Miracle-dz/UniFAR-FTUs huggingface dataset:
New heterologous modules for classical or PCR‐based gene disruptions in Saccharomyces cerevisiae

We have constructed and tested a dominant resistance module, for selection of S. cerevisiae transformants, which entirely consists of heterologous DNA. This kanMX module contains the known kanr open reading‐frame of the E. coli transposon Tn903 fused to transcriptional and translational control sequences of the TEF gene of the filamentous fungus Ashbya gossypii. This hybrid module permits efficient selection of transformants resistant against geneticin (G418). We also constructed a lacZMT reporter module in which the open reading‐frame of the E. coli lacZ gene (lacking the first 9 codons) is fused at its 3′ end to the S. cerevisiae ADH1 terminator. KanMX and the lacZMT module, or both modules together, were cloned in the center of a new multiple cloning sequence comprising 18 unique restriction sites flanked by Not I sites. Using the double module for constructions of in‐frame substitutions of genes, only one transformation experiment is necessary to test the activity of the promotor and to search for phenotypes due to inactivation of this gene. To allow for repeated use of the G418 selection some kanMX modules are flanked by 470 bp direct repeats, promoting in vivo excision with frequencies of 10–3–10–4. The 1·4 kb kanMX module was also shown to be very useful for PCR based gene disruptions. In an experiment in which a gene disruption was done with DNA molecules carrying PCR‐added terminal sequences of only 35 bases homology to each target site, all twelve tested geneticin‐resistant colonies carried the correctly integrated kanMX module.
Anti‐HCV therapies in chimeric scid‐Alb/uPA mice parallel outcomes in human clinical application

Compounds with in vitro anti‐hepatitis C virus (HCV) activity are often advanced directly into clinical trials with limited or no in vivo efficacy data. This limits prediction of clinical efficacy of compounds in the HCV drug pipeline, and may expose human subjects to unnecessary treatment effects. The scid‐Alb‐uPA mouse supports proliferation of transplanted human hepatocytes and subsequent HCV infection. Cohorts of genotype 1a HCV‐infected mice were treated with interferon α‐2b(IFN‐α), BILN‐2061 (anti‐NS3 protease), or HCV371 (anti‐NS5B polymerase). Mice treated with 1350IU/g/day IFN‐α intramuscularly for 10 to 28 days demonstrated reduced viral titers compared with controls in all five experiments (P < .05, t test); viral titers rebounded after treatment withdrawal. A more pronounced antiviral effect with IFN‐α was seen in genotype 3a–infected mice. Pilot studies with BILN2061 confirmed exposure to 10X replicon EC50 at trough and reduced viral titer over 2 log at 4 days. In a second 7‐day study, mean HCV RNA titers dropped 1.1 log in BILN2061‐treated animals, 0.6 log in IFN‐treated mice, and rose 0.2 log in controls (P = .013, ANOVA). Pre‐existing mutants with partial resistance to BILN2061 were identified by sequencing both the human inoculum and sera from treated mice. The polymerase inhibitor HCV371 yielded a decline in HCV titers of 0.3 log relative to vehicle‐treated controls (P = NS). Performance of all three antiviral regimens in the chimeric mouse model paralleled responses in humans. In conclusion, this system may help selection of lead compounds for advancement into human trials with an increased likelihood of clinical success while broadening the tools available for study of the biology of HCV infection. (HEPATOLOGY 2006;43:1346–1353.)
Air pollution, obesity, genes and cellular adhesion molecules

