Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding and addressing the impact of wiring congestion during technology mapping

Traditionally, interconnect effects are taken into account duringlogic synthesis via wireload models, but their ineffectiveness forDSM technologies has been demonstrated and various physicalsynthesis approaches have been spawned to address the problem. Ofparticular interest is that logic block size is no longer dictatedexclusively by total cell area, yet synthesis optimizationobjectives are aimed specifically at minimizing the number and sizeof cells. Methodologies that incorporate congestion within thelogic synthesis objective function have been proposed in[9][10][11] and [15]; however, as we will demonstrate, predictingthe true congestion prior to layout is not possible, and theefficacy of any approach can only be evaluated after routing iscompleted within the fixed die size. In this paper we propose apractical, complete methodology which first performscongestion-aware technology mapping using a global weighting factorfor the cost function [15], and then applies incremental localizedunmapping and remapping on congested areas. This complete approachaddresses the problem that one global factor is not ideally suitedfor all regions of the designs. Most importantly, through theapplication of this methodology to industrial examples we will showthat any attempt at a purely top-down single-pass congestion-awaretechnology mapping is merely wishful thinking.
Symbolic derivation of dynamic equations of motion for robot manipulators using Piogram symbolic method

An algorithm for both manual and automatic derivation of dynamic models of robotic manipulators using the Piogram symbolic method is presented. A program is also developed based on the Newton-Euler formalism by the Piogram symbolic representation method, which is applicable to manipulators of any degree of freedom. Two examples are given to illustrate how to use this program for dynamic equation generation. It is shown that the method has the advantage of simplifying the manipulation process, and thus a large amount of memory space and computing time when the method is implemented in a computer program. >
IAR3 Encodes an Auxin Conjugate Hydrolase from Arabidopsis

Amide-linked conjugates of indole-3-acetic acid (IAA) are putative storage or inactivation forms of the growth hormone auxin. Here, we describe the Arabidopsis iar3 mutant that displays reduced sensitivity to IAA–Ala. IAR3 is a member of a family of Arabidopsis genes related to the previously isolated ILR1 gene, which encodes an IAA–amino acid hydrolase selective for IAA–Leu and IAA–Phe. IAR3 and the very similar ILL5 gene are closely linked on chromosome 1 and comprise a subfamily of the six Arabidopsis IAA-conjugate hydrolases. The purified IAR3 enzyme hydrolyzes IAA–Ala in vitro. iar3 ilr1 double mutants are more resistant than either single mutant to IAA–amino acid conjugates, and plants overexpressing IAR3 or ILR1 are more sensitive than is the wild type to certain IAA–amino acid conjugates, reflecting the overlapping substrate specificities of the corresponding enzymes. The IAR3 gene is expressed most strongly in roots, stems, and flowers, suggesting roles for IAA-conjugate hydrolysis in those tissues.
Modulation of the P1 Plasmid Partition Protein ParA by ATP, ADP, and P1 ParB*

ParA is an essential P1 plasmid partition protein. It represses transcription of the par genes (parA and parB) and is also required for a second, as yet undefined step in partition. ParA is a ParB-stimulated ATPase that binds to a specific DNA site in the parpromoter region. ATP binding and hydrolysis by ParA affect ParA activities in vitro. ATP and ADP binding stimulate ParA DNA binding and dimerization; however, ATP hydrolysis has a negative effect on DNA binding. Our current experiments reveal that ATP binding and hydrolysis affect ParA conformation and ParA sensitivity to ParB. Nucleotide binding assays show that ParA binds ATP better than ADP (K d values of 33 and 50 μm, respectively). Interaction with these nucleotides as well as ATP hydrolysis by ParA alter ParA conformation as established by CD and ParA sensitivity to heat denaturation. Finally, we show that ParB stimulates ParA DNA binding. This stimulation requires ATP hydrolysisin vitro, suggesting that one role for ATP hydrolysisin vivo is to make ParA repressor sensitive to ParB. Our observations lead to the suggestion that ATP binding and hydrolysis have separable roles in ParA repressor function and perhaps in ParA partition functions as well.
Graph-based collective classification for tweets

