Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbon-Source-Dependent Expression of thePalkB Promoter from the Pseudomonas oleovoransAlkane Degradation Pathway

ABSTRACT Pseudomonas oleovorans GPo1 can metabolize medium-chain-length alkanes by means of an enzymatic system whose induction is regulated by the AlkS protein. In the presence of alkanes, AlkS activates the expression of promoter PalkB, from which most of the genes of the pathway are transcribed. In addition, expression of the first enzyme of the pathway, alkane hydroxylase, is known to be influenced by the carbon source present in the growth medium, indicating the existence of an additional overimposed level of regulation associating expression of the alk genes with the metabolic status of the cell. Reporter strains bearingPalkB-lacZ transcriptional fusions were constructed to analyze the influence of the carbon source on induction of thePalkB promoter by a nonmetabolizable inducer. Expression was most efficient when cells grew at the expense of citrate, decreasing significantly when the carbon source was lactate or succinate. When cells were grown in Luria-Bertani rich medium,PalkB was strongly down-regulated. This effect was partially relieved when multiple copies of the gene coding for the AlkS activator were present and was not observed when the promoter was moved to Escherichia coli, a heterologous genetic background. Possible mechanisms responsible for PalkB regulation are discussed.
Joint Design of Energy-Efficient Clustering and Data Recovery for Wireless Sensor Networks

The two-layer network structure has been widely adopted in wireless sensor networks (WSNs) for managing sensor nodes. In such a structure, the low layer nodes communicate with their cluster head, followed by the cluster-head nodes communicating with the base station operating in either a one-hop or a multi-hop manner. The main focus of node-clustering algorithms is minimizing energy consumption due to strictly limited resources in WSNs. Also, WSNs are data intensive networks with the capability of providing users with accurate data. Unfortunately, data missing is common in WSNs. In this paper, we propose a novel joint design of sensor nodes clustering and data recovery, where the WSNs is organized in a two-layer manner with our developed clustering algorithm, and then, the missing data are recovered based on this two-layer structure. Furthermore, in the proposed clustering algorithm, we take both the energy-efficiency and data forecasting accuracy into consideration and investigate the tradeoff between them. This is based on the key observation that the high energy-efficiency of the network can be achieved by reducing the distances among the nodes in a cluster, while the accuracy of the forecasting results can be improved by increasing the correlation of the data stream among the nodes in a cluster. Simulation results demonstrate that our joint design outperforms the existing algorithms in terms of energy consumption and forecasting accuracy.
Empirical Evidence on Taxis' Route Choice Set Using GPS Data

In this paper, the route choice set of taxi trips is examined empirically, using the global positioning system (GPS) data of a taxi dispatch center in Shanghai. There are four main types of route choice set generation models, and the k-shortest models are the most widely used. Two types of k-shortest route choice sets are generated - one type has the routes with the shortest distances, and the other has the shortest travel times. The comparison between the route choice set and the observed route is presented in this paper. The results show that the k-shortest choice set generation model works well on taxi trips, and most of the taxi trips follow either the shortest or fastest routes.
Cheaper Reasoning with Ownership Types – Work in Progress –

We use ownership types to facilitate program verification. Namely, an assertion that has been established for a part of the heap which is unaffected by some execution will still hold after this execution. We use ownership and effects, and extend them to assertions to be able to make the judgement as to which executions do not affect which assertions. We describe the ideas in terms of an example, and outline the formal system.
Subgraph sparsification and nearly optimal ultrasparsifiers

We consider a variation of the spectral sparsification problem where we are required to keep a subgraph of the original graph. Formally, given a union of two weighted graphs G and W and an integer k, we are asked to find a k-edge weighted graph Wk such that G+Wk is a good spectral sparsifer of G+W. We will refer to this problem as the subgraph (spectral) sparsification. We present a nontrivial condition on G and W such that a good sparsifier exists and give a polynomial-time algorithm to find the sparsifer. As an application of our technique, we show that for each positive integer k, every n-vertex weighted graph has an (n-1+k)-edge spectral sparsifier with relative condition number at most n/k log n, ~O(log log n) where ~O() hides lower order terms. Our bound nearly settles a question left open by Spielman and Teng about ultrasparsifiers. We also present another application of our technique to spectral optimization in which the goal is to maximize the algebraic connectivity of a graph (e.g. turn it into an expander) with a limited number of edges.
Imaging , Diagnosis , Prognosis Pharmacokinetically Stabilized Cystine Knot Peptides That Bind Alpha-v-Beta-6 Integrin with Single-Digit Nanomolar Af fi nities for Detection of Pancreatic Cancer