Objectives Particulate matter has been associated with acute cardiovascular outcomes, but our understanding of the mechanism is incomplete. We examined the association between particulate matter and cell adhesion molecules. We also investigated the modifying effect of genotype and phenotype variation to gain insight into the relevant biological pathways for this association. Methods We used mixed regression models to examine the association of PM2.5 (particulate matter ≤2.5 μm in diameter) and black carbon with serum concentrations of soluble intercellular adhesion molecule (sICAM-1) and soluble vascular cell adhesion molecule (sVCAM-1), markers of endothelial function and inflammation, in a longitudinal study of 809 participants in the Normative Ageing Study (1819 total observations). We also examined whether this association was modified by genotype, obesity or diabetes status. Genes selected for analyses were either related to oxidative stress, endothelial function, lipid metabolism or metal processing. Results Black carbon during the 2 days prior to blood draw was significantly associated with increased sVCAM-1 (4.5% increase per 1 μg/m3, 95% CI 1.1 to 8.0). Neither pollutant was associated with sICAM-1. Larger effects of black carbon on sVCAM were seen in subjects with obesity (p=0.007) and who were GSTM1 null (p=0.02). Conclusions Black carbon is associated with markers of endothelial function and inflammation. Genes related to oxidative defence may modify this association.
Childhood maltreatment modifies the relationship of depression with hippocampal volume

Background. Childhood maltreatment (CM) may modify the relationship between major depressive disorder (MDD) and hippocampal volume reduction. To disentangle the impact of MDD and CM on hippocampal volume we investigated the association between MDD and hippocampal volume in persons with and without a history of CM in two independent cohorts. Method. We used data of 262 participants from the Netherlands Study of Depression and Anxiety (NESDA) (mean age 37 years, 32% male) and 636 participants from the SMART-Medea study (mean age 61 years, 81% male). In both studies a 12-month diagnosis of MDD and CM were assessed using a diagnostic interview. Hippocampal volume was measured in NESDA using FreeSurfer software on 3-T magnetic resonance (MR) images and in SMART it was manually outlined on 1.5-T MR images. With analysis of covariance adjusted for intracranial volume, age, gender and lifestyle factors we estimated the effects of MDD and CM on hippocampal volume. Results. In both cohorts CM was not significantly associated with hippocampal volume. After pooling the data MDD was associated with smaller hippocampal volume (B = −138.90 mm3, p = 0.05) and the interaction between MDD and CM reached significance (p = 0.04); in participants with CM, MDD was related to smaller hippocampal volume (NESDA: B = −316.8 mm3, p = 0.02; SMART: B = −407.6, p = 0.046), but not in participants without CM (p > 0.05). Conclusions. Our study shows that in two independent cohorts, particularly in individuals with CM, a diagnosis of MDD is related to smaller hippocampal volume. Prospective studies are needed to further determine through which mechanism CM may amplify the relationship between MDD and hippocampal volume.
Influence of non-monetary information signals of the USA on the Ukrainian stock market volatility

The Ukrainian PFTS stock index volatility reaction as a whole and its constituent economic sectors (“Basic Materials”, “Financials”, “Industrials”, “Oil &amp; Gas”, “Telecommunications”, “Utilities”) to seven non-monetary US information signals (“Consumer price index”, “Personal spending”, “Unemployment rate”, “Gross domestic product”, “Industrial production”, “Consumer confidence”, “Housing starts”) was carried out for the period 2000–2017 on the basis of closing stock quotations in the trading day format. To assess the “surprise” component direct influence nature of the USA selected non-monetary information signals on the PFTS stock index, an AR-GARCH econometric modelling device was used. The results achieved clearly indicate the presence of some PFTS stock index economic sectors heterogeneous reaction to the United States individual non-monetary information signals announcement. For example, such economic sectors as “Basic Materials”, “Financials”, and “Oil &amp; Gas” volatility response to the US non-monetary information signal “Consumer price index” “surprise” components the opposite of the overall PFTS stock index reaction. It can also be concluded that the United States non-monetary information signals influence on the Ukrainian stock market volatility depends not only on the financial cycle phase and data frequency, but also on the PFTS stock index economic sector.
Optimal Determination of Antenna Height and Power in a Mass per Swath Width Sense for a Given Incidence Angle

An optimal antenna height and power determination is proposed for the cost-effective implementation of the spaceborne stripmap synthetic aperture radar (SAR) satellite. For a given azimuth resolution, the antenna height and the average transmitted RF power of the SAR antenna are determined so that the mass per swath width of a SAR satellite can be minimized with the constraints on the signal-to-noise ratio (SNR) and ambiguities, given the SAR geometry (an altitude and an incidence angle) and radar wavelength. The illustrative design example shows that the mass per swath width of a SAR satellite, obtained from the proposed optimization, for the required SNR (SNRreq = 10 dB) and the specified incidence angle (eta = 45 deg), is about 72% of that resulted from utilizing the minimum antenna height.
Vision-based control of a quadrotor for an object inspection scenario

