Miracle-dz/UniFAR-FTUs huggingface dataset:
A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)

OMIM's task of cataloging the association between human phenotypes and their causative genes (the Morbid Map of the Genome) and classifying and naming newly recognized disorders is growing rapidly. Establishing the relationship between genotype and phenotype has become increasingly complex. New technologies such as genome‐wide association studies (GWAS) and array comparative genomic hybridization (aCGH) define “risk alleles” that are inherently prone to substantial interpretation and modification. In addition, whole exome and genome sequencing are expected to result in many reports of new mendelian disorders and their causative genes. In preparation for the onslaught of new information, we have launched a new Website to allow a more comprehensive and structured view of the contents of OMIM and to improve interconnectivity with complementary clinical and basic science genetics resources. This article focuses on the content of OMIM, the process and intent of disease classification and nosology, and anticipated improvements in our new Website (http://www.omim.org). Hum Mutat 32:1–4, 2011. © 2011 Wiley‐Liss, Inc.
Two algorithms for correcting phase aberration in a computer-controlled ultrasonic imaging system

Spatial inhomogeneities in the acoustic velocity of tissues degrade the performance of medical ultrasonic imaging systems. Two algorithms which can correct the phase aberration induced by the inhomogeneities are presented. The first algorithm adjusts the phases of signals transmitted and received from individual channels in a phased array scanner, one group of adjacent elements at a time. The second algorithm is based on the assumption that a phases error profile can be approximated by a sum of sine waves and the phase aberration can be corrected by subtracting components of the sum. Comparisons of the two algorithms are presented. <<ETX>>
Machine learning identifies specific habitats associated with genetic connectivity in Hyla squirella

The goal of this study was to identify and differentiate the influence of multiple habitat types that span a spectrum of suitability for Hyla squirella, a widespread frog species that occurs in a broad range of habitat types. We collected microsatellite data from 675 samples representing 20 localities from the southeastern USA and used machine‐learning methodologies to identify significant habitat features associated with genetic structure. In simulation, we confirm that our machine‐learning algorithm can successfully identify landscape features responsible for generating between‐population genetic differentiation, suggesting that it can be a useful hypothesis‐generating tool for landscape genetics. In our study system, we found that H. squirella were spatially structured and models including specific habitat types (i.e. upland oak forest and urbanization) consistently explained more variation in genetic distance (median pR2 = 47.78) than spatial distance alone (median pR2 = 23.81). Moreover, we estimate the relative importance that spatial distance, upland oak and urbanized habitat have in explaining genetic structure of H. squirella. We discuss how these habitat types may mechanistically facilitate dispersal in H. squirella. This study provides empirical support for the hypothesis that habitat‐use can be an informative correlate of genetic differentiation, even for species that occur in a wide range of habitats.
PCA BASED FACE RECOGNITION ON REDUCED DIMENSIONS

Face recognition has been a fast growing, challenging and interesting research field in computer vision, pattern recognition and machine learning communities with real time applications. A large number of face recognition algorithms have been developed in last decades on both analytic and holistic approach of image based face recognition.PCA is the linear method based on holistic approach which perform dimension reduction and Gabor wavelet is the most efficient method for feature extraction so hybrid approach utilize for recognition task. This paper explains the reduced dimension statistic for Face recognition
The influence of ERP system to the company performance seen through innovation process, information quality, and information sharing as the intervening variables

Enterprise Resource Planning (ERP) system is an integrated information technology that combines all departments in a company with a single data entry. The ERP system is used to obtain quality information so that the head of the companies can easily make decisions accurately and timely. The information is also distributed among all related departments through sharing information. The quality information can improve the innovation process and company performance. Based on the questionnaires distributed to manufacturing companies in East Java and the data processed by SEM PLS, there are several conclusions. First, the ERP directly influences the information sharing but does not significantly influence the information quality. Second, innovation sharing influences directly the information quality and innovation process, but it does not give impacts to the operational performance. Third, the innovation quality has an impact on the innovation process and the operational performance. Fourth, the innovation process has a positive and significant impact directly to the operational performance
A new species of small-eared shrew (Mammalia, Eulipotyphla, Cryptotis) from the Lacandona rain forest, Mexico

