Miracle-dz/UniFAR-FTUs huggingface dataset:
Localization of NaK ATPase on cultured human retinal pigment epithelium.

PURPOSE To localize NaK ATPase sites on cultured human retinal pigment epithelium (RPE). METHODS Cultured human RPE from fetal, 2-year-old, and 21-year-old donors was grown to confluence in microporous culture wells for 4 months to 2 years, mounted in a small-volume Ussing chamber, and perfused with growth medium. Ouabain (10(-5)-M) was applied to the basal and apical sides of the RPE. Changes in transepithelial resistance (Rt), transepithelial potential (TEP), and apical and basal membrane potentials were measured. RESULTS Application of ouabain to the basal side of RPE produced a small sustained increase in TEP after 6 minutes and, simultaneously, small depolarizations of both apical and basal membranes. During the continued presence of ouabain on the basal side, application of ouabain to the apical side produced a significantly larger TEP decrease and greater depolarization of both membranes. Significant changes in Rt were not observed. CONCLUSIONS These results indicate that NaK ATPase sites are present on both the apical and basolateral membranes of cultured human RPE. The greater effect of ouabain when applied to the apical side suggests that functional NaK ATPase sites are more abundant on the apical membrane.
Realistic delay modeling in satisfiability-based timing analysis

Circuit delay computation taking into account the existence of false paths represents a significant and computationally complex problem. Existing research work has focused mainly on path sensitization models and algorithms, and on gate and interconnect delay models. Nevertheless, work in these two main areas has evolved separately, and so most path sensitization models and algorithms assume very rudimentary gate and interconnect delay models. In this paper we propose a modeling framework for circuit delay computation as a sequence of instances of propositional satisfiability. This framework is used to capture several path sensitization models under the unit delay model. Moreover several algorithms for propositional satisfiability are evaluated seeking to illustrate the computational challenges posed by the circuit delay computation problem. Finally, realistic delay models taking into account extracted interconnect delays and fanout data are incorporated into the proposed circuit delay computation framework in order to experimentally evaluate its application.
Prediction and Analysis of Protein Hydroxyproline and Hydroxylysine

Background Hydroxylation is an important post-translational modification and closely related to various diseases. Besides the biotechnology experiments, in silico prediction methods are alternative ways to identify the potential hydroxylation sites. Methodology/Principal Findings In this study, we developed a novel sequence-based method for identifying the two main types of hydroxylation sites – hydroxyproline and hydroxylysine. First, feature selection was made on three kinds of features consisting of amino acid indices (AAindex) which includes various physicochemical properties and biochemical properties of amino acids, Position-Specific Scoring Matrices (PSSM) which represent evolution information of amino acids and structural disorder of amino acids in the sliding window with length of 13 amino acids, then the prediction model were built using incremental feature selection method. As a result, the prediction accuracies are 76.0% and 82.1%, evaluated by jackknife cross-validation on the hydroxyproline dataset and hydroxylysine dataset, respectively. Feature analysis suggested that physicochemical properties and biochemical properties and evolution information of amino acids contribute much to the identification of the protein hydroxylation sites, while structural disorder had little relation to protein hydroxylation. It was also found that the amino acid adjacent to the hydroxylation site tends to exert more influence than other sites on hydroxylation determination. Conclusions/Significance These findings may provide useful insights for exploiting the mechanisms of hydroxylation.
An Efficient Framework for Incremental Graph Computation

Graph computation has become increasingly popular in emerging applications such as social networks and web graphs. In practice, graph is typically large and frequently updated with small changes. However, traditional graph processing systems process the evolving graph in a batch manner. To accelerate these large-scale graph applications, this paper proposes an efficient message reuse framework for incremental graph computation, called IncTracker. IncTracker automatically detects the input data changes and only processes the "changed" vertices by employing an efficient, fine-grained reuse mechanism. By reusing the intermediate messages and results of previous runs, the proposed framework can efficiently avoid redundant message communication in iterations. We compare the framework with Pregel on several SNAP datasets. The results show that the speedup ranges from 1.10x to 2.26x and the network traffic is significantly reduced when the incremental changes from 0% to 20%.
Building parameterized action representations from observation

