Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical and genetic characterization of a large primary open angle glaucoma pedigree

ABSTRACT Purpose: To both characterize the clinical features of large primary open angle glaucoma (POAG) pedigree from a village in southern India and to investigate the genetic basis of their disease. Materials and methods: Eighty-four members of a large pedigree received complete eye examinations including slit lamp examination, tonometry, gonioscopy, and ophthalmoscopy. Some were further studied with perimetry. Those diagnosed with POAG were tested for disease-causing mutations in the myocilin and optineurin genes with Sanger sequencing. Results: Fourteen of 84 family members were diagnosed with POAG, while eight were clinically judged to be POAG-suspects. The family structure and the pattern of glaucoma in the pedigree are complex. Features of glaucoma in this pedigree include relatively early age at diagnosis (mean 50 ± 14 years) and maximum intraocular pressures ranging from 14 to 36 mm Hg with a mean of 23 mm Hg ± 6.5 mm Hg. Patients had an average central corneal thickness (mean 529 ± 37.8 microns) and moderate cup-to-disc ratios (0.74 ± 0.14). No mutations were detected in myocilin, optineurin, or TANK binding kinase 1 (TBK1). Conclusions: We report a five-generation pedigree with a complex pattern of POAG inheritance that includes 22 POAG patients and glaucoma suspects. Although the familial clustering of POAG in this pedigree is consistent with dominant inheritance of a glaucoma-causing gene, mutations were not detected in genes previously associated with autosomal dominant glaucoma, suggesting the involvement of a novel disease-causing gene in this pedigree.
Membrane Transporters as Mediators of Cisplatin Effects and Side Effects

Transporters are important mediators of specific cellular uptake and thus, not only for effects, but also for side effects, metabolism, and excretion of many drugs such as cisplatin. Cisplatin is a potent cytostatic drug, whose use is limited by its severe acute and chronic nephro-, oto-, and peripheral neurotoxicity. For this reason, other platinum derivatives, such as carboplatin and oxaliplatin, with less toxicity but still with antitumoral action have been developed. Several transporters, which are expressed on the cell membranes, have been associated with cisplatin transport across the plasma membrane and across the cell: the copper transporter 1 (Ctr1), the copper transporter 2 (Ctr2), the P-type copper-transporting ATPases ATP7A and ATP7B, the organic cation transporter 2 (OCT2), and the multidrug extrusion transporter 1 (MATE1). Some of these transporters are also able to accept other platinum derivatives as substrate. Since membrane transporters display a specific tissue distribution, they can be important molecules that mediate the entry of platinum derivatives in target and also nontarget cells possibly mediating specific effects and side effects of the chemotherapeutic drug. This paper summarizes the literature on toxicities of cisplatin compared to that of carboplatin and oxaliplatin and the interaction of these platinum derivatives with membrane transporters.
Social behavior recognition in continuous video

We present a novel method for analyzing social behavior. Continuous videos are segmented into action `bouts' by building a temporal context model that combines features from spatio-temporal energy and agent trajectories. The method is tested on an unprecedented dataset of videos of interacting pairs of mice, which was collected as part of a state-of-the-art neurophysiological study of behavior. The dataset comprises over 88 hours (8 million frames) of annotated videos. We find that our novel trajectory features, used in a discriminative framework, are more informative than widely used spatio-temporal features; furthermore, temporal context plays an important role for action recognition in continuous videos. Our approach may be seen as a baseline method on this dataset, reaching a mean recognition rate of 61.2% compared to the expert's agreement rate of about 70%.
Adaptive Hybrid Feature Extraction for Leaf Image Classification by Support Vector Machine

In leaf image classification or retrieval fields, hybrid features are widely used to represent the information in various aspects by combining a number of sub-features linearly. However, the importance degrees of sub-features are often ignored by assigning the weights in an ad-hoc fashion without a solid theoretical basis. In this paper, a new type of adaptive hybrid features is proposed by using kernel trick of support vector machine (SVM), in which the weights can be adaptively selected. All weights are obtained by solving an optimization problem to maximize the discriminability of features. Experimental results of leaf image classification show that SVMs with new features significantly outperform those with traditional ones in terms of test accuracy.
Adaptive Tracking Games for Coupled Stochastic Linear Multi-Agent Systems: Stability, Optimality and Robustness

