Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial patterns of pulmonary tuberculosis incidence and their relationship to socio-economic status in Vitoria, Brazil.

OBJECTIVE To investigate spatial patterns of the incidence of pulmonary tuberculosis (TB) and its relationship with socio-economic status in Vitoria, Espirito Santo, Brazil. DESIGN In a 4-year, retrospective, territory-based surveillance study of all new pulmonary TB cases conducted in Vitoria between 2002 and 2006, spatial patterns of disease incidence were compared using spatial clustering statistics (Anselin's local indicators of spatial association [LISA] and Getis-Ord Gi* statistics), smoothed empirical Bayes estimates and model-predicted incidence rates. Spatial Poisson models were fit to examine the relationship between socio-economic status and TB incidence. RESULTS A total of 651 TB cases were reported across 78 neighborhoods, with rates ranging from 0 to 129 cases per 100,000 population. Moran's I indicated strong spatial autocorrelation among incidence rates (0.399, P < 0.0001), and four areas of high incidence were identified by LISA and Gi* statistics. Smoothed spatial empirical Bayes estimates demonstrate that two of these areas range from 70 to 90 cases/100,000, while the other two range from 40 to 70 cases/100,000. TB incidence and socio-economic status had a significant curvilinear relationship (P = 0.02). CONCLUSIONS Data derived from these spatial statistical tools will help TB control programs to allocate TB resources to those populations most at risk of increasing TB rates and to target areas where TB control efforts need to be concentrated.
The Evolutionary Sequence of Post-Starburst Galaxies

© 2017 The Authors. There are multiple ways in which to select post-starburst galaxies in the literature. In this work, we present a study into how two well-used selection techniques have consequences on observable post-starburst galaxy parameters, such as colour, morphology and environment, and how this affects interpretations of their role in the galaxy duty cycle. We identify a master sample of Hδ strong (EWHδ> 3A) post-starburst galaxies from the value-added catalogue in the seventh data release of the Sloan Digital Sky Survey (SDSS DR7) over a redshift range 0.01 -2.5A) but one having an additional cut onEWHα (> -3A). We examine the differences in observables and AGN fractions to see what effect the Hα cut has on the properties of post-starburst galaxies and what these differing samples can tell us about the duty cycle of post-starburst galaxies. We find that Hδ strong galaxies peak in the 'blue cloud', E+As in the 'green valley' and pure E+As in the 'red sequence'. We also find that pure E+As have a more early-type morphology and a higher fraction in denser environments compared with the Hδ strong and E+A galaxies. These results suggest that there is an evolutionary sequence in the post-starburst phase from blue discy galaxies with residual star formation to passive red early-types.
A conceptual brain machine interface system

While even a single bit output can impart a great deal of improvement in quality of life to patients, a richer vocabulary could obviously mean an even greater degree of control. This paper discusses ideas about extending previous results of using a support vector machine (SVM) based brain machine interface (BMI) to include multiple directions and magnitudes. It also investigates the number of neurons needed to create an accurate two direction result.
Stability, L1-gain and controller design for switched positive delay systems with uncertainties

By employing mode-dependent average dwell time (MDADT) switching, the problems of robust stability, L1-gain performance and controller design are addressed for switched delay positive systems with polytopic uncertainty. First, sufficient stability and L1-gain conditions are established for the considered system with a class of multiple copositive Lyapunov-Krasovskii function approach. Then, with the aid of the derived results ahead, state-feedback controllers are developed to make sure that the corresponding system is stable with L1-gain performance. All the proposed conditions can be solved by LMI toolbox. Finally, we take an example to verify the effectiveness of the results.
Controlling Real Time Sound Spatialization Using The Radiodrum

We present a real-time, multi-channel rendering system with the radiodrum controller as an intuitive, handson interface to a 3D spatialization system. The radiodrum is a virtual controller and interface that allows for very rapid tracking of two augmented drum sticks in 3D space. We have combined this interface with a real time 3D visualization system that allows a user to control the position of sound sources using an array of loudspeakers, typically setup in a cube model inside a rectangular room. To generate the auditory scene, we use a model that is a combination of an image source model and a model developed by Moore in which virtual sounds are positioned and moved using a combination of delay lines.
Mining Association Rules Related to Protein-Protein Interactions

