Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli in settled-dust and air samples collected in residential environments in Mexico City

Escherichia coli, an important indicator of the presence of fecal material, was isolated from indoor and outdoor environments in Mexico City. The heterogeneity of E. coli was represented by 89 serotypes, most of them coming from settled-dust indoor samples; 21% of them presented antibiotic multiresistance. The numbers of plasmids were higher among the antibiotic-resistant strains. The results of this study suggest that intestinal infections produced by environmental strains could be of more epidemiological impact than previously thought.
FoxP1 Protein Shows Differential Layer Expression in the Parahippocampal Domain among Bird Species

Different bird orders show diversity in neural capabilities supported by variations in brain morphology. The parahippocampal domain in the medial pallium, together with the hippocampus proper, plays an important role in memory skills. In the present work, we analyze the expression pattern of the FoxP1 protein in the parahippocampal area of four different bird species: the nonvocal learner birds quail and chicken (Galliformes) and two vocal learner birds, i.e. the zebra finch (Passeriformes) and the budgerigar (Psittaciformes), at different developmental and adult stages. We also analyze the expression of the calbindin protein in quails and zebra finches. We observed differences in the FoxP1 parahippocampal layer among bird species. In quails, chickens, and budgerigar, FoxP1 cells were located in the outer layers of the lateral and caudolateral parahippocampal sectors. In contrast, FoxP1 immunoreactive cells appeared in the inner layer of the same sectors in the zebra finch parahippocampal domain. These differences suggest two possibilities: either the FoxP1-positive cells described in quails, chickens, and budgerigars are a different population than the one described in the zebra finch, or there are changes in the pattern of radial migration in the parahippocampal area among birds. In the present study, we show that FoxP1 expression is more similar between quails, chickens, and budgerigars than between budgerigars and zebra finches in the parahippocampal area. This result contrasts with previous data in other telencephalic structures, like the calbindin-positive projection neurons described in the striatum of budgerigars and zebra finches but not in quails and chickens. All of these data point to diversity in the evolution of different morphological characters and, therefore, a mosaic model for telencephalic evolution in birds.
STEM CELL RESEARCH: FUTURE IMPLICATIONS FOR INTERNAL MEDICINE

Over the last 20-30 years, signifi cant advances have occurred in diagnose and treatment of human disease. Notwithstanding the progress in both the quality and effectiveness of overall medical treatment, the U.S. and Europe are faced with a growing threat to the national health care systems mainly because by 2030, the number of Americans and Europeans over 65 will double (1). This will create an increasingly large group at high risk for debilitating, life threatening and costlyto-treat diseases such as cardiovascular disease, diabetes, osteoporosis and arthritis, and neurodegenerative disorders. Cardiovascular diseases remain the leading cause of death in the Western world. In addition, cardiovascular disorders are associated with signifi cant morbidity which requires expensive surgical procedures and lengthy hospitalizations(2,3). It is estimated that 50% of adults between the ages of 55 and 64 years have
sbmC, a stationary‐phase induced SOS Escherichia coli gene, whose product protects cells from the DNA replication inhibitor microcin B17

Microcin B17 (MccB17) is a ribosomally synthesized peptide antibiotic of 43 amino acids that induces double‐strand breaking of DNA in a DNA gyrase‐dependent reaction. As a consequence, the SOS regulon is induced and massive DNA degradation occurs. In this work we have characterized an Escherichia coli gene, sbmC, that in high copy number determines high cell resistance to MccB17. sbmC encodes a cytoplasmic polypeptide of 157 amino acids (Mr, 18 095) that has been visualized in SDS—polyacrylamide gels. The gene is located at min 44 of the E. coli genetic map, close to the sbcB gene. sbmC expression is induced by DNA‐damaging agents and, also, by the entry of cells into the stationary growth phase. A G → T transversion at the fifth nucleotide of the quasicanonical LexA‐box preceding the gene makes recA cells 16‐fold more resistant to exogenous MccB17. The gene product, SbmC, also blocks MccB17 export from producing cells. Altogether, our results suggest that SbmC recognizes and sequesters MccB17 in a reversible way.
A readout circuit implementation to reduce the flicker noise in MEMS electrothermal sensors