Distributed adaptive tracking-type games are investigated for a class of coupled stochastic linear multi-agent systems with uncertainties of unknown structure parameters, external stochastic disturbances, unmodeled dynamics, and unknown agents' interactions. The control goal is to make the states of all the agents converge to a desired function of the population state average (PSA). Due to the fact that only local information is available for each agent, the control is distributed. For the time-invariant parameter case, the extended least-squares algorithm, Nash certainty equivalence (NCE) principle, and certainty equivalence (CE) principle are used to estimate the unknown parameters and the PSA term, and to design adaptive control, respectively. Under some mild conditions, it is shown that the closed-loop system is almost surely uniformly stable with respect to the population number N; the estimate for the PSA term is strongly consistent; the adaptive control is almost surely an asymptotic Nash equilibrium. When the dynamics of each agent contains time-varying parameters and unmodeled dynamics, the projected least mean square (LMS) algorithm, NCE principle, and CE principle are adopted to estimate the unknown time-varying parameters, and the unknown PSA term, and to design robust adaptive control, respectively. In addition to stability of the closed-loop system and consistency of the PSA estimate, the control law is shown to be robust Nash equilibrium with respect to the unmodeled dynamics, the variation of the unknown parameters, and the external disturbances. Two numerical examples are given to illustrate the methods and results of this paper.
An Osgoodian perspective on WordNet

According to Osgood's “Semantic Differential” theory, the connotative meaning of most adjectives can be rated on a scale, the ends of which are antonymic adjectives. Such a pair of antonymic adjectives is called a factor. Osgood and his colleagues found that most of the variance in the text affecting judgment was explained by only three major factors: the evaluative factor (e.g., good-bad), the potency factor (e.g., strong-weak), and the activity factor (e.g., active-passive). The method described in this article defines an ontology-supported topological calculus over the senses of the words and takes into account all categories of content words (not only adjectives). Each set of synonyms is associated with a new mark-up which generalizes the usual subjectivity annotation (positive, negative, and objective) according to a user-based multi-criteria differential semantics model.
Diurnal analysis of surface Urban Heat Island using spatially enhanced satellite derived LST data

The importance of studying the Urban Heat Island (UHI) phenomenon has increased over the years due to the processes of urbanization and industrialization. Thermal remote sensing imagery has been extensively utilized for surface UHI (SUHI) studies. However, the low image acquisition frequency of most sensors limits its use. The Institute for Astronomy, Astrophysics, Space Applications and Remote Sensing, of the National Observatory of Athens (NOA/IAASASRS) has developed a system that produces land surface temperature (LST) time series by downscaling data retrieved from MSGSEVIRI (Meteosat Second Generation - Spinning Enhanced Visible and Infrared Imager) geostationary satellite. The system has been designed specifically to facilitate urban climate studies, by producing LST datasets that combine high spatial and temporal resolution. Moreover, the large number of LST image data produced, enables their utilization to a number of different applications. In this work, LST data from the NOA/IAASARS system have been employed for the study of the diurnal evolution of the SUHI phenomenon for Athens (GR), Istanbul (TR) and Rome (IT). The results obtained refer to the summer of 2014 and highlight the intensity and temporal variation of this phenomenon for each city employed in this study.
Symbolic Computing with Incremental Mind-maps to Manage and Mine Data Streams - Some Applications

In our understanding, a mind-map is an adaptive engine that basically works incrementally on the fundament of existing transactional streams. Generally, mind-maps consist of symbolic cells that are connected with each other and that become either stronger or weaker depending on the transactional stream. Based on the underlying biologic principle, these symbolic cells and their connections as well may adaptively survive or die, forming different cell agglomerates of arbitrary size. In this work, we intend to prove mind-maps' eligibility following diverse application scenarios, for example being an underlying management system to represent normal and abnormal traffic behaviour in computer networks, supporting the detection of the user behaviour within search engines, or being a hidden communication layer for natural language interaction.
CELLULAR RECEPTORS: BINDING OF RADIOACTIVELY LABELED ANTI-ALLOANTISERUM

