Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Tuberculosis (TB) Prevention Effectiveness in Children of Bacillus Calmette-Guérin (BCG) Vaccines from Different Sources, Kazakhstan

Background Except during a 1-year period when BCG vaccine was not routinely administered, annual coverage of infants with Bacillus Calmette-Guérin (BCG) in Kazakhstan since 2002 has exceeded 95%. BCG preparations from different sources (Japan, Serbia, and Russia) or none were used exclusively in comparable 7-month time-frames, September through March, in 4 successive years beginning in 2002. Our objective was to assess relative effectiveness of BCG immunization. Methods/Findings We compared outcomes of birth cohorts from the 4 time-frames retrospectively. Three cohorts received vaccine from one of three manufacturers exclusively, and one cohort was not vaccinated. Cohorts were followed for 3 years for notifications of clinical TB and of culture-confirmed TB, and for 21 months for TB meningitis notifications. Prevention effectiveness based on relative risk of TB incidence was calculated for each vaccinated cohort compared to the non-vaccinated cohort. Although there were differences in prevention effectiveness observed among the three BCG vaccines, all were protective. The Japanese vaccine (currently used in Kazakhstan), the Serbian vaccine, and the Russian vaccine respectively were 69%, 43%, and 22% effective with respect to clinical TB notifications, and 92%, 82%, and 51% effective with respect to culture confirmed TB. All three vaccines were >70% effective with respect to TB meningitis. Limitations Potential limitations included considerations that 1) the methodology used was retrospective, 2) multiple risk factors could have varied between cohorts and affected prevention effectiveness measures, 3) most cases were clinically diagnosed, and TB culture-positive case numbers and TB meningitis case numbers were sparse, and 4) small variations in reported population TB burden could have affected relative risk of exposure for cohorts. Conclusions/Significance All three BCG vaccines evaluated were protective against TB, and prevention effectiveness varied by manufacturer. When setting national immunization policy, consideration should be given to prevention effectiveness of BCG preparations.
Age Accumulation in Peritoneal Membrane and Cavity during Peritoneal Dialysis and Its Effect on Peritoneal Structure and Function

T he conventional dialysis solutions contain a high concentration of glucose to induce sufficient ultra filtration and to maintain fluid balance in uremic patients. During continuous ambulatory peritoneal dialysis (CAPD), the peritoneal cavity is therefore continuously exposed to high glucose for a long time. Histological examination of the peritoneum from peritoneal dialysis patients revealed duplication of submesothelial basement membrane in both diabetic and non diabetic patients and acceleration of preexisting duplication of capillary basement membrane in diabetic patients (1-4). These histologic changes, similar to diabetic complications, are believed to be due to continuous exposure of the peritoneum to an unphysiologic ally high concentration of glucose. Hyperglycemia is associated with the presence or progression of complications in non insulin-dependent diabetes mellitus (NIDDM) (1,5) and insulindependent diabetes mellitus (IDDM) (2). One of the major consequences of prolonged hyperglycemia is accelerated formation of advanced glycosylation endproducts (AGEs) on long-lived structural proteins (3). AGEs are excreted mainly by the kidneys and, therefore, serum level increases as renal function decreases (4). AGE peptide levels in spent dialysate in PD patients is higher than plasma levels (6,7). Peritoneal accumulation of AGEs was reported in PD patients (8,9). Exogenous administration of AGEs induced an increase in vascular permeability in normal animals (10) and the accumulation of AGE induced structural and functional alterations of tis sue proteins (11). Peritoneal accumulation of AGEs, structural and functional alterations of tissue proteins, and increased permeability of the peritoneal vasculature may re
Bayesian hypothesis testing for one bit compressed sensing with sensing matrix perturbation

This letter proposes a low-computational Bayesian algorithm for noisy sparse recovery in the context of one bit compressed sensing with sensing matrix perturbation. The proposed algorithm which is called BHT-MLE comprises a sparse support detector and an amplitude estimator. The support detector utilizes Bayesian hypothesis test, while the amplitude estimator uses an ML estimator which is obtained by solving a convex optimization problem. Simulation results show that BHT-MLE algorithm offers more reconstruction accuracy than that of an ML estimator (MLE) at a low computational cost.
Species-Specific Secondary Metabolite Production in Marine Actinomycetes of the Genus Salinispora

ABSTRACT Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.
Calibration of distance measures for unsupervised query-by-example

Retrieving information from the ever-increasing amount of unannotated audio and video recordings requires techniques such as unsupervised pattern discovery or query-by-example. In this paper we focus on queries that are specified in the form of an audio snippet containing the desired word or expression excised from the target recordings. The task is to retrieve alland-only the instances whose match score with the query meet an absolute criterion. For this purpose we introduce a distance measure between two acoustic vectors that can be calibrated in a completely unsupervised manner. The use of that measure also allows the use of a fast matching approach, which makes it possible to skip more than 97% of full-fledged DTW without affecting performance in terms of precision and recall. We demonstrate the effectiveness of the proposals with query-byexample experiments conducted on a read speech corpus for English and a spontaneous speech corpus for Dutch.
Evaluation of energy-efficiency in lighting systems using sensor networks

