Miracle-dz/UniFAR-FTUs huggingface dataset:
A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner

RNA polymerase II (pol II) is required for the transcription of all protein-coding genes and as such represents a major enzyme whose activity is tightly regulated. Transcriptional initiation therefore requires numerous general transcriptional factors and cofactors that associate with pol II at the core promoter to form a pre-initiation complex. Transcription factor IIA (TFIIA) is a general cofactor that binds TFIID and stabilizes the TFIID–DNA complex during transcription initiation. Previous studies showed that TFIIA can make contact with the DNA sequence upstream or downstream of the TATA box, and that the region bound by TFIIA could overlap with the elements recognized by another factor, TFIIB, at adenovirus major late core promoter. Whether core promoters contain a DNA motif recognized by TFIIA remains unknown. Here we have identified a core promoter element upstream of the TATA box that is recognized by TFIIA. A search of the human promoter database revealed that many natural promoters contain a TFIIA recognition element (IIARE). We show that the IIARE enhances TFIIA-promoter binding and enhances the activity of TATA-containing promoters, but represses or activates promoters that lack a TATA box. Chromatin immunoprecipitation assays revealed that the IIARE activates transcription by increasing the recruitment of pol II, TFIIA, TAF4, and P300 at TATA-dependent promoters. These findings extend our understanding of the role of TFIIA in transcription, and provide new insights into the regulatory mechanism of core promoter elements in gene transcription by pol II.
Disturbance rejection control with H∞ optimized observer for vibration suppression of piezoelectric smart structures

In this paper, a disturbance rejection (DR) control with H∞ optimized observer is developed for vibration suppression of smart structures considering model uncertainties and measurement noise. An electro-mechanically coupled dynamic finite element (FE) model of piezoelectric smart structures is firstly built for control design. Based on the dynamic FE model, the H∞ optimized observer is designed with a dynamic feedback gain which is calculated by H∞ mixed sensitivity optimization. Expected response speed and robustness to model uncertainties and measurement noise are obtained by configuring proper weighting functions. In the closed-loop system, estimated disturbances and state variables are fed back through a conventional DR controller to counteract disturbances and stabilize the system. In order to validate the DR control with H∞ optimized observer, vibration suppression simulations of a piezoelectric smart beam are implemented in the absence and presence of model uncertainties and measurement noise, respectively. Furthermore, DR control with generalized proportional integral observer and DR control with high-gain proportional integral observer are added for comparison. Results show that excellent vibration suppression performance and better robustness to model uncertainties and measurement noise are achieved by the DR control with H∞ optimized observer.
Enhanced iNOS Expression in Leukocytes and Circulating Endothelial Cells Is Associated with the Progression of Coronary Artery Lesions in Acute Kawasaki Disease

Nitric oxide (NO) serves many vasoprotective roles, but the massive release of NO causes arterial wall degeneration. We investigated whether enhanced nitric oxide synthase (iNOS) expression in peripheral blood leukocytes and circulating endothelial cells mirrors the progression of coronary arterial lesions in 55 children with acute Kawasaki disease (KD), including 24 with and 31 without coronary artery lesions (CAL). Patients were treated with i.v. gamma-globulin at the time of diagnosis and blood samples were collected before and after treatment. The cellular origin of NO synthesis was determined by flow cytometric analysis of iNOS expression in peripheral blood, and by immunohistochemical analysis of circulating endothelial cells and coronary arteries. iNOS expression in neutrophils peaked at the time of diagnosis, but did not peak in monocytes until 2 wk post onset of disease. Levels were significantly higher in both cell types in patients with CAL (p = 0.001 and p = 0.035, respectively). In addition, the number of circulating endothelial cells and levels of iNOS expression were higher in patients with CAL (p = 0.011 and p = 0.012, respectively). Immunohistochemical analysis of the coronary arteries from three patients with acute KD revealed iNOS immunoreactivity in endothelial cells, as well as infiltrating monocytes/macrophages in the aneurysms. We conclude that the expression of iNOS in peripheral blood leukocytes, as well as circulating endothelial cells, correlates with the severity of coronary arterial wall injury and the progression of CAL in patients with acute KD.
Tachyon Dynamics and the Effective Action Approximation

