Miracle-dz/UniFAR-FTUs huggingface dataset:
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system

Significance Correlation of expression between genes can offer useful hints regarding their function or underlying regulatory mechanism. Today, large amounts of expression data are publicly available, allowing researchers to estimate expression correlation over thousands of samples. However, extracting information from correlation data is not straightforward, because underlying expression data are generated by different laboratories working on different cell types and under different conditions. Here we present Immuno-Navigator, a database for correlation of expression in cells of the immune system, which addresses these issues. We present examples of ways our database can be used for generating hypotheses for further experimental analysis. We demonstrate how it recapitulates known facts in immunology and successfully predicts key regulators in naturally occurring regulatory T cells. High-throughput gene expression data are one of the primary resources for exploring complex intracellular dynamics in modern biology. The integration of large amounts of public data may allow us to examine general dynamical relationships between regulators and target genes. However, obstacles for such analyses are study-specific biases or batch effects in the original data. Here we present Immuno-Navigator, a batch-corrected gene expression and coexpression database for 24 cell types of the mouse immune system. We systematically removed batch effects from the underlying gene expression data and showed that this removal considerably improved the consistency between inferred correlations and prior knowledge. The data revealed widespread cell type-specific correlation of expression. Integrated analysis tools allow users to use this correlation of expression for the generation of hypotheses about biological networks and candidate regulators in specific cell types. We show several applications of Immuno-Navigator as examples. In one application we successfully predicted known regulators of importance in naturally occurring Treg cells from their expression correlation with a set of Treg-specific genes. For one high-scoring gene, integrin β8 (Itgb8), we confirmed an association between Itgb8 expression in forkhead box P3 (Foxp3)-positive T cells and Treg-specific epigenetic remodeling. Our results also suggest that the regulation of Treg-specific genes within Treg cells is relatively independent of Foxp3 expression, supporting recent results pointing to a Foxp3-independent component in the development of Treg cells.
Evolution of CFTR protein distribution in lung tissue from normal and CF human fetuses

In order to determine whether or not CFTR protein distribution differs between the airways of fetuses with Cystic Fibrosis (CF) from the airways of normal fetuses we studied the distribution pattern of the CFTR protein in lung. Cases of normal and CF human fetuses as well as cases of normal neonates were examinated. Our aim was to establish whether CFTR expression during pregnancy could be correlated with the maturation of the airways, and to compare normal and CF samples. We hypothesized that any difference between normal and CF fetal lung in CFTR protein expression could be related to a functional change appearing in early development even if no morphological differences could be detected at the light microscopic level. The distribution of CFTR protein progressively increased from 10 weeks of gestation (WG) to mid‐gestation, but thereafter decreased until term. The CFTR protein was first detected in the cytoplasm of undifferentiated epithelial cells. Before mid‐gestation, the immunostaining was strongly positive in bronchi, in sub‐mucosal glands, and in lung parenchyma. Then, it became localized to the apical zone of the epithelial cells. This pattern correlated with differentiation during the second half of gestation. The main difference observed between normal and CF fetuses was a 3‐week delay in detectability of the CFTR protein expression in the latter until 15 weeks of gestation. These results support the hypothesis of an early functional change. Abnormal fetal lung CFTR protein regulation could give rise to a predisposition to the post‐natal inflammatory changes of the airways that characterize CF disease. 2007;42:1032–1040. © 2007 Wiley‐Liss, Inc.
Mechanical Properties of Recycled Steel Tire Fibres in Concrete

Tyre production is increasing every year due to the increase of vehicle sales. The generation and disposal of waste are inherent to life itself and have presented very serious problems to the human community in Malaysia. Recently, some research has been devoted to the use of recycled steel tire fibres (RSF) in concrete. This study is focusing on the use of RSF in concrete mix. The different volume of RSF was used in concrete mix to fabricated and tested. In particular, concrete obtain by adding RSF evidence a satisfactory improvement, mostly in cracking control, compressive strength, flexural strength and also tensile strength. On the other hand, compressive, flexural and tensile strength was positively affected by the addition of RSF. More percentage of volume fractions (Vf) added will give high number of bonding in concrete to delay the crack growth. It gives high result in tensile strength. Moreover, the workability of the concrete reinforced with RSF was significantly affected.
Intraspecific brood parasitism: a strategy for floating females in the European starling

