julilili42/papers huggingface dataset:
Asymptotically flat extensions of CMC Bartnik data
2017-03-24

Let be a metric on the -sphere with positive Gaussian curvature and be a positive constant. Under suitable conditions on , we construct smooth, asymptotically flat -manifolds with non-negative scalar curvature, with outer-minimizing boundary isometric to and having mean curvature , such that near infinity is isometric to a spatial Schwarzschild manifold whose mass can be made arbitrarily close to a constant multiple of the Hawking mass of . Moreover, this constant multiplicative factor depends only on and tends to as tends to . The result provides a new upper bound of the Bartnik mass associated to such boundary data.
Assessment of building heights from pléiades satellite imagery for the Nyarugenge sector, Kigali, Rwanda
2017-03-24

Quantitative and qualitative information about land-use and buildings are important for spatial planning decision processes. The proposed study determines the suitability of multispectral information and stereoscopic-derived heights of Pléiades tri-stereoscopic satellite imagery for the identification of building footprints and the assessment of building heights. The study area is the Nyarugenge sector in the center of the City of Kigali. A tri-stereoscopic Pléiades satellite scene was used to process a digital surface model. An object-based image analysis provided the basic geometries and respective variables, which served as input features for a Support Vector Machine based classification. The comparison of the building footprints with ground reference information indicates a high accuracy. The assessment of building heights led to mixed results. The heights of buildings were derived with medium to high accuracies for building blocks with a well-developed road network or open spaces, which allowed the assessment of the elevation of the terrain surface. In densely built-up areas, with a lack of road accessibility and located mainly on steep slopes, the derived heights of single buildings or building blocks did not produce satisfying results. However, for urban planners, policy and decision makers, the method yields a high potential in analyzing and monitoring urban areas.Keywords - building extraction, DSM, remote sensing, SVM, Pléiades
Embodied Agency
2017-03-25

Is bodily awareness a condition on bodily action? I approach this question by weaving an argument based on considerations from action theory, the phenomenology of embodied agency, and from the psychology and neuroscience of action. In this paper, I discuss two accounts on which bodily awareness is a condition on bodily action. The first is an influential philosophical account from O'Shaughnessy, which claims that bodily awareness is necessary for the online control of bodily action. I argue that there are empirical counterexamples to O'Shaughnessy's account. Instead I propose an account on which the capacity for bodily awareness is a condition on our capacity for ordinary bodily action. This alternative account does justice to the causal and functional character of ordinary bodily action as well as its phenomenology. It is also consistent with the psychology and neuroscience of action. I provide a two‐stage argument for my view. The first stage shows that a sense of the spatial possibilities of one's body is a condition on intentionally acting with one's body. The second stage demonstrates that bodily awareness is a condition on a normal afferented agent's sense of the actions open to him through examining the role of bodily awareness in motor imagery and the role of motor imagery in preparatory processes for everyday actions.
Membrane Associated Progesterone Receptors: Promiscuous Proteins with Pleiotropic Functions – Focus on Interactions with Cytochromes P450
2017-03-26

Membrane-associated progesterone receptors (MAPR) are a group of four rather small, partially homologous proteins, which share a similar non-covalent heme-binding domain that is related to cytochrome b5, a well-known functional interaction partner of microsomal cytochrome P450 (CYP) monooxygenase systems. Apart from their structural similarities the four proteins progesterone membrane component 1 (PGRMC1, also referred to as IZA, sigma-2 receptor, Dap1), PGRMC2, neudesin (NENF) and neuferricin (CYB5D2) display surprisingly divergent and multifunctional physiological properties related to cholesterol/steroid biosynthesis, drug metabolism and response, iron homeostasis, heme trafficking, energy metabolism, autophagy, apoptosis, cell cycle regulation, cell migration, neural functions, and tumorigenesis and cancer progression. The purpose of this mini-review is to briefly summarize the structural and functional properties of MAPRs with particular focus on their interactions with the CYP system. For PGRMC1, originally identified as a non-canonical progesterone-binding protein that mediates some immediate non-genomic actions of progesterone, available evidence indicates mainly activating interactions with steroidogenic CYPs including CYP11A1, CYP21A2, CYP17, CYP19, CYP51A1, and CYP61A1, while interactions with drug metabolizing CYPs including CYP2C2, CYP2C8, CYP2C9, CYP2E1, and CYP3A4 were either ineffective or slightly inhibitory. For the other MAPRs the evidence is so far less conclusive. We also point out that experimental limitations question some of the previous conclusions. Use of appropriate model systems should help to further clarify the true impact of these proteins on CYP-mediated metabolic pathways.
Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies
2017-03-27

Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.
Maximizing gender equality by minimizing course choice options? Effects of obligatory coursework in math on gender differences in STEM.
2017-03-27

Math achievement, math self-concept, and vocational interests are critical predictors of STEM careers and are closely linked to high school coursework. Young women are less likely to choose advanced math courses in high school, and encouraging young women to enroll in advanced math courses may therefore bring more women into STEM careers. We looked at a German statewide educational reform that required all students to take advanced math courses and examined differential effects of the reform on young men and women’s math achievement, math self-concept, vocational interests, and field of study at university. We compared data from 4,730 students before the reform and 4,715 students after the reform. We specified multiple regression models and tested main effects of gender and cohort as well as the effect of the Cohort × Gender interaction on all outcomes. All outcomes showed clear gender differences favoring young men before the reform. However, the reform was associated with different effects for young men and women: Whereas gender differences in math achievement were smaller after the reform, differences between young men and women in math self-concept and realistic and investigative vocational interests were larger after the reform than before. Gender differences in the field of study at university did not differ between before and after the reform. Results suggest that reducing course choice options in high school does not automatically increase gender equality in STEM fields. (PsycINFO Database Record (c) 2017 APA, all rights reserved)
Vocational qualification as safety-net? Education-to-work transitions of higher education dropouts in Germany
2017-03-27

Abstract Background In Germany, almost 15 per cent of all first-year students leave higher education without obtaining a degree. The German post-secondary educational system is tracked however, and many dropouts enter the labour market with pre-tertiary vocational training certificates. We therefore examine if higher education dropouts benefit from these vocational qualifications obtained outside higher education and use vocational credentials as a safety net. Methods Using data from the German National Educational Panel Study (NEPS Starting Cohort 6), this study employs Cox and OLS regression models to examine the labour market transition of higher education dropouts. We distinguish the actual transitions (finding a job) from the occupational status of the first job. Results Our results suggest that higher education dropouts without pre-tertiary vocational qualifications have more difficulties finding a job, compared to dropouts with pre-tertiary vocational qualifications. Comparing the occupational status of dropouts with and without pre-tertiary vocational qualifications, we find that these are not associated with a higher occupational status. Conclusions We conclude that pre-tertiary vocational qualifications do serve as a safety net in case of drop out, because they protect from protracted pathways into the labour market. Apart from this we do not find evidence for additional returns of vocational certificates in terms of occupational status.
Myosin-1E interacts with FAK proline-rich region 1 to induce fibronectin-type matrix
2017-03-27

Significance Focal adhesion kinase (FAK) is an intensely studied protein involved in many medically relevant biological processes, including cancer. Despite the large interest in FAK, a promising strategy to target FAK therapeutically is elusive. Here, we show that a region within the FAK protein that contains autophosphorylation site tyrosine (Y) 397 is essential for FAK activity in vivo. Myosin-1E (MYO1E), an actin-dependent molecular motor protein, directly interacts with FAK to induce Y397 autophosphorylation, which, in turn, causes changes in gene expression commonly observed in aggressive cancer. Our findings are significant because they further delineate FAK function in vivo and identify the MYO1E–FAK interaction as a possible Achilles’ heel for cancer.
Dermasence refining gel modulates pathogenetic factors of rosacea in vitro
2017-03-27

Summary Background Over the counter cosmetics sold for local treatment of slight to moderate rosacea often state the claim of actively modulating rosacea pathogenesis. Factors involved in the pathogenesis of this common yet complex skin disorder include kallikrein‐related peptidase 5 ( KLK 5), LL ‐37, as well as protease‐activated receptor 2 ( PAR 2) and vascular endothelial growth factor ( VEGF ). Objective The objective was to prove the modulating effect of the cosmetic skin care agent Dermasence Refining Gel ( DRG ) on factors involved in rosacea pathogenesis. Methods We analyzed the effect of DRG on the expression of KLK 5, LL ‐37, PAR 2, and VEGF in an in vitro skin model of human reconstituted epidermis. Results The expression of CAMP ( LL ‐37 gene, fold change −4.19 [±0.11]), VEGFA (fold change −2.55 [±0.12]) and PAR 2 (−1.33 [±0.12]) was reduced, KLK 5 expression increased (fold change 2.06 (±0.08)) after 18 h of treatment with DRG in comparison to treatment with the matrix gel only. The reduction in CAMP expression was significant ( P &lt;.01). The protein expression of all four inflammatory markers was markedly reduced after 18 hours of DRG treatment in comparison to baseline (0 hour), by measure of fluorescence intensity. Conclusion We show evidence explaining the anti‐inflammatory effect of Dermasence Refining Gel in rosacea pathogenesis in vitro. The adjunctive use of DRG in mild to moderate rosacea as a topical cosmetic seems medically reasonable.
Low incidence of the immune reconstitution inflammatory syndrome among HIV-infected patients starting antiretroviral therapy in Gabon: a prospective cohort study
2017-03-27

