Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptidyl-Prolyl-cis/trans-Isomerases Mip and PpiB of Legionella pneumophila Contribute to Surface Translocation, Growth at Suboptimal Temperature, and Infection

The gammaproteobacterium Legionella pneumophila is the causative agent of Legionnaires’ disease, an atypical pneumonia that manifests itself with severe lung damage. L. pneumophila, a common inhabitant of freshwater environments, replicates in free-living amoebae and persists in biofilms in natural and man-made water systems. ABSTRACT The gammaproteobacterium Legionella pneumophila is the causative agent of Legionnaires’ disease, an atypical pneumonia that manifests itself with severe lung damage. L. pneumophila, a common inhabitant of freshwater environments, replicates in free-living amoebae and persists in biofilms in natural and man-made water systems. Its environmental versatility is reflected in its ability to survive and grow within a broad temperature range as well as its capability to colonize and infect a wide range of hosts, including protozoa and humans. Peptidyl-prolyl-cis/trans-isomerases (PPIases) are multifunctional proteins that are mainly involved in protein folding and secretion in bacteria. In L. pneumophila the surface-associated PPIase Mip was shown to facilitate the establishment of the intracellular infection cycle in its early stages. The cytoplasmic PpiB was shown to promote cold tolerance. Here, we set out to analyze the interrelationship of these two relevant PPIases in the context of environmental fitness and infection. We demonstrate that the PPIases Mip and PpiB are important for surfactant-dependent sliding motility and adaptation to suboptimal temperatures, features that contribute to the environmental fitness of L. pneumophila. Furthermore, they contribute to infection of the natural host Acanthamoeba castellanii as well as human macrophages and human explanted lung tissue. These effects were additive in the case of sliding motility or synergistic in the case of temperature tolerance and infection, as assessed by the behavior of the double mutant. Accordingly, we propose that Mip and PpiB are virulence modulators of L. pneumophila with compensatory action and pleiotropic effects.
Three-dimensional carrier-envelope-phase map of focused few-cycle pulsed Gaussian beams

We derive an analytical expression that describes the complete three-dimensional carrier-envelope phase (CEP) distribution of in the focal volume of ultrashort pulsed Gaussian beams focused by spherical mirrors or lenses. The focal CEP map depends on the so-called factor $g$ specifying the frequency-dependence of the beam width of the source few-cycle pulse, on its chirp and on the small chromatic aberration introduced by a lens without appreciably distorting or broadening the few-cycle pulse. We show how to tailor the CEP map of mirror-focused and lens-focused few-cycle pulses in order to produce negligible transversal and axial CEP variations in specific regions of the focal volume for phase-sensitive interactions of light with matter taking place in a volume or on a surface. We propose a quasi-achromatic doublet lens that can implement in practice these tailored CEP distributions.
Cannabidiol regulates the expression of hypothalamus-pituitary-adrenal axis-related genes in response to acute restraint stress

Background: Research interest has grown around the potential therapeutic use of cannabidiol in mood-related disorders, due to its anxiolytic and antidepressant-like effects. These have been partially attributed to its action as an allosteric modulator of 5-HTR1A. However, the exact mechanism supporting cannabidiol properties remains unclear. Aims: To assess the effects of cannabidiol on different targets of the hypothalamus-pituitary-adrenal axis under baseline and stress conditions. Methods: We administered cannabidiol (5 mg/kg, 15 mg/kg or 30 mg/kg, intraperitoneally) or vehicle to male C57BL/6J mice 90 min before single restraint stress exposure (20 min). Using real-time polymerase chain reaction analysis, we measured alterations in the relative gene expression of corticotropin-releasing factor in the paraventricular nucleus, pro-opiomelanocortin in the arcuate nucleus of the hypothalamus, glucocorticoid receptor in the hippocampus, and serotonin 5-HTR1A receptor in the hippocampus and amygdala. Results: Under baseline conditions, cannabidiol did not modify any element of the hypothalamus-pituitary-adrenal axis. In contrast, all doses induced alterations in 5-HTR1A in the amygdala and hippocampus. Interestingly, cannabidiol at low (5 mg/kg) and intermediate doses (15 mg/kg) successfully blocked the effects induced by acute stress on corticotropin-releasing factor, pro-opiomelanocortin and glucocorticoid receptor gene expression. Also, restraint stress induced the opposite effects in 5-HTR1A gene expression in the hippocampus and amygdala, an effect not seen in mice treated with cannabidiol at low doses. Conclusions: Taken together, these data suggest the ability of cannabidiol to regulate acute stress hypothalamus-pituitary-adrenal axis activation might be explained, at least in part, by its action on 5-HTR1A receptors.
Regional classification: The case of the Visegrad Four

