Miracle-dz/UniFAR-FTUs huggingface dataset:
GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism

Ocular albinism type 1 (OA), caused by mutations in the OA1 gene, encodes a G-protein coupled receptor, OA1, localized in melanosomal membranes of the retinal pigment epithelium (RPE). This disorder is characterized by both RPE macro-melanosomes and abnormal decussation of ganglion cell axons at the brain’s optic chiasm. We demonstrated previously that Oa1 specifically activates Gαi3, which also signals in the Oa1 transduction pathway that regulates melanosomal biogenesis. In this study, we screened the human Gαi3 gene, GNAI3, in DNA samples from 26 patients who had all clinical characteristics of OA but in whom a specific mutation in the OA1 gene had not been found, and in 6 normal control individuals. Using the Agilent HaloPlex Target Enrichment System and next-generation sequencing (NGS) on the Illumina MiSeq platform, we identified 518 variants after rigorous filtering. Many of these variants were corroborated by Sanger sequencing. Overall, 98.8% coverage of the GNAI3 gene was obtained by the HaloPlex amplicons. Of all variants, 6 non-synonymous and 3 synonymous were in exons, 41 in a non-coding exon embedded in the 3’ untranslated region (UTR), 6 in the 5’ UTR, and 462 in introns. These variants included novel SNVs, insertions, deletions, and a frameshift mutation. All were found in at least one patient but none in control samples. Using computational methods, we modeled the GNAI3 protein and its non-synonymous exonic mutations and determined that several of these may be the cause of disease in the patients studied. Thus, we have identified GNAI3 as a second gene possibly responsible for X-linked ocular albinism.
Adaptive equalization of multiple-input multiple-output (MIMO) channels

The paper proposes and investigates a new approach to adaptive spatio-temporal equalization for MIMO (multiple-input multiple-output) channels. A system with n transmit and m (m/spl ges/n) receiver antennas is assumed. A decision feedback equalizer is considered. A least squares solution is first formulated, based on which a recursive solution using Riccati recursions is proposed. The proposed solution is tested by simulating the MIMO system. It is shown that the adaptive solution achieves the same performance as the optimum least squares solution. The effect of the nondiagonal channel elements (acting as interference) on the system performance is also studied. It has been shown that in order to achieve better performance, the interference from nondiagonal channel elements needs to be minimized. This can be done by using orthogonal transmission. Moreover the proposed solution do not require channel identification and will also enable equalizer adaptation to channel changes.
IMPACT ASSESSEMENT OF SEWERAGE DRAIN ON TUBEWELL WATER QUALITY USING MT3D MODEL

In last few decades, the demand of fresh water is rising magnificently due to rapid increase in population and food demand. A large quantity of groundwater is being used for irrigation due to shortage of surface water. In Pakistan the availability and quality of groundwater has been affected due to rapid urbanization and over exploitation. This research was conducted to assess the impact of sewerage drain at Jaranwala Drain on groundwater quality and evaluate the rate at which drain is deteriorating the groundwater quality. MODFLOW and MT3D models were used to calculate concentrations for different time intervals in aquifer at the end of year 2014. The results showed that the concentration of 723 mg/l was travelled 320 m towards pumping well for simulation time of 35 days in all three layers. After 1096 days of simulation, the travelled distance towards the pumping well was 1000, 970 and 920 m with concentration of 7020, 5630 and 5120 mg/l in the first, second and third layer, respectively. It was concluded that the horizontal movement of the concentration was very high as compared to the vertical movement. It was also concluded that if sewerage drain is passing near agricultural land then tubewell installation on two kilometers or away from drain is safe to avoid the contamination of tubewell water.
Improving Design Diversity Using Graph Based Evolutionary Algorithms

Graph based evolutionary algorithms (GBEAs) have been shown to have superior performance to evolutionary algorithms on a variety of evolutionary computation test problems as well as on some engineering applications. One of the motivations for creating GBEAs was to produce a diversity of solutions with little additional computational cost. This paper tests that feature of GBEAs on three problems: a real-valued multi-modal function of varying dimension, the plus-one-recall-store (PORS) problem, and an applied engineering design problem. For all of the graphs studied the number of different solutions increased as the connectivity of the graph underlying the algorithm decreased. This indicates that the choice of graph can be used to control the diversity of solutions produced. The availability of multiple solutions is an asset in a product realization system, making it possible for an engineer to explore design alternatives.
Understanding Edge Connectivity in the Internet through Core Decomposition