Purpose:Detection of pancreatic cancer remains a high priority and effective diagnostic tools are needed for clinical applications. Many cancer cells overexpress integrin avb6, a cell surface receptor being evaluated as a novel clinical biomarker. Experimental Design: To validate this molecular target, several highly stable cystine knot peptides were engineered by directed evolution to bind specifically and with high affinity (3–6 nmol/L) to integrin avb6. The binders do not cross-react with related integrin avb5, integrin a5b1, or tumor-angiogenesis–associated integrin, avb3. Results: Positron emission tomography showed that these disulfide-stabilized peptides rapidly accumulate at tumors expressing integrin avb6. Clinically relevant tumor-to-muscle ratios of 7.7 2.4 to 11.3 3.0 were achieved within 1 hour after radiotracer injection. Minimization of off-target dosing was achieved by reformatting avb6-binding activities across various natural and pharmacokinetically stabilized cystine knot scaffolds with different amino acid content. We show that the primary sequence of a peptide scaffold directs its pharmacokinetics. Scaffolds with high arginine or glutamic acid content suffered high renal retention ofmore than 75% injected dose per gram (%ID/g). Substitution of these amino acids with renally cleared amino acids, notably serine, led to significant decreases in renal accumulation of less than 20%ID/g 1 hour postinjection (P < 0.05, n 1⁄4 3). Conclusions: We have engineered highly stable cystine knot peptides with potent and specific integrin avb6-binding activities for cancer detection. Pharmacokinetic engineering of scaffold primary sequence led to significant decreases in off-target radiotracer accumulation. Optimization of binding affinity, specificity, stability, and pharmacokinetics will facilitate translation of cystine knots for cancer molecular imaging. Clin Cancer Res; 18(3); 839–49. 2011 AACR.
Tourism Satellite Account for India

With the growing recognition of tourism as a source of employment generating growth in the country, improved understanding of what tourism is, its role in the economy and its relationship to other parts of the economy is important. The Tourism Satellite Account (TSA) is a new framework recently adopted by the United Nations Statistical Commission that provides an important platform towards forging improved understanding of the structure and role of tourism in the economy. Estimates using the TSA framework have the advantage of being credible, with the methodology now widely accepted, and internationally comparable. This study presents India's pilot TSA, in the form of various tables suggested by the World Tourism Ogranization (WTO). The tables present a disaggregated picture of various components of tourism in the country, as well as explaning the method of arriving at estimates of tourism sector's role in the economy. Using the TSA methodology, tourism value added is 2.78 percent of GDP in terms of direct impact, and 5.83 percent of GDP when indirect effects are also included. Similarly, tourism's share in total number of jobs is 4.59 percent, rising to 8.27 percent when indirect effects are also included.These estimates do not include the role of another growing segment of tourism in the country, namely (same) day tourism. The presentation in this report is divided into two parts. Since the TSA framework is new and not very widely familiar in India, the first part provides a brief introduction to the concepts and issues. In Part II, the methodology and the basic findings of the TSA for India are presented.
Communicating affect via flight path Exploring use of the Laban Effort System for designing affective locomotion paths

People and animals use various kinds of motion in a multitude of ways to communicate their ideas and affective state, such as their moods or emotions. Further, people attribute affect and personalities to movements of even non-life like entities based solely on the style of their motions, e.g., the locomotion style of a geometric shape (how it moves about) can be interpreted as being shy, aggressive, etc. We investigate how robots can leverage this locomotion-style communication channel for communication with people. Specifically, our work deals with designing stylistic flying-robot locomotion paths for communicating affective state. To author and unpack the parameters of affect-oriented flying-robot locomotion styles we employ the Laban Effort System, a standard method for interpreting human motion commonly used in the performing arts. This paper describes our adaption of the Laban Effort System to author motions for flying robots, and the results of a formal experiment that investigated how various Laban Effort System parameters influence people's perception of the resulting robotic motions. We summarize with a set of guidelines for aiding designers in using the Laban Effort System to author flying robot motions to elicit desired affective responses.
Link-based event detection in email communication networks

People's email communications can be modeled as graphs with vertices representing email accounts and edges representing email communications. Email communication data usually comes in as continuous data stream. Event detection aims to identify abnormal email communications that serve as analogs of real-world events imposed upon the data stream. The goal is to understand the communications behaviors of the subjects. The contents of emails are often not available or protected by privacy, which makes linkage information the only resource we can rely on. We propose a link-based event detection method that clusters vertices with similar communication patterns together and then, considers deviations from each vertex's individual profile, as well as its cluster profile. Experiments show that this method performs well on both Enron and our own email datasets.
Temporal and latitudinal variations of stratospheric trace gases - A critical comparison between theory and experiment