Rat alloantisera of the following specificities were obtained after single skin graft rejection: DA anti-BN, BN anti-DA, DA anti-Lewis, and Lewis anti-DA. Anti-alloantibodies were raised by injecting the first two alloantisera into (DA x BN)F1 hosts and the last two alloantisera into (DA x Lewis)F1 hosts. In this manner, four anti-alloantisera were raised: anti-(DA anti-BN), anti-(BN anti-DA), anti-(DA anti-Lewis), and anti-(Lewis anti-DA). From each anti-alloantiserum a gamma globulin fraction was prepared and trace labeled with 125I. The labeled anti-alloantibodies could be shown to be fixed preferentially by red cells coated with the alloantibody used to induce them. They were also preferentially fixed by normal rat lymphoid cells presumed to carry recognition structures similar to alloantibody. For instance, anti-(DA anti-BN) was fixed by BN red cells coated with DA anti-BN and by normal DA lymphoid cells presumed to carry RS(BN). Conversely, anti-(BN anti-DA) was fixed by DA red cells coated with BN anti-DA and by normal BN lymphoid cells, carrying RS(DA). Absorption and inhibition experiments showed that alloantibodies and normal lymphoid cells compete for the same labeled anti-alloantibodies. We conclude that cellular receptors and circulating alloantibody are antigenically similar: They have the same aliotype.
Improved modulation Technique for voltage fed quasi-Z-source DC/DC converter

A new shoot-through pulse width modulation (PWM) technique for voltage fed quasi-Z-source DC/DC converters is presented. One advantage of the technique is it minimizes switching losses in the converter by minimizing the number of switching commutations of the active devices in the intermediate H-bridge. The duration of the active and shoot-through states are independently controllable, allowing the shoot-through duty cycle to reach its maximum limit (Dst, max = 0.5), thus enabling a high voltage gain suitable for applications with renewable energy sources (fuel cells, photovoltaics) and other applications requiring a large voltage boost. In addition, the switches achieve zero voltage switching (ZVS) which reduce EMI and improves efficiency of the converter. A 500W prototype converter was implemented demonstrating improved performance with the new modulation technique.
Adaptive learning interface used physiological signals

The purpose of the article is the development of an interface which closely adapts to the individual. By quantifying the frustration as the human manipulates machines from a biomedical signal and making it into teaching signals of machine learning (ML), we aim at the development of a system in which the machine adapts to the human. The authors extract the characteristic vector of whether the examinee is in discomfort or not from electroencephalograms (EEG) and electromyograms (EMG). An artificial neural network (ANN) is employed to extract the vector. For the machine learning, reinforcement learning is used and the rewards are an extracted signal from physiological signals. As a basic experiment for extracting discomfort and comfort from the physiological signals, the EEG measurement experiment was carried out under an unpleasant sound environment for 20 examinees. The input signals to ANN for the characteristic vector extraction was examined. By affixing piezoelectric films on the eyebrow, the movement of the eyebrow was measured. Finally, the results of measuring EEG and EMG simultaneously under the situation in which frustration accumulated for the examinee are shown. We use reinforcement learning (RL) to control the behavior of the Khepera robot.
Enhancing a Multi-Agent System with Evolving Logic Programs

This paper reports on a fertile marriage between madAgents, a Java and Prolog based multi-agent platform, and EVOLP, a logic programming based language to represent and reason about evolving knowledge. The resulting platform was implemented using a combination of Java, XSB Prolog and Smodels. The paper begins with an introductory section and a general description of the platform and supported architecture, to progress with the formal semantic characterisation, a small example and details concerning the implementation, to end with a brief comparison with other related systems and some final conclusions.
Noninvasive Vascular Elastography With Plane Strain Incompressibility Assumption Using Ultrafast Coherent Compound Plane Wave Imaging