Recently, protein-protein interactions are systematically examined with the yeast two-hybrid method [2, 4]. As a result, a large quantity of information about protein-protein interactions is accumulated. However, general information or knowledge about interactions is not so much identified although a lot of individual interactions are identified using such methods. On the other hand, the technique to extract useful information or knowledge hidden in vast data, which is called “data mining”, attracts a great deal of attention, and several researches applying data mining to bioinformatics have already been done [3]. For this reason, we are studying and developing a system to discover knowledge or useful information related to protein-protein interactions from accumulated protein-protein interaction data, using the “association rules discovery” algorithm [1] that is a popular method of data mining.
Acidic urine pH is associated with elevated levels of free urinary benzidine and N-acetylbenzidine and urothelial cell DNA adducts in exposed workers.

We evaluated the influence of urine pH on the proportion of urinary benzidine (BZ) and N-acetylbenzidine present in the free, unconjugated state and on exfoliated urothelial cell DNA adduct levels in 32 workers exposed to BZ in India. Postworkshift urine pH was inversely correlated with the proportions of BZ (r = -0.78; P < 0.0001) and N-acetylbenzidine (r = -0.67; P < 0.0001) present as free compounds. Furthermore, the average of each subject's pre- and postworkshift urine pH was negatively associated with the predominant urothelial DNA adduct (P = 0.0037, adjusted for urinary BZ and metabolites), which has been shown to cochromatograph with a N-(3'-phosphodeoxyguanosin-8-yl)-N'-acetylbenzidine adduct standard. Controlling for internal dose, individuals with urine pH < 6 had 10-fold higher DNA adduct levels compared to subjects with urine pH > or = 7. As reported previously, polymorphisms in NAT1, NAT2, and GSTM1 had no impact on DNA adduct levels. This is the first study to demonstrate that urine pH has a strong influence on the presence of free urinary aromatic amine compounds and on urothelial cell DNA adduct levels in exposed humans. Because there is evidence that acidic urine has a similar influence on aromatic amines derived from cigarette smoke, urine pH, which is influenced by diet, may be an important susceptibility factor for bladder cancer caused by tobacco in the general population.
Developmental and regional expression of three new members of the ras‐gene family in the mouse brain

We have examined the expression in the mouse nervous system of three new members of the ras protooncogene family: rab1, rab2, and rab3. Each of these genes was transcribed into messenger RNAs with different molecular weights. These transcripts had specific developmental and regional patterns of expression. In particular, for the three genes, the ratio between the heavy and light mRNAs depended strongly on developmental stage and brain region. The use of pure neuronal and glial cultures revealed that the high molecular weight transcripts were enriched in neurons and that, in the case of rab2 and rab3, their expression increased with neuronal differentiation. These results are discussed considering the sequence identities between these genes and the yeast YPT1 and sec‐4 genes, which are known to be implicated in post‐Golgi vesicular transport and cytoskeletal stabilization. We propose that the rab genes might be of importance in the regulation of these two processes within the developing and adult nervous system.
This is the closest I have come to being compared to a doctor: Views of medical students on clinical clerkship in an Interprofessional Training Unit

Background: The need for interprofessional education has been apparent for decades and in 2004, we established the first Interprofessional Training Unit (ITU) in Denmark. Nursing, occupational therapy and physiotherapy students were in the ITU for its first 2 years and in 2006, medical students joined in. The students in collaboration run a ward with eight beds under the supervision of trained personnel. Methods: A questionnaire consisting questions concerning the interprofessional meetings, the rounds, teaching, learning about own profession, learning about other professions and finally an overall assessment of their stay in the ITU was filled in by 55 medical students. To validate and deepen the questionnaire, 22 medical students participated in a group interview concentrating on the students’ evaluation of fulfilment of the goals for the ITU. The transcripted interview and the written comments in the questionnaire were analysed using Systematic Text Condensation. Results: Our results showed that the medical students in the ITU developed their professional knowledge and capability simultaneous with the learning of interprofessional collaboration. The students valued the teaching methods because the students were in the forefront and treated as professionals. The students demanded more homogeneous instruction and a better introduction to the ITU. Conclusion: A stay in an ITU with a safe learning environment can increase both uniprofessional and interprofessional learning for medical students. The students stressed the importance of supervision before and after carrying out a hospital task.
Visualization of fetal intra‐abdominal organs in second‐trimester severe oligohydramnios by intraperitoneal infusion