Unmanned aerial vehicles (UAVs) have gained special attention in recent years, among others in monitoring and inspection applications. In this paper, a less explored application field is proposed, railway inspection, where UAVs can be used to perform visual inspection tasks such as semaphore, catenary, or track inspection. We focus on lightweight UAVs, which can detect many events in railways (for example missing indicators or cabling, or obstacles on the tracks). An outdoor scenario is developed where a quadrotor visually detects a railway semaphore and flies around it autonomously, recording a video of it for offline post-processing. For these tasks, we exploit object detection methods from literature, and develop a visual servoing technique. Additionally, we perform a thorough comparison of several object detection approaches before selecting a preferred method. Then, we show the performance of the presented filtering solutions when they are used in servoing, and conclude our experiments with evaluating real outdoor flight trajectories using an AR.Drone 2.0 quadrotor.
Self‐consciousness and Alzheimer's disease

Objectives– To propose a neuropsychological study of the various aspects of self‐consciousness (SC) in Alzheimer's disease. Methods– Forty‐five patients with probable mild or moderate AD were included in the study. Severity of their dementia was assessed by the Mini Mental State (MMS). Fourteen questions were prepared to evaluate SC. Results– No significant correlations were found between SC score and educational level, age, and duration of disease. A significant correlation was found between SC score and the severity of dementia, whereas frontal disturbances were just short of the significance threshold. The various aspects of SC were not impaired to the same degree. The most disturbed ones were awareness of cognitive deficiencies, moral judgements and prospective memory. The least disturbed aspects were awareness of identity and of mental representation of the body. Items relating to anosognosia and moral judgements were significantly correlated with the MMS score, whereas affective state, body representation disorders, prospective memory, and capacities for introspection were not related to the severity of the dementia. Consciousness of identity was sound, regardless of MMS score. Conclusions– AD clearly induces an heterogeneous impairment of SC. SC requires a convergence of many neural networks. In AD, neuronal alterations involve many cortical areas and information sent to the associative frontal cortex from memory, language and visuospatial areas is lacking or disturbed. Thus, the sequential order of successive stimuli cannot be maintained by the heteromodal associative cortex (dorsal convexity of the prefrontal cortex), and the supramodal associative cortex (located rostrally in the frontal lobes) is unable to provide reliable monitoring and assessment of simultaneous neural cognitive networks carrying insufficient and inadequate input. The core deficiency in AD patients might be impaired SC equated with the disability to maintain sequential and simultaneous “attention to life”. The Self‐Consciousness Questionnaire, a clinical scale providing multidimensional measurement, indicates that different aspects of consciousness are not correlated with overall cognitive deficiency as determined by the MMSE.
Involvement of Asada-Halliwell Pathway During Phytoremediation of Chromium (VI) in Brassica juncea L. Plants

Brassica juncea (Indian mustard) L. plants were exposed to different concentrations (0.0, 0.1, 0.3 and 0.5 mM) of Chromium (Cr) and harvested after 30 and 60 days of sowing for the analysis of growth parameters, metal uptake and oxidative stress markers. Significant accumulation of Cr (VI) by B. juncea L. plants resulted in the reduced growth and modulations in the pool of various biochemical stress markers. The toxic effects of Cr (VI) on growth and other stress markers (protein content, lipid peroxidation and antioxidative enzymes viz.SOD, CAT, POD, APOX, GR, DHAR and MDHAR) in B. juncea L. were observed to be concentration and time dependent. Effect of Cr (VI) on biochemical parameters was differential and their maximum activities of SOD, POD, APX, GR, DHAR and lipid peroxidation were recorded at 0.5 mM concentration in 30 days old plants. Whereas, trend in the activities of most of the stress markers was reversed in 60 days old plants. The results obtained from the study suggested that Cr (VI) stress inhibited growth of B. juncea L. plants is directly interrelated with its accumulation and resulted in the modulation in activities of various stress markers.
Association of body position with sleep architecture and respiratory disturbances in children with obstructive sleep apnea

