Miracle-dz/UniFAR-FTUs huggingface dataset:
TCRklass: A New K-String–Based Algorithm for Human and Mouse TCR Repertoire Characterization

The next-generation sequencing technology has promoted the study on human TCR repertoire, which is essential for the adaptive immunity. To decipher the complexity of TCR repertoire, we developed an integrated pipeline, TCRklass, using K-string–based algorithm that has significantly improved the accuracy and performance over existing tools. We tested TCRklass using manually curated short read datasets in comparison with in silico datasets; it showed higher precision and recall rates on CDR3 identification. We applied TCRklass on large datasets of two human and three mouse TCR repertoires; it demonstrated higher reliability on CDR3 identification and much less biased V/J profiling, which are the two components contributing the diversity of the repertoire. Because of the sequencing cost, short paired-end reads generated by next-generation sequencing technology are and will remain the main source of data, and we believe that the TCRklass is a useful and reliable toolkit for TCR repertoire analysis.
Potential Association of INMT Nonsynonymous Variant (His46Pro) with Hirschsprung's Disease

Background: Hirschsprung's disease (HSCR) is a congenital disorder which is characterized by the lack of ganglion cells in part of or the entire colon, resulting in intestinal obstruction and other related symptoms. Recently, our group has conducted a genome-wide association study in Korean HSCR cases and controls to identify novel markers in other genes. Objectives: The present research aimed to further study the potential association of INMT with HSCR by conducting a replication study. Methods: A total of 15 INMT single nucleotide polymorphisms (SNPs) were analyzed for the association with HSCR in 187 HSCR patients and 283 controls. Analyses were also conducted for subtypes of HSCR (short-segment, long-segment, and total colonic aganglionosis). Results: A nonsynonymous SNP rs77743549 (His46Pro) was significantly associated with the increased risk of HSCR (odds ratio = 1.77; corrected p = 0.002). Furthermore, this rs77743549 retained its association with all subtypes of HSCR (p = 0.006-0.002 under the codominant model). A global test showed that rs77743549 was associated with the length of aganglionosis (p = 0.00004). Conclusion: Although further replications and functional evaluations are needed, our study suggests that rs77743549 of INMT may be associated with the risk for HSCR and/or the development of the enteric nervous system.
Bio-inspired redistribution of urban traffic flow using a social network approach

In present days, the road network in any major city faces the constant pressure of accommodating an ever increasing number of vehicles while conserving a congestion-free status. However, identifying key intersections that will soon become congested is a difficult task, performed by tedious, thorough simulations; even more difficult is to adapt the road network so as to increase its efficiency and avoid congestion. We argue upon the social component of road traffic and propose an alternative way to detect hotspots leading to congestion by using techniques borrowed from complex network analysis. We will use the betweenness centrality and argue upon its power-law distribution, which we set out to redistribute and equalize. The paper introduces a genetic algorithm that redistributes the betweenness values at a community level in a city by changing street directions and number of available lanes in order to reduce (and possibly even eliminate) congestion hotspots. Experimental results in terms of reducing traffic loads from hotspots and transferring to neighboring streets yield an improvement with a factor of up to 90% times without adding significant costs or modifying the existing infrastructure.
Generation of a Replication-Competent, Propagation-Deficient Virus Vector Based on the Transmissible Gastroenteritis Coronavirus Genome