Fetal intraperitoneal infusion of saline was performed in two patients with severe oligohydramnios at 24 and 25 weeks' gestation in order to enhance visualization of intra‐abdominal organs. Renal agenesis was easily diagnosed. The technique can be considered as an alternative to artificial instillation of amniotic fluid in the differential diagnosis of conditions associated with severe oligohydramnios.
Urinary excretion of choline metabolites following choline administration in normals and patients with hepatobiliary diseases.

Choline has been recommended for the treatment of hepatic diseases, especially those of nutritional origin, and for the prevention of arteriosclerosis. Little is known of its fate after oral or intravenous administration. A recent Spanish report (1) that patients with liver diseases and dogs with experimental hepatic damage excrete in the urine considerably more than normal of a substance precipitated by Reinecke salt (and considered as choline by the authors) after large doses of choline given orally, suggested that the utilization of choline might be altered in hepatobiliary disease. In addition, studies with radiophosphorous (2) indicate a reduced rate of phospholipid formation in the presence of hepatocellular damage and an increased rate in biliary obstruction, suggesting that less choline might appear in the urine than normal in obstructive jaundice and more than normal in liver cell damage. To test these hypotheses and to investigate the fate of choline after its oral adrministration 1 ) the identity of the reineckate precipitated from the urine was determined, and 2) the influence upon its excretion of physiologic conditions as well as hepatobiliary diseases was studied.
Association of pregnancy outcome with cytokine gene polymorphisms in HEV infection during pregnancy

Hepatitis E virus (HEV) infection is associated with high maternal and fetal mortalities. The aim of the study was to find cytokine gene polymorphisms in relation to HEV infection during pregnancy. A total of 262 pregnant and 208 non‐pregnant women with hepatitis, 262 healthy pregnant and 208 non‐pregnant women as controls. The study group were pregnant and non‐pregnant women with HEV infection, not infected with HEV and controls. Genotyping was carried out by PCR‐RFLP and ARMS‐PCR methods. The frequencies of TNF‐α −308 A allele & AA genotype, IFN‐γ +874 T allele & TT genotypes were significantly higher in pregnant women with HEV infection compared to other groups. The frequency of TGF‐β1 codon 10 +869 T allele &TT genotype and codon 25 +915 G allele & GG genotype were significantly higher in pregnant women compared to non‐pregnant women with HEV infection. The frequency of IL‐6‐174 GG genotype was significantly higher in pregnant women with HEV infection compared to not infected with HEV and controls. Cytokine gene polymorphisms shows association with preterm delivery (TNF‐α −308 AA, IFN‐γ +874 AA, TGF‐β1 codon 10 +869 TT & codon 25 GG genotypes), low birth weight (TNF‐α −308 GG & IL‐6 −174 CC genotypes), fetal loss (IL‐6‐174 CC genotype), and small for date (IL‐6‐174 CC & TGF‐β1 codon 10 +869 TC genotypes) of HEV infected pregnant women compared to not infected with HEV and controls. These findings suggest that cytokines gene polymorphisms were found to be associated with pregnant women with HEV infection and adverse pregnancy outcome. J. Med. Virol. 86:1366–1376, 2014. © 2014 Wiley Periodicals, Inc.
Genetic susceptibility to environmental toxicants in ALS