There is a paucity of data on the immune reconstitution inflammatory syndrome (IRIS) in the Central African region. We followed ART-naive HIV-infected patients initiating antiretroviral therapy in an HIV clinic in Gabon, for 6 months. Among 101 patients, IRIS was diagnosed in five. All IRIS cases were mucocutaneous manifestations. There were no cases of tuberculosis (TB) IRIS, but active TB (n = 20) was associated with developing other forms of IRIS (p = 0.02). Six patients died. The incidence of IRIS is low in Gabon, with mild, mucocutaneous manifestations.
Sensing Magnetic Fields with a Giant Quantum Wave
2017-03-27

Microscopic imaging of local magnetic fields provides a window into the organizing principles of complex and technologically relevant condensed-matter materials.However, a wide variety of intriguing strongly correlated and topologically nontrivial materials exhibit poorly understood phenomena outside the detection capability of state-of-the-art high-sensitivity high-resolution scanning probe magnetometers.We introduce a quantum-noise-limited scanning probe magnetometer that can operate from room-to-cryogenic temperatures with unprecedented dc-field sensitivity and micron-scale resolution.The Scanning Quantum Cryogenic Atom Microscope (SQCRAMscope) employs a magnetically levitated atomic Bose-Einstein condensate (BEC), thereby providing immunity to conductive and blackbody radiative heating.The SQCRAMscope has a field sensitivity of 1.4 nT per resolution-limited point (approximately 2 μm) or 6 nT= ffiffiffiffiffiffi Hz p per point at its duty cycle.Compared to point-by-point sensors, the long length of the BEC provides a naturally parallel measurement, allowing one to measure nearly 100 points with an effective field sensitivity of 600 pT= ffiffiffiffiffiffi Hz p for each point during the same time as a point-by-point scanner measures these points sequentially.Moreover, it has a noise floor of 300 pT and provides nearly 2 orders of magnitude improvement in magnetic flux sensitivity (down to 10 -6 Φ 0 = ffiffiffiffiffiffi Hz p) over previous atomic probe magnetometers capable of scanning near samples.These capabilities are carefully benchmarked by imaging magnetic fields arising from microfabricated wire patterns in a system where samples may be scanned, cryogenically cooled, and easily exchanged.We anticipate the SQCRAMscope will provide charge-transport images at temperatures from room temperature to 4 K in unconventional superconductors and topologically nontrivial materials.
Radial and Peroneal Nerve Grafting: Functional Results
2017-03-27

Background: Lesions of the Peroneal nerve are considered to have a poorer prognosis than those of the radial nerve.We suppose that the quality of the graft bed is one reason for this observation. Materials and Methods:Results after grafting of radial and Peroneal nerves were investigated in cases without additional tendon transfer.Clinical follow-up and chart review was performed.Results: 6 sural nerve graftings of the radial and 5 graftings of the Peroneal nerve were included.4 of 6 radial grafts were placed extra-anatomically.5 patients with complete wrist drop eventually achieved wrist extension, 4 of them after extra-anatomical graft placement.1 of 5 Peroneal grafts was placed extra-anatomically.Weakness in foot elevation could significantly be improved in 2 of 5 patients. Conclusions:Good functional recovery can be achieved by extra-anatomic positioning of radial nerve grafts.Results for Peroneal nerve grafts are inferior, possibly, among other factors, because improvement of graft bed vascularization by extra-anatomic graft positioning is less feasible here.
National German Audit of Diagnosis, Treatment, and Teaching in Secondary Adrenal Insufficiency
2017-03-28