The electrothermal displacement sensors are doped silicon resistors. The electrical current through the doped silicon generates flicker and thermal noise which degrades the sensitivity of these sensors. We propose an alternative readout method in which driving the silicon heaters with a high frequency voltage instead of a dc voltage leads to a lower flicker noise. The output of the sensor, in a simple wheatstone bridge configuration, is amplified by a low noise differential amplifier which attenuates the heating high frequency voltage as a common mode input. The proposed technique has been applied to a MEMS electrothermal sensor fabricated in the standard silicon on insulator (SOI) process. Experimental results demonstrate an 8dB improvement in SNR compared to the conventional measurement technique. The achieved noise floor is less than -100 dBVrms around the 20 Hz measured signal which translates to equation to 0.1nm/√(Hz) displacement noise in a MEMS nanopositioner.
Intratumoral injection of dendritic cells in combination with local hyperthermia induces systemic antitumor effect in patients with advanced melanoma

Dendritic cells (DC) are potent antigen‐presenting cells that can present tumor antigens chaperoned by heat shock proteins (HSPs), while local hyperthermia (LHT) can increase the expression of HSPs. In this study, we determine if intratumoral injection of immature DC after LHT (LHT+IT‐DC) induces systemic antitumor immunity in patients with advanced melanoma, and investigate the potential immunological mechanisms involved in the treatments. Patients were randomly assigned to intratumoral administration of autologous immature DC triweekly, with (LHT+IT‐DC, arm A, n = 9) or without (IT‐DC, arm B, n = 9) LHT. Our results showed that there were no grade 3/4 toxicities. The time to progress (TTP) of arm A was 5 months, significantly longer than that in arm B (2 months, p < 0.05). However, the overall survival time had no statistical difference (13 months vs. 6 months, p > 0.05) between the 2 groups. Our ELISPOT assay showed a significantly increased melanoma‐specific IFN‐γ production in arm A, suggesting that LHT+IT‐DC was more effective in the induction of cytotoxic T lymphocytes (CTL) than IT‐DC alone. Furthermore, we detected an increased HSPs expression 4 hr after the first LHT, an enhanced Th1/Th2 chemokines production 24 hr after the first LHT+IT‐DC treatment, a promoted migration of DC to afferent lymph nodes, and a decreased infiltration of regulatory T cells (CD4+CD25+) and an increased infiltration of active CTL (CD8+CD28+) 48 hr after the third DC injection in arm A patients. Therefore, LHT+IT‐DC can induce effective specific antitumor immunity and facilitate a Th1‐polarized immune response in patients with advanced melanoma. © 2007 Wiley‐Liss, Inc.
An E3 ubiquitin ligase: c‐Cbl

Casitas B‐lineage lymphoma (Cbl) is an E3 ubiquitin ligase of many tyrosine kinase receptors. The authors previously detected c‐Cbl mutation and low protein expression in non‐small cell lung cancer (NSCLC). Therefore, it was hypothesized that overexpression of wild‐type c‐Cbl (c‐Cbl WT) exhibits tumor growth inhibition.
Evolution of Secondary Metabolite Genes in Three Closely Related Marine Actinomycete Species

ABSTRACT The marine actinomycete genus Salinispora is composed of three closely related species. These bacteria are a rich source of secondary metabolites, which are produced in species-specific patterns. This study examines the distribution and phylogenetic relationships of genes involved in the biosynthesis of secondary metabolites in the salinosporamide and staurosporine classes, which have been reported for S. tropica and S. arenicola, respectively. The focus is on “Salinispora pacifica,” the most recently discovered and phylogenetically diverse member of the genus. Of 61 S. pacifica strains examined, 15 tested positive for a ketosynthase (KS) domain linked to the biosynthesis of salinosporamide K, a new compound in the salinosporamide series. Compound production was confirmed in two strains, and the domain phylogeny supports vertical inheritance from a common ancestor shared with S. tropica, which produces related compounds in the salinosporamide series. There was no evidence for interspecies recombination among salA KS sequences, providing further support for the geographic isolation of these two salinosporamide-producing lineages. In addition, staurosporine production is reported for the first time for S. pacifica, with 24 of 61 strains testing positive for staD, a key gene involved in the biosynthesis of this compound. High levels of recombination were observed between staD alleles in S. pacifica and the cooccurring yet more distantly related S. arenicola, which produces a similar series of staurosporines. The distributions and phylogenies of the biosynthetic genes examined provide insight into the complex processes driving the evolution of secondary metabolism among closely related bacterial species.
Axisymmetric Wall Jet Development in Confined Jet Impingement