Virtual worlds may be inhabited by intelligent agents who interact by performing various simple and complex actions. If the agents are human-like (embodied), their actions may be generated from motion capture or procedural animation. In this thesis, we introduce the CaPAR interactive system which combines both these approaches to generate agent-size neutral representations of actions within a framework called Parameterized Action Representation (PAR). Just as a person may learn a new complex physical task by observing another person doing it, our system observes a single trial of a human performing some complex task that involves interaction with self or other objects in the environment and automatically generates semantically rich information about the action. This information can be used to generate similar constrained motions for agents of different sizes. Human movement is captured by electromagnetic sensors. By computing motion zero-crossings and geometric spatial proximities, we isolate significant events, abstract both spatial and visual constraints from an agent's action, and segment a given complex action into several simpler subactions. We analyze each independently and build individual PARs for them. Several PARs can be combined into one complex PAR representing the original activity. Within each motion segment, semantic and style information is extracted. The style information is used to generate the same constrained motion in other differently sized virtual agents by copying the end-effector velocity profile, by following a similar end-effector trajectory, or by scaling and mapping force interactions between the agent and an object. The semantic information is stored in a PAR. The extracted style and constraint information is stored in the corresponding agent and object models.
Control theoretic properties of physiological controller motifs

Identifying biophysical mechanisms that provide regulation and control is essential for our understanding of living systems. However, the distance between life sciences and control theory can be a challenge. Here, we describe, and show the control theoretic properties of a set of biochemical reaction schemes, so-called controller motifs. These controller motifs have similarities with industrial control systems, and have properties such as setpoints, integral gain, and setpoint weight. Once identified, a system understanding of such mechanisms can help synthetic biologists in selecting suitable targets to alter in construction of new biological systems. From a control theoretic viewpoint we identify which biochemical rate constant or property affect the setpoint and the dynamic response of a biophysical controller motif. We also show how a biological system consisting of two antagonistic regulatory mechanisms can be compared to a control engineering problem of controlling the water level in a tank. The similarity between biological systems and control engineering provides theoretical insight, and clears the way to an engineer's approach to synthetic biology.
Characterization of Francisella tularensis Schu S4 mutants identified from a transposon library screened for O-antigen and capsule deficiencies

The lipopolysaccharide (LPS) and O-antigen polysaccharide capsule structures of Francisella tularensis play significant roles in helping these highly virulent bacteria avoid detection within a host. We previously created pools of F. tularensis mutants that we screened to identify strains that were not reactive to a monoclonal antibody to the O-antigen capsule. To follow up previously published work, we characterize further seven of the F. tularensis Schu S4 mutant strains identified by our screen. These F. tularensis strains carry the following transposon mutations: FTT0846::Tn5, hemH::Tn5, wbtA::Tn5, wzy::Tn5, FTT0673p/prsA::Tn5, manB::Tn5, or dnaJ::Tn5. Each of these strains displayed sensitivity to human serum, to varying degrees, when compared to wild-type F. tularensis Schu S4. By Western blot, only FTT0846::Tn5, wbtA::Tn5, wzy::Tn5, and manB::Tn5 strains did not react to the capsule and LPS O-antigen antibody 11B7, although the wzy::Tn5 strain did have a single O-antigen reactive band that was detected by the FB11 monoclonal antibody. Of these strains, manB::Tn5 and FTT0846 appear to have LPS core truncations, whereas wbtA::Tn5 and wzy::Tn5 had LPS core structures that are similar to the parent F. tularensis Schu S4. These strains were also shown to have poor growth within human monocyte derived macrophages (MDMs) and bone marrow derived macrophages (BMDMs). We examined the virulence of these strains in mice, following intranasal challenge, and found that each was attenuated compared to wild type Schu S4. Our results provide additional strong evidence that LPS and/or capsule are F. tularensis virulence factors that most likely function by providing a stealth shield that prevents the host immune system from detecting this potent pathogen.
Freezing and Thawing Human Embryonic Stem Cells

Since James Thomson et al developed a technique in 1998 to isolate and grow hES in culture, freezing cells for later use and thawing and expanding cells from a frozen stock have become important procedures performed in routine hES cell culture. Since hES cells are very sensitive to the stresses of freezing and thawing, special care must taken. Here we demonstrate the proper technique for rapidly thawing hES cells from liquid nitrogen stocks, plating them on mouse embryonic feeder cells, and slowly freezing them for long-term storage.
World of Attitudes in Research Article Discussion Sections: A Cross-Linguistic Perspective

This study aimed to account for metadiscourse variations in the discussion sections of articles written in Persian and English and published in Iranian as well as international scholarly journals in English Language Teaching and Psychiatry. For this purpose, 90 research article discussions were selected, and then hedges and boosters were identified based on the taxonomies of metadiscourse markers. The results of the quantitative and qualitative analyses revealed significant differences in frequency, type, and functions of these devices in the texts. These differences might be attributed to lack of awareness of the conventional rules of English rhetoric, limited and fragile knowledge of academic English by Persian writers, and lack of explicit instruction and exposure to pragmatic and sociolinguistic rules of English by Persian researchers. Further research in other disciplines will help to make more accurate generalizations about the role of metadiscourse markers in research articles.
Parametric methods for pole assignment