Plane strain tensor estimation using non-invasive vascular ultrasound elastography (NIVE) can be difficult to achieve using conventional focus beamforming due to limited lateral resolution and frame rate. Recent developments in compound plane wave (CPW) imaging have led to high speed and high resolution imaging. In this study, we present the performance of NIVE using coherent CPW. We show the impact of CPW beamforming on strain estimates compared to conventional focus sequences. To overcome the inherent variability of lateral strains, associated with the low lateral resolution of linear array transducers, we use the plane strain incompressibility to constrain the estimator. Taking advantage of the approximate tenfold increase in frame rate of CPW compared with conventional focus imaging, we introduce a time-ensemble estimation approach to further improve the elastogram quality. By combining CPW imaging with the constrained Lagrangian speckle model estimator, we observe an increase in elastography quality (~10 dB both in signal-to-noise and contrast-to-noise ratios) over a wide range of applied strains (0.02 to 3.2%).
The double-stranded RNA-activated protein kinase PKR is dispensable for regulation of translation initiation in response to either calcium mobilization from the endoplasmic reticulum or essential amino acid starvation.

The alpha-subunit of eukaryotic initiation factor eIF2 is a preferred substrate for the double-stranded RNA-activated protein kinase, PKR. Phosphorylation of eIF2alpha converts the factor from a substrate into a competitive inhibitor of the guanine nucleotide exchange factor, eIF2B, leading to a decline in mRNA translation. Early studies provided evidence implicating PKR as the kinase that phosphorylates eIF2alpha under conditions of cell stress such as the accumulation of misfolded proteins in the lumen of the endoplasmic reticulum, i.e., the unfolded protein response (UPR). However, the recent identification of a trans-microsomal membrane eIF2alpha kinase, termed PEK or PERK, suggests that this kinase, and not PKR, might be the kinase that is activated by misfolded protein accumulation. Similarly, genetic studies in yeast provide compelling evidence that a kinase termed GCN2 phosphorylates eIF2alpha in response to amino acid deprivation. However, no direct evidence showing activation of the mammalian homologue of GCN2 by amino acid deprivation has been reported. In the present study, we find that in fibroblasts treated with agents that promote the UPR, protein synthesis is inhibited as a result of a decrease in eIF2B activity. Furthermore, the reduction in eIF2B activity is associated with enhanced phosphorylation of eIF2alpha. Importantly, the magnitude of the change in each parameter is identical in wildtype cells and in fibroblasts containing a chromosomal deletion in the PKR gene (PKR-KO cells). In a similar manner, we find that during amino acid deprivation the inhibition of protein synthesis and extent of increase in eIF2alpha phosphorylation are identical in wildtype and PKR-KO cells. Overall, the results show that PKR is not required for increased eIF2alpha phosphorylation or inhibition of protein synthesis under conditions promoting the UPR or in response to amino acid deprivation.
The Effect of Tuberculosis on Mortality in HIV Positive People: A Meta-Analysis

Background Tuberculosis is a leading cause of death in people living with HIV (PLWH). We conducted a meta analysis to assess the effect of tuberculosis on mortality in people living with HIV. Methods Meta-analysis of cohort studies assessing the effect of tuberculosis on mortality in PLWH. To identify eligible studies we systematically searched electronic databases (until December 2008), performed manual searches of citations from relevant articles, and reviewed conference proceedings. Multivariate hazard ratios (HR) of mortality in PLWH with and without tuberculosis, estimated in individual cohort studies, were pooled using random effect weighting according to “Der Simonian Laird method” if the p-value of the heterogeneity test was <0.05. Results Fifteen cohort studies were systematically retrieved. Pooled overall analysis of these 15 studies estimating the effect of tuberculosis on mortality in PLWH showed a Hazard Ratio (HR) of 1.8 (95% confidence interval (CI): 1.4–2.3). Subanalysis of 8 studies in which the cohort was not exposed to highly active antiretroviral therapy (HAART) showed an HR of 2.6 (95% CI: 1.8–3.6). Subanalysis of 6 studies showed that tuberculosis did not show an effect on mortality in PLWH exposed to HAART: HR 1.1 (95% CI: 0.9–1.3). Conclusion These results provide an indication of the magnitude of benefit to an individual that could have been expected if tuberculosis had been prevented. It emphasizes the need for additional studies assessing the effect of preventing tuberculosis or early diagnosis and treatment of tuberculosis in PLWH on reducing mortality. Furthermore, the results of the subgroup analyses in cohorts largely exposed to HAART provide additional support to WHO's revised guidelines, which include promoting the initiation of HAART for PLWH co-infected with tuberculosis. The causal effect of tuberculosis on mortality in PLWH exposed to HAART needs to be further evaluated once the results of more cohort studies become available.
NUAT: A non-uniform access time memory controller