Global calculations of stratospheric HOx, Clx, and NOx are presented which include the effects of planetary albedo and diurnal and seasonal variations of the insolation. Comparisons are made with a wide range of atmospheric measurements at different latitudes and altitudes. Agreement between theory and observations is generally within a factor of 2. The theory appears to explain adequately the major features of latitude and seasonal distributions of NO2 and HNO3. The results indicate that mesospheric OH makes an appreciable contribution to the total OH column abundance and strongly suggest that nitrogen oxides exist principally in the form of HNO3 at high latitudes in winter. There are difficulties in reconciling OH, ClO, and O3 observations in the upper stratosphere.
A Comparison of Children Learning New Words from Robots , Tablets , & People

This work investigates young children’s perceptions of social robots in a learning context. Because social robots are a relatively new technology, direct comparison to more familiar means of learning could give us useful insights. Here, we compared the efficacy of three sources of information (human, robot, and tablet/iPad) with respect to children’s rapid learning of new words. Our results suggested that in this simple case, all three interlocutors served equally well as providers of new words. However, children strongly preferred learning with the robot, and considered it to be more like a person than like an iPad. Follow-up work will examine more complex learning tasks.
Human gait classification using combined HMM & SVM hybrid classifier

The paper describes the work on human gait recognition using Hidden Markov Model (HMM), Support Vector Machine (SVM) and Hybridized classifiers (developed using both HMM and SVM). Human gait data obtained from CASIA gait database were segmented to locate major human body part and generate corresponding stick view in order to extract gait features. A total of 25 features were obtained using the length of body parts and major joint angles along with other features and classified using HMM, SVM and Hybridized classifiers. The Hybridized classifier outperforms individual classifiers by 11.25% and 18.14% during training and testing respectively.
AtLAZY1 is a signaling component required for gravitropism of the Arabidopsis thaliana inflorescence.

The present study identified a family of six A. thaliana genes that share five limited regions of sequence similarity with LAZY1, a gene in Oryza sativa (rice) shown to participate in the early gravity signaling for shoot gravitropism. A T-DNA insertion into the Arabidopsis gene (At5g14090) most similar to LAZY1 increased the inflorescence branch angle to 81° from the wild type value of 42°. RNA interference lines and molecular rescue experiments confirmed the linkage between the branch-angle phenotype and the gene consequently named AtLAZY1. Time-resolved gravitropism measurements of atlazy1 hypocotyls and primary inflorescence stems showed a significantly reduced bending rate during the first hour of response. The subcellular localization of AtLAZY1 protein was investigated to determine if the nuclear localization predicted from the gene sequence was observable and important to its function in shoot gravity responses. AtLAZY1 fused to green fluorescent protein largely rescued the branch-angle phenotype of atlazy1, and was observed by confocal microscopy at the cell periphery and within the nucleus. Mutation of the nuclear localization signal prevented detectable levels of AtLAZY1 in the nucleus without affecting the ability of the gene to rescue the atlazy1 branch-angle phenotype. These results indicate that AtLAZY1 functions in gravity signaling during shoot gravitropism, being a functional ortholog of rice LAZY1. The nuclear pool of the protein appears to be unnecessary for this function, which instead relies on a pool that appears to reside at the cell periphery.
DC-to-DC converter with no magnetic elements and enhanced regulation

A switched-capacitor-based (SC) step-up DC converter is proposed. It contains no inductors and transformers, thus it can be realized in small size, exhibiting low weight and high power density. Two switched-capacitor circuits, operating in antiphase in each half-cycle, are used to control the energy flow from an unregulated voltage source to a regulated output. The capacitors are charged and discharged according to a designed sequence. To enhance the line and load regulation capability, in each half-cycle, each charging interval is split into two subintervals, which are followed by noncharging subintervals whose duration is dictated by the pulsewidth modulation (PWM) feedback circuit. The new converter is advantageous for applications in which significant line drops are likely to occur.
A Nucleic-Acid Hydrolyzing Single Chain Antibody Confers Resistance to DNA Virus Infection in HeLa Cells and C57BL/6 Mice

Viral protein neutralizing antibodies have been developed but they are limited only to the targeted virus and are often susceptible to antigenic drift. Here, we present an alternative strategy for creating virus-resistant cells and animals by ectopic expression of a nucleic acid hydrolyzing catalytic 3D8 single chain variable fragment (scFv), which has both DNase and RNase activities. HeLa cells (SCH7072) expressing 3D8 scFv acquired significant resistance to DNA viruses. Virus challenging with Herpes simplex virus (HSV) in 3D8 scFv transgenic cells and fluorescence resonance energy transfer (FRET) assay based on direct DNA cleavage analysis revealed that the induced resistance in HeLa cells was acquired by the nucleic acid hydrolyzing catalytic activity of 3D8 scFv. In addition, pseudorabies virus (PRV) infection in WT C57BL/6 mice was lethal, whereas transgenic mice (STG90) that expressed high levels of 3D8 scFv mRNA in liver, muscle, and brain showed a 56% survival rate 5 days after PRV intramuscular infection. The antiviral effects against DNA viruses conferred by 3D8 scFv expression in HeLa cells as well as an in vivo mouse system can be attributed to the nuclease activity that inhibits viral genome DNA replication in the nucleus and/or viral mRNA translation in the cytoplasm. Our results demonstrate that the nucleic-acid hydrolyzing activity of 3D8 scFv confers viral resistance to DNA viruses in vitro in HeLa cells and in an in vivo mouse system.
Predicting Initial Claims for Unemployment Benefits