ABSTRACT Replication-competent propagation-deficient virus vectors based on the transmissible gastroenteritis coronavirus (TGEV) genome that are deficient in the essential E gene have been developed by complementation within E+ packaging cell lines. Cell lines expressing the TGEV E protein were established using the noncytopathic Sindbis virus replicon pSINrep21. In addition, cell lines stably expressing the E gene under the CMV promoter have been developed. The Sindbis replicon vector and the ectopic TGEV E protein did not interfere with the rescue of infectious TGEV from full-length cDNA. Recombinant TGEV deficient in the nonessential 3a and 3b genes and the essential E gene (rTGEV-Δ3abΔE) was successfully rescued in these cell lines. rTGEV-Δ3abΔE reached high titers (107 PFU/ml) in baby hamster kidney cells expressing porcine aminopeptidase N (BHK-pAPN), the cellular receptor for TGEV, using Sindbis replicon and reached titers up to 5 × 105 PFU/ml in cells stably expressing E protein under the control of the CMV promoter. The virus titers were proportional to the E protein expression level. The rTGEV-Δ3abΔE virions produced in the packaging cell line showed the same morphology and stability under different pHs and temperatures as virus derived from the full-length rTGEV genome, although a delay in virus assembly was observed by electron microscopy and virus titration in the complementation system in relation to the wild-type virus. These viruses were stably grown for >10 passages in the E+ packaging cell lines. The availability of packaging cell lines will significantly facilitate the production of safe TGEV-derived vectors for vaccination and possibly gene therapy.
Pros and cons of permutation tests in clinical trials.

Hypothesis testing, in which the null hypothesis specifies no difference between treatment groups, is an important tool in the assessment of new medical interventions. For randomized clinical trials, permutation tests that reflect the actual randomization are design-based analyses for such hypotheses. This means that only such design-based permutation tests can ensure internal validity, without which external validity is irrelevant. However, because of the conservatism of permutation tests, the virtues of permutation tests continue to be debated in the literature, and conclusions are generally of the type that permutation tests should always be used or permutation tests should never be used. A better conclusion might be that there are situations in which permutation tests should be used, and other situations in which permutation tests should not be used. This approach opens the door to broader agreement, but begs the obvious question of when to use permutation tests. We consider this issue from a variety of perspectives, and conclude that permutation tests are ideal to study efficacy in a randomized clinical trial which compares, in a heterogeneous patient population, two or more treatments, each of which may be most effective in some patients, when the primary analysis does not adjust for covariates. We propose the p-value interval as a novel measure of the conservatism of a permutation test that can be defined independently of the significance level. This p-value interval can be used to ensure that the permutation test have both good global power and an acceptable degree of conservatism.
Fully Autonomous UAV

Ardu-pilot Mega (APM ver.2.6) is the Flight Controller used in this project. It is a professional quality open-source auto-piloting firmware that is based on the Arduino Mega platform. This autopilot can also control fixed-wing aircraft, multi-rotor helicopters, as well as traditional helicopters. It is an autopilot capable of autonomous flight stabilization, way-point based navigation and two way telemetry with Xbee wireless modules. Supporting 8 RC channels with 4 serial ports. Ardu-Pilot Mega consists of the main processor board which has all the complex sensors like Accelerometer, Gyroscope, Compass Module, and to this we've externally interfaced a GPS module, for GPS waypoint navigation. By using APM 2.6 module as the base we're trying out to make our Multirotor completely autonomous i.e, no human interference, the only thing we do, is give some GPS co-ordinates and a fixed altitude and a Hover speed to the APM module. Thus the model hovers to the co-ordinates and shoots the entire footage using a 'C. C. D camera module' and lively streams using 'TS832 multichannel Transmitter', to the 'RC832 -32 Channel receiver', which converts the received signal to pixels and shows the Live footage on screen. This entire setup on the ground is powered by 'Lithium polymer batteries' and is known as the Ground station when connected to a Computer. In Addition to this an open-source Android application will be exploited for usage through which all the commanding can be done directly.
Telephone Modem Access Improves Diabetes Control in Those with Insulin-Requiring Diabetes