With rapid development of micro-processors, off-chip memory access becomes a system bottleneck. DRAM, a main memory in most computers, has concentrated only on capacity and bandwidth for decades to achieve high performance computing. However, DRAM access latency should also be considered to keep the development trend in multi-core era. Therefore, we propose NUAT which is a new memory controller focusing on reducing memory access latency without any modification of the existing DRAM structure. We only exploit DRAM's intrinsic phenomenon: electric charge variation in DRAM cell capacitors. Given the cost-sensitive DRAM market, it is a big advantage in terms of actual implementation. NUAT gives a score to every memory access request and the request with the highest score obtains a priority. For scoring, we introduce two new concepts: Partitioned Bank Rotation (PBR) and PBR Page Mode (PPM). First, PBR is a mechanism that draws information of access speed from refresh timing and position; the request which has faster access speed gains higher score. Second, PPM selects a better page mode between open- and close-page modes based on the information from PBR. Evaluations show that NUAT decreases memory access latency significantly for various environments.
Cytoreductive therapy in 108 adults with systemic mastocytosis: Outcome analysis and response prediction during treatment with interferon‐alpha, hydroxyurea, imatinib mesylate or 2‐chlorodeoxyadenosine

Cytoreductive therapy in systemic mastocytosis (SM) includes several drugs whose individual merit has not been well characterized. We retrospectively studied 108 Mayo Clinic patients who met the 2008 WHO diagnostic criteria for SM and received at least one cytoreductive drug. The numbers of patients who were evaluable for response to treatment with interferon‐alpha with or without prednisone (IFN‐α), hydroxyurea (HU), imatinib mesylate (IM) or 2‐chlorodeoxyadenosine (2‐CdA) were 40, 26, 22, and 22, respectively. The corresponding overall (major) response rates, according to recently published consensus criteria, were 53% (18%), 19% (0%), 18% (9%), and 55% (37%). The respective overall response rates in indolent SM, aggressive SM and SM associated with another clonal hematological nonmast cell lineage disease (SM‐AHNMD) were 60%, 60%, 45% for IFN‐α, 0, 0, 21% for HU, 14%, 50%, 9% for IM and 56%, 50%, 55% for 2‐CdA. The absence of mast cell mediator release symptoms in IFN‐α‐treated patients and presence of circulating immature myeloid cells in 2‐CdA‐treated patients predicted inferior response. TET2 mutational status did not influence treatment response. Although the major response rates with these four cytoreductive agents were still suboptimal and HU was mainly used in patients with SM‐AHNMD, the current study favors 2‐CdA or IFN‐α as first‐line current therapy in SM and identifies patients who are likely to respond to such therapy. Am. J. Hematol. , 2009. © 2009 Wiley‐Liss, Inc.
An Analysis Tool for Social Networks and Other Relational Data Senior Design 2009-2010

In recent years, social networking has become an integral part of life for students, professionals, and the general population alike. With different sites catering to different types of people, there are more and more ways for people to get involved. Social networks have gone beyond a casual hobby and have the potential to shape the ways people go about everyday life. As these sites grow in popularity, many people have amassed large networks with various types of connections to other users. As a result, while only a small amount of data may be available about a given individual, there is likely a vast amount of information about people they have chosen to be connected to through these websites. And as more people join every day, people’s networks are expanding as more opportunities to establish links come about. This phenomenon is relatively new, so research in the area of social network data is young, but growing quickly. In order to aid future research on social networks, a software package was developed to allow analysis on network data. It was developed with the intention of being an allpurpose research tool, with the ability to store large amounts of data and do simple analysis on it. Users are able to create networks and output their findings, based on a few simple output options. A custom query language was also developed with the system in order to allow users to examine whole networks at a time and ask network-based questions, rather than focus on the individuals.