Since the biggest enlargement of the European Union in 2004, the EU cohesion policy has made a significant contribution to spreading growth and prosperity across the European territory. Despite this, the cohesion policy is still confronted with persistent economic, social and territorial disparities among countries and regions and weakened economic growth and competitiveness. The aim of the paper is to evaluate regional disparities in the case of the Visegrad Four (V4) countries in the year 2010 and to propose an alternative method of regional classification that could be helpful for the efficient allocation of European funds. In the paper, an analysis of the disparities in the V4 NUTS 2 regions is undertaken on the basis of cluster analysis. The three determined clusters confirm that NUTS 2 regions with capital cities (Praha, Bratislavský kraj, Mazowieckie and Kozep-Magyarorszag) still occupy the dominant positions in comparison with other regions in the V4. Significant disparities between clusters are visible, especially regarding the economic and innovative performance and territorial cohesion.
A second-order dynamical approach with variable damping to nonconvex smooth minimization

ABSTRACT We investigate a second-order dynamical system with variable damping in connection with the minimization of a nonconvex differentiable function. The dynamical system is formulated in the spirit of the differential equation which models Nesterov's accelerated convex gradient method. We show that the generated trajectory converges to a critical point, if a regularization of the objective function satisfies the Kurdyka- Lojasiewicz property. We also provide convergence rates for the trajectory formulated in terms of the Lojasiewicz exponent.
What medical education can learn from the fashion industry

The letter by O’Connor (2018) describing the integration of structured student-specific activities into the ICU ward rounds (WRs) was of particular interest to me as a final year medical student. Evidence suggests that structured and goal orientated WRs are an effective way to teach medical students and improve WR competencies (Krautter et al. 2014). However, such WRs are not typical of those experienced by students. Learning opportunities do present themselves on WRs; however, students are often delegated tasks such as writing in patient notes or taking blood. These are essential skills and are important duties of junior doctors. Additionally it is beneficial for students to be integrated into the team and feel they are doing activities that assist the WR. However, these are often the only specific and consistent ways in which students are involved and these can detract from other learning opportunities. Therefore I am unsurprised that student-specific activities, aimed at aiding involvement and learning, were greeted with enthusiasm. Not only would it allow greater, and relevant, participation but also, as described by O’Connor (2018), more feedback on the development of clinical skills. Medical students recognize that WR must prioritize patient care and that Consultant job plans have limited time set aside for WRs. Realistically any additional staff that would be required to support a WR, such as that described by O’Connor (2018), is unlikely to come to fruition given that staffing shortages are commonplace. I would therefore propose a blended approach, reasoning that such studentspecific activities need not be done for every patient. Indeed just a few specified, integrated and goal-orientated learning opportunities per WR would greatly increase student engagement and focus their learning. In conclusion, I believe that while WRs do present learning opportunities, students are not consistently involved in a meaningful way. Integrating a few student-specific activities could therefore significantly enhance the learning outcomes from WRs as well as the enjoyment for the clinical team themselves.
What is the relationship between the breech presentation and hip dysplasia ? An experimental study on a rat model

The relationship between breech presentation and Developmental Dysplasia of the Hip (DDH) had been demonstrated through epidemiological methods, but the mechanism of such correlation and the pathological process of breech-related hip dysplasia remain unclarified. The purposes of this study were: (1) to establish an animal model to best simulate breech presentation; (2) to investigate how breech presentation influenced the severity of DDH and (3) to analyze the pathological development of the acetabulum and the femoral head. Newborn rats were swaddled to keep the hip flexed and knees extended to simulate human breech presentation. At 0, 2, 4, 6, 8 day after birth the specimen of the rats was stained and postero-anterior pelvic picture of the rat skeletons were taken to observe the relationship of the acetabulum and the femoral head. Sections of the hip were stained with Safranin O-Fast Green to assess the histopathologic changes of the acetabulum and the femoral head. In the pelvic pactures, cartilage acetabular index (CAI), center-edge angle (CEA) and acetabular diameter/depth ratio (D/D) were measured. The incidence of DDH increased and the severity aggravated with the swaddling time. CAI in the experiment group was significantly larger than that of the control group since day 2. CEA decreased with time in the experiment group, while D/D increased obviously. Pathological changes of the hip joint emerged in the early stage of breech presentation, and aggravated with growth. Lateral bending of the ischium and thinner articular cartilage were observed in the dysplastic hips. In conclusion, the more time in breech position, the more incidence and severity of DDH. Breech-related DDH was a chronic process that proceeded from mild dysplasia to subluxation and then to frank dislocation.
Determinants of Borrowers' Default in P2P Lending under Consideration of the Loan Risk Class