Abstract Great heterogeneity seems to exist regarding diagnosis, therapy, and teaching of patients with secondary adrenal insufficiency (SAI) across Germany resulting in different diagnosis and treatment strategies. The aim of the work was to present the first national audit on diagnosis, treatment, and patient teaching of SAI reflecting common clinical practice in Germany. A self-designed questionnaire was sent via e-mail to all members of the German Endocrine Society (approx. 120 centers). Returned questionnaires (response rate 38.3%) were checked for duplicity of institutions and analyzed. Diagnostic testing focuses on those patients with relevant risk for adrenal insufficiency. Basal serum cortisol is mostly used as screening test. Short synacthen and CRH tests are the preferred confirmatory tests, however, cut-off values vary due to different assays used. Patients with radiation, second surgery, progressive disease or new symptoms are followed by serial re-testing. Perioperative management and frequency of postoperative re-evaluations differ among centers. Hydrocortisone is the preferred glucocorticoid for replacement therapy, but daily doses vary considerably (10–30 mg/day). Some centers perform hormone measurements for dose adjustment of glucocorticoid replacement therapy whereas others rely on clinical judgement. Patients’ teaching is done in 84% of centers, but only half of the centers include patients’ relatives. Homogeneity exists in patients’ teaching regarding intercurrent illnesses (fever, diarrhoea). Recommendations regarding dose adaptations in situations such as sport-activities, dental-procedures, or coughing are highly variable. This first national audit reveals great heterogeneity among German centers and could improve patients’ care in SAI, for example, by initiating new trials and developing clinical practice guidelines.
Reply to the Letter to the Editor by D. D’Arcangelo et al.: “Ion Channels in Brain Metastasis”—Ion Channels in Cancer Set up and Metastatic Progression Ion Channels in Brain Metastasis
2017-03-28

In their comment on our review article entitled Ion Channels in Brain Metastasis, Dr. D’Arcangelo et al. describe their recent report on aberrant ion channel expression in several cancer entities in order to provide information complementary to that which is presented in our article [1].[..]
BioContainers: an open-source and community-driven framework for software standardization
2017-03-29

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/.
Sleep disturbances and mental strain in university students: results from an online survey in Luxembourg and Germany
2017-03-29

Objectives\\n\\nThis study examined the prevalence of sleep disturbances and mental strain in students from two European countries, Luxembourg and Germany.\\nMethods\\n\\nA total of 2831 students took part in an online survey, with 2777 students from Germany and 184 students from Luxembourg. Sleep disturbances were assessed with the Pittsburgh Sleep Quality Index and the Epworth Sleepiness Scale, and aspects of mental strain using the Patient Health Questionnaire, the Social-Interactive-Anxiety Scale, the self-efficacy questionnaire and the test anxiety questionnaire. In addition, we also assessed students’ chronotypes.\\nResults\\n\\nAcross the whole sample mean scores on the sleep questionnaires were above the cut-off for clinically relevant sleep problems, indicating an increased prevalence of sleep disturbances in students from both countries. Sleep quality was impaired in 42.8%, and 17.9% showed clinically relevant scores. Overall 25.5% reported elevated depression and 13.3% social phobia symptoms, while 45% indicated elevated stress levels. Sleep quality, daytime sleepiness, chronotype, depression scores, stress levels, test anxiety, and self-efficacy differed significantly between men and women, but there were no differences between countries.\\nConclusions\\n\\nSleep disturbances and mental strain in students are common, with the current results replicating previous findings. Students from Luxembourg and Germany are affected equally.
The geometrical shape of mesenchymal stromal cells measured by quantitative shape descriptors is determined by the stiffness of the biomaterial and by cyclic tensile forces
2017-03-29

Controlling mesenchymal stromal cell (MSC) shape is a novel method for investigating and directing MSC behaviour in vitro. it was hypothesized that specifigc MSC shapes can be generated by using stiffness-defined biomaterial surfaces and by applying cyclic tensile forces. Biomaterials used were thin and thick silicone sheets, fibronectin coating, and compacted collagen type I sheets. The MSC morphology was quantified by shape descriptors describing dimensions and membrane protrusions. Nanoscale stiffness was measured by atomic force microscopy and the expression of smooth muscle cell (SMC) marker genes (ACTA2, TAGLN, CNN1) by quantitative reverse-transcription polymerase chain reaction. Cyclic stretch was applied with 2.5% or 5% amplitudes. Attachment to biomaterials with a higher stiffness yielded more elongated MSCs with fewer membrane protrusions compared with biomaterials with a lower stiffness. For cyclic stretch, compacted collagen sheets were selected, which were associated with the most elongated MSC shape across all investigated biomaterials. As expected, cyclic stretch elongated MSCs during stretch. One hour after cessation of stretch, however, MSC shape was rounder again, suggesting loss of stretch-induced shape. Different shape descriptor values obtained by different stretch regimes correlated significantly with the expression levels of SMC marker genes. Values of approximately 0.4 for roundness and 3.4 for aspect ratio were critical for the highest expression levels of ACTA2 and CNN1. Thus, specific shape descriptor values, which can be generated using biomaterial-associated stiffness and tensile forces, can serve as a template for the induction of specific gene expression levels in MSC. Copyright © 2017 John Wiley & Sons, Ltd.