Abstract The diversity and distribution of mammals in the American tropics remain incompletely known. We describe a new species of small-eared shrew (Soricidae, Cryptotis) from the Lacandona rain forest, Chiapas, southern Mexico. The new species is distinguished from other species of Cryptotis on the basis of a unique combination of pelage coloration, size, dental, cranial, postcranial, and external characters, and genetic distances. It appears most closely related to species in the Cryptotis nigrescens species group, which occurs from southern Mexico to montane regions of Colombia. This discovery is particularly remarkable because the new species is from a low-elevation habitat (approximately 90 m), whereas most shrews in the region are restricted to higher elevations, typically > 1,000 m. The only known locality for the new shrew is in one of the last areas in southern Mexico where relatively undisturbed tropical vegetation is still found. The type locality is protected by the Mexican government as part of the Yaxchilán Archaeological Site on the border between Mexico and Guatemala. Resumen La diversidad y distribución de las musarañas en el trópico americano son, aún, parcialmente conocidas. Aquí presentamos la descripción de una nueva especie de musaraña de orejas cortas (Soricidae, Cryptotis) con base en dos ejemplares de museo colectados en la selva Lacandona, Chiapas, en el sur de Mexico. La nueva especie se puede distinguir de otras especies del género por una combinación de características que incluye la coloración del pelaje, el tamaño, caracteres dentales, craneales, postcraneales y distancias genéticas. El nuevo taxón podría estar relacionado al grupo de especies Cryptotis nigrescens, cuyas especies habitan desde el sur de Mexico hasta las montañas de Colombia. El descubrimiento es particularmente notable ya que la especie nueva habita en tierras bajas (cerca de los 90 m), mientras que la mayoría de las especies en la región están restringidas a elevaciones mayores a los 1000 m. La única localidad para la nueva especie descrita se ubica en la selva Lacandona, una de las últimas áreas al sur de Mexico con vegetación tropical que permanecen sin alterar. La localidad tipo se encuentra en una zona protegida por el gobierno federal mexicano, ya que es parte de la Zona Arqueológica Yaxchilán, ubicada en la frontera entre Mexico y Guatemala.
Mapping of a locus (mdoA) that affects the biosynthesis of membrane-derived oligosaccharides in Escherichia coli

Mutants of Escherichia coli defective in the newly discovered mdoA locus are blocked at an early stage in the biosynthesis of membrane-derived oligosaccharides. The mutation has now been mapped and found to be located near 23 min on the E. coli chromosome between putA and pyrC. The mdoA mutants are defective in the membrane-localized component of the glucosyl transferase system described by Weissborn and Kennedy (A. C. Weissborn and E. P. Kennedy, Fed. Proc. 42:2122, 1983).
In vitro Antioxidant Properties of Underutilized Baccaurea angulata Fruit

Six different crude extracts were obtained from the skin, pulp and whole fruit freeze-dried samples of Baccaurea angulata, an underutilized tropical fruit from Borneo Island of Malaysia. The effect of solvents on; total phenolic contents, total flavonoid contents, total carotene contents, free radical scavenging activities, phosphatidylcholine peroxidation inhibition activities and qualitative-quantitative compositions of ascorbic acid, carnosic, catechin, cinnamic and myricetin using using ultra high performance liquid chromatography were determined using their respective assays. The results indicated that methanol extracts contain higher TPC, TFC and TCC than PBS extracts for the various fruits' parts. Methanol extracts also showed remarkable antiradical activity. A strong correlation was also found between pulp and whole fruit. Overall, the variations in the UHPLC results among the various extracts were consistent with the results obtained for TPC, TFC, TCC, DPPH radical scavenging activity and lipid peroxidation inhibition activities of the various crude extracts, especially, methanol extracts. Keywords—Antioxidants, Baccaurea angulata, Lipid peroxidation, Underutilized.
Microscopic Magnetic Characterization Of Submicron Cobalt Islands Prepared Using Self Assembled Polymer Masking Technique

Patterns of submicron cobalt islands were created on silicon by using self-assembled co-polymers as etching masks. The synthesis conditions were varied to create specific magnetic island morphologies. The magnetic structure and magnetization reversal of interconnected, as well as interacting and non-interacting islands were systematically studied using magnetic force microscopy. Differences in magnetic characteristics were observed and correlated with the thin film morphologies. The result of these studies include the transition from single to multidomain configuration as a function of island size, domain boundary characteristics near coercivity, evidence of magnetization rotation with increasing reverse magnetic field, and evidence of collective switching behavior in interacting single domain islands.
Reducing Truncation Error of Non-Uniform Grid Size in FDTD Methods using the Complementary Derivatives Method (CDM)

The finite-difference time-domain (FDTD) method and its variants such as the ADI-FDTD, are very versatile and general numerical schemes suitable for efficient solution of a wide class of electromagnetic problems. Using non-uniform grid size in FDTD-based methods to resolve fine structures can reduce the computational domain and therefore lead to a reduction of the computational cost (time and computer memory). However, for high-accuracy problems, using different grid size increases the truncation error at the boundary domains having different grid size. To address this problem, in this work, we introduce the complementary derivatives method, henceforth referred to as CDM. The method is essentially an interpolation scheme enforced at the boundary. Numerical results will be presented to show that the CDM can maintain second-order accuracy throughout the computational domain
A Psychoacoustically Motivated Technique for the Automatic Transcription of Chords from Musical Audio