We study the determinants of borrowers’ default in P2P lending with a new data set consisting of 70,673 loan observations from the Lending Club. Previous research identified a number of default determining variables but did not distinguish between different loan risk levels. We define four loan risk classes and test the significance of the default determining variables within each loan risk class. Our findings suggest that the significance of most variables depends on the loan risk class. Only a few variables are consistently significant across all risk classes. The debt-to-income ratio, inquiries in the past six months and a loan intended for a small business are positively correlated with the default rate. Annual income and credit card as loan purpose are negatively correlated.
Lunar occultation of the diffuse radio sky: LOFAR measurements between 35 and 80 MHz

We present radio observations of the Moon between 35 and 80 MHz to demonstrate a novel technique of interferometrically measuring large-scale diffuse emission extending far beyond the primary beam (global signal) for the first time. In particular, we show that (i) the Moon appears as a negative-flux source at frequencies 35 z > 12) and the Epoch of Reionization (12 > z > 5).
Efficacy of rhizobacteria for growth promotion in sorghum under greenhouse conditions and selected modes of action studies

SUMMARY The screening of rhizobacteria for growth promotion of sorghum (Sorghum bicolour (L.) Moench) was conducted under greenhouse conditions for a total of 78 bacteria isolated from the rhizosphere of sorghum in Ethiopia, and 86 isolates from the rhizosphere and rhizoplane of grasses in South Africa. Three isolates from Ethiopia, all identified as Bacillus cereus, enhanced growth promotion by resulting in statistically significant increases in at least five parameters. Of these, B. cereus (KBE7-8) resulted in significant increase in shoot and root biomass. Among effective isolates from South Africa, B. cereus (NAS4-3) and Stenotrophomonas maltophilia (KBS9-B) showed significant increases in all the parameters measured. The isolates which resulted in significant growth promotion colonized the roots effectively with a count up to ⩾108 cfu/g. In the study conducted to elucidate the possible modes of action by these effective isolates, indole 3-acetic acid-like substances were detected in culture filtrates of the isolates ranging from 4·2 μg/ml by Serratia marcescens (KBS9-R) to 22·8 μg/ml by B. cereus (KBS5-H) in the presence of 2 mg tryptophan/g nutrient broth solution. Higher rates of solubilization of tricalcium phosphate on Pikovskaya agar medium were shown by Chryseomonas luteola (KBS5-F), S. marcescens (KBS6-H) and B. cereus (KBE9-1). There is very limited knowledge of the use of rhizobacteria in agriculture in Ethiopia and South Africa. The current study therefore generates valuable information towards application of plant growth promoting rhizobacteria as alternatives to chemical fertilizers.
Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica

Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. To address this limitation, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which functional determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified mutations that led to high lipid accumulation and eliminated pseudohyphal morphology.
Comparison of 2D and 3D PET for cerebral FDG in human subjects

The authors compared 12 pairs of cerebral [/sup 18/F]-fluoro-deoxyglucose (FDG) 2D/3D image sets from a GE/Advance PET scanner, incorporating the actual corrections used on human subjects. Differences in resolution consistent with other published values were found. There is a significant difference in axial resolution between 2D and 3D, and the authors focused on this as it is a scanner feature that cannot be readily changed. Previously published values for spatial axial resolution in 2D and 3D modes were used to model the differential axial smoothing at each image voxel. This model was applied to the 2D FDG images, and the resulting smoothed data indicate the published differences in axial resolution between 2D and 3D modes can account for 30-40% of the differences between these image sets. The authors then investigated the effect this difference might have on analysis typically performed on human FDG data. A phantom containing spherical hot- and cool-spots in a warm background to mimic a typical human cerebral FDG PET scan was scanned for a variety of time durations (30, 15, 5, 1 min). Only for the 1-minute frame (total counts 2D:6M, 3D:30M) is there an advantage to using 3D mode; for the longer frames which are more typical of a human FDG protocol, the reliability for extracting regions-of-interest is the same for either mode while 2D mode shows better quantitative accuracy.
Submission from CMU towards 1 st MultiTarget Speaker Detection and Identification Challenge

In this document, we present the entry from CMU towards MCE 2018 [1]. This begins with a brief description of the tasks and evaluation framework. We show via experiments that inverted Euclidean distance can be used instead of cosine distance. Based on this, we make a submission based on learning a similarity metric using Siamese nets optimized using euclidean distance between the representations.
The Genomic Basis of Tumor Regression in Tasmanian Devils (Sarcophilus harrisii)