In this paper, we address the problem of classifying tweets into topical categories. Because of the short, noisy and ambiguous nature of tweets, we propose to collectively conduct the classification by exploiting the context information (i.e. related tweets) other than individually as in conventional text classification methods. In particular, we augment the content-based representation of text with tweets sharing same #hashtag or URL, which results in a tweet graph. We then formulate the tweet classification task under a graph optimization framework. We investigate three popular approaches, namely, Loopy Belief Propagation (LBP), Relaxation Labeling (RL), and Iterative Classification Algorithm (ICA). Extensive experiment results show that the graph-based tweet classification approach remarkably improves the performance, while the ICA model with relationship of sharing the same #hashtag gives the best result on separate tweet graph.
An improved test for Haemophilus influenzae precipitins in the serum of patients with chronic respiratory disease

The detection of antibacterial precipitins in the serum of patients with chronic lower respiratory infections has been shown to be of great value in the assessment of pathogenicity of the corresponding bacterial species in the sputum. The test used hitherto, however, is time-consuming and cumbersome owing to the need to distinguish, by immunoelectrophoresis, between antibodies specific to the organism in question and those which react with antigens common to various Gram-negative species. A method has now been devised for the preparation of an extract of Haemophilus influenzae containing species-specific antigens only. Use of this extract obviates the need for immuno-electrophoresis and improves the sensitivity of the test.
Near optimal linear quadratic regulator for a singularly perturbed linear stochastic system with multiplicative white noise perturbations and Markovian jumping

We study the optimal control of a class of singularly perturbed linear stochastic systems (SPLSS) with Markovian jumping parameters. After establishing an asymptotic structure for the stabilizing solution of the coupled stochastic algebraic Riccati equations (CSAREs), a parameter-independent composite controller is derived. Furthermore, the cost degradation in a reduced-order controller is also discussed.
Redesign of retrovirus packaging cell lines to avoid recombination leading to helper virus production

Retrovirus vectors can be made in the absence of helper virus by using retrovirus packaging cell lines. Helper-free virus is critical for a variety of gene transfer studies. The most useful packaging cell lines contain helper virus DNA from which the signal required for packaging of the viral RNA genome into virions has been deleted. However, we showed that the ability to package virus is conferred at very low frequency to cells infected with virus from these packaging cell lines, presumably by low-frequency transmission of the deleted virus genome. In addition, these packaging cell lines can interact with some retroviral vectors to yield replication-competent virus. We constructed packaging cell lines containing helper virus DNA that had several alterations in addition to deletion of the packaging signal. The new packaging cells retained the useful features of previously available lines but did not yield helper virus after introduction of any of the vectors tested, and transfer of the packaging function was not detected.
Effects of Group Experiential Cognitive Therapy for the Treatment of Panic Disorder with Agoraphobia

A treatment protocol, called experiential cognitive therapy (ExCT), was developed. It integrated traditional cognitive behavior therapy (CBT) with virtual reality exposure for the treatment of panic disorder with agoraphobia (PDA). The objective of this study was to test the efficacy of short-term (four sessions) ExCT compared with a traditional 12-session panic control program (PCP) for the treatment of PDA. Forty patients diagnosed as having PDA by the diagnostic criteria of DSM-IV were randomly assigned to ExCT and PCP groups of 20 patients each. The treatment effects were measured with self-report questionnaires, including the BDI, STAI, ASI, PBQ, ACQ, and BSQ. The authors also assessed high end-state functioning (HES), including the success rate of stopping or reducing medication at post-treatment and 6-month follow-up. In all ratings, both ExCT and PCP groups showed significant improvement post-treatment compared with pre-treatment scores. There were no significant differences between the two treatment groups in HES and medication discontinuation at post-treatment, but there was a significant difference in medication discontinuation at 6-month follow-up. These results suggested that although short-term effectiveness of ExCT might be comparable to the effectiveness of PCP, long-term effectiveness of ExCT might be relatively inferior to the effectiveness of PCP.
11β-Hydroxyprogesterone Acts as a Mineralocorticoid Agonist in Stimulating Na+ Absorption in Mammalian Principal Cortical Collecting Duct Cells

