Miracle-dz/UniFAR-FTUs huggingface dataset:
Drift and conservation of differential exon usage across tissues in primate species

Significance In higher organisms, most genes consist of several disconnected regions (exons), which are combined in various ways to produce several different gene transcripts from the same gene. Such alternative exon usage is thought to contribute to the ability of organisms to generate different cell types and tissues from a single genome. However, recent evidence has also suggested that much alternative exon usage might be noise with no particular function. We reconcile these two views by comparing how exons are used in different tissues and for which exons these usage patterns across tissues change or stay similar (are “conserved”) in several primate species. The latter case is an indication that the pattern is of functional importance, and our analysis quantifies how widespread such cases are. Alternative usage of exons provides genomes with plasticity to produce different transcripts from the same gene, modulating the function, localization, and life cycle of gene products. It affects most human genes. For a limited number of cases, alternative functions and tissue-specific roles are known. However, recent high-throughput sequencing studies have suggested that much alternative isoform usage across tissues is nonconserved, raising the question of the extent of its functional importance. We address this question in a genome-wide manner by analyzing the transcriptomes of five tissues for six primate species, focusing on exons that are 1:1 orthologous in all six species. Our results support a model in which differential usage of exons has two major modes: First, most of the exons show only weak differences, which are dominated by interspecies variability and may reflect neutral drift and noisy splicing. These cases dominate the genome-wide view and explain why conservation appears to be so limited. Second, however, a sizeable minority of exons show strong differences between tissues, which are mostly conserved. We identified a core set of 3,800 exons from 1,643 genes that show conservation of strongly tissue-dependent usage patterns from human at least to macaque. This set is enriched for exons encoding protein-disordered regions and untranslated regions. Our findings support the theory that isoform regulation is an important target of evolution in primates, and our method provides a powerful tool for discovering potentially functional tissue-dependent isoforms.
Design of current-mode modular programmable analog CMOS FLC

One of the active areas of fuzzy logic applications is control systems. In this paper presents a proposed Fuzzy Logic Controller FLC chip utilized a novel Membership Function Circuit MFC which can be made programmable. This membership function features of large dynamic range, high current driving, high noise immunity and is simply tunable by setting some voltages on IC pins. Each input of controller has five membership functions and output has seven singletons. A new structure for Min/Max operators, and also, a new current-mode divider circuit with very small area, very low power consumption and high speed and accurate are presented, which are compatible to the proposed MFC, are also given. This controller is a general-purpose two-input one-output fuzzy controller that can be implemented in 0.08-mm2 in 0.35-μm CMOS technology BSIM3v3. For general control tasks, input-output inference of FLC is voltage/voltage. The maximum delay in output of FLC is about 67-ns that correspond to 15-MFLIPS Fuzzy Logic Inference per Second and power consumption is 2.5-mW.
Implementation of an Integral Sliding Mode Controller for a Pneumatic Cylinder Position Servo Control System

In this paper, an integral sliding mode control for a proportional valve pneumatic cylinder position control system was proposed to realize position regulating and tracking control. The key feature of this control scheme is using of multi-variable parameters design sliding surface method for the pneumatic servo system to improve the control performances. The validity of the proposed control scheme is verified through practical testing on an experimental pneumatic cylinder servo system device. In the cases of step, multi-step, and sinusoidal level position command inputs, the test results show that the proposed control scheme is capable of improving the tracking precision.
Effect of oral antacid administration on the pharmacokinetics of intravenous doxycycline

The effect of oral antacid administration on the pharmacokinetics of intravenous doxycycline was studied. In a randomized crossover design, six healthy male volunteers received an infusion of 200 mg of doxycycline hyclate on two occasions separated by 7 days. On one occasion, subjects were given 30 ml of aluminum hydroxide orally four times a day for 4 days, beginning 2 days prior to doxycycline dosing. Blood and urine samples were collected up to 48 and 96 h after the infusion, respectively, and were analyzed by a microbial assay. Values for volume of distribution at steady state, nonrenal clearance, urine recovery, and urine pH were not statistically different among treatment groups. With concomitant antacid therapy, the half-life of intravenous doxycycline was shortened from 16.2 +/- 2.6 to 11.2 +/- 1.2 h (P = 0.003), and total body clearance increased from 37.4 +/- 6.5 to 54.1 +/- 12.3 ml/min (P = 0.008). Area under the concentration-time curve for serum was decreased by 18 to 44%, with a 22 to 41% increase in renal clearance. Although the increase in nonrenal clearance ranged from 11 to 128%, the high variability led to a nonsignificant difference (P = 0.07). Concomitant oral antacid therapy may significantly enhance the clearance of intravenous doxycycline.
A Brief Historical Account and Introduction to the Earth Science Curriculum Project.