The non-redundant parametrization of the pole assignment problem for a n-th order system with m inputs allows to express the solution of the problem in term of n(m - 1) free parameters. These parameters can be used to fulfill additional requirements on the closed-loop system as for instance minimum norm feedback gain matrix, well conditioned eigenvector set, maximum stability radius. One of reliable numerical methods for pole assignment is the so-called Schur method. An extension of this method is proposed which computes the solution of the pole assignment problem corresponding to a non-redundant parameter set. Several possibilities are further investigated to compute minimum norm feedback matrices. An improved approach to compute minimum Frobenius-norm feedback relying on a redundant parametrization is also discussed.
Efficacy of atenolol and captopril in reducing risk of macrovascular and microvascular complications in type 2 diabetes: UKPDS 39

Abstract Objective: To determine whether tight control of blood pressure with either a β blocker or an angiotensin converting enzyme inhibitor has a specific advantage or disadvantage in preventing the macrovascular and microvascular complications of type 2 diabetes. Design: Randomised controlled trial comparing an angiotensin converting enzyme inhibitor (captopril) with a β blocker (atenolol) in patients with type 2 diabetes aiming at a blood pressure of <150/<85 mm Hg. Setting: 20 hospital based clinics in England, Scotland, and Northern Ireland. Subjects: 1148 hypertensive patients with type 2 diabetes (mean age 56 years, mean blood pressure 160/94 mm Hg). Of the 758 patients allocated to tight control of blood pressure, 400 were allocated to captopril and 358 to atenolol. 390 patients were allocated to less tight control of blood pressure. Main outcome measures: Predefined clinical end points, fatal and non-fatal, related to diabetes, death related to diabetes, and all cause mortality. Surrogate measures of microvascular and macrovascular disease included urinary albumin excretion and retinopathy assessed by retinal photography. Results: Captopril and atenolol were equally effective in reducing blood pressure to a mean of 144/83 mm Hg and 143/81 mm Hg respectively, with a similar proportion of patients (27% and 31%) requiring three or more antihypertensive treatments. More patients in the captopril group than the atenolol group took the allocated treatment: at their last clinic visit, 78% of those allocated captopril and 65% of those allocated atenolol were taking the drug (P<0.0001). Captopril and atenolol were equally effective in reducing the risk of macrovascular end points. Similar proportions of patients in the two groups showed deterioration in retinopathy by two grades after nine years (31% in the captopril group and 37% in the atenolol group) and developed clinical grade albuminuria ≥300 mg/l (5% and 9%). The proportion of patients with hypoglycaemic attacks was not different between groups, but mean weight gain in the atenolol group was greater (3.4 kg v 1.6 kg). Conclusion: Blood pressure lowering with captopril or atenolol was similarly effective in reducing the incidence of diabetic complications. This study provided no evidence that either drug has any specific beneficial or deleterious effect, suggesting that blood pressure reduction in itself may be more important than the treatment used.
Implementation of Fully Self-Aligned Homojunction Double-Gate a-IGZO TFTs

A simple method of fabricating fully self-aligned double-gate (SADG) homojunction a-IGZO TFTs is proposed and experimentally demonstrated for the first time. The self-alignment between the bottom- and top-gates is realized with one backside-illuminated photolithographic step; and that between the source/drain regions and the two gates is formed by both argon plasma treatment and hydrogen doping. The resulting overlap between the gate and source/drain regions is about 0.3 μm. Excellent symmetry between bidirectional transfer characteristics in the fabricated SADG TFTs is observed. Moreover, the dynamic threshold voltage operation is well demonstrated, and the driving capability, electrical stress effects under tied and separate gate biases are investigated.
Salusins, newly identified regulators of hemodynamics and mitogenesis, increase in polycystic ovarian syndrome

In the current study, we aimed to investigate whether serum salusin α and β levels are different in PCOS subjects. Fifty women with PCOS and 50 healthy, age- and body mass index matched controls were included to the prospective cross-sectional study. All subjects underwent venous blood drawing on the early follicular phase after an overnight fasting. Serum salusin α and β levels were measured with EIA, and ELISA respectively. The relationships between serum salusin levels and anthropometric and metabolic parameters were also assessed. Plasma salusin α and β levels were higher in women with PCOS compared to control group. Serum salusin α level correlated positively with salusin β and fasting serum insulin levels. The serum salusin β levels were correlated positively with HOMA-IR, TG, LDL-C, LH, FSH, and total testosterone levels. Our results indicate that salusins, newly identified regulators of hemodynamics and mitogenesis, are increased within the serum of women with PCOS.
Facial Mimicry Versus Perspective-Taking: Decoding Instructional Sets As Empathy-Inducing Strategies