The binding of mineralocorticoid hormones to the mineralocorticoid receptor is the first step in a cascade of events leading to the stimulation of Na + reabsorption by renal cortical collecting duct (CCD) principal cells. The agonist properties of mineralocorticoid hormones are linked to contacts between their 21-hydroxyl group and Asn770, a residue of the ligand-binding domain of the human mineralocorticoid receptor (hMR). Here, we investigate whether the presence of a hydroxyl group at position 11, 17, or 20 could also alter the activity of progesterone (P), a mineralocorticoid antagonist without the 21-hydroxyl group. Both 17α-hydroxyprogesterone (17OHP) and 20α-hydroxyprogesterone (20OHP) antagonized the aldosterone-induced trans -activation activity (IC 50 : 17OHP, 10 −7 M; 20OHP, 10 −8 M) of the hMR transiently expressed in COS-7 cells lacking steroid receptors. In cultured mouse mpkCCD cl4 principal cells, 17OHP and 20OHP also prevented the aldosterone-stimulated amiloride-sensitive component of the short-circuit current (Ams I sc ), reflecting Na + absorption mediated by the epithelial Na + channel (ENaC). In contrast, 11β-hydroxyprogesterone (11OHP) activated the transiently expressed hMR in COS-7 cells in a dose-dependent manner (ED 50 : 10 −8 M) and, like aldosterone, stimulated Ams I sc in mpkCCD cl4 cells. Docking 11OHP within the hMR-ligand-binding domain homology model revealed that the agonist activity of 11OHP is caused by contacts between its 11β-hydroxyl group and Asn770. Furthermore, 11OHP was unable to activate the mutant hMR/N770A, in which Ala is substituted for Asn at position 770. These findings demonstrate that in the absence of the 21-hydroxyl group, the 11β-hydroxyl group can produce the contact with the hMR-Asn770 required for the hMR activation leading to stimulated Na + absorption.
BRAF in Papillary Thyroid Carcinoma

Novel genetic findings about papillary thyroid carcinoma identify BRAF gene as a subject of great interest. Involvement of BRAF gene in pathogenesis of PTC, diagnostic value and the putative prognostic significance of its T1799A mutation are summarized in this article. Furthermore, a particular attention is focused to the role of pre-operative detection of BRAF mutation in the FNAB specimens of thyroid nodules and to the use of this gene as target for an effective cancer therapy.
An Emotion Affected Action Selection Mechanism for Multiple Virtual Agents

This paper presents an action selection mechanism, for virtual flocking animals, inspired by ethology and theories of emotion. We investigate how emotions, in this case fear, affect behaviour, considering deer and sheep as exemplary flocking mammals. The paper also describes and applies a mechanism to measure different types of flocking, using singular values and entropy to compute complexity. Results show that emotion can be used to regulate two competing and vital behaviours like those seen in herding animals: the group behaviour (herding) and the individual behaviour (grazing), thus demonstrating that emotion is a functional organiser of group behaviour
Fgf signaling instructs position-dependent growth rate during zebrafish fin regeneration