Recently effective actions have been extensively used to describe tachyon condensation in string theory. While the various effective actions which have appeared in the literature have very similar properties for static configurations, they differ for time-dependent tachyons. In this paper we discuss general properties of non-linear effective Lagrangians which are first order in derivatives. In particular we show that some observed properties, such as asymptotically vanishing pressure, are rather generic features, although the quantative features differ. On the other hand we argue that certain features of marginal tachyon profiles are beyond the reach of any first order Lagrangian description. We also point out that an effective action, proposed earlier, captures the dynamics of tachyons well.
A comparison of four methods for cognitive load measurement

Recognizing users' cognitive load during tasks is among the most important considerations for adaptive automation and interface evaluation. This paper compares four methods of measuring user cognitive load, that is, subjective rating of task difficulty, task completion time, performance accuracy and eye activity based physiological measurement. In order to be practically useful, the measurement should be sensitive to task difficulty variation and accurately predict user cognitive load. In this study, we examined the sensitivity and accuracy of these measures for five levels of cognitive load. ANOVA tests and Gaussian mixture model classification results show that subjective rating of task difficulty is the most effective measure, meanwhile eye activity based measure is as sensitive and accurate as using task completion time to classify two or more cognitive load levels, but has the relative advantage of being a real time measure and not requiring a specific action.
Genetic Analysis and QTL Mapping of Seed Coat Color in Sesame (Sesamum indicum L.)

Seed coat color is an important agronomic trait in sesame, as it is associated with seed biochemical properties, antioxidant content and activity and even disease resistance of sesame. Here, using a high-density linkage map, we analyzed genetic segregation and quantitative trait loci (QTL) for sesame seed coat color in six generations (P1, P2, F1, BC1, BC2 and F2). Results showed that two major genes with additive-dominant-epistatic effects and polygenes with additive-dominant-epistatic effects were responsible for controlling the seed coat color trait. Average heritability of the major genes in the BC1, BC2 and F2 populations was 89.30%, 24.00%, and 91.11% respectively, while the heritability of polygenes was low in the BC1 (5.43%), in BC2 (0.00%) and in F2 (0.89%) populations. A high-density map was constructed using 724 polymorphic markers. 653 SSR, AFLP and RSAMPL loci were anchored in 14 linkage groups (LG) spanning a total of 1,216.00 cM. The average length of each LG was 86.86 cM and the marker density was 1.86 cM per marker interval. Four QTLs for seed coat color, QTL1-1, QTL11-1, QTL11-2 and QTL13-1, whose heritability ranged from 59.33%–69.89%, were detected in F3 populations using CIM and MCIM methods. Alleles at all QTLs from the black-seeded parent tended to increase the seed coat color. Results from QTLs mapping and classical genetic analysis among the P1, P2, F1, BC1, BC2 and F2 populations were comparatively consistent. This first QTL analysis and high-density genetic linkage map for sesame provided a good foundation for further research on sesame genetics and molecular marker-assisted selection (MAS).
Wearable Sensors Integrated with Virtual Reality: A Self-Guided Healthcare System Measuring Shoulder Joint Mobility for Frozen Shoulder

Frozen shoulder is a common clinical shoulder condition. Measuring the degree of shoulder joint movement is crucial to the rehabilitation process. Such measurements can be used to evaluate the severity of patients' condition, establish rehabilitation goals and appropriate activity difficulty levels, and understand the effects of rehabilitation. Currently, measurements of the shoulder joint movement degree are typically conducted by therapists using a protractor. However, along with the growth of telerehabilitation, measuring the shoulder joint mobility on patients' own at home will be needed. In this study, wireless inertial sensors were combined with the virtual reality interactive technology to provide an innovative shoulder joint mobility self-measurement system that can enable patients to measure their performance of four shoulder joint movements on their own at home. Pilot clinical trials were conducted with 25 patients to confirm the feasibility of the system. In addition, the results of correlation and differential analyses compared with the results of traditional measurement methods exhibited a high correlation, verifying the accuracy of the proposed system. Moreover, according to interviews with patients, they are confident in their ability to measure shoulder joint mobility themselves.
Frequency splitting analysis of magnetically-coupled resonant wireless power transfer