Abstract The Internet is a complex network composed of several networks: the autonomous systems. Each of them is designed with the aim of transporting information efficiently. This information is carried over routes, which are discovered by routing protocols, such as the border gateway protocol (BGP). The protocols may find possible paths between nodes whenever they exist, or even find paths satisfying specific constraints, e.g., a certain quality of service (QoS). Here, we study connectivity as a network attribute related to both situations; we provide a formal lower bound to it based on core decomposition and low-complexity algorithms to find it. Then we apply these algorithms to analyze maps obtained from the prominent Internet mapping projects, and use the LaNet-vi open-source software for their visualization.
Relations of APOE promoter polymorphisms to LDL cholesterol and markers of subclinical atherosclerosis in young adults Published, JLR Papers in Press, March 9, 2006.

The common apolipoprotein E (apoE) gene (APOE) ϵ2/ϵ3/ϵ4 polymorphism explains part of serum lipid variation, and polymorphisms in the APOE promoter region have been proposed to participate in the regulation of serum lipid levels within the most common APOE ϵ3/ϵ3 genotype group. We determined APOE −219G/T and +113G/C promoter genotypes and estimated APOE haplotypes in 525 participants of the Cardiovascular Risk in Young Finns Study. We studied the associations of the APOE promoter polymorphisms and their haplotypes with cross-sectional and longitudinal serum lipid and apolipoprotein concentrations as well as with flow-mediated dilatation (FMD), carotid artery compliance (CAC), and intima-media thickness (IMT) within the APOE ϵ3/ϵ3 carriers. We found no significant association between the APOE promoter genotypes and serum lipids [low density lipoprotein-cholesterol (LDL-C), HDL-C, and triglycerides], apolipoproteins (apoA-I and apoB), or brachial artery FMD, CAC, or carotid IMT in either men or women. In longitudinal analyses in males, the carriers of heterozygous genotypes (−219G/T or +113G/C) and, furthermore, carriers of the −219T/+113C/ϵ3 haplotype had significantly higher LDL-C and total cholesterol concentrations throughout the 21 year follow-up period compared with homozygous G allele carriers or noncarriers of the −219T/+113C/ϵ3 haplotype. Such associations were not found in females. In summary, the APOE promoter polymorphisms −219G/T and +113G/C as well as their haplotype are associated with longitudinal changes in LDL-C and total cholesterol concentrations in young Finnish males but do not seem to be major determinants for FMD, CAC, or carotid IMT in males or females.
Background and foreground modeling using nonparametric kernel density estimation for visual surveillance

Automatic understanding of events happening at a site is the ultimate goal for many visual surveillance systems. Higher level understanding of events requires that certain lower level computer vision tasks be performed. These may include detection of unusual motion, tracking targets, labeling body parts, and understanding the interactions between people. To achieve many of these tasks, it is necessary to build representations of the appearance of objects in the scene. This paper focuses on two issues related to this problem. First, we construct a statistical representation of the scene background that supports sensitive detection of moving objects in the scene, but is robust to clutter arising out of natural scene variations. Second, we build statistical representations of the foreground regions (moving objects) that support their tracking and support occlusion reasoning. The probability density functions (pdfs) associated with the background and foreground are likely to vary from image to image and will not in general have a known parametric form. We accordingly utilize general nonparametric kernel density estimation techniques for building these statistical representations of the background and the foreground. These techniques estimate the pdf directly from the data without any assumptions about the underlying distributions. Example results from applications are presented.
Epigenetic silencing and tissue independent expression of a novel tetracycline inducible system in double‐transgenic pigs