The flow field surrounding an axisymmetric, confined, impinging jet was investigated with a focus on the early development of the triple-layered wall jet structure. Experiments were conducted using stereo particle image velocimetry at three different confinement gap heights (2, 4, and 8 jet diameters) across Reynolds numbers ranging from 1000 to 9000. The rotating flow structures within the confinement region and their interaction with the surrounding flow were dependent on the confinement gap height and Reynolds number. The recirculation core shifted downstream as the Reynolds number increased. For the smallest confinement gap height investigated, the strong recirculation caused a disruption of the wall jet development. The radial position of the recirculation core observed at this small gap height was found to coincide with the location where the maximum wall jet velocity had decayed to 15% of the impinging jet exit velocity. After this point, the self-similarity hypothesis failed to predict the evoluti.
Modified EOX (Epirubicin, Oxaliplatin and Capecitabine) as palliative first-line chemotherapy for gastroesophageal adenocarcinoma.

BACKGROUND The efficacy of triple-drug combination regimens such as epirubicin, oxaliplatin and capecitabine (EOX) is superior to standard cisplatin/5-fluorouracil, but considerable toxicity needs to be taken into account in patients with upper gastrointestinal adenocarcinoma. Therefore, we aimed to establish a modified version of the EOX regimen with improved tolerability for these patients. PATIENTS AND METHODS Patients received palliative first-line chemotherapy with a modified EOX regimen repeated every three weeks (epirubicin 50 mg/m(2) i.v. , day 1; oxaliplatin 130 mg/m(2) i.v. , day 1; capecitabine at a twice-daily dose of 1000 mg/m(2) p.o. for two weeks). RESULTS Out of 51 patients, partial remission was observed in five (10.2%) and stable disease in 31 (60.8%). Progression-free survival was four months, and overall survival twelve months. CONCLUSION Modified EOX was generally well-tolerated and, therefore, further investigation within prospective clinical trials is warranted.
Estimation in Independent Observer Line Transect Surveys for Clustered Populations

Summary. This paper introduces a framework for animal abundance estimation in independent observer line transect surveys of clustered populations. The framework generalizes an approach given in Chen (1999, Environmental and Ecological Statistics6, in press) to accommodate heterogeneity in detection caused by cluster size and other covariates. Both parametric and nonparametric estimators for the local effective search widths, given the covariates, can be derived from the framework. A nonparametric estimator based on conditional kernel density estimation is proposed and studied owing to its flexibility in modeling the detection functions. A real data set on harbor porpoise in the North Sea is analyzed.
A new point estimate method for stochastic optimal operation of smart distribution systems considering demand response programs

Smart Distribution Systems (SDS) with different technologies in Distributed Energy Resources (DER) and different load management facilities require proper operation strategies with considering the stochastic behavior of decision variables. Accordingly, this paper proposes a new Point Estimate Method (PEM) for optimal operation of SDS considering Demand Response Programs (DRP) under uncertainty in load and generation. In this paper optimal scheduling of DER units is investigated from economic and reliability viewpoints and also, the effect of DRP on operation of SDS is studied. The network is assumed to be supplied by renewable energy resources and Energy Storage Systems (ESS). The optimization aim is to minimize the operation and maintenance costs, power loss cost and cost of energy not supplied (ENS) simultaneously. The uncertainties of load demand and renewable power generation are considered using PEM approach as remarkable tool to handle the uncertainty. Ant colony optimization (ACO) is employed to minimize the objective function as a powerful optimization algorithm. The effectiveness and efficiency of the proposed approach are validated on PG&E 69-bus distribution system. The obtained results show that the proposed framework can be considered as an efficient tool in optimal operation of future distribution networks.
Influence factors on the development of obesity in 3-year-old children based on the Toyama study.