Much of human interaction and communication comprises verbal and nonverbal information. While verbal communication contains important lexical information, research has shown that nonverbal communication is often more important to the success of an interaction than is verbal. Improper use and interpretations of nonverbal communication have been shown to be related to social and personal distress due, in part, to a lack of understanding and empathy for the target. Previous research has identified both perspective-taking and facial mimicry as potential strategies that can be used to understand or decode nonverbal communication, which promote empathic responding and prosocial behaviors toward a target. The current study sought to understand better these two decoding strategies by presenting participants with an interpersonal situation (a betrayal) that would require the use of empathic responding to achieve conflict resolution between friends. The results demonstrated that when individuals engaged in either of the two decoding strategies, they reported significantly higher empathic understanding of the target and self-other overlap (a prosocial outcome) relative to those not instructed to engage in a particular strategy. These findings support the use of both nonverbal decoding strategies (perspective-taking and facial mimicry) as means of enhancing interpersonal communication.
Whittaker supports for representations of reductive groups

Let $F$ be either $\mathbb{R}$ or a finite extension of $\mathbb{Q}_p$, and let $G$ be a finite central extension of the group of $F$-points of a reductive group defined over $F$. Also let $\pi$ be a smooth representation of $G$ (Frechet of moderate growth if $F=\mathbb{R}$). For each nilpotent orbit $\mathcal{O}$ we consider a certain Whittaker quotient $\pi_{\mathcal{O}}$ of $\pi$. We define the Whittaker support WS$(\pi)$ to be the set of maximal $\mathcal{O}$ among those for which $\pi_{\mathcal{O}}\neq 0$. In this paper we prove that all $\mathcal{O}\in\mathrm{WS}(\pi)$ are quasi-admissible nilpotent orbits, generalizing some of the results in [Moe96,JLS16]. If $F$ is $p$-adic and $\pi$ is quasi-cuspidal then we show that all $\mathcal{O}\in\mathrm{WS}(\pi)$ are $F$-distinguished, i.e. do not intersect the Lie algebra of any proper Levi subgroup of $G$ defined over $F$. We also give an adaptation of our argument to automorphic representations, generalizing some results from [GRS03,Shen16,JLS16,Cai] and confirming some conjectures from [Ginz06]. Our methods are a synergy of the methods of the above-mentioned papers, and of our preceding paper [GGS17].
Feature Modeling for Context-Aware Software Product Lines

One of the first activities to develop a software product line is the feature analysis. This activity produces a feature model to represent commonalities and variabilities among products of a product line. Contextaware applications use context information to provide services and relevant information for their users. One of the challenges to build a context-aware product line is how to represent context information in a feature model. This paper proposes a modeling notation, called UbiFEX, for representing context information and defining context adaptive rules in a feature model.
Bio-inspired machine learning in microarray gene selection and cancer classification

Microarray technology today has the ability of having the whole genome spotted on a single chip. It allows the biologist to inspect thousands of gene activities simultaneously. Machine learning approaches are suited and used to discovering the complex relationships between genes under controlled experimental conditions and classify microarray data by identifying a subset of informative genes embedded in a large data set that involves multiple classes and is infected with the high dimensionality noise. In this paper, a hybrid system integrates genetic algorithms and decision tree is proposed for genes expression analysis and prediction to their functionality for cancer classification. The learning capacity of decision trees used in the base learning systems is boosted by feature selection method. Experiments present preliminary results to demonstrate the capability of hybrid system to mine accurate classification rules for classifying prediction in comparable to traditional machine learning algorithms.
Going beyond sentences when applying tree kernels

We go beyond the level of individual sentences applying parse tree kernels to paragraphs. We build a set of extended trees for a paragraph of text from the individual parse trees for sentences and learn short texts such as search results and social profile postings to take advantage of additional discourse-related information. Extension is based on coreferences and rhetoric structure relations between the phrases in different sentences. We evaluate our approach, tracking relevance classification improvement for multi-sentence search task. The search problem is formulated as classification of search results into the classes of relevant and irrelevant, learning from the Bing search results. We compare performances of individual sentence kernels with the ones for extended parse trees and show that adding discourse information to learning data helps to improve classification results.
Compressive Sensing Time Reversal MIMO Radar: Joint Direction and Doppler Frequency Estimation

This letter applies compressive sensing (CS) and time reversal (TR) to multiple-input and multiple-output (MIMO) radars to derive a novel algorithm for joint estimation of the direction of arrival, direction of departure, and Doppler information on potential targets embedded in an environment with rich clutter. The CSTR/MIMO radar uses multipath constructively and offers significant performance gains over its CS/MIMO counterpart without TR in our Monte Carlo simulations.