The applicability of tightly regulated transgenesis in domesticated animals is severely hampered by the present lack of knowledge of regulatory mechanisms and the long generation intervals. To capitalize on the tightly controlled expression of mammalian genes made possible by using prokaryotic control elements, we have used a single‐step transduction to introduce an autoregulative tetracycline‐responsive bicistronic expression cassette (NTA) into transgenic pigs. Transgenic pigs carrying one NTA cassette showed a mosaic transgene expression restricted to single muscle fibers. In contrast, crossbred animals carrying two NTA cassettes with different transgenes, revealed a broad tissue‐independent and tightly regulated expression of one cassette, but not of the other one. The expression pattern correlated inversely with the methylation status of the NTA transcription start sites indicating epigenetic silencing of one NTA cassette. This first approach on tetracycline regulated transgene expression in farm animals will be valuable for developing precisely controlled expression systems for transgenes in large animals relevant for biomedical and agricultural biotechnology. —Kues, W.A. , Schwinzer, R. , Wirth, D. , Verhoeyen, E. , Lemme, E. , Hermann, D. , Barg‐Kues, B. , Hauser, H. , Wonigeit, K. , and Niemann, H. Epigenetic silencing and tissue independent expression of a novel tetracycline inducible system in double‐transgenic pigs. FASEBJ. 20, E357–E366 (2006)
A Grid-Based k-Nearest Neighbor Join for Large Scale Datasets on MapReduce

Because MapReduce supports efficient parallel data processing, MapReduce-based query processing algorithms have been widely studied. Among various query types, k-nearest neighbor join, which aims to produce the k nearest neighbors of each point of a dataset from another dataset, has been considered most important in data analysis. Existing k-NN join query processing algorithms on MapReduce suffer from high index construction and computation costs which make them unsuitable for big data processing. In this paper, we propose a new grid-based k-NN join query processing algorithm on MapReduce. First, we design a dynamic grid index that represents the distribution of join datasets. Based on this index, we prune out unnecessary cells for the join with the distance-based filtering. This can reduce the data transmission and computation overheads. From performance analysis, we show that our algorithm outperforms the existing scheme up to seven times in terms of query processing time while achieving high query result accuracy.
Quantum picturalism

Why did it take us 50 years since the birth of the quantum mechanical formalism to discover that unknown quantum states cannot be cloned? Yet, the proof of the ‘no-cloning theorem’ is easy, and its consequences and potential for applications are immense. Similarly, why did it take us 60 years to discover the conceptually intriguing and easily derivable physical phenomenon of ‘quantum teleportation’? We claim that the quantum mechanical formalism doesn't support our intuition, nor does it elucidate the key concepts that govern the behaviour of the entities that are subject to the laws of quantum physics. The arrays of complex numbers are kin to the arrays of 0s and 1s of the early days of computer programming practice. Using a technical term from computer science, the quantum mechanical formalism is ‘low-level’. In this review we present steps towards a diagrammatic ‘high-level’ alternative for the Hilbert space formalism, one which appeals to our intuition. The diagrammatic language as it currently stands allows for intuitive reasoning about interacting quantum systems, and trivialises many otherwise involved and tedious computations. It clearly exposes limitations such as the no-cloning theorem, and phenomena such as quantum teleportation. As a logic, it supports ‘automation’: it enables a (classical) computer to reason about interacting quantum systems, prove theorems, and design protocols. It allows for a wider variety of underlying theories, and can be easily modified, having the potential to provide the required step-stone towards a deeper conceptual understanding of quantum theory, as well as its unification with other physical theories. Specific applications discussed here are purely diagrammatic proofs of several quantum computational schemes, as well as an analysis of the structural origin of quantum non-locality. The underlying mathematical foundation of this high-level diagrammatic formalism relies on so-called monoidal categories, a product of a fairly recent development in mathematics. Its logical underpinning is linear logic, an even more recent product of research in logic and computer science. These monoidal categories do not only provide a natural foundation for physical theories, but also for proof theory, logic, programming languages, biology, cooking, … So the challenge is to discover the necessary additional pieces of structure that allow us to predict genuine quantum phenomena. These additional pieces of structure represent the capabilities nature has provided us with to manipulate entities subject to the laws of quantum theory.
The determination of high-risk pregnancy: the use of antenatal scoring system.