Environmental toxicants such as heavy metals, pesticides, and chemicals appear to be risk factors for sporadic amyotrophic lateral sclerosis (SALS). An impaired ability to break down these toxicants because of differences in detoxification genes could underlie some cases of this disease. We therefore examined the frequencies of single nucleotide polymorphisms (SNPs) in 186 SALS patients and 186 controls at the allele, genotype, and haplotype levels for the metallothionein (MT) family of genes, metal transcription factor‐1 (MTF‐1), and glutathione synthetase (GSS). Exposure to heavy metals, solvents/chemicals, and pesticides/herbicides was assessed by questionnaire, and gene‐toxicant interactions were analyzed. An intronic SNP upstream of MT‐Ie differed in SALS patients and controls at the allele and genotype levels. Haplotypes covering MT‐I isoforms also differed between the two groups. Alleles and genotypes of one MTF‐1 SNP differed in female SALS patients. One GSS haplotype interacted with both metals and solvents/chemicals to increase the risk of the disease. Differences in genes involved in handling toxicants, and interactions between toxicants and these genes, appear to be present in some patients with SALS. This suggests that impaired detoxification mechanisms play a role in SALS. © 2007 Wiley‐Liss, Inc.
ASSESSING NOVEL GENES ASSOCIATED WTIH STARCH CONTENT IN MAIZE THROUGH TRANSCRIPT PROFILING ANALYSIS

Presently there is increased interest in studying and improving crops for production of bio-fuels. Improving starch concentration in maize (Zea mays L.) would likely be a great asset for the ethanol industry. From the cross of the high starch maize line Illinois Low Protein cycle 90 (ILP) × B73 backcrossed to B73, 150 S1, 138 S3, and 138 S3 testcross lines were developed. Transcript profiling analysis was employed to assess differences in gene expression between selected high and low starch S1 families and testcross progenies. Two time points, 15 and 20 days after pollination (DAP), were evaluated. A model was implemented to identify overall differentially expressed genes in the two populations. In addition, the contrast of the 15 vs. 20 DAP was used to identify genes that increased or decreased relative expression during seed development. A total of 89 genes with consistent expression patterns across time points and populations were selected. None of the genes evaluated were found significant in the 15 vs. 20 DAP contrast indicating no major changes in gene expression between high and low families occur between the two time points. Only two known starch biosynthesis related genes were identified. One, alpha amylase inhibitor (AAI), showed the highest fold difference in expression among all genes represented on the chip. Further expression differential of this gene was evaluated in RT-PCR which strengthened the hypothesis of the gene being related to final starch concentration present in materials derived from ILP×B73. Our results strongly support a likely function of AAI gene in final starch accumulated in ILP×B73 derived materials. In order for higher starch concentration materials to serve as useful donors to commercial hybrids, they should provide reasonably competitive grain yields. Thus in the oral presentation we provide information on yield trial performance of testcross hybrids of ILP/B73 derived materials in relation to commercial checks and experimental hybrids derived from PVP released materials. *Present Address: 7963 Paseo Aliso, Carlsbad, CA 92009
Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors

Components of multiprotein complexes are routinely determined by using proteomic approaches. However, this information lacks functional content except when new complex members are identified. To analyze quantitatively the abundance of proteins in human Mediator we used normalized spectral abundance factors generated from shotgun proteomics data sets. With this approach we define a common core of mammalian Mediator subunits shared by alternative forms that variably associate with the kinase module and RNA polymerase (pol) II. Although each version of affinity-purified Mediator contained some kinase module and RNA pol II, Mediator purified through F-Med26 contained the most RNA pol II and the least kinase module as demonstrated by the normalized spectral abundance factor approach. The distinct forms of Mediator were functionally characterized by using a transcriptional activity assay, where F-Med26 Mediator/RNA pol II was the most active. This method of protein complex visualization has important implications for the analysis of multiprotein complexes and assembly of protein interaction networks.
Structure of butterfly scales: Patterning in an insect cuticle