Based on four-coil magnetically-coupled resonant wireless power transfer, this paper demonstrates, explains, and analyzes the frequency splitting phenomena with the circuit theory. Firstly, we build the complete and simplified models to describe the whole system. Then the frequency splitting phenomena are displayed and further explained by measuring and describing the amplitude-frequency and phase-frequency characteristics of the input impedance. Three related factors, i.e. the source internal resistance, the mutual inductance of the source coil and the sending coil, and the mutual inductance of the load coil and the receiving coil, are studied. Theoretical calculations and experimental results provide a sound basis for the explanation.
Evolution of blood lead levels in urban French population (1979-1995).

BACKGROUND The aim of the Council Directive of 29 March 1977 of the European Union was to measure non-occupational lead exposure levels in the general adult populations of European countries through biological monitoring. In France, such measurements were carried out during 1979 and 1982 in eight metropolitan areas (having more than 500 000 inhabitants), a period during which the lead content of petrol was decreased. The aim of this study conduct in 1995 was to evaluate the exposure trend to lead. METHODS In 1995 this measurement was repeated, only in the three largest urban areas (Paris, Marseilles and Lyons). The same sampling method used in the first two campaigns was retained to ensure that the results of 1995 could be compared with those from 1979 and 1982. RESULTS In these three metropolitan areas, the average blood lead levels decreased by the order of 60 microg/l between the beginning of the 1980's and 1995. This represents a fall of more than 50%. CONCLUSIONS Certainly car pollution is not the only vector of dissemination of lead in the centre of urban zones, but it is there that the most sustained efforts at eradication have been made. The improvement we have observed is probably due to the policy of eliminating lead from petrol. In conclusion, the blood lead levels in French urban populations seem to have greatly decreased from those of the early 1980s.
Technical Cashew Nutshell Liquid in Diets of Growing Meat-Type Quails

12/May/2018 Approved: 16/October/2018 ABStRACt The aim of this study was to evaluate the inclusion of technical cashew nutshell liquid (TCNSL) in European quails ( Coturnix coturnix coturnix ) diets from 1 to 35 days of age on the performance, carcass traits, and development of the digestive organs. 575 quails were distributed in a completely randomized design with five treatments (0%, 0.25%, 0.50%, 0.75%, and 1.00% TCNSL), five replicates, and 23 birds per experimental unit. Live performance was evaluated by weight gain, average feed intake, and feed to conversion ratio. The relative weight of the digestive organs (proventriculus, gizzard, pancreas, liver, small intestine, and large intestine), length of the small and large intestine, and carcass and parts yield (breast, wing, and leg) were determined at the end of the experimental period (35 days). The supplementation of quail diets with TCNSL did not influence live performance or carcass and parts yields. The relative weights of the proventriculus, gizzard, pancreas, small intestine, and large intestine, and the length of the small intestine and large intestine were not affected by the dietary inclusion of TCNSL. However, TCNSL supplementation had a quadratic effect ( p< 0.05) on liver relative weight, with the lowest relative weight predicted at 0.33% TCNSL. Quails fed 1% TCNSL showed higher liver relative weight compared with those fed the TCNSL-free diets. The dietary inclusion of up to 1% TCNSL did not influence the performance, carcass traits, or development of the digestive organs
Focusing of General Bistatic SAR Configuration Data With 2-D Inverse Scaled FFT