During appendage regeneration in urodeles and teleosts, tissue replacement is precisely regulated such that only the appropriate structures are recovered, a phenomenon referred to as positional memory. It is believed that there exists, or is quickly established after amputation, a dynamic gradient of positional information along the proximodistal (PD) axis of the appendage that assigns region-specific instructions to injured tissue. These instructions specify the amount of tissue to regenerate, as well as the rate at which regenerative growth is to occur. A striking theme among many species is that the rate of regeneration is more rapid in proximally amputated appendages compared with distal amputations. However, the underlying molecular regulation is unclear. Here, we identify position-dependent differences in the rate of growth during zebrafish caudal fin regeneration. These growth rates correlate with position-dependent differences in blastemal length, mitotic index and expression of the Fgf target genes mkp3, sef and spry4. To address whether PD differences in amounts of Fgf signaling are responsible for position-dependent blastemal function, we have generated transgenic fish in which Fgf receptor activity can be experimentally manipulated. We find that the level of Fgf signaling exhibits strict control over target gene expression, blastemal proliferation and regenerative growth rate. Our results demonstrate that Fgf signaling defines position-dependent blastemal properties and growth rates for the regenerating zebrafish appendage.
Egg consumption and risk of coronary heart disease and stroke: dose-response meta-analysis of prospective cohort studies

Objective To investigate and quantify the potential dose-response association between egg consumption and risk of coronary heart disease and stroke. Design Dose-response meta-analysis of prospective cohort studies. Data sources PubMed and Embase prior to June 2012 and references of relevant original papers and review articles. Eligibility criteria for selecting studies Prospective cohort studies with relative risks and 95% confidence intervals of coronary heart disease or stroke for three or more categories of egg consumption. Results Eight articles with 17 reports (nine for coronary heart disease, eight for stroke) were eligible for inclusion in the meta-analysis (3 081 269 person years and 5847 incident cases for coronary heart disease, and 4 148 095 person years and 7579 incident cases for stroke). No evidence of a curve linear association was seen between egg consumption and risk of coronary heart disease or stroke (P=0.67 and P=0.27 for non-linearity, respectively). The summary relative risk of coronary heart disease for an increase of one egg consumed per day was 0.99 (95% confidence interval 0.85 to 1.15; P=0.88 for linear trend) without heterogeneity among studies (P=0.97, I2=0%). For stroke, the combined relative risk for an increase of one egg consumed per day was 0.91 (0.81 to 1.02; P=0.10 for linear trend) without heterogeneity among studies (P=0.46, I2=0%). In a subgroup analysis of diabetic populations, the relative risk of coronary heart disease comparing the highest with the lowest egg consumption was 1.54 (1.14 to 2.09; P=0.01). In addition, people with higher egg consumption had a 25% (0.57 to 0.99; P=0.04) lower risk of developing hemorrhagic stroke. Conclusions Higher consumption of eggs (up to one egg per day) is not associated with increased risk of coronary heart disease or stroke. The increased risk of coronary heart disease among diabetic patients and reduced risk of hemorrhagic stroke associated with higher egg consumption in subgroup analyses warrant further studies.
A hardware time manager implementation for the Xenomai real-time kernel of embedded Linux

Nowadays, the use of embedded operating systems in different embedded projects is subject to a tremendous growth. Embedded Linux is becoming one of those most popular EOSs due to its modularity, efficiency, reliability, and cost. One way to make it hard real-time is to include a real-time kernel like Xenomai. One of the key characteristics of a Real-Time Operating System (RTOS) is its ability to meet execution time deadlines deterministically. So, the more precise and flexible the time management can be, the better it can handle efficiently the determinism for different embedded applications. RTOS time precision is characterized by a specific periodic interrupt service controlled by a software time manager. The smaller the period of the interrupt, the better the precision of the RTOS, the more it overloads the CPU, and though reduces the overall efficiency of the RTOS. In this paper, we propose to drastically reduce these overheads by migrating the time management service of Xenomai into a configurable hardware component to relieve the CPU. The hardware component is implemented in a Field Programmable Gate Array coupled to the CPU. This work was achieved in a Master degree project where students could apprehend many fields of embedded systems: RTOS programming, hardware design, performance evaluation, etc.
Efficient relational keyword search system