science, which has had a long and varied career as a secondary school subject, is now enjoying a period of rapid increase in enrollment, due in part to a growing disenchantment of most scientists and science educators with general science courses, and in part to a rebirth of interest in the earth and its environs. The rapid advance of science and technology during and following World War II has created the revolution in science education of
Neuritogenic Actions of Botulinum Neurotoxin A on Cultured Motor Neurons

Botulinum neurotoxins (BoNTs) are extremely potent neuromuscular poisons that act through soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein cleavage to inhibit neurotransmitter release. The ability of BoNT serotype A (BoNT/A) to eliminate localized transmitter release at extremely low doses is well characterized. In the current study, we investigated the less understood characteristic of BoNT/A to induce nerve outgrowth, sometimes referred to as sprouting. This phenomenon is generally considered a secondary response to the paralytic actions of BoNT/A, and other potential factors that may initiate this sprouting have not been investigated. Alternatively, we hypothesized that BoNT/A induces sprouting through presynaptic receptor activation that is independent of its known intracellular actions on the soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) synaptosomal associated protein of 25 kDa (SNAP-25). To test this, the effects of BoNT/A application on neurite outgrowth were examined using primary cultures enriched with motor neurons isolated from embryonic mouse spinal cord. In this system, BoNT/A potently stimulated neuritogenesis at concentrations as low as 0.01 nM. The neuritogenic effects of BoNT/A exposure were concentration dependent and antagonized by Triticum vulgaris lectin, a known competitive antagonist of BoNT. Similar results were observed with the isolated BoNT/A binding domain, revealing that neuritogenesis could be initiated solely by the binding actions of BoNT/A. In addition, the presence or absence of SNAP-25 cleavage by BoNT/A was not a determinant factor in BoNT/A-induced neuritogenesis. Collectively, these results suggest that binding of BoNT/A to the motor neuronal membrane activates neuritogenesis through as yet undetermined intracellular pathway(s), independent of its known action on vesicular release.
Calibration method for extending single-layer LIDAR to multi-layer LIDAR

This paper uses a single-layer LIDAR system mounted on a pan-tilt unit to obtain multi-layer information. A calibration method for extending the single-layer information to multi-layer information is proposed. In order to obtain multi-layer information from single-layer LIDAR, the LIDAR system has to tilt the scanning plane at various angles and integrate those scanning planes to construct a three-dimensional model. Ideally, the tilt axis should pass through the center of the scanner. However, since the LIDAR system is mounted on a pan-tilt unit, the tilt axis passes through the motor of the pan-tilt unit, rather than the center of the LIDAR scanner. The positions of the scanning center form a circle. A calibration scheme for transforming all scanning data with respect to one scanning center is proposed. Experimental results show that with the proposed method, the shift error is reduced significantly and the standard deviation of measured distances is reduced to 17% of that for uncalibrated results.
Culture and eating disorders classification.

OBJECTIVE This paper discusses cultural considerations for classification of eating disorders. METHOD The literature on epidemiology and phenomenology of eating disorders in culturally diverse populations was selectively reviewed to identify methodologic challenges in classification and characterization of prevalence and phenomenology. RESULTS Prevalence of eating disorders among culturally diverse populations is incompletely characterized. Few studies address the epidemiology of eating disorders or provide qualitative data on variation in presentation in these populations. Unrecognized cultural diversity may result in misclassification of cases. CONCLUSION Development of culturally valid assessments, ethnographic data on indigenous nosologic correlates and idioms of distress, and attention to phenomenologic diversity may have critical impact on understanding clinical presentations and risk factors that may be culturally particular. A flexible classificatory system for the eating disorders may help to encompass their culturally based phenomenologic diversity, facilitate culturally sensitive and strategic prevention strategies, and reduce ethnic disparities in access to care for them.
Targeted therapy for esophagogastric cancers: a review

The incidence of esophagogastric cancers is increasing rapidly in the Western population. Despite better understanding of the biology and intense research in the treatment of these cancers, the long-term survival remains poor both in the locally advanced and metastatic settings. The addition of combined modality strategies has resulted in modest improvement in 5-year survival rates. A number of biologic agents targeting epidermal-derived growth factor receptor, vascular endothelial derived growth factor and its receptor, and mammalian target of rapamycin (mTOR) are being currently evaluated in Phase II and III clinical trials. Some of these, like trastuzumab, cetuximab, and bevacizumab, have shown promising results. This review provides a brief overview of the recent developments in biologic agents for the treatment of esophagogastric cancers.
Improving light field camera sample design with irregularity and aberration