This paper presents a bistatic focusing solution for the general case, when transmitter and receiver trajectories move along nonparallel trajectories with different velocities. The approach in this paper is based on the point target reference spectrum for an arbitrary bistatic configuration, derived from our previous publications. Based on various simulations, the validity of the formula for both airborne and spaceborne configurations is demonstrated. Focusing for special bistatic azimuth time-invariant configurations, "tandem" and "translationally invariant" constellations are accomplished. All focusing algorithms have been developed in an interactive data language and verified with adequate simulation results. The bistatic algorithm was further successfully applied to real bistatic data acquired by the German Research Establishment for Applied Natural Sciences' PAMIR and AER-II synthetic aperture radar systems. Processing in the general case turns out to be additionally truly azimuth time variant. It is solved by implementing a novel two-dimensional inverse-scaled fast Fourier transform algorithm
Using Text Similarity to Detect Social Interactions not Captured by Formal Reply Mechanisms

In modeling social interaction online, it is important to understand when people are reacting to each other. Many systems have explicit indicators of replies, such as threading in discussion forums or replies and retweets in Twitter. However, it is likely these explicit indicators capture only part of people's reactions to each other, thus, computational social science approaches that use them to infer relationships or influence are likely to miss the mark. This paper explores the problem of detecting non-explicit responses, presenting a new approach that uses tf-idf similarity between a user's own tweets and recent tweets by people they follow. Based on a month's worth of posting data from 449 ego networks in Twitter, this method demonstrates that it is likely that at least 11% of reactions are not captured by the explicit reply and retweet mechanisms. Further, these uncaptured reactions are not evenly distributed between users: some users, who create replies and retweets without using the official interface mechanisms, are much more responsive to followees than they appear. This suggests that detecting non-explicit responses is an important consideration in mitigating biases and building more accurate models when using these markers to study social interaction and information diffusion.
Reli: Hardware/software Checkpoint and Recovery scheme for embedded processors

Checkpoint and Recovery (CR) allows computer systems to operate correctly even when compromised by transient faults. While many software systems and hardware systems for CR do exist, they are usually either too large, require major modifications to the software, too slow, or require extensive modifications to the caching schemes. In this paper, we propose a novel error-recovery management scheme, which is based upon re-engineering the instruction set. We take the native instruction set of the processor and enhance the microinstructions with additional micro-operations which enable checkpointing. The recovery mechanism is implemented by three custom instructions, which recover the registers which were changed, the data memory values which were changed and the special registers (PC, status registers etc.) which were changed. Our checkpointing storage is changed according to the benchmark executed. Results show that our method degrades performance by just 1.45% under fault free conditions, and incurs area overhead of 45% on average and 79% in the worst case. The recovery takes just 62 clock cycles (worst case) in the examples which we examined.
A model for reticular dysgenesis shows impaired sensory organ development and hair cell regeneration linked to cellular stress

ABSTRACT Mutations in the gene AK2 are responsible for reticular dysgenesis (RD), a rare and severe form of primary immunodeficiency in children. RD patients have a severely shortened life expectancy and without treatment die, generally from sepsis soon after birth. The only available therapeutic option for RD is hematopoietic stem cell transplantation (HSCT). To gain insight into the pathophysiology of RD, we previously created zebrafish models for Ak2 deficiencies. One of the clinical features of RD is hearing loss, but its pathophysiology and causes have not been determined. In adult mammals, sensory hair cells of the inner ear do not regenerate; however, their regeneration has been observed in several non-mammalian vertebrates, including zebrafish. Therefore, we used our RD zebrafish models to determine whether Ak2 deficiency affects sensory organ development and/or hair cell regeneration. Our studies indicated that Ak2 is required for the correct development, survival and regeneration of sensory hair cells. Interestingly, Ak2 deficiency induces the expression of several oxidative stress markers and it triggers an increased level of cell death in the hair cells. Finally, we show that glutathione treatment can partially rescue hair cell development in the sensory organs in our RD models, pointing to the potential use of antioxidants as a therapeutic treatment supplementing HSCT to prevent or ameliorate sensorineural hearing deficits in RD patients. Summary: A zebrafish model of reticular dysgenesis reveals hair cell developmental deficits that can be partially rescued by antioxidants, pointing to their potential use as a therapeutic treatment for reticular dysgenesis patients.
Human Protein MCM6 on HeLa Cell Chromatin*