BACKGROUND Obesity in childhood increases the risk of obesity in adulthood. Obesity in adulthood is a risk factor for chronic diseases such as hypertension and atherosclerosis. Therefore, it is important to eliminate factors influencing the development of obesity in children from the viewpoint of preventive medicine. The purpose of this study is to elucidate the relationship between obesity and lifestyle in 3-year-old children in a case-control study. METHODS Subjects were selected from the Toyama study at health checkups for 3-year-old children which are done routinely by local governments in Japan on all children of that age. A special questionnaire consisting of items on lifestyle and environmental factors of the children and past histories of parents was distributed to the Toyama study participants beforehand and was collected at the checkup. Matched-pair comparisons were performed between obese children whose body mass index was 18 or more (N = 427) and control children (N = 854) matched by sex and birth month. Multivariate stepwise conditional logistic regression analysis was also applied to assess the influence of confounding factors. RESULTS The following six factors significantly influenced the development of obese 3-year-old children using the Mantel-Haenszel method: the mother's job, limited playtime outdoors (1 hour or less), snacking irregularity, an overweight father (body mass index >/= 24), an overweight mother (body mass index >/= 24), and overweight at birth (birth weight >/= 3,500 g). An overweight mother or father, limited playtime outdoors, overweight at birth, and snacking irregularity were significantly related to obesity in 3-year-old children after adjusting for confounding factors by multivariate stepwise conditional logistic regression analysis. CONCLUSIONS We have suggested several factors influencing the development of obesity in 3-year-old Japanese children: parental overweight and overweight at birth as host factors, physical inactivity and snacking irregularity as behavioral factors, the mother's job as an environmental factor.
Comparison of Three Receiver Designs for Optical Wireless Communications using White LEDs

Three visible light optical wireless communication systems using asymmetrically clipped optical orthogonal frequency division multiplexing (ACO-OFDM) and white light emitting diodes (LEDs) are compared. The LEDs considered have a larger modulation bandwidth for the blue optical frequencies than for the rest of the transmitted optical spectrum. It is shown that for typical parameter values, a novel diversity combining receiver has slightly greater capacity than a system optimized for reception of blue light only, and that both have greater capacity than a system designed to receive the entire visible light spectrum.
Identification of ammonia and carbon monoxide based on the hysteresis of a gas-sensitive SiC field effect transistor

In this work gate bias cycled operation (GBCO) is used on a gas-sensitive SiC field effect transistor (“GasFET”) to increase the sensitivity and selectivity. Gate bias ramps introduce strong hysteresis in the sensor signal. The shape of this hysteresis is shown to be an appropriate feature both for the discrimination of various gases (NH3, CO, NO, CH4) and also different gas concentrations (250 and 500 ppm). The shape is very sensitive to ambient conditions. Thus, the influence of oxygen concentration and relative humidity as well as sensor temperature is investigated and reasons for the observed signal changes are discussed.
Modelling the application of adaptive optics to wide‐field microscope live imaging

Wide‐field fluorescence microscopy is an essential tool in modern cell biology. Unfortunately the image quality of fluorescence microscopes is often significantly degraded due to aberrations that occur under normal imaging conditions. In this article, we examine the use of adaptive optics technology to dynamically correct these problems to achieve close to ideal diffraction limited performance. Simultaneously, this technology also allows ultra‐rapid focusing without having to move either the stage or the objective lens. We perform optical simulations to demonstrate the degree of correction that can be achieved.
Liver dysfunction in chronic lymphocytic leukemia: Prevalence, outcomes, and pathological findings