OBJECTIVE To assess whether modem access improves diabetes control in IDDM patients. RESEARCH DESIGN AND METHODS Forty-two patients participated in the study and were followed for 12 wk. The patients were randomly divided into two groups at baseline, a modem group and a control group. There were no significant differences between HbA1c, random blood glucose, and weight between the groups at the beginning of the study. Patients were asked to perform five blood glucose determinations/day (before breakfast, before lunch, afternoon [1500], before dinner, and at bedtime) twice/week. The modem group transferred their data over the phone once/week. The control group would bring in their results on their regular visits every 6 wk. Patients in the modem group were counseled every week over the telephone after transferring results to adjust insulin and food intake if necessary. RESULTS In the modem group, HbA1c improved from 0.106 to 0.092 (13.20%). The control group improved from 0.112 to 0.102 (8.9%). There was no significant change in weight, random blood glucose, or insulin. CONCLUSIONS The use of telephone modem-based patient-monitoring systems in diabetes clinical research seems to stimulate the patient to keep closer control of blood glucose levels. It might be especially useful in rural settings, for which this study was designed.
Rearrangements in Thyroid Hormone Receptor Charge Clusters That Stabilize Bound 3,5′,5-Triiodo-L-thyronine and Inhibit Homodimer Formation*

In this study, we investigated how thyroid hormone (3,5′,5-triiodo-l-thyronine, T3) inhibits binding of thyroid hormone receptor (TR) homodimers, but not TR-retinoid X receptor heterodimers, to thyroid hormone response elements. Specifically we asked why a small subset of TRβ mutations that arise in resistance to thyroid hormone syndrome inhibit both T3 binding and formation of TRβ homodimers on thyroid hormone response elements. We reasoned that these mutations may affect structural elements involved in the coupling of T3 binding to inhibition of TR DNA binding activity. Analysis of TR x-ray structures revealed that each of these resistance to thyroid hormone syndrome mutations affects a cluster of charged amino acids with potential for ionic bond formation between oppositely charged partners. Two clusters (1 and 2) are adjacent to the dimer surface at the junction of helices 10 and 11. Targeted mutagenesis of residues in Cluster 1 (Arg338, Lys342, Asp351, and Asp355) and Cluster 2 (Arg429, Arg383, and Glu311) confirmed that the clusters are required for stable T3 binding and for optimal TR homodimer formation on DNA but also revealed that different arrangements of charged residues are needed for these effects. We propose that the charge clusters are homodimer-specific extensions of the dimer surface and further that T3 binding promotes specific rearrangements of these surfaces that simultaneously block homodimer formation on DNA and stabilize the bound hormone. Our data yield insight into the way that T3 regulates TR DNA binding activity and also highlight hitherto unsuspected T3-dependent conformational changes in the receptor ligand binding domain.
Impainting SONAR images by exemplar-based algorithm

An essential problem in image processing is the recovery of lost or damaged data, which can be done by inpainting. In the recent years, a large variety of image inpainting algorithms have been proposed in the literature. This paper presents a comparison between two exemplar based image inpainting algorithms, in the case of SONAR images. A number of simulations on real SONAR images prove the effectiveness of these algorithms in reconstructing the affected parts of the images. The performance is analyzed in terms of the visual quality and comparing the Peak Signal to Noise Ratio.
Differential Viral Fitness Between H1N1 and H3N8 Avian Influenza Viruses Isolated from Mallards (Anas platyrhynchos)

SUMMARY Homosubtypic and heterosubtypic immunity in mallards (Anas platyrhynchos) play an important role in the avian influenza virus (AIV) diversity. The mechanisms of AIV replication among wild birds and the role of immunity in AIV diversity have thus not been completely clarified. During the monitoring of AI circulation among wild waterfowl in 2007–2008, two viruses (H3N8 and H1N1) were isolated from ducks caught in a funnel trap located in La Hulpe wetland in Belgium. H3N8 viruses were revealed to be more prevalent in the mallard population than was H1N1, which might suggest a better adaptation to this species. In order to investigate this hypothesis, we characterized both isolated viruses biologically by experimental inoculation. Virus excretion and humoral response induced by both isolated viruses were evaluated in mallards after a first infection followed by a homo- or heterosubtypic reinfection under controlled experimental conditions. The H1N1 virus had a delayed peak of excretion of 4 days compared to the H3N8, but the virus shedding was more limited, earlier, and shorter after each reinfection. Moreover, the H3N8 virus could spread to all ducks after homo- or heterosubtypic reinfections and during a longer period. Although the humoral response induced by both viruses after infection and reinfection could be detected efficiently by competitive ELISA, only a minimal H1 antibody response and almost no H3-specific antibodies could be detected by the HI test. Our results suggest that the H3N8 isolate replicates better in mallards under experimental controlled conditions.
Characterization of 38 microsatellite loci in the European blackbird, Turdus merula (Turdidae, AVES)