All music, and especially pop music, is based upon ‘chords’: structured combinations of musical notes that harmonise when sounded together. However, because of the presence of inharmonic spectral peaks known as ‘upper partials’ within most musical sounds, current techniques for automatically transcribing chords from musical audio suffer from varying degrees of inaccuracy as these upper partials obscure the actual perceived sound during computerised analysis. Since different musical instruments exhibit different upper partial signatures, blending multiple elements in a mix worsens this effect due to their interference with one another. In this thesis a psychoacoustically motivated technique for processing audio is simulated to evaluate its effectiveness upon chord transcription. The human auditory system is imitated by taking four ‘streams’ from songs – individual tracks corresponding to the bass, vocals, drums and other instrumentation – and mixing these in various proportions to determine whether, by reducing the interference of these streams with one another, better chord recognition performance can be achieved with a subset of them. A total of 434 audio files corresponding to 62 individual chords are analysed using an algorithmic technique for automatic chord estimation. It is demonstrated that the best chord recognition performance over the sample set is achieved by partial removal of the drums, vocals and bass, whilst leaving other instrumentation at full signal level. This achieves a significant 40.33% increase in chord transcription accuracy compared to the original unseparated chord samples, showing that it is theoretically possible to improve chord recognition performance by separating audio streams within a song. This result assists the development of more accurate chord recognition techniques in fields such as music information retrieval and also provides some insight into the principles behind human music perception.
Adiponectin in renal disease – a review of the evidence as a risk factor for cardiovascular and all-cause mortality

Adiponectin, an adipokine, was discovered in 1995. The initial evidence led to the study of adiponectin as a determinant of insulin sensitivity and blood glucose levels. The literature then evolved to reports of the inverse association of adiponectin with incident Type 2 diabetes mellitus and coronary heart disease. Shortly thereafter, reports of a positive association with heart failure and mortality appeared and were replicated. We review here the basic science evidence and clinical studies of the role of renal function and kidney disease as a determinant of adiponectin.
Personalised news filtering and recommendation system using Chi-square statistics-based K-nearest neighbour (χ2SB-KNN) model

ABSTRACT Recommendation problem has been extensively studied by researchers in the field of data mining, database and information retrieval. This study presents the design and realisation of an automated, personalised news recommendations system based on Chi-square statistics-based K-nearest neighbour (χ2SB-KNN) model. The proposed χ2SB-KNN model has the potential to overcome computational complexity and information overloading problems, reduces runtime and speeds up execution process through the use of critical value of χ2 distribution. The proposed recommendation engine can alleviate scalability challenges through combined online pattern discovery and pattern matching for real-time recommendations. This work also showcases the development of a novel method of feature selection referred to as Data Discretisation-Based feature selection method. This is used for selecting the best features for the proposed χ2SB-KNN algorithm at the preprocessing stage of the classification procedures. The implementation of the proposed χ2SB-KNN model is achieved through the use of a developed in-house Java program on an experimental website called OUC newsreaders’ website. Finally, we compared the performance of our system with two baseline methods which are traditional Euclidean distance K-nearest neighbour and Naive Bayesian techniques. The result shows a significant improvement of our method over the baseline methods studied.
Activity-dependent dephosphorylation of paxillin contributed to nociceptive plasticity in spinal cord dorsal horn

Abstract The enzymatic activity of protein tyrosine kinase Src is subjected to the regulation by C-terminal Src kinase (CSK) and protein tyrosine phosphatases (PTPs). Aberrant Src activation in the spinal cord dorsal horn is pivotal for the induction and development of nociceptive behavioral sensitization. In this study, we found that paxillin, one of the well-characterized cell adhesion components involved in cell migration and survival, integrated CSK and PTPs' signaling to regulate Src-dependent nociceptive plasticity. Paxillin localized at excitatory glutamatergic synapses in the spinal dorsal horn of mice, and the phosphorylation of Tyr118 on paxillin was necessary to associate with and target CSK at synapses. After peripheral tissue injury, the enhanced neuronal activity stimulated N-methyl-D-aspartate (NMDA) subtype glutamate receptors, which initiated PTPs' signaling to catalyze Tyr118 dephosphorylation. The reduced Tyr118 phosphorylation disrupted paxillin interaction with CSK, leading to the dispersal of CSK out of synapses. With the loss of CSK-mediated inhibition, Src activity was persistently increased. The active Src potentiated the synaptic transmission specifically mediated by GluN2B subunit–containing NMDA receptors. The active Src also facilitated the induction of long-term potentiation of C fiber–evoked field potentials and exaggerated painful responses. In complete Freund's adjuvant–injected mice, viral expression of phosphomimicking paxillin mutant to resume CSK synaptic localization repressed Src hyperactivity. Meanwhile, this phosphomimicking paxillin mutant blunted NMDA receptor–mediated synaptic transmission and alleviated chronic inflammatory pain. These data showed that PTPs-mediated dephosphorylation of paxillin at Tyr118 was involved in the modification of nociceptive plasticity through CSK-Src signaling.
Efficient numerical solution of the time-dependent Schrödinger equation for deep tunneling