AIMS A standardized antenatal scoring system is not available in order to detect high-risk pregnancies at primary health care units in Turkey. The authors aimed to evaluate the applicability of the "Knox scoring system" in Turkey. MATERIALS AND METHODS One hundred and twenty-nine pregnant women were included in study. They were assessed upon admission and then the same women were reassessed at the onset of labor by Knox scoring system. RESULTS The Knox scoring system identified 65 pregnant women (50.4%) as high-risk upon admission while 22 pregnant women (17.1%) as high-risk at the onset of labor. Twelve pregnant women (9.3%) (one case of perinatal death and 11 cases of perinatal morbidity) had poor perinatal outcomes during the study period. The Knox scoring form administered upon admission yielded 58% sensitivity, 50% specificity, and 10% positive predictive value, while 91% sensitivity, 90% specificity, and 50% positive predictive value at the onset of labor. The diagnostic value of the Knox scoring system for determining high-risk pregnancies was not found statistically significant regarding admission (ROC value: 0.655; p > 0.05), while statistically significant regarding the onset of labor (ROC value: 0.946; p < 0.05). CONCLUSIONS The use of the Knox scoring system for determining high-risk pregnancies seems to be effective at the onset of labor.
Mycobacterial Phenolic Glycolipids Selectively Disable TRIF-Dependent TLR4 Signaling in Macrophages

Phenolic glycolipids (PGLs) are cell wall components of a subset of pathogenic mycobacteria, with immunomodulatory properties. Here, we show that in addition, PGLs exert antibactericidal activity by limiting the production of nitric oxide synthase (iNOS) in mycobacteria-infected macrophages. PGL-mediated downregulation of iNOS was complement receptor 3-dependent and comparably induced by bacterial and purified PGLs. Using Mycobacterium leprae PGL-1 as a model, we found that PGLs dampen the toll-like receptor (TLR)4 signaling pathway, with macrophage exposure to PGLs leading to significant reduction in TIR-domain-containing adapter-inducing interferon-β (TRIF) protein level. PGL-driven decrease in TRIF operated posttranscriptionally and independently of Src-family tyrosine kinases, lysosomal and proteasomal degradation. It resulted in the defective production of TRIF-dependent IFN-β and CXCL10 in TLR4-stimulated macrophages, in addition to iNOS. Our results unravel a mechanism by which PGLs hijack both the bactericidal and inflammatory responses of host macrophages. Moreover, they identify TRIF as a critical node in the crosstalk between CR3 and TLR4.
Experiments in voice quality modification of natural speech signals: the spectral approach

Voice quality is currently a key issue in speech synthesis research. The lack of realistic intra-speaker voice quality variation is an important source of concern for concatenation-based synthesis methods. A challenging problem is to reproduce the voice quality changes that are occuring in natural speech when the vocal e ort is varying. A new method for voice quality modi cation is presented. It takes advantage of a spectral theory for voice source signal representation. An algorithm based on periodic-aperiodic decomposition and spectral processing (using the short-term Fourier transform) is described. The use of adaptive inverse ltering in this framework is also discussed. Applications of this algorithm may include: pre-processing of speech corpora, modi cation of voice quality parameters together with intonation in synthesis, voice transformation. Some experiments are reported, showing convincing voice quality modi cations for various speakers.
Biotic controls on Holocene fire frequency in a temperate mountain forest, Czech Republic

Mountain spruce–beech–fir mixed forests are an important type of vegetation at higher elevations in temperate Europe. We aimed to determine how fire disturbances have affected long‐term vegetation dynamics and to assess their contribution to soil formation. We detected fire episodes using a soil charcoal record extensively dated based on 14C and combined with pollen and macrocharcoal records from a local peat bog. Altitudinal shifts of the timberline during the Younger Dryas–Holocene transition seem to be responsible for an abrupt occurrence of fire at 11 200 cal a BP. The minimum fire frequency estimation based on dated soil charcoal particles showed variation during the early to mid‐Holocene in response to climatic changes. A marked decrease of fire frequency since 6200 cal a BP is attributed to the transformation of vegetation from Picea abies‐dominated forests into mixed Fagus sylvatica–Abies alba stands. Once Fagus sylvatica established a dense canopy a profound alteration of the disturbance regime occurred, leading to the exclusion of fire, and has indirectly accelerated the process of podzolization. Thus, the synergistic effects of biotic change are capable of amplifying a climatic impulse, illustrating the important influence of bottom‐up controls on fire regimes and soil development.
Presynaptic localization of an AMPA‐type glutamate receptor in corticostriatal and thalamostriatal axon terminals