In many bird species, there is a floating population of females that are excluded from breeding because of competition for limited breeding resources. Female floaters may enhance their reproductive success by engaging in intraspecific brood parasitism. We studied female floaters in a population of European starlings, Sturnus vulgaris, in order to determine their identity and potential parasitic behaviour. Females were caught after being attracted to nestboxes with artificial nests during 1993-1995. None of the females was known to have a nest of her own at capture but 47% of the females either laid an egg in the nest or carried a fully developed egg within the reproductive tract, indicating that they were intraspecific brood parasites. The floating females were significantly younger and smaller than breeding females. Of 13 females equipped with radiotransmitters and followed daily, all but one started a breeding attempt of their own after 3-8 days and the majority settled as secondary females or mated with males where the original female had disappeared. This suggests that females that are unable to compete successfully for nest sites or males early in the breeding season may use intraspecific brood parasitism to enhance reproductive success during the period that they are constrained from breeding. The importance of settling rapidly because of a seasonal decline in reproductive success may also promote the evolution of intraspecific brood parasitism in the starling. The relative reproductive success of combining egg dumping with breeding compared with traditional breeding will depend on the costs of delaying breeding as well as the probability of finding a mate later in the breeding season. Copyright 1999 The Association for the Study of Animal Behaviour.
Optimal speed estimation in natural image movies predicts human performance.

Accurate perception of motion depends critically on accurate estimation of retinal motion speed. Here, we first analyze natural image movies to determine the optimal space-time receptive fields for encoding local motion speed in a given direction. Next, from the receptive field responses to natural stimuli, we determine the neural computations that are optimal for combining and decoding the responses into estimates of speed. The computations show how selective, invariant speed-tuned units might be constructed by the nervous system. The space-time receptive fields (which are direction-tuned but not speed-tuned) and the speed-tuned units exhibit strong similarities to neurons in cortex. Then, in a psychophysical experiment using matched naturalistic stimuli, we show that human performance closely parallels optimal performance. Indeed, a single free parameter accurately predicts the detailed shapes of a large set of psychometric functions. For each human observer, this parameter accounts for more than 95% of the variance in the discrimination data with natural stimuli. The optimal observer also provides excellent predictions of human performance with classic artificial stimuli (e.g. drifting gabors). Importantly, the optimal observer for speed estimation was not designed to match human performance. Rather, it was constructed to maximize the accuracy of speed estimates in natural image movies given the constraints of the visual system's front end. We conclude i) that many properties of speed selective neurons and human speed discrimination performance are predicted by the optimal computations, and ii) that natural stimulus variation affects optimal and human observers almost identically. Meeting abstract presented at VSS 2015.
Interaction of the A1 Subunit of Factor VIIIa and the Serine Protease Domain of Factor X Identified by Zero-length Cross-linking

Summary We have previously used a solid phase binding assay to localize a Factor X (FX) interactive site to the acidic C-terminus of the A1 subunit of FVIIIa (Lapan KA, Fay PJ. J Biol Chem 1997; 272: 2082-2088). The complex of FVIII-FX was made covalent following reaction with the zero-length cross-linking reagent 1-ethyl-3-(3-dimethylaminopropyl-)carbodiimide hydrochloride (EDC). Western blotting of the thrombin-cleaved complex showed that the A1 subunit of FVIIIa associated with FX heavy chain. The FX-A1 product was also detected following cross-linking to the A1/A3-C1-C2 dimer, but not the activated protein C-cleaved A1336/A3-C1-C2 form, indicating that a residue(s) in the region spanning Met337-Arg372 contributed to the intermolecular ion pair(s). A synthetic peptide to this acidic region (FVIII337-372) cross-linked to FX and the product was alkaline resistant indicating that amide linkage(s) were formed. Sequence analysis of the FX-FVIII337-372 adduct suggested that the first 12 NH2-terminal residues of the FX and peptide do not participate in cross-link formation. Conversion of the cross-linked product to FXa by RVV-X showed that the peptide was associated with the serine protease-forming domain of the heavy chain. These results indicate that the association of FVIIIa and FX occurs from a salt linkage(s) formed between residues of the A1 acidic C-terminus of the cofactor (within residues 349-372) and the serine protease-forming domain of the substrate.
A review of participant satisfaction, stress and anxiety associated with video assisted feedback in simulation based medical education