We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirty‐seven loci were identified by testing 242 loci that had been originally isolated in other avian species. One additional locus was isolated from a European blackbird genomic library. All loci were characterized in 20–29 blackbirds from a population in the Czech Republic and displayed between two and 16 alleles, with observed heterozygosity ranging from 0.04 to 1.00. Thirty‐seven loci could be assigned a chromosome location in the zebra finch (Taeniopygia guttata) genome based on sequence homology.
Effect of Solvent Polarity and Viscosity on the Guest Binding Dynamics with Bile Salt Aggregates †

Bile salts form supramolecular aggregates with two binding sites with different properties. The guest binding dynamics to the aggregates and guest protection from species in the aqueous phase were investigated using fluorescence and laser flash photolysis experiments. Sodium cholate, deoxycholate and taurodeoxycholate were used as bile salts and acetonitrile or ethylene glycol were added as co‐solvents to water in order to alter the binding properties of 1‐ethylnaphthalene and 1‐naphthyl‐1‐ethanol with the aggregates. The binding dynamics are faster and protection efficiencies are lower for guests bound to cholate and in the presence of either co‐solvent.
How Young Girls Change Their Landing Technique Throughout the Adolescent Growth Spurt

Background: Despite the rapid musculoskeletal changes experienced by girls throughout the adolescent growth spurt, little is known about how their lower limb landing technique changes during this time. Purpose: To investigate the longitudinal changes in the 3-dimensional lower limb kinematics, joint moments, and muscle activation patterns displayed by girls when performing a horizontal landing task throughout their adolescent growth spurt. Study Design: Descriptive laboratory study. Methods: A total of 33 healthy 10- to 13-year-old girls, in Tanner stage II, with a maturity offset of −6 to −4 months (time from peak height velocity) were recruited. According to her maturity offset, each participant was tested up to 4 times during the 12 months of her growth spurt (maturity offset: test 1 = −6 to −4 months; test 2 = 0 months; test 3 = 4 months; test 4 = 8 months). During each test session, participants performed a horizontal leap movement, during which ground-reaction forces (1000 Hz), lower limb muscle activity (1000 Hz), and kinematic data (100 Hz) were collected. Results: Throughout the growth spurt, girls displayed a decrease in knee flexion (P = .028), increase in hip flexion (P = .047), increase in external knee abduction moments (P = .008), and decrease in external hip adduction moments (P = .003) during the landing movement. Conclusion: During their adolescent growth spurt, pubescent girls displayed a change in the strategy with which they controlled their lower limb to land after performing a horizontal leap movement. This change in the landing strategy has the potential to increase the risk of anterior cruciate ligament injuries toward the latter stages of the adolescent growth spurt. Clinical Relevance: The outcomes of this research provide a greater understanding of the changes in the landing strategy used by pubescent girls throughout the adolescent growth spurt. This can assist in the development of screening tools designed to determine “at-risk” landing biomechanics during puberty.
Detection of the 113p53 protein isoform: A p53-induced protein that feeds back on the p53 pathway to modulate the p53 response in zebrafish