Abstract Understanding the genetic basis of disease-related phenotypes, such as cancer susceptibility, is crucial for the advancement of personalized medicine. Although most cancers are somatic in origin, a small number of transmissible cancers have been documented. Two such cancers have emerged in the Tasmanian devil (Sarcophilus harrisii) and now threaten the species with extinction. Recently, cases of natural tumor regression in Tasmanian devils infected with the clonally contagious cancer have been detected. We used whole-genome sequencing and FST-based approaches to identify the genetic basis of tumor regression by comparing the genomes of seven individuals that underwent tumor regression with those of three infected individuals that did not. We found three highly differentiated candidate genomic regions containing several genes related to immune response and/or cancer risk, indicating that the genomic basis of tumor regression was polygenic. Within these genomic regions, we identified putative regulatory variation in candidate genes but no nonsynonymous variation, suggesting that natural tumor regression may be driven, at least in part, by differential host expression of key loci. Comparative oncology can provide insight into the genetic basis of cancer risk, tumor development, and the pathogenicity of cancer, particularly due to our limited ability to monitor natural, untreated tumor progression in human patients. Our results support the hypothesis that host immune response is necessary for triggering tumor regression, providing candidate genes that may translate to novel treatments in human and nonhuman cancers.
Experimental validation on effects of pulsed electric field treatment on the sensory quality of vegetable juices

Pulsed electric field (PEF) treatment is one of the non-thermal methods of food processing. PEF technology has been reported and recognized by a number of food researchers as an alternate method of conventional thermal processing for fluid and semi-fluid foods. Recently, the PEF technique application has been exploited in the field of extraction of bio-molecules, drying enhancement and enzyme activity modification. PEF has also proved significant and more effective application with moderate thermal treatment for food preservation as hurdle technology. Although significant work was found in the domain of milk and fruit juice processing and preservation, but limited reported work was found in the area of application of PEF for vegetable juice processing while no reported work was found on PEF treatment of mint and curry leaves juices. This paper reports about application of PEF and its effects in sensory qualities of the vegetable juices after a specified treatment. Few vegetable juices were treated, i.e. cabbage, cucumber, bitter gourd along with mint leaves and curry leaves. No changes in sensory properties were found between treated and untreated samples.
CDNA: A Context-Aware Notification System for Driver Interruption

Inopportune driver notifications are a real problem that may cause distractions and interruptions in traffic, and hence accidents. Notifications on mobile devices are one of the ways by which drivers are interrupted, reaching extremely high amounts in a normal day. Despite that, notifications are valued by users and they are part of the common use of smartphones. Therefore, how to lessen the interruptive potential of notifications without eliminating them completely? To mitigate this problem, the present work proposes a context-aware notification system with the identification of opportune and inopportune moments for drivers notification. The proposed system uses smartphone sensors (gyroscope and GPS) to infer if the driver may be interrupted in a specific moment to receive a notification. Preliminary experiments were performed with people in real driving situations to verify if the system could identify opportune and inopportune moments, and found results indicate that is possible to identify these moments with a general accuracy of 88%.
Titan interaction with Saturn's magnetosphere: Voyager 1 results revisited

[1] We investigate the details of Titan's interaction with Saturn's magnetosphere, which includes formation and location of an ionopause, mass loading via ion pickup, and the effects of finite gyroradii. We present new interpretations of the Voyager 1 plasma instrument measurements not addressed by Hartle et al. (1982). Pickup ions H+ and H2+ dominate in the outermost region with respect to Titan's “ionopause,” followed by CH4+ at intermediate distances and N2+ just outside the “ionopause. ” Mass loading and slowing down of the ambient plasma is observed to increase as the pickup ion mass increases with decreasing radial distance from Titan's ionosphere. H2 and CH4 are molecules not originally included in the exosphere of Titan by Hartle and coworkers, and the pickup ions of H2+ and CH4+ are a new feature of our model calculations and should be present in Titan's exospheric region. Therefore Titan could be an important source of carbon to Saturn's magnetosphere. Finite gyroradius effects are identified in the plasma interaction with Titan's atmosphere, which results in an asymmetric removal of ambient plasma from Titan's exosphere region. The finite gyroradius effects also show that the observed hot keV ion component of the ambient plasma is a heavy ion such as N+/O+. A minimum “ionopause” altitude of 4800 km is estimated by a new approach using mass loading.
Testing the Technologies : Demonstration Grid-Connected Photovoltaic Projects in Japan

Title Testing the Technologies : Demonstration Grid-Connected Photovoltaic Projects in Japan Author(s) Hara, Ryoichi; Kita, Hiroyuki; Tanabe, Takayuki; Sugihara, Hiroyuki; Kuwayama, Akira; Miwa, Shuya Citation IEEE Power and Energy Magazine, 7(3), 77-85 https://doi.org/10.1109/MPE.2009. 932310 Issue Date 2009-05 Doc URL http://hdl.handle. net/2115/38532 Rights (c) 2009 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. Type article File Information 7-3_p77-85.pdf