The numerical challenge associated with the time-dependent approach to the general problem of the decay of a metastable state by quantum tunneling is discussed and methods towards its application to concrete problems are presented. In particular, different artificial boundary conditions were implemented in order to reduce the reflections of the wave packet at the numerical boundaries. They are illustrated and optimized for the deep tunneling case of ground state proton decay.
X Chromosome Dosage Compensation in Drosophila

Abstract Dosage compensation in Drosophila is achieved by increasing the transcription of genes on the male X chromosome. Recent advances in the study of dosage compensation indicate that the chromatin composition of the male X chromosome is distinct from that of female X chromosomes or of the autosomes in either sex. At least two dosage compensation regulatory proteins (MLE and MSL-1) and a specific acetylated isoform of histone H4 (H4 Ac16) associate predominantly with hundreds of sites along the length of the X chromosome in male and not in female nuclei. In this review, we discuss these findings in the context of the relationship between gene expression and local chromatin structure.
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches

Monoamine oxidase A (MAO A) is an enzyme that catalyzes the oxidation of neurotransmitter amines. A functional polymorphism in the human MAOA gene (high- and low- MAOA) has been associated with distinct behavioral phenotypes. To investigate directly the biological mechanism whereby this polymorphism influences brain function, we recently measured the activity of the MAO A enzyme in healthy volunteers. When found no relationship between the individual’s brain MAO A level and the MAOA genotype, we postulated that there are additional regulatory mechanisms that control the MAOA expression. Given that DNA methylation is linked to the regulation of gene expression, we hypothesized that epigenetic mechanisms factor into the MAOA expression. Our underplaying assumption was that the differences in an individual’s genotype play a key role in the epigenetic potential of the MAOA locus and, consequently, determine the individual’s level of MAO A activity in the brain. As a first step towards experimental validation of the hypothesis, we performed a comprehensive bioinformatic analysis aiming to interrogate genomic features and attributes of the MAOA locus that might modulate its epigenetic sensitivity. Major findings of our analysis are the following: (1) the extended MAOA regulatory region contains two CpG islands (CGIs), one of which overlaps with the canonical MAOA promoter and the other is located further upstream; both CGIs exhibit sensitivity to differential methylation. (2) The uVNTR’s effect on the MAOA’s transcriptional activity might have epigenetic nature: this polymorphic region resides within the MAOA’s CGI and itself contains CpGs, thus, the number of repeating increments effectively changes the number of methylatable cytosines in the MAOA promoter. An array of in silico analyses (the nucleosome positioning, the physical properties of the local DNA, the clustering of transcription-factor binding sites) together with experimental data on histone modifications and Pol 2 sites and data from the RefSeq mRNA library suggest that the MAOA gene might have an alternative promoter. Based on our findings, we propose a regulatory mechanism for the human MAOA according to which the MAOA expression in vivo is executed by the generation of tissue-specific transcripts initiated from the alternative promoters (both CGI-associated) where transcriptional activation of a particular promoter is under epigenetic control.
Human Biochemistry of the Isoprostane Pathway*

Free radicals derived primarily from molecular oxygen have been implicated in a variety of human disorders including atherosclerosis, cancer, neurodegenerative diseases, and aging (1). Damage to tissue biomolecules, including lipids, proteins, and DNA, by free radicals is postulated to contribute importantly to the pathophysiology of oxidative stress. Lipids are readily attacked by free radicals resulting in the formation of a number of peroxidation products. One class of oxidation products formed in abundance in vitro and in vivo is the isoprostanes (IsoPs),2 which were discovered by our laboratory in 1990. IsoPs are a series of prostaglandin (PG)-like compounds produced by the free radical-catalyzed peroxidation of arachidonic acid independent of the cyclooxygenase (2). Over the past 20 years, we and others have carried out a large number of studies defining the basic chemistry and biochemistry involved in the formation and metabolism of the IsoPs. In addition, we have shown that levels of IsoPs are increased in a number of human diseases, and it is currently recognized that measurement of these molecules is the most accurate analytical method to assess oxidative injury in vivo. Further, a number of IsoPs have been found to possess potent biological activity and thus are likely also mediators of oxidant injury (3). In recent years, additional related compounds, derived from various polyunsaturated fatty acids such as eicosapentaenoic acid (EPA) (4) and docosahexaenoic acid (DHA) (5), have been discovered to be formed as products of the IsoP pathway. It is the purpose herein to summarize our current knowledge regarding the IsoPs including the chemistry and biochemistry of their formation, the utility of measuring these compounds as markers of in vivo oxidant stress, and their pharmacological properties.