In modern energy aware buildings, lighting control systems are put in place so to maximise the energy-efficiency of the lighting system without effecting the comfort of the occupant. In many cases this involves utilising a set of presence sensors, with actuators, to determine when to turn on/off or dim lighting, when it is deemed necessary. Such systems are installed using standard tuning values statically fixed by the system installer. This can cause inefficiencies and energy wastage as the control system is never optimised to its surrounding environment. In this paper, we investigate a Wireless Sensor Network (WSN) as a viable tool that can help in analysing and evaluating the energy-efficiency of an existing lighting control system in a low-cost and portable solution. We introduce LightWiSe (LIGHTting evaluation through WIreless SEnsors), a wireless tool which aims to evaluate lighting control systems in existing office buildings. LightWiSe determines points in the control system that exhibit energy wastage and to highlight areas that can be optimised to gain a greater efficiency in the system. It will also evaluate the effective energy saving to be obtained by replacing the control system with a more judicious energy saving solution. During a test performed in an office space, with a number of different lighting control systems we could highlight a number of areas to reduce waste and save energy. Our findings show that each system tested can be optimised to achieve greater efficiency. LightWiSe can highlight savings in the region of 50% to 70% that are achievable through optimising the current control system or installing an alternative.
Capsicum chinensis L. growth and nutraceutical properties are enhanced by biostimulants in a long-term period: chemical and metabolomic approaches

Two biostimulants, one derived from alfalfa plants (AH) and the other obtained from red grape (RG), were chemically characterized using enzyme linked immuno-sorbent assays, Fourier transform infrared (FT-IR) and Raman spectroscopies. Two doses (50 and 100 mL L−1 for RG, and 25 and 50 mL L−1 for AH) of biostimulants were applied to Capsicum chinensis L. plants cultivated in pots inside a tunnel. The experimental design consisted of the factorial combination of treatment (no biostimulant, plus AH, plus RG) at three doses (zero, low, and high) and two time-course applications (at the second and fourth week after transplantation) and the effects were recorded at flowering and maturity. Both biostimulants contained different amounts of indoleacetic acid and isopentenyladenosine; the AH spectra exhibited amino acid functional groups in the peptidic structure, while the RG spectra showed the presence of polyphenols, such as resveratrol. These results revealed that at flowering, RG and AH increased the weights of fresh leaves and fruits and the number of green fruits, whereas at maturity, the biostimulants most affected the fresh weight and number of red fruits. At flowering, the leaves of the treated plants contained high amounts of epicatechin, ascorbic acid, quercetin, and dihydrocapsaicin. At maturity, the leaves of the treated plants exhibited elevated amounts of fructose, glucose, chlorogenic, and ferulic acids. Moreover, green fruits exhibited a high content of chlorogenic acid, p-hydroxybenzoic acid, p-coumaric acid and antioxidant activity, while both AH- and RG-treated red fruits were highly endowed in capsaicin. The 1H high-resolution magic-angle spinning (HRMAS)-nuclear magnetic resonance (NMR) spectra of red fruits revealed that both products induced a high amount of NADP+, whereas RG also increased glucose, fumarate, ascorbate, thymidine and high molecular weight species. Our results suggested that AH and RG promoted plant growth and the production of secondary metabolites, such as phenols.
Current Account Reversals and Growth: The Direct Effect Central and Eastern Europe 1923-2000

According to economic theory, the capital inflows reversal – so-called sudden stop – has a significant negative effect on economic growth. This paper investigates the direct impact of current account reversals on growth in Central and Eastern European countries. Two steps to conduct the analysis are applied. In the first step we estimate the standard growth equation augmented by an effect of the current account reversal. We find that after a current account reversal the growth rate declines by 1.10 percentage points in the current year. The subsequent analysis of the adjustment dynamics builds upon the notion of convergence. We find the unconditional and conditional convergence coefficients to be - 0.47 and -0.52, respectively. This implies that the consequences of the reversal are likely eliminated after 3.3 years when the actual growth rate is back at its equilibrium level, ceteris paribus. Finally, the cumulative loss associated with a sudden stop in capital flows is about 2.3 percentage points. We infer that Central and Eastern European countries are relatively flexible in terms of adjustment and reallocation of resources given the findings in similar literature examining either a more general sample or concentrating on rather different regions.
Hypocretins (Orexins) Regulate Serotonin Neurons in the Dorsal Raphe Nucleus by Excitatory Direct and Inhibitory Indirect Actions