Conclusions. Sleep position in children with obstructive sleep apnea (OSA) did not affect the sleep architecture. Supine position had a significant influence on respiratory parameters and gas exchange. Lateral position did not affect respiratory parameters in children aged 3–5 years and little affected gas exchange except right lateral decubitus (RLD) position in children aged 11–13 years. Children with OSA breathe best when in the left lateral decubitus (LLD) position. Objective. To analyze the relationship between OSA and body position during sleep in children. Subjects and methods. A total of 45 consecutive children (age class A: 3–5 years, n=15; B: 6–10 years, n=14; C: 11–13 years, n=16) with OSA were studied. The following variables were evaluated: apnea hypopnea index (AHI) in supine, LLD, and RLD positions, sleep architecture, respiratory parameters, and oxygen saturation. Results. There were no no significant differences in AHI between LLD AHI, RLD AHI, and supine position in age class A, LLD AHI was significantly lower than supine AHI in age classes B and C. There was no correlation between position AHI and sleep architecture. There was no correlation between lateral position AHI and the parameters of respiratory disturbance in age class A. The parameters of respiratory disturbance were related to LLD and RLD position in age class B; supine and RLD position in age class C were similar. Position AHI was related to some of the parameters of gas exchange except for RLD AHI in age classes A and B.
Re‐innervation and recovery of rat soleus muscle and motor unit function after nerve crush

In this study we have investigated the effects of peripheral nerve crush on the contractile properties of the adult rat soleus muscle. The soleus nerve was crushed close to the muscle and functional re‐innervation was assessed by the measurement of the force produced by contraction induced by electrical nerve stimulation. Whole soleus muscle and single motor unit (MU) properties were studied at increasing re‐innervation times 7–56 days after crush. Results showed progressive re‐innervation as 50% of the axotomized motoneurones had re‐innervated their muscle 7 days after crush, 72% at 14 days and re‐innervation was complete at 28 days. The force parameters recovered more slowly. Tetanic contractions faded at high frequency stimulation, which did not occur in the control muscle. This disruption in the tetanic response was more pronounced in single MUs. Our results demonstrate for the first time a process of progressive axonal re‐innervation by the axotomized motoneurones and provide a functional picture of the effective restoration of the neuromuscular function.
Profitability vs. Credit Score Models—A New Approach to Short Term Credit in the UK

The profitability lending model was initially discussed by Eisenbeis [1] who suggested that it might be possible to build a lending model that prevailed the traditional scorecard models. In this paper, we study a unique dataset from a personal loan company based in the United Kingdom, which offered overdraft-style short-term loans to individuals with low and high credit scores during the last few years. Our results conclude that credit score does not significantly impact profitability in the overdraft market. Moreover, we argue that, assuming a good understanding of low credit score individuals, a business model that grants loans to these “new” customers is as sustainable and commercially viable as lending to higher credit profile applicants.
Prevalence of Multiple Sclerosis Door-to-Door Survey in Maltepe, Istanbul, Turkey

Background: The prevalence of multiple sclerosis (MS) in Istanbul, Turkey, is unknown. We investigated the prevalence of MS in the district of Maltepe, Istanbul, Turkey. Methods: This was a cross-sectional field research study using door-to-door sampling. Maltepe is a district of Istanbul beside the sea of Marmara (population 359,298 from 2000 census). The two-phase study screened 32,531 subjects using the Poser criteria for clinical diagnosis. The χ2 test was used for analyses of frequency distributions. Results: 33 of 32,531 people were diagnosed with MS. Their average age was 41 ± 12.0 years (43 ± 12.7 years for females and 37 ± 9.6 years for males). The prevalence of MS in Maltepe was 101.4/100,000 within the total population (118.7/100,000 in the female and 76.0/100,000 in the male populations). Conclusions: The prevalence rates of MS in the Turkish population living in a district of Istanbul are considerably higher than we thought. And the prevalence rate is much higher than neighboring countries. They are similar to those recently recorded in Sicily and Germany. These figures suggest that the prevalence rate of MS is not totally dependent upon geographical variation. However, the research of our results needs to be confirmed with further investigations in order to determine the prevalence of MS in Turkey with confidence.
Improved Immunogenicity and Protective Efficacy of a Tuberculosis DNA Vaccine Encoding Ag85 by Protein Boosting