The prevalence of liver dysfunction and its association with outcomes in patients with previously untreated chronic lymphocytic leukemia (CLL) is unknown. Newly diagnosed (<12 months) previously untreated CLL patients seen at Mayo Clinic, Rochester, MN between 9/1993 and 4/2016 who had baseline assessment of at least one liver function test (LFT) were included in this analysis. The prevalence of liver dysfunction at baseline, proportion of patients who acquired LFT abnormalities, time to first therapy (TTFT) and overall survival (OS) were assessed. An abnormal LFT was present in 82/2336 (3.5%) patients at diagnosis and was associated with advanced Rai stage (Rai III–IV) (21% vs. 6%; P < .001), lower hemoglobin (13.1 g/dL vs. 13.9 g/dL; P < .001), and lower platelet count (187 × 109/L vs. 200 × 109/L; P = .03). Additionally, 236 patients with normal LFTs at diagnosis developed acquired liver dysfunction during follow‐up. Patients with abnormal LFTs at diagnosis had a shorter OS compared to those with normal LFTs (HR 1.80 95% CI 1.13‐2.87; P = .014, adjusted for age, sex, Rai stage, and treatment), although TTFT was not different. Of 52 patients who underwent a liver biopsy, CLL was present in liver tissue in 39/52 (73%) patients, with the portal tracts the most common region involved. Histopathology findings of liver involvement by CLL had limited correlation with choice of CLL therapy. In conclusion, approximately 1 of 25 newly diagnosed CLL patients has abnormal LFTs at diagnosis. Although the TTFT was not different among patients with abnormal LFTs, these patients have a shorter OS compared to those with normal LFTs.
Association of COMT gene polymorphisms with systemic atherosclerosis in elderly Japanese.

AIM Atherosclerotic disease is a major health problem among the elderly, which arises from a complex interaction between genetic and environmental factors. The catechol-O-methyltransferase (COMT) gene encodes an enzyme that degrades catecholamines and estrogens to less active metabolites. The objective of this study was to examine whether polymorphisms of the COMT gene affected the severity of atherosclerotic disease in a Japanese elderly population. METHOD A total of 1536 autopsy cases of hospital deaths were assessed for the degree of pathological atherosclerotic index (PAI), coronary stenotic index (CSI) and intracranial stenotic index (ICAI), which were obtained by macroscopic examination of the luminal surface of formalin-fixed arteries. Two single nucleotide polymorphisms (SNPs) in the COMT gene, rs4633 (C/T) and rs4680 (G/A) were genotyped. The rs4680 (G/A) corresponds to a functional SNP with the substitution of valine to methionine. RESULT The CC genotype of rs4633 (C/T) and the GG genotype of rs4680 (G/A) showed a significantly higher degree of PAI and the association remained positive after adjustment for age, hypertension, diabetes, smoking and drinking (p=0.035 and p=0.031, respectively). There were no significant associations between COMT genotypes and CSI or ICAI. When male and female subjects were analyzed separately, the association was observed only in female subjects (p=0.012 and p=0.027) after adjustment for age, hypertension, diabetes, smoking and drinking. CONCLUSION The functional SNP in the COMT gene associated with the severity of atherosclerosis in a Japanese elderly population, whereby the influence of the genotype appears to be stronger in females than in males.
Human immunodeficiency virus integrase protein requires a subterminal position of its viral DNA recognition sequence for efficient cleavage

Retroviral integration requires cis-acting sequences at the termini of linear double-stranded viral DNA and a product of the retroviral pol gene, the integrase protein (IN). IN is required and sufficient for generation of recessed 3' termini of the viral DNA (the first step in proviral integration) and for integration of the recessed DNA species in vitro. Human immunodeficiency virus type 1 (HIV-1) IN, expressed in Escherichia coli, was purified to near homogeneity. The substrate sequence requirements for specific cleavage and integration of retroviral DNA were studied in a physical assay, using purified IN and short duplex oligonucleotides that correspond to the termini of HIV DNA. A few point mutations around the IN cleavage site substantially reduced cleavage; most other mutations did not have a drastic effect, suggesting that the sequence requirements are limited. The terminal 15 bp of the retroviral DNA were demonstrated to be sufficient for recognition by IN. Efficient specific cutting of the retroviral DNA by IN required that the cleavage site, the phosphodiester bond at the 3' side of a conserved CA-3' dinucleotide, be located two nucleotides away from the end of the viral DNA; however, low-efficiency cutting was observed when the cleavage site was located one, three, four, or five nucleotides away from the terminus of the double-stranded viral DNA. Increased cleavage by IN was detected when the nucleotides 3' of the CA-3' dinucleotide were present as single-stranded DNA. IN was found to have a strong preference for promoting integration into double-stranded rather than single-stranded DNA.