Simulation acts as a replication of components of a clinical situation and allows a learner to practice in an ‘artificial’ and controlled simulated environment with guided exposure. Feedback of the trainee’s performance during and after the simulation activity is an essential component of simulation training. The affective domain (how participants feel) is the most often neglected domain in higher education but can be used to assess the effect of a learning activity or intervention. Studies suggest participant satisfaction with, and perception of, simulation training was enhanced by video assisted feedback of their performance. Although studies have established a link between simulation training and stress/anxiety this association has not been investigated to determine whether VAF results in a beneficial level of stress and anxiety or a detrimental level.
Blood pressure profile in elderly patients with hypertension or heart failure

Wstęp Ciśnienie tętnicze podlega nieustannym wahaniom zarówno u osób z prawidłowym ciśnieniem, jak i u chorych z nadciśnieniem tętniczym. Ta zmienność ciśnienia (BPV, blood pressure variability) odzwierciedla indywidualny charakter autonomicznej regulacji czynności układu sercowo-naczyniowego [1]. Ciśnienie podlega zmienności krótkoterminowej powodowanej wysiłkiem fizycznym oraz bodźcami behawioralnymi i emocjonalnymi, a także długotrwałej, związanej z różnicami ciśnienia w okresie snu i czuwania. Zmienność ciśnienia w dużym stopniu zależy od funkcji baroreceptorów tętniczych [2]. Zmiana ich wrażliwości przyczynia się do nasilenia zmienności ciśnienia. Pogorszenie funkcji baroreceptorów obserwuje się zarówno w procesie starzenia, jak i w nadciśnieniu tętniczym [3, 4]. W przypadku nadciśnienia jednoAbstract Background. Aim of the study was to assess blood pressure (BP) profile among elderly patients treated from hypertension or heart failure. Material and methods. In elderly normotensive (NT), treated hypertensives (HT) and patients with treated stable systolic heart failure (HF) 24-hour ambulatory BP (Spacelabs 90207) were measured. Mean values and variability (SD) of systolic, diastolic, mean and pulse pressures (SBP, DBP, MAP, PP) were obtained. Moreover, morning surge (MS) of SBP, nocturnal dipping of BP and ambulatory arterial stiffness index (AASI) were calculated. The groups were compared applying the Kruskal-Wallis test (ANOVA rang). Results. Studied population consisted of 51 persons: 10 NT, 27 with controlled HT and 14 with stabled HF. Groups were similar in age, mean 24h and night of BP values, but differed in daytime BP (SBP; 126,6 ± 7,6 v. 135,0 ± 10,6 v. 126,6 ± 15,3 mm Hg, p = 0,03; DBP: 78,7 ± 7,0 v. 77,4 ± 9,2 v. 72,6 ± 9,6 mm Hg, p = 0,04; MAP: 95,2 ± 6,8 v. 98,4 ± 8,1 v. 92,3 ± 10,7 mm Hg, p = 0,03). Variability significantly differed between groups only with reference to SBP during 24 h (13,5 ± 2,9 v. 14,7 ± 4,0 v. 13,0 ± 3,0 mm Hg, p = 0,02) and to daytime PP (7,8 ± 1,4 v. 10,3 ± 2,1 v. 9,1 ± 1,4 mm Hg, p = 0,004). Morning surge, dipping and AASI were similar among studied groups. Conclusions. Despite treatment and controlled values of BP it was still observed unfavorable features of BP profile among elderly patients with hypertension or heart failure. Gerontol. Pol. 2009; 17, 4: 188–194
IMPROVED DEVICE SCALING & PROCESS SIMPLIFICATION THROUGH ADVANCED ION IMPLANTATION TECHNIQUES