ABSTRACT C57BL/6 mice were vaccinated with plasmid DNA encoding Ag85 fromMycobacterium tuberculosis, with Ag85 protein in adjuvant, or with a combined DNA prime-protein boost regimen. While DNA immunization, as previously described, induced robust Th1-type cytokine responses, protein-in-adjuvant vaccination elicited very poor cytokine responses, which were 10-fold lower than those observed with DNA immunization alone. Injection of Ag85 DNA-primed mice with 30 to 100 μg of purified Ag85 protein in adjuvant increased the interleukin-2 and gamma interferon (IFN-γ) response in spleen two- to fourfold. Further, intracellular cytokine analysis by flow cytometry also showed an increase in IFN-γ-producing CD4+ T cells in DNA-primed–protein-boosted animals, compared to those that received only the DNA vaccination. Moreover, these responses appeared to be better sustained over time. Antibodies were readily produced by all three methods of immunization but were exclusively of the immunoglobulin G1 (IgG1) isotype following protein immunization in adjuvant and preferentially of the IgG2a isotype following DNA and DNA prime-protein boost vaccination. Finally, protein boosting increased the protective efficacy of the DNA vaccine against an intravenousM. tuberculosis H37Rv challenge infection, as measured by CFU or relative light unit counts in lungs 1 and 2 months after infection. The capacity of exogenously given protein to boost the DNA-primed vaccination effect underlines the dominant role of Th1-type CD4+ helper T cells in mediating protection.
Enhancing Genome-Enabled Prediction by Bagging Genomic BLUP

We examined whether or not the predictive ability of genomic best linear unbiased prediction (GBLUP) could be improved via a resampling method used in machine learning: bootstrap aggregating sampling (“bagging”). In theory, bagging can be useful when the predictor has large variance or when the number of markers is much larger than sample size, preventing effective regularization. After presenting a brief review of GBLUP, bagging was adapted to the context of GBLUP, both at the level of the genetic signal and of marker effects. The performance of bagging was evaluated with four simulated case studies including known or unknown quantitative trait loci, and an application was made to real data on grain yield in wheat planted in four environments. A metric aimed to quantify candidate-specific cross-validation uncertainty was proposed and assessed; as expected, model derived theoretical reliabilities bore no relationship with cross-validation accuracy. It was found that bagging can ameliorate predictive performance of GBLUP and make it more robust against over-fitting. Seemingly, 25–50 bootstrap samples was enough to attain reasonable predictions as well as stable measures of individual predictive mean squared errors.
Two schemes for pulse compression in gas-filled kagomé-PCF

Two schemes for multi-μJ pulse compression in noble-gas-filled hollow-core kagomé-PCF are demonstrated and compared. A fiber-plus-chirped-mirror combination compresses 150 fs, 9.5 μJ pulses to 26 fs, and soliton-effect compression produces sub 7 fs pulses.
Optimization Methods of Torque Density for Developing the Neodymium Free SPOKE-Type BLDC Motor

In this paper, we propose a method for optimizing the torque density to develop a SPOKE-type brushless direct current (BLDC) motor that does not require the use of a neodymium permanent magnet. Recently, the price of neodymium magnets has increased significantly owing to the rising prices of rare-earth minerals. Therefore, here we developed a method to maximize the torque density by using ferrite magnets instead of neodymium magnets. The proposed model was inserted into the auxiliary magnets in the center of a rotor after changing the existing interior permanent magnet-type BLDC motor to a SPOKE-type motor, and the effective air-gap flux density $(B_{g})$ was maximized. We also developed an optimization tool to determine the volume of a magnet that would generate the maximum torque at a SPOKE-type motor structure including an auxiliary magnet. We manufactured a SPOKE-type motor designed using these optimization tools. Finally, we compared and analyzed finite element method simulation results and experimental results.