All butterfly and moth scales and bristles are made of non‐living insect cuticle. Each is the product of a single epithelial cell, and all share the same basic architecture. However, some are highly specialized, and their cuticle is further elaborated into stacks of thin‐films, lattices, or other minute structures, many of which first came to our attention because they interact, with light to produce structural colors. The scale cell forms the scale by extruding a projection of itself and secreting around it the outer epicuticle, a thin cuticular envelope which will form the outermost layer of the scale. The inner layers of cuticle, collectively called the procuticle, are secreted thereafter and go on to form the lattices, pillars, or other internal structures of the scale. We believe that the pattern‐forming mechanisms used by the cell to shape the cuticle into its finished form include elastic buckling of the outer epicuticle to produce external folds, and “masking” of certain areas of the original epicuticular envelope to produce thin spots which will break through to become windows. Varied though they be, all insect cuticular patterns have common basic elements, which suggests that our findings may be generalized to other highly patterned insect cuticles, particularly those formed by single cells. © 1994 Wiley‐Liss, Inc.
A patient fatality following the ingestion of a small amount of chlorfenapyr

Chlorfenapyr has been used worldwide for agricultural pest control since 1995. Despite its widespread use, acute human poisoning data are insufficient; only a small number of fatalities from chlorfenapyr poisoning have been reported. The signs and symptoms of chlorfenapyr toxicity include nausea, vomiting, fever, rhabdomyolysis, among others. In addition, central nervous system effects in association with delayed toxicity have also been observed. Here, we detail a fatality resulting from delayed chlorfenapyr toxicity following the ingestion of a small amount of pesticide.
Gridded Aclar: preparation methods and use for correlative light and electron microscopy of cell monolayers, by TEM and FIB–SEM

Aclar, a copolymer film with properties very similar to those of tissue culture plastic, is a versatile substrate to grow cells for light (including fluorescence) and electron microscopic applications in combination with both chemical fixation and cryoimmobilization. In this paper, we describe complete procedures to perform correlative light and electron microscopy using Aclar as substrate for the culture of cell monolayers to be finally embedded in plastic. First, we developed straightforward, efficient and flexible ways to mark the surface of the Aclar to create substrates to locate cells first at the light microscopy and then the electron microscopy level. All the methods enable the user to self‐design gridded Aclar pieces, according to the purpose of the experiments, and create a large number of substrates in a short time. Second, we confirmed that marked Aclar supports the normal growth and morphology of cells. Third, we validated the correlative light and electron microscopy procedure using Aclar. This validation was done for the high‐resolution analysis of endothelial cells using transmission electron microscopy and focused ion beam–scanning electron microscopy in combination with the use of fluorescence, phase contrast and/or bright field microscopy to map areas of interest at low resolution. The methods that we present are diverse, easy to implement and highly reproducible, and emphasize the versatility of Aclar as a cell growth substrate for diverse microscopic applications.
The Role of Climatic Anomalies and Soil Moisture in the Decline of Drought-Prone Forests

Increased intensity and duration of droughts and high-temperature events have been associated with forest decline in many parts of the world, and these decline events are expected to become more common under climate change. There is, therefore, a need for monitoring and modeling of forest decline. We used a regional forest condition monitoring program (DEBOSCAT) to study the spatial distribution of decline events in 2012 in Catalonia (Northeastern Spain) and their relationship with climatic factors. In 2012, this dataset was collected after an extraordinarily dry summer, and allowed the study of decline events in eight dominant tree species. We fitted a logistic model to predict forest decline probability as a function of species, precipitation and temperature anomalies, solar radiation, and remotely sensed soil moisture data from the Soil Moisture and Ocean Salinity Mission (SMOS). Broadleaved species were more affected by decline events than conifers. The statistical model explained almost 40% of forest decline occurrence, wherein almost 50% of this variability was explained by species effect, with broadleaved trees being generally more sensitive to the studied factors than conifers. Climatically wetter areas and those more exposed to radiation were more likely to be affected, suggesting better adaptation of forests in dry areas. In general, more damaged forests were characterized by high-positive temperature anomalies, lower than average rainfall, and low soil moisture in summer 2012. The most vulnerable species was Fagus sylvatica, a Euro-Siberian species, contrasting with Pinus halepensis, a typically Mediterranean species, which showed low sensitivity to drought.