Advanced ion implantation techniques are being used to solve device scaling issues through the use of equivalent scaling methodology. These include vertical device isolation and manufacture of SOI wafers by hydrogen or oxygen ion implantation, improved lateral device isolation through parallel beam high energy implantation, higher-k gate material modification through selected impurity implantation such as nitrogen into silicon dioxide, improved device Leff control through zero tilt shallow junction implantation and high tilt implantation for gate overlap control. Additional cost savings and 2 to 4 mask count reduction have been achieved through post-gate implant (PoGI) process simplification technique. Besides beam-line single wafer implanter designs, new cluster module designs are appearing using plasma doping techniques.
PARTICLE IMAGE VELOCIMETRY MEASUREMENTS OF THE CAVITATING FLOW IN A REAL SIZE TRANSPARENT VCO NOZZLE

The difficulties of micro PIV measurements in high speed flow measurements in small orifices are discussed. A backlit micro PIV system was developed to measure the flow within real size transparent VCO nozzle with orifices of 150 μm in diameter. Using refractive index matching the resolution of the PIV images reaches almost the diffraction limit. Larger tracer particles than with conventional PIV are needed but a much lower light energy level of the illuminating light pulses, that have to be incoherent. A double pulse Nd-Yag laser and fluorescence medium together with a filter are used to produce the incoherent light. Both the visualization of the cavitation as well as the micro-PIV results seem to indicate that cavitation collapses or decays is a deterministic manner within the orifice of a cavitating transparent VCO nozzle. fuel was injected into atmospheric conditions to obtain longer series of images and thus to be able to average the results. The experiments presented here are a continuation of the work presented in [1] and [2]. PROBLEMS OF USING PIV IN NOZZLE ORIFICES WITH CAVITATION The first question that has to be answered when using PIV is how thick the light sheet should be to obtain an adequate spatial resolution and at the same time thick enough to reduce the number of out of plane motions of the tracers? The thickness of the light sheet should be much smaller than the typical scale of velocity gradients of the flow. In the present case it would mean a light sheet thickness much smaller than the orifice diameter, i.e. 150 μm. For example Fath et al. [3] performed visualization experiments using laser light sheets at the orifice exit under atmospheric conditions. The calculated sheet thickness they could produce was order of 40 μm. Walter [4] performed PIV measurements in transparent nozzles using a light sheet with 18 μm thickness. However, when using the standard PIV set-up in cavitating flows the scattered light intensity from the interface between liquid and vapour is much stronger than the light scattered by the tracers. Therefore, Walter used a fluorescent tracers and a filter to block the light scattered by the cavitation surfaces. However, the light energy per laser pulse had to be limited (3 mJ) to avoid damage to the nozzle material (Perspex). The resulting fluorescence intensity is therefore low and a camera with image intensifier is then necessary, which causes an increase of noise in the images. Elaborate evaluation is then needed to obtain the velocity from the images. Walther used a phase averaging procedure to reduce the signal to noise ratio of the correlation peak. Summarizing these results the effort needed a er I IL SS08-7-1
Rough Lipopolysaccharide of Brucella abortus RB51 as a Common Antigen for Serological Detection of B. ovis, B. canis, and B. abortus RB51 Exposure Using Indirect Enzyme Immunoassay and Fluorescence Polarization Assay