Conventional camera designs usually shun sample irregularities and lens aberrations. We demonstrate that such irregularities and aberrations, when properly applied, can improve the quality and usability of light field cameras. Examples include spherical aberrations for the mainlens, and misaligned sampling patterns for the microlens and photosensor elements. These observations are a natural consequence of a key difference between conventional and light field cameras: optimizing for a single captured 2D image versus a range of reprojected 2D images from a captured 4D light field. We propose designs in mainlens aberrations and microlens/photosensor sample patterns, and evaluate them through simulated measurements and captured results with our hardware prototype.
Polyreactive natural antibodies in transplantation

Purpose of review Antibody-mediated rejection (ABMR), especially in its chronic manifestation, is increasingly recognized as a leading cause of late graft loss following solid organ transplantation. In recent years, autoantibodies have emerged as a significant component of the humoral response to allografts alongside anti-human leukocyte antigen antibodies. These include polyreactive antibodies also known as natural antibodies (Nabs) secreted by innate B cells. A hallmark of Nabs is their capacity to bind altered self such as oxidized lipids on apoptotic cells. This review provides an overview of these overlooked antibodies and their implication in the pathophysiology of ABMR. Recent findings New evidence reported in the past few years support a contribution of immunoglobulin (Ig) G Nabs to ABMR. Serum IgG Nabs levels are significantly higher in patients with ABMR compared with control kidney transplant recipients with stable graft function. Pretransplant IgG Nabs are also associated with ABMR and late graft loss. IgG Nabs are almost exclusively of the IgG1 and IgG3 subclasses and have the capacity to activate complement. Summary In conclusion, Nabs are important elements in host immune responses to solid organ grafts. The recent description of their implication in ABMR and late kidney graft loss warrants further investigation into their pathogenic potential.
Integration of Network Topological and Connectivity Properties for Neuroimaging Classification

Rapid advances in neuroimaging techniques have provided an efficient and noninvasive way for exploring the structural and functional connectivity of the human brain. Quantitative measurement of abnormality of brain connectivity in patients with neurodegenerative diseases, such as mild cognitive impairment (MCI) and Alzheimer's disease (AD), have also been widely reported, especially at a group level. Recently, machine learning techniques have been applied to the study of AD and MCI, i.e., to identify the individuals with AD/MCI from the healthy controls (HCs). However, most existing methods focus on using only a single property of a connectivity network, although multiple network properties, such as local connectivity and global topological properties, can potentially be used. In this paper, by employing multikernel based approach, we propose a novel connectivity based framework to integrate multiple properties of connectivity network for improving the classification performance. Specifically, two different types of kernels (i.e., vector-based kernel and graph kernel) are used to quantify two different yet complementary properties of the network, i.e., local connectivity and global topological properties. Then, multikernel learning (MKL) technique is adopted to fuse these heterogeneous kernels for neuroimaging classification. We test the performance of our proposed method on two different data sets. First, we test it on the functional connectivity networks of 12 MCI and 25 HC subjects. The results show that our method achieves significant performance improvement over those using only one type of network property. Specifically, our method achieves a classification accuracy of 91.9%, which is 10.8% better than those by single network-property-based methods. Then, we test our method for gender classification on a large set of functional connectivity networks with 133 infants scanned at birth, 1 year, and 2 years, also demonstrating very promising results.
On Kalman filter for stochastic system with correlated noises based on event-triggered sampling

In this paper, an event-triggered sensor data transmission scheme for Kalman filtering, whose goal is to guarantee a good trade off between estimation quality and transmission rate, is considered in a linear stochastic system with correlated process and measurement noise. We prove an upper bound on system performance to design this transmission strategy which decides the transfer time of the data packet in detail. A numerical example is given to verify the potential and effectiveness of the theoretical results.
Chromatin and transcription

The compaction of DNA into chromatin in the eukaryotic nucleus poses many obstacles to transcription. Individual nucleosomes as well as higher order structures limit access of cis‐acting regulatory elements to trans‐acting factors. The structural nature of this inhibition and the mechanisms by which chromatin is remodeled to facilitate the regulation of gene expression have remained puzzles for many years. Recent advances highlight the intimate and dynamic interplay between transcription proteins and components of chromatin, providing new clues to long‐standing questions. A transcriptional adaptor complex has been discovered to house histone acetylase activity. A chromatin remodeling “machine” has been found to be part of the RNA polymerase II holoenzyme. Identification of new factors that affect the organization of functional chromatin domains in yeast, flies, and mammals provides new insights into the organization of higher order chromatin structures, as well as the nature of boundaries that restrict these domains. These compelling discoveries and others define a new and exciting threshold for our understanding of the many connections between chromatin and transcription. —Edmondson, D. G. , Roth, S. Y. Chromatin and transcription. FASEB J. 10, 1173‐1182 (1996)
Self-Reported Atrial Fibrillation and Risk of Stroke in the Reasons for Geographic and Racial Differences in Stroke (REGARDS) Study