Minichromosome maintenance (Mcm) proteins perform essential functions regulating the replication of chromatin. Human cells, like other eukaryotic cells, express at least six Mcm proteins conserved in the central region. We have earlier described the primary structures of five human Mcm proteins, but the primary structure of the sixth human Mcm protein, MCM6, was identified only recently. We now use antibodies, specific for the MCM6 protein, to assess its intranuclear distribution. We find that a fraction of MCM6 protein occurs in the nucleosol, forming multiprotein complexes with other Mcm proteins. More importantly, we use for the first time micrococcal nuclease as a tool to investigate the association of MCM6 protein with chromatin. After short digestion times, a considerable fraction of the MCM6 protein is released from chromatin as a multiprotein complex that includes other Mcm proteins as well. In addition, fractions of MCM3 and MCM6 proteins are released by nuclease digestion as monomeric proteins indicating that at least these two Mcm proteins may also occur as single molecules on chromatin. The data also suggest that the chromatin regions with bound Mcm proteins are more vulnerable to nuclease attack than bulk chromatin and may therefore differ in the arrangement of nucleosomes.
Learning by demonstration from multiple agents in humanoid robots

In this paper we present a novel hand gesture recognition system for adaptive learning of human interactions for intuitive human-robot interactions. The proposed system tracks upper body hand gestures of two interacting human agents simultaneously with the help of a motion tracking camera. High dimensional spatio-temporal gesture data is modelled onto low dimensional latent space by means of principal component analysis (PCA) yet maintaining maximum spatial information. Mapping between these low dimensional motion data is learned by non-linear learning algorithms like Radial Basis Function Neural Network (RBFN) and Long Short Term Memory Neural Network (LSTM). Finally learned interaction models can be used by robot to perform similar interactions with a human partner. In order to evaluate accuracy of gestures performed by the robot, the paper presents novel approach to find optimum number of neurons required in the hidden layer of a three layered artificial neural network to produce the desired gesture. Gestures are performed by both, a simulated virtual robot and a physical humanoid robot platform.
Charcot‐Marie‐Tooth type X: unusual phenotype of a novel CX32 mutation

Background: X‐linked Charcot‐Marie‐Tooth disease (CMTX), caused by mutations in the gene encoding connexin32, is the second most common form of inherited demyelinating neuropathy, next to CMT 1A, and accounts for 10–20% of all hereditary demyelinating neuropathies.
Oral glucose tolerance test for preoperative assessment of liver function in liver resection

Backgrounds/Aims We intended to determine the role of the Oral glucose tolerance test (OGTT), in addition to volumetry, in preoperative assessment of patients undergoing liver resection. Methods This was a prospective study conducted at a tertiary care hospital, between February 2009 and February 2011. OGTT curve (parabolic/linear), linearity index (LI) and Parenchymal Hepatic Resection Rate (PHRR) were correlated with postoperative outcomes in terms of postoperative liver failure (PLF), by 50-50 criteria, morbidity, mortality and hospital stay. Results Of the 33 patients included in the study, 23 (69.7%) patients underwent major liver resections. Hepatocellular carcinoma (30.3%) was the leading indication. The overall postoperative morbidity rate was 72.7%, but major complications occurred in 3 (9.1%) patients only. There was no 90-day mortality. The 50-50 criteria were met by 3 patients undergoing major resection. Significant correlation was noted between the linear OGTT curve and the overall hospital stay (12.1 days vs. 9.6 days in parabolic; p=0.04). Patients with linear OGTT met the 50-50 criteria more often (18%) than those having a parabolic curve (4.5%; p=0.25). Although the OGTT was more often linear with occurrence of morbidity (41.7% vs 11.1%), major morbidity (66.7% vs 30%) and PLF by 50-50 criteria (66.7% vs 30%), it was not statistically significant. The linearity index was marginally lower (0.9 vs 1.2) in the presence of major morbidity and PLF by 50-50 criteria. Conclusions Linear OGTT affects the PLF and major morbidity, therein impacting the hospital stay. OGTT LI and PHRR can help predict postoperative outcome for a given extent of liver resection.