One of the strongest leading indicators of economic activity is the number of people who file for unemployment benefits. Macroeconomists Robert Gordon and James Hamilton have recently examined the historical evidence. According to Hamilton's summary: ". in each of the last six recessions, the recovery began within 8 weeks of the peak in new unemployment claims. "In an earlier blog post, we suggested that Google Trends/Search Insights data could be useful in short term predictions of economic variables. Given the importance of initial claims as a macroeconomic predictor, we thought it would be useful to try to forecast this economic metric. The initial claims data is available from the Department of Labor, while the Google Trends data for relevant categories is available here.We applied the methodology outlined in our earlier paper, building a model to forecast initial claims using the past values of the time series, and then added the Google Trends variables to see how much they improved the forecast. We found a 15.74% reduction in mean absolute error for one-week ahead out, of sample forecasts. Most economists would consider this to be a significant boost. Details of our analysis may be found in this paper. The bottom line is that initial claims have been generally declining from their peak and that, so far at least, the Google query data is forecasting further short term declines. It would be good news indeed if this particular Google trend continues.
LRP-1: Functions, Signaling and Implications in Kidney and Other Diseases

Low-density lipoprotein (LDL)-related protein-1 (LRP-1) is a member of LDL receptor family that is implicated in lipoprotein metabolism and in the homeostasis of proteases and protease inhibitors. Expression of LRP-1 is ubiquitous. Up-regulation of LRP-1 has been reported in numerous human diseases. In addition to its function as a scavenger receptor for various ligands, LRP-1 has been shown to transduce multiple intracellular signal pathways including mitogen-activated protein kinase (MAPK), Akt, Rho, and the integrin signaling. LRP-1 signaling plays an important role in the regulation of diverse cellular process, such as cell proliferation, survival, motility, differentiation, and transdifferentiation, and thus participates in the pathogenesis of organ dysfunction and injury. In this review, we focus on the current understanding of LRP-1 signaling and its roles in the development and progression of kidney disease. The role and signaling of LRP-1 in the nervous and cardiovascular systems, as well as in carcinogenesis, are also briefly discussed.
A Review Paper on Fingerprint Image Enhancement with Different Methods

: Image enhancement plays an important role in Fingerprint Recognition System. In this paper, we study the different techniques of enhancement of a fingerprint image in which have been used in previous work. There are so many techniques for enhancement which uses so many different image processing approaches. During study some approaches are found in spatial domain, frequency domain, some are neural network based and some are fuzzy based. Most of the fingerprint techniques use contextual filters or multi-resolution filters whose parameters depends on the local ridge frequency and orientation . The main drawback of these methods lie in the fact that false estimate of local ridge direction will lead to poor enhancement. But the estimate of local ridge directions is unreliable in the areas corrupted by noise where enhancement is most needed.
Genome-Wide Expression Analysis of Burkholderia pseudomallei Infection ina Hamster Model of Acute Melioidosis

ABSTRACT Burkholderia pseudomallei is the causative agent of melioidosis and represents a potential bioterrorism threat. In the current studies we have examined gene expression in B. pseudomallei in an animal model of acute melioidosis using whole-genome microarrays. Gene expression profiles were generated by comparing transcriptional levels of B. pseudomallei-expressed genes in infected hamster organs including liver, lung, and spleen following intraperitoneal and intranasal routes of infection to those from bacteria grown in vitro. Differentially expressed genes were similar in infected livers irrespective of the route of infection. Reduced expression of a number of housekeeping genes suggested a lower bacterial growth rate during infection. Energy production during growth in vivo involved specific biochemical pathways such as isomerization of 3-phosphoglycerate, catabolism of d-glucosamine and inositol, and biosynthesis of particular amino acids. In addition, the induction of genes known to be involved in oxidative phosphorylation including ubiquinol oxidase, ferredoxin oxidoreductase, and formate dehydrogenase enzymes suggested the use of alternative pathways for energy production, while the expression of genes coding for ATP-synthase and NADH-dehydrogenase enzymes was reduced. Our studies have identified differentially expressed genes which include potential virulence genes such as those for a putative phospholipase C and a putative two-component regulatory system, and they have also provided a better understanding of bacterial metabolism in response to the host environment during acute melioidosis.