Background and Purpose— We compared the associations of self-reported atrial fibrillation (AF) and ECG-detected AF with incident stroke in the Risk of Stroke in the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study. Methods— In this analysis, 27 109 participants aged 45 years or older without previous stroke were included. Stroke cases were identified and adjudicated during an average of 4.4 years of follow-up. Cox proportional hazards analysis was used to calculate hazard ratios (HR) of self-reported AF, ECG-detected AF, and AF detected by either method with incident stroke. We also examined the predictive ability of the Framingham Stroke Risk Score (FSRS) when the component AF was defined by different methods. Results— After adjustment for components of the FSRS, self-reported AF, ECG-detected AF, and AF by either method were predictive of incident stroke (HR, 1.41; 95% CI, 1.05–1.88; HR, 1.90; 95% CI, 1.10–3.27; HR, 1.53; 95% CI, 1.16–2.01, respectively). When self-report, ECG, or either method, separately, were considered as the method of AF ascertainment in the FSRS, the HR per 1% increase in the FSRS were identical across AF ascertainment methods (HR, 1.04; 95% CI, 1.03–1.04; HR, 1.04; 95% CI, 1.04–1.05; HR, 1.04; 95% CI, 1.03–1.04; respectively). Conclusions— Self-reported AF is a strong predictor of stroke that can be used interchangeably or in combination with ECG-detected AF in stroke risk prediction models.
Reduction of Oxidative Stress and Inflammation by Blunting Daily Acute Glucose Fluctuations in Patients With Type 2 Diabetes: Role of Dipeptidyl Peptidase-IV Inhibition. Diabetes Care 2012;35:2076–2082

OBJECTIVE Evaluate the effects of two dipeptidyl peptidase-IV (DPP-4) inhibitors, sitagliptin and vildagliptin, known to have different efficacy on mean amplitude of glycemic excursions (MAGE), on oxidative stress, and on systemic inflammatory markers in patients with type 2 diabetes. RESEARCH DESIGN AND METHODS A prospective, randomized, open-label PROBE design (parallel group with a blinded end point) study was performed in 90 patients with type 2 diabetes inadequately controlled by metformin. The study assigned 45 patients to receive sitagliptin (100 mg once daily; sitagliptin group) and 45 patients to receive vildagliptin (50 mg twice daily; vildagliptin group) for 12 weeks. MAGE, evaluated during 48 h of continuous subcutaneous glucose monitoring, allowed an assessment of daily glucose fluctuations at baseline and after 12 weeks in all patients. Assessment of oxidative stress (nitrotyrosine) and systemic levels of inflammatory markers interleukin (IL)-6 and IL-18 was performed at baseline and after 12 weeks in all patients. RESULTS HbA(1c), fasting and postprandial glucose, MAGE, and inflammatory and oxidative stress markers were similar between the groups at baseline. After 12 weeks, MAGE (P < 0.01) was lower in the vildagliptin group than in the sitagliptin group. After treatment, HbA(1c) and postprandial glucose evidenced similar changes between the groups (P = NS). Vildagliptin treatment was associated with a stronger decrease in nitrotyrosine (P < 0.01), IL-6 (P < 0.05), and IL-18 (P < 0.05) than sitagliptin treatment. Nitrotyrosine and IL-6 changes significantly correlated with changes in MAGE but not in fasting glucose and HbA(1c). CONCLUSIONS MAGE reduction is associated with reduction of oxidative stress and markers of systemic inflammation in type 2 diabetic patients. These effects were greater in the vildagliptin group than in the sitagliptin group.
Peering and querying e-catalog communities

More and more suppliers are offering access to their product or information portals (also called e-catalogs) via the Web. The key issue is how to efficiently integrate and query large, intricate, heterogeneous information sources such as e-catalogs. Traditional data integration approach, where the development of an integrated schema requires the understanding of both structure and semantics of all schemas of sources to be integrated, is hardly applicable because of the dynamic nature and size of the Web. We present WS-CatalogNet: a Web services based data sharing middleware infrastructure whose aims is to enhance the potential of e-catalogs by focusing on scalability and flexible aspects of their sharing and access.
Test-cost sensitive naive Bayes classification

Inductive learning techniques such as the naive Bayes and decision tree algorithms have been extended in the past to handle different types of costs mainly by distinguishing different costs of classification errors. However, it is an equally important issue to consider how to handle the test costs associated with querying the missing values in a test case. When the value of an attribute is missing in a test case, it may or may not be worthwhile to take the effort to obtain its missing value, depending on how much the value results in a potential gain in the classification accuracy. In this paper, we show how to obtain a test-cost sensitive naive Bayes classifier (csNB) by including a test strategy which determines how unknown attributes are selected to perform test on in order to minimize the sum of the mis-classification costs and test costs. We propose and evaluate several potential test strategies including one that allows several tests to be done at once. We empirically evaluate the csNB method, and show that it compares favorably with its decision tree counterpart.