and synaptic transmission. In a group of neurodegenerative diseases, such as Alzheimer disease and other tauopathies, conformational changes in Tau are associated with the initial stages of disease pathology. Folding of Tau into the MC1 conformation, where the amino acids at residues 7–9 interact with residues 312–342, is one of the earliest pathological alterations of Tau in Alzheimer disease. The mechanism of this conformational change in Tau and the subsequent effect on function and association to microtubules is largely unknown. Recent work by our group and others suggests that members of the Hsp70 family play a significant role in Tau regulation. Our new findings suggest that heat shock cognate (Hsc) 70 facilitates Tau-mediated microtubule polymerization. The association of Hsc70 with Tau was rapidly enhanced following treatment with microtubule-destabilizing agents. The fate of Tau released from the microtubule was found to be dependent on ATPase activity of Hsc70. Microtubule destabilization also rapidly increased the MC1 folded conformation of Tau. An in vitro assay suggests that Hsc70 facilitates formation of MC1 Tau. However, in a hyperphosphorylating environment, the formation of MC1 was abrogated, but Hsc70 binding to Tau was enhanced. Thus, under normal circumstances, MC1 formation may be a protective conformation facilitated by Hsc70. However, in a diseased environment, Hsc70 may preserve Tau in a more unstructured state, perhaps facilitating its pathogenicity.
On the Maximum Luminosity of Galaxies and Their Central Black Holes: Feedback from Momentum-driven Winds

We investigate large-scale galactic winds driven by momentum deposition. Momentum injection is provided by (1) radiation pressure produced by the continuum absorption and scattering of photons on dust grains and (2) supernovae (momentum injection by supernovae is important even if the supernova energy is radiated away). Radiation can be produced by a starburst or active galactic nucleus (AGN) activity. We argue that momentum-driven winds are an efficient mechanism for feedback during the formation of galaxies. We show that above a limiting luminosity, momentum deposition from star formation can expel a significant fraction of the gas in a galaxy. The limiting, Eddington-like luminosity is LM ≃ (4fgc/G)σ4, where σ is the galaxy velocity dispersion and fg is the gas fraction; the subscript M refers to momentum driving. A starburst that attains LM moderates its star formation rate and its luminosity does not increase significantly further. We argue that elliptical galaxies attain this limit during their growth at z ≳ 1 and that this is the origin of the Faber-Jackson relation. We show that Lyman break galaxies and ultraluminous infrared galaxies have luminosities near LM. Since these starbursting galaxies account for a significant fraction of the star formation at z ≳ 1, this supports our hypothesis that much of the observed stellar mass in early-type galaxies was formed during Eddington-limited star formation. Star formation is unlikely to efficiently remove gas from very small scales in galactic nuclei, i.e., scales much smaller than that of a nuclear starburst. This gas is available to fuel a central black hole (BH). We argue that a BH clears gas out of its galactic nucleus when the luminosity of the BH itself reaches ≈LM. This shuts off the fuel supply to the BH and may also terminate star formation in the surrounding galaxy. As a result, the BH mass is fixed to be MBH ≃ (fgκes/πG2)σ4, where κes is the electron scattering opacity. This limit is in accord with the observed MBH-σ relation.
Emotion recognition from helpdesk messages

This paper describes system for emotion recognition which can be used to determine the priority of messages on the first level of helpdesk services. An algorithm used in this paper uses artificial intelligence (SVM classifier) and can recognize 5 different emotions. The used emotional classes were based on acoustic model which was inspired by acoustic emotion recognition research works. The proposed system has evaluated 5 classifiers and identifies a dominant emotion class. This work also describes a small database which was created on the basis of the selected helpdesk messages. The database was used in training and testing of the mentioned classifier. Success of classifier achieved in this work is 76.63% and impact of the proposed optimization methods on the final model accuracy has been proven.
Design and simulation of 1-DOF tactile sensor for gripping force measurement