Keyword-based search is popularized in Information Retrieval (IR) communities and Internet search engines on the Web. Nowadays, social networking, micro-blogging, and other data-driven websites store large amounts of information in relational databases. But searching in databases users need to know a database schema and a query language. The usability of Database is severely limited unless easier ways to access databases are developed. While traditional database management systems offer powerful query languages, they do not allow keyword-based search. Keyword search techniques on the Web cannot directly be applied to databases because the data on the Internet and database are in different forms. Therefore, we propose a search system for relational data with our proposed methods that can support keyword-based search over relational database. The main contributions of this system compose of the direct indexing of records in database, the schema based queries for relevant answers, and ranking of the relevant answer sets. As long as the database table records can be extended, this system can be easily extendable for further searching records from tables.
A fuzzy logic CC-PWM three-phase AC/DC converter

The paper deals with a PWM AC/DC converter based on the fuzzy control of the output capacitor charge/discharge process. The proposed control system satisfies sinusoidal input currents, unity power factor and constant output voltage by means of an optimised management of the energy exchanged between the AC supply and the output capacitor. The simulations show a very good dynamic behaviour of the system at both start-up and load current step variations.
Assessment of Body Volume Using Three‐Dimensional Photonic Scanning

Abstract: Measurement of body volume (BV) can be used to estimate body composition using two‐ or multicomponent models. The traditional approach, underwater weighing (UWW), is awkward and unsuitable for many subjects. A newer alternative, whole body air displacement plethysmography (ADP), is less demanding but still unsuitable for young children, who may not remain still during the measurement. We have, therefore, considered whether a novel approach, three‐dimensional photonic scanning, is a viable alternative. Duplicate measurements of body volume were obtained in 22 adults (11 of each sex; mean [SD] BMI, 21.8 [2.5] kg/m2) by UWW, ADP, and a Hamamatsu Bodyline Scanner (HBS) (Hamamatsu, Japan). Subjects wore a tight‐fitting swimming costume for all three measurements, which were performed within one day of each other. Scans lasted 10 seconds, with the subject standing in a predefined position. The body surface skin was reconstructed using a B‐spline‐fitting model. In UWW, lung volume (LV) was measured simultaneously with underwater weight. In ADP and HBS, LV was predicted from weight and height. Results were compared using correlation and Bland and Altman analysis. Correlation analysis indicated that the scanner successfully ranked subjects in terms of BV. However, Bland and Altman analysis demonstrated that, relative to both UWW and ADP, HBS measured BV without bias but with limits of agreement between individuals of >2 liters, equivalent to approximately 20% fat. Scan precision was 0.57 liters, or 4.1% fat. Although HBS cannot yet measure BV with sufficient accuracy to predict fatness, much of the error is probably due to difficulties in standardizing LV during the scan. Simultaneous measurement of LV with volume by HBS is expected to improve limits of agreement substantially. Occlusion is also an important source of error. The method offers many advantages over alternative techniques, because the measurement is brief, noninvasive, and suitable for repeat measurements.
Whole‐exome sequencing identifies a homozygous donor splice‐site mutation in STAG3 that causes primary ovarian insufficiency

Primary ovarian insufficiency (POI) is the depletion or loss of normal ovarian function, which cause infertility in women before the age of 40 years. Two homozygous germline truncation mutations in STAG3 gene had been reported to causes POI in consanguineous families. Here, we aimed to identify the genetic cause of POI in 2 affected sisters manifested with primary amenorrhea and partial development of secondary sexual characters with normal range of height of a consanguineous Han Chinese family. Whole‐exome and Sanger sequencing identified a homozygous donor splice‐site mutation (NM_012447.2: c.1573+5G>A) in the STAG3 gene. RT‐PCR revealed that the mutation causes loss of wild‐type donor splice‐site which leads to aberrant splicing of STAG3 mRNA and consecutive formation of STAG3 alternative transcript (p.Leu490Thrfs*10) . This is the first report of splice‐site mutation of STAG3 gene causes POI in 2 Han Chinese patients.