The hypocretins (hcrt1 and hcrt2) are expressed by a discrete population of hypothalamic neurons projecting to many regions of the CNS, including the dorsal raphe nucleus (DRN), where serotonin (5-HT) neurons are concentrated. In this study, we investigated responses to hcrts in 216 physiologically identified 5-HT and non-5-HT neurons of the DRN using intracellular and whole-cell recording in rat brain slices. Hcrt1 and hcrt2 induced similar amplitude and dose-dependent inward currents in most 5-HT neurons tested (EC50, ∼250 nm). This inward current was not blocked by the fast Na+ channel blocker TTX or in a Ca2+-free solution, indicating a direct postsynaptic action. The hcrt-induced inward current reversed near −18 mV and was primarily dependent on external Na+ but not on external or internal Ca2+, features typical of Na+/K+ nonselective cation channels. At higher concentrations, hcrts also increased spontaneous postsynaptic currents in 5-HT neurons (EC50, ∼450–600 nm), which were TTX-sensitive and mostly blocked by the GABAA antagonist bicuculline, indicating increased impulse flow in local GABA interneurons. Accordingly, hcrts were found to increase the basal firing of presumptive GABA interneurons. Immunolabeling showed that hcrt fibers projected to both 5-HT and GABA neurons in the DRN. We conclude that hcrts act directly to excite 5-HT neurons primarily via a TTX-insensitive, Na+/K+ nonselective cation current, and indirectly to activate local inhibitory GABA inputs to 5-HT cells. The greater potency of hcrts in direct excitation compared with indirect inhibition suggests a negative feedback function for the latter at higher levels of hcrt activity.
Controlling risk in a lightning-speed trading environment

A small group of high-frequency algorithmic trading firms have invested heavily in technology to leverage the nexus of high-speed communications, mathematical advances, trading and high-speed computing. By doing so, they are able to complete trades at lightning speeds. High-frequency algorithmic trading strategies rely on computerized quantitative models that identify which type of financial instruments to buy or sell (e.g., stocks, options or futures), as well as the quantity, price, timing and location of the trades. These so-called black boxes are capable of reading market data, transmitting thousands of order messages per second to an exchange, cancelling and replacing orders based on changing market conditions and capturing price discrepancies with little or no human intervention.
Deep API Programmer: Learning to Program with APIs

We present DAPIP, a Programming-By-Example system that learns to program with APIs to perform data transformation tasks. We design a domain-specific language (DSL) that allows for arbitrary concatenations of API outputs and constant strings. The DSL consists of three family of APIs: regular expression-based APIs, lookup APIs, and transformation APIs. We then present a novel neural synthesis algorithm to search for programs in the DSL that are consistent with a given set of examples. The search algorithm uses recently introduced neural architectures to encode input-output examples and to model the program search in the DSL. We show that synthesis algorithm outperforms baseline methods for synthesizing programs on both synthetic and real-world benchmarks.
Generating Descriptions of Nouns in Software from Program Comments

Software developers surmise roles and workings of functions or variables for program comprehension judging from its identiﬁers. It is diﬃcult to surmise appropriately if engineers have little knowledge and experiment of software development, because sometimes word’s meanings in identiﬁers are diﬀerent form in natural language. This paper proposes a method to generate descriptions of nouns which are used in identiﬁers automatically that helps surmising identiﬁers. The description is generated from comments in source code by using natural language process and extracting notes for noun.
TGF‐β1, GDF‐5, and BMP‐2 Stimulation Induces Chondrogenesis in Expanded Human Articular Chondrocytes and Marrow‐Derived Stromal Cells

Replacement of degenerated cartilage with cell‐based cartilage products may offer a long‐term solution to halt arthritis' degenerative progression. Chondrocytes are frequently used in cell‐based FDA‐approved cartilage products; yet human marrow‐derived stromal cells (hMSCs) show significant translational potential, reducing donor site morbidity and maintaining their undifferentiated phenotype with expansion. This study sought to investigate the effects of transforming growth factor β1 (TGF‐β1), growth/differentiation factor 5 (GDF‐5), and bone morphogenetic protein 2 (BMP‐2) during postexpansion chondrogenesis in human articular chondrocytes (hACs) and to compare chondrogenesis in passaged hACs with that of passaged hMSCs. Through serial expansion, chondrocytes dedifferentiated, decreasing expression of chondrogenic genes while increasing expression of fibroblastic genes. However, following expansion, 10 ng/mL TGF‐β1, 100 ng/mL GDF‐5, or 100 ng/mL BMP‐2 supplementation during three‐dimensional aggregate culture each upregulated one or more markers of chondrogenic gene expression in both hACs and hMSCs. Additionally, in both cell types, the combination of TGF‐β1, GDF‐5, and BMP‐2 induced the greatest upregulation of chondrogenic genes, that is, Col2A1, Col2A1/Col1A1 ratio, SOX9, and ACAN, and synthesis of cartilage‐specific matrix, that is, glycosaminoglycans (GAGs) and ratio of collagen II/I. Finally, TGF‐β1, GDF‐5, and BMP‐2 stimulation yielded mechanically robust cartilage rich in collagen II and GAGs in both cell types, following 4 weeks maturation. This study illustrates notable success in using the self‐assembling method to generate robust, scaffold‐free neocartilage constructs using expanded hACs and hMSCs. Stem Cells 2015;33:762–773
Effect of Organic Solvents on the Yield of Solvent-Tolerant Pseudomonas putida S12