This paper presents the design and simulation of a quantum tunneling composite (QTC) based tactile sensor structure for gripping force measurement. The design presents a tactile sensing element capable 1-DOF force sensing in the z-direction. QTC is a novel electrically conductive elastomeric matrix-nanostructured nickel powder composite. QTC has extremely large, reversible increases in conductivity when compressed, stretched, bent, or twisted. These properties are exploited to design a tactile sensor capable of measuring a dynamic force over the sensor area. QTC has some drawbacks which have limited its use to a simple pressure switch. One drawback of QTC is that it acts as a complete conductor beyond a certain stage of compression. Another is that it takes considerable time to return to the initial shape after compression. The proposed sensor design is able to overcome these drawbacks by extending the range of operation of QTC and rapidly returning the QTC to its unloaded shape. This design allows for the use of QTC as a simple, cheap force sensor. The design can be further optimized to match the characteristics of the proposed sensor with the force range of a given application. The design and simulation of the sensor structure is described. This sensor is to be connected via a data acquisition system to a computer, which converts the data into a color contour map using LabView and MATLAB to measure and display the pressure distribution in real-time.
Transmitter Optimization and Beamforming Optimality Conditions for Double-Scattering MIMO Channels

We investigate the capacity of a general class of MIMO channels, known as double-scattering channels. Our results assume perfect channel state information (CSI) at the receiver and statistical CSI at the transmitter. We first derive the optimal capacity-achieving signaling directions, and show that they correspond to the eigenvectors of the transmit spatial correlation matrix. We then derive new simple closed-form power allocation policies which are shown to yield negligible capacity loss compared with the optimal power allocation policy, without requiring complicated numerical optimization methods to compute. Finally we derive a necessary and sufficient condition for which a beamforming approach (i.e. rank-1 transmission) achieves the ergodic capacity.
Normal Forms and Normalization for Probabilistic Databases under Sharp Constraints

The data deluge is defined by increasing amounts of large data with increasing degree of uncertainty. In a recent response, probabilistic databases are receiving a great deal of interest from research and industry. One popular approach to probabilistic databases is to extend traditional relational database technology to handle uncertainty. In this approach probabilistic databases are probability distributions over a collection of possible worlds of relational databases. On the one hand, research has seen various efforts to extend query evaluation from relational to probabilistic databases. On the other hand, updates have not received much attention at all. In this paper we show that well-known syntactic normal form conditions capture probabilistic databases with desirable update behavior. Such behavior includes the absence of data redundancy, insertion, deletion, and modification anomalies. We further show that standard normalization procedures can be applied to standard representations of probabilistic databases to obtain database schemata that satisfy the normal form condition, and can thus be updated efficiently.
Saliency driven total variation segmentation

This paper introduces an unsupervised color segmentation method. The underlying idea is to segment the input image several times, each time focussing on a different salient part of the image and to subsequently merge all obtained results into one composite segmentation. We identify salient parts of the image by applying affinity propagation clustering to efficiently calculated local color and texture models. Each salient region then serves as an independent initialization for a figure/ground segmentation. Segmentation is done by minimizing a convex energy functional based on weighted total variation leading to a global optimal solution. Each salient region provides an accurate figure/ ground segmentation highlighting different parts of the image. These highly redundant results are combined into one composite segmentation by analyzing local segmentation certainty. Our formulation is quite general, and other salient region detection algorithms in combination with any semi-supervised figure/ground segmentation approach can be used. We demonstrate the high quality of our method on the well-known Berkeley segmentation database. Furthermore we show that our method can be used to provide good spatial support for recognition frameworks.
On the Load Balancing Techniques for GPU Applications Based on Prefix-Scan

Prefix-scan is one of the most common operation and building block for a wide range of parallel applications for GPUs. It allows the GPU threads to efficiently find and access in parallel to the assigned data. Nevertheless, the workload decomposition and mapping strategies that make use of prefix-scan can have a significant impact on the overall application performance. This paper presents a classification of the mapping strategies at the state of the art and their comparison to understand in which problem they best apply. Then, it presents Multi-Phase Search, an advanced dynamic technique that addresses the workload unbalancing problem by fully exploiting the GPU device characteristics. In particular, the proposed technique implements a dynamic mapping of work-units to threads through an algorithm whose complexity is sensibly reduced with respect to the other dynamic approaches in the literature. The paper shows, compares, and analyses the experimental results obtained by applying all the mapping techniques to different datasets, each one having very different characteristics and structure.