The neostriatum is known to receive glutamatergic projections from the cerebral cortex and thalamic nuclei. Vesicular glutamate transporters 1 and 2 (VGluT1 and VGluT2) are located on axon terminals of corticostriatal and thalamostriatal afferents, respectively, whereas VGluT3 is found in axon terminals of cholinergic interneurons in the neostriatum. In the present study, the postsynaptic localization of ionotropic glutamate receptors was examined in rat neostriatum by the postembedding immunogold method for double labelling of VGluT and glutamate receptors. Immunoreactive gold particles for AMPA receptor subunits GluR1 and GluR2/3 were frequently found not only on postsynaptic but also on presynaptic profiles immunopositive for VGluT1 and VGluT2 in the neostriatum, and GluR4‐immunoreactive particles were observed on postsynaptic and presynaptic profiles positive for VGluT1. Quantitative analysis revealed that 27–45% of GluR1‐, GluR2‐, GluR2/3‐ and GluR4‐immunopositive particles found in VGluT1‐ or VGluT2‐positive synaptic structures in the neostriatum were associated with the presynaptic profiles of VGluT‐positive axons. In contrast, VGluT‐positive presynaptic profiles in the neostriatum showed almost no immunoreactivity for NMDA receptor subunits NR1 or NR2A/B. Furthermore, almost no GluR2/3‐immunopositive particles were observed in presynaptic profiles of VGluT3‐positive (cholinergic) terminals that made asymmetric synapses in the neostriatum, or in those of VGluT1‐ or VGluT2‐positive terminals in the neocortex. The present results indicate that AMPA receptor subunits but not NMDA receptor subunits are located on axon terminals of corticostriatal and thalamostriatal afferents, and suggest that glutamate released from these axon terminals controls the activity of the terminals through the presynaptic AMPA autoreceptors.
Ectopic T-bet Expression Licenses Dendritic Cells for IL-12-Independent Priming of Type 1 T Cells In Vitro1

T-bet (TBX21) is a transcription factor required for the optimal development of type 1 immune responses. Although initially characterized for its intrinsic role in T cell functional polarization, endogenous T-bet may also be critical to the licensing of type 1-biasing APCs. Here, we investigated whether human dendritic cells (DC) genetically engineered to express high levels of T-bet (i.e., DC.Tbet) promote superior type 1 T cell responses in vitro. We observed that DC.Tbet were selective activators of type 1 effector T cells developed from the naive pool of responder cells, whereas DC.Tbet and control DC promoted type 1 responses equitably from the memory pool of responder cells. Naive T cells primed by (staphylococcal enterotoxin B or tumor-associated protein-loaded) DC.Tbet exhibited an enhancement in type 1- and a concomitant reduction in Th2- and regulatory T cell-associated phenotype/function. Surprisingly, DC.Tbets were impaired in their production of IL-12 family member cytokines (IL-12p70, IL-23, and IL-27) when compared with control DC, and the capacity of DC.Tbet to preferentially prime type 1 T cell responses was only minimally inhibited by cytokine (IL-12p70, IL-23, IFN-γ) neutralization or receptor (IL-12Rβ2, IL-27R) blockade during T cell priming. The results of transwell assays suggested the DC.Tbet-mediated effects are predominantly the result of direct DC-T cell contact or their close proximity, thereby implicating a novel, IL-12-independent mechanism by which DC.Tbets promote improved type 1 functional polarization from naive T cell responders. Given their superior type 1 polarizing capacity, DC.Tbet may be suitable for use in vaccines designed to prevent/treat cancer or infectious disease.