Isoforms of p53 have been described in both zebrafish and human systems based on sensitive analysis of RNA using PCR-based methods. Despite consistent evidence of the existence of these isoforms at the RNA level it has been difficult to detect the endogenous proteins in a physiological setting. In the zebrafish we have previously shown that the mRNA encoding the ∆113p53 is abundantly induced in whole embryos following induction of the p53 response by radiation, CDK inhibitors and chemotherapeutic drugs. Using a set of monoclonal antibodies raised against different domains of ZFp53 we now show for the first time clear evidence for the controlled expression of a truncated form of the ZFp53 protein, ∆113p53. The protein is present at very low levels but is induced by transcriptionally active full-length ZFp53 following the exposure of zebrafish embryos to the CDK inhibitor roscovitine. Induction of the protein is completely ZFp53 dependent and morpholinos that specifically block the expression of endogenous D113p53 protein selectively enhance the expression of some but not all ZFp53 responsive genes. We map the p53 response elements in the ∆113p53 promoter using functional assays and identify an region at 1593-1612 in intron 4 of ZFp53, as being crucial in the full-length promoter. Thus the endogenous D113p53 protein, which oligomerises with the full-length ZFp53 protein, can act as a selective dominant negative inhibitor of the ZFp53 response, creating a distinct feedback response that varies the nature of the p53 response over time after exposure to an inducing signal.
Variation in the Composition and Pore Function of Major Outer Membrane Pore Protein P2 of Haemophilus influenzae from Cystic Fibrosis Patients

ABSTRACT We investigated the relationship between susceptibility to β-lactam antibiotics and variation in the major outer membrane protein P2 (OmpP2; also called porin) of persistent nonencapsulatedHaemophilus influenzae isolated from cystic fibrosis patients. Nine OmpP2 variants were selected from two distinctH. influenzae strains from two patients extensively treated with β-lactam antibiotics. The variants differed in their susceptibilities to at least two β-lactam antibiotics. By detergent extraction and column chromatography, OmpP2 was purified from two variants that were derived from strain 70 and that differed notably in their susceptibilities to β-lactam antibiotics. The proteins were reconstituted into black lipid membranes for measurement of porin function. OmpP2 from the more resistant isolate (isolate 70b) had a smaller channel conductance than OmpP2 of the more susceptible isolate (isolate 70f). DNA sequencing of ompP2 of these isolates revealed single nonsynonymous base differences; there were changes in the amino acid sequence corresponding to surface-exposed loops 4, 5, 6, and 8. Changes in loops 4, 5, and 6 were previously shown to result in antigenic differences. Beside these mutations, variants of strain 70 showed additional mutations in loop 1 and nonexposed loop 3. Taken together, our results suggest that in variants of strain 70, nonsynonymous point mutations accumulated both in the sequences ofompP2 coding for antigen-variable loops and in other loops, notably, loops 1 and 3. The latter changes are suggested to affect the permeability of the porin channel.
Dietary supplementation with sodium bicarbonate improves calcium absorption and eggshell quality of laying hens during peak production

Abstract The advantage of supplemental sodium bicarbonate (NaHCO3) on eggshell quality in laying hens changes with age. Besides increasing calcium (Ca) secretion in the eggshell gland, it may improve Ca absorption in the intestine or kidney. Hy-Line Brown layers (n = 384), 25 weeks of age, were allocated to two treatment groups in two experiments, each of which included 4 replicates of 24 hens. Hens were fed a basal diet (control) or the basal diet containing 3 g NaHCO3 g/kg for 50 or 20 weeks in Experiment 1 or 2, respectively. A 24-h continuous lighting regimen was used to allow hens to consume the dietary supplements during the period of active eggshell formation. In Experiment 1, particularly from 25 to 50 weeks of age, and in Experiment 2, NaHCO3 supplementation favoured hen-d egg production at the expense of lower egg weight. The increased eggshell thickness should have nothing to do with the additional eggshell formation, because of the unchanged egg mass and daily eggshell calcification. At 35 weeks of age in both experiments, NaHCO3 supplementation increased duodenal expression of calbindin-d28k (CaBP-D28k) protein, contributing to higher Ca retention and balance. From 50 to 75 weeks of age in Experiment 1, the hens had little response to NaHCO3 supplementation and showed a negative trend on eggshell thickness and strength. It is concluded that dietary supplementation with 3 g NaHCO3 g/kg improves Ca absorption and eggshell quality of laying hens during the peak but not late production period, with the introduction of continuous lighting.