Abstract Rough lipopolysaccharide (RLPS) antigens were prepared from cultures of Brucella abortus RB51, B. ovis, and B. canis. The preparations were standardized by weight and tested with sera from cattle immunized with B. abortus RB51, sheep infected with B. ovis, and dogs infected with B. canis. Populations of unexposed animals of each species were also tested. The tests used were the indirect enzyme immunoassay (IELISA) using RLPS and the fluorescence polarization assay (FPA) using RLPS core fractions, labeled with fluorescein isothiocyanate. The IELISA using B. abortus RB51 RLPS antigen resulted in sensitivity and specificity values of 94.8% and 97.3%, respectively, when testing bovine sera, 98.5% and 97.8% when testing ovine sera, and 95.8% and 100% when testing dog sera. The IELISA using B. ovis RLPS antigen gave sensitivity and specificity values of 80.5% and 91.7%, respectively with bovine sera, 98.9% and 93.8% with sheep sera, and 70.8% and 79.8% with dog sera. The IELISA using B. canis RLPS antigen resulted in sensitivity and specificity values of 97.0% and 97.4%, respectively, with bovine sera, 96.2% and 96.3% with sheep sera, and 95.8% and 98.8% with dog sera. Labeling RLPS core from B. ovis and B. canis with fluorescein was not successful. B. abortus RB51 core labeled with fluorescein resulted in sensitivity and specificity values of 93.5% and 99.8%, respectively, with bovine sera and 78.1% and 99.0% with sheep sera. It was not possible to test the dog sera in the FPA.
"Lion and Man": Upper and Lower Bounds

Given a lion and a man, their initial positions, and restrictions on their ranges and speeds, how quickly can the lion get within a given distance from the man? We consider the case in which the lion and man are restricted to the interior of a circle and each is limited to the same speed. INFORMS Journal on Computing , ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
MODELING , IDENTIFICATION , AND ADAPTIVE MANEUVERING OF CYBERSHIP II : A COMPLETE DESIGNWITH EXPERIMENTS

Good nonlinear maneuvering models, including numerical values, for control of ships are hard to find. This paper presents a complete modeling, identification, and control design for maneuvering a ship along a desired path. A variety of references have been applied to describe the ship model, its difficulties, limitations, and possible simplifications for the purpose of automatic control design. The numerical values of the parameters in the model are identified in towing tests and adaptive maneuvering experiments for a scaled model ship in a marine control laboratory. Copyright c ° 2004 IFAC
Central neuronal projections and neuromuscular organization of the basal region of the shore crab leg

The musculature and associated skeleton, peripheral nervous system, and central projections of motor and sensory neurones of the two basal (thoracic and coxal) segments of the shore crab leg (fifth pereiopod, P5) were examined in vivo and with methylene blue or cobalt staining.
A 600mV Baseband Analog Filter for UMTS Receivers

In this paper an approach for the design of low-voltage analog active-RC filters is presented. This technique is based on the use of different common mode levels at the opamp inputs and the filter inputs and outputs. A design example of a 600mV supply voltage 4th order low-pass analog filter for UMTS receivers is reported. The filter is designed in a 0.13mum CMOS technology with a 600mV supply voltage. The filter features a wide swing performance (THD = -40dB@800mVpp,differential output signal amplitude), and high dynamic range (47 dB)
Indian Diabetes Risk Score Helps to Distinguish Type 2 from Non-Type 2 Diabetes Mellitus (GDRC-3)

Aim: The aim of this study was to investigate whether the Indian Diabetes Risk Score (IDRS) could assist in classifying type 2 diabetes mellitus (T2DM) and non-T2DM among patients attending clinics in India. Methods: Patient records from 2006 through 2009 were taken from the clinical database of a tertiary care diabetes hospital in Chennai, Southern India. A total of 8747 patients with diabetes, diagnosed by a physician either as type 1 diabetes mellitus (T1DM), T2DM, or other types were included for analysis. The IDRS, based on age, abdominal obesity, family history of diabetes, and physical activity, was calculated for each patient at first visit to our clinic. Receiver operating characteristic (ROC) curves were generated to obtain optimal IDRS cut points for predicting T2DM and non-T2DM. Results: Of the 8747 patient records analyzed, 204 (2.3%) were classified as non-T2DM and 8543 (97.7%) as T2DM. In ROC analysis, an IDRS ≥60 [area under the curve (AUC), 0.894; sensitivity, 83.8%; specificity, 81.0%] was predictive of T2DM, while an IDRS <60 (AUC, 0.882; sensitivity, 79.9%; specificity, 83.8%) was predictive of non-T2DM. Conclusions: The IDRS, a simple, cost-effective risk score, can assist in classifying T2DM versus non-T2DM among clinic patients in India.