ABSTRACT Solvent-tolerant microorganisms are useful in biotransformations with whole cells in two-phase solvent-water systems. The results presented here describe the effects that organic solvents have on the growth of these organisms. The maximal growth rate of Pseudomonas putida S12, 0.8 h−1, was not affected by toluene in batch cultures, but in chemostat cultures the solvent decreased the maximal growth rate by nearly 50%. Toluene, ethylbenzene, propylbenzene, xylene, hexane, and cyclohexane reduced the biomass yield, and this effect depended on the concentration of the solvent in the bacterial membrane and not on its chemical structure. The dose response to solvents in terms of yield was linear up to an approximately 200 mM concentration of solvent in the bacterial membrane, both in the wild type and in a mutant lacking an active efflux system for toluene. Above this critical concentration the yield of the wild type remained constant at 0.2 g of protein/g of glucose with increasing concentrations of toluene. The reduction of the yield in the presence of solvents is due to a maintenance higher by a factor of three or four as well as to a decrease of the maximum growth yield by 33%. Therefore, energy-consuming adaptation processes as well as the uncoupling effect of the solvents reduce the yield of the tolerant cells.
Design and Application of Compact and Highly Tolerant Polarization-Independent Waveguides

In this paper, the design, fabrication, and application of a highly tolerant polarization-independent optical-waveguide structure suited for operation in the third communication window is presented. The waveguide structure has been optimized toward minimized sensitivity to technological tolerances and low fabrication complexity. The tolerance analysis has been based on the typical processing tolerances of the widely applied silicon-oxynitride technology, being plusmn3times10 -4 in refractive index, plusmn1% in thickness, and plusmn0.1 mum in channel width. The optimized waveguide design fulfills the criterion of a channel birefringence within 5times10-5, including processing tolerance. It also enables a fiber-to-chip coupling loss below 1 dB/facet and is suited for the realization of low-loss bends with a radius down to 600 mum. Based on this waveguide design, a passband-flattened optical wavelength filter with 50-GHz free spectral range has been realized and tested. The measured TE-TM shift of 0.03 nm confirms the polarization dependence of the optical waveguides being as low as 3times10-5
A novel homozygous nonsense mutation in CABP4 causes congenital cone-rod synaptic disorder.

PURPOSE The purpose of this study was to identify the causative gene defect in two siblings with an uncharacterized cone-rod dysfunction and to describe the clinical characteristics. METHODS Genome-wide homozygosity mapping, with a 250K SNP-array followed by a search for candidate genes, was performed. The patients underwent ophthalmic examination, including elaborate electroretinography. RESULTS In a Dutch sib pair, a shared 9-Mb homozygous region was found on 11q13.1-q13.5 that encompasses the CABP4 gene, previously implicated in autosomal recessive incomplete congenital stationary night blindness (CSNB2) in two small families. A novel homozygous p.Arg216X mutation in CABP4 was detected in the sib pair. Quantitative RT-PCR on RNA isolated from patient lymphoblast cells showed no nonsense-mediated degradation of mutant CABP4 mRNA. Clinically, patients presented with reduced visual acuity, photophobia, and abnormal color vision, but they did not experience night blindness. Electroretinograms showed electronegative mixed rod-cone responses and severely reduced cone responses, as in CSNB2. Isolated rod responses, however, were (sub)normal. CONCLUSIONS A novel homozygous nonsense mutation in CABP4 in two siblings resulted in a phenotype with severely reduced cone function and only negligibly reduced rod function on electroretinography and psychophysical testing. Since these patients and two of three previously described patients do not experience night blindness, the name CSNB2 is confusing for patients as well as clinicians. Therefore, the authors propose to name the phenotype congenital cone-rod synaptic disorder.
Middleware and programming support for agent systems

JADE (Java Agent Development Framework) is a software environment to build agent systems for the management of networked information resources in compliance with the FIPA2000 specifications for interoperable intelligent multi-agent systems. JADE offers an agent middleware to implement efficient FIPA2000 compliant multi-agent systems and supports their development through the availability of a predefined programmable agent model, an ontology development support, and a set of management and testing tools. This paper describes the main features of the JADE system and introduces some of the most important projects based on the JADE software.