julilili42/papers huggingface dataset:
Haves and have nots must find a better way: The case for open scientific hardware
2018-09-27

Many efforts are making science more open and accessible; they are mostly concentrated on issues that appear before and after experiments are performed: open access journals, open databases, and many other tools to increase reproducibility of science and access to information. However, these initiatives do not promote access to scientific equipment necessary for experiments. Mostly due to monetary constraints, equipment availability has always been uneven around the globe, affecting predominantly low-income countries and institutions. Here, a case is made for the use of free open source hardware in research and education, including countries and institutions where funds were never the biggest problem.
Selective Inhibition of the Lactate Transporter MCT4 Reduces Growth of Invasive Bladder Cancer
2018-09-27

Abstract The significance of lactate transporters has been recognized in various cancer types, but their role in urothelial carcinoma remains mostly unknown. The aim of this study was to investigate the functional importance of the monocarboxylate transporter (MCT) 4 in preclinical models of urothelial carcinoma and to assess its relevance in patient tumors. The association of MCT4 expression with molecular subtypes and outcome was determined in The Cancer Genome Atlas (TCGA) cohort and two independent cohorts of patients with urothelial carcinoma. Silencing of MCT4 was performed using siRNAs in urothelial carcinoma cell lines. Effects of MCT4 inhibition on cell growth, apoptosis, and production of reactive oxygen species (ROS) were assessed. Moreover, effects on lactate efflux were determined. The in vivo effects of MCT4 silencing were assessed in an orthotopic xenograft model. MCT4 expression was higher in the basal subtype. Decreased MCT4 methylation and increased RNA and protein expression were associated with worse overall survival (OS). Inhibition of MCT4 led to a reduction in cell growth, induction of apoptosis, and an increased synthesis of ROS. MCT4 inhibition resulted in intracellular accumulation of lactate. In vivo, stable knockdown of MCT4 reduced tumor growth. The expression of MCT4 in urothelial carcinoma is associated with features of aggressive tumor biology and portends a poor prognosis. Inhibition of MCT4 results in decreased tumor growth in vitro and in vivo. Targeting lactate metabolism via MCT4 therefore provides a promising therapeutic approach for invasive urothelial carcinoma, especially in the basal subtype.
Do Occupational and Patient Safety Culture in Hospitals Share Predictors in the Field of Psychosocial Working Conditions? Findings from a Cross-Sectional Study in German University Hospitals
2018-09-27

Background: In the healthcare sector, a comprehensive safety culture includes both patient care-related and occupational aspects. In recent years, healthcare studies have demonstrated diverse relationships between aspects of psychosocial working conditions, occupational, and patient safety culture. The aim of this study was to consider and test relevant predictors for staff’s perceptions of occupational and patient safety cultures in hospitals and whether there are shared predictors. From two German university hospitals, 381 physicians and 567 nurses completed a questionnaire on psychosocial working conditions, occupational, and patient safety culture. Two regression models with predictors for occupational and patient safety culture were conceptually developed and empirically tested. In the Occupational Safety Culture model, job satisfaction (β = 0.26, p ≤ 0.001), work‒privacy conflict (β = −0.19, p ≤ 0.001), and patient-related burnout (β = −0.20, p ≤ 0.001) were identified as central predictors. Important predictors in the Patient Safety Culture model were management support for patient safety (β = 0.24, p ≤ 0.001), supervisor support for patient safety (β = 0.18, p ≤ 0.001), and staffing (β = 0.21, p ≤ 0.001). The two models mainly resulted in different predictors. However, job satisfaction and leadership seem to play an important role in both models and can be used in the development of a comprehensive management of occupational and patient safety culture.
Structural design of the echinoid’s trabecular system
2018-09-27

The multi-plated skeleton of echinoids is made of the stereom, a light-weight construction which resembles a micro-beam framework. Although the two-dimensional design of the stereom has been studied, its spatial architecture is only little known. It is, however, imperative to understand the spatial architecture of the trabecular system in order to interpret its structural principles of this load-bearing construction. The echinoid's trabecular system is thus analyzed in-depth with respect to eight topological descriptors. The echinoid's plates are divided into two regions, the center of which consists of an unordered stereom, and the margin which consists of an ordered stereom. The eight trabecular descriptors indicate that the basal topology of the two plate regions are similar. The trabecular system predominantly consists of short and stocky trabeculae that show little tortuosity. The majority of trabeculae intersect in a 3N configuration, where three trabeculae intersect in one common node. Trabeculae in the 3N configuration intersect in an angle of around 120° resulting in a planar and triangular motif. These planar elements, when arranged in an angular off-set, can resist multi-dimensional loads. Results also show that the trabecular orientation perpendicular to the plate's surface is at an angle of 60°. The trabecular orientation in the plate's horizontal plane is directional. Both trabecular orientations reflect a construction which is capable of resisting applied loads and can distribute these loads over the entire skeleton. The spatial architecture of the echinoid's trabecular system is thus considered to be a performative light-weight and load-bearing system.
Clinical application of advanced MR methods in children: points to consider
2018-09-27

Abstract The application of both functional MRI and diffusion MR tractography prior to a neurosurgical operation is well established in adults, but less so in children, for several reasons. For this review, we have identified several aspects (task design, subject preparation, actual scanning session, data processing, interpretation of results, and decision‐making) where pediatric peculiarities should be taken into account. Further, we not only systematically identify common issues, but also provide solutions, based on our experience as well as a review of the pertinent literature. The aim is to provide the clinician as well as the imaging scientist with information that helps to plan, conduct, and interpret such a clinically‐indicated exam in a way that maximizes benefit for, and minimizes the burden on the individual child.
Birdtracks for SU(N)
2018-09-27

I gently introduce the diagrammatic birdtrack notation, first for vector algebra and then for permutations. After moving on to general tensors I review some recent results on Hermitian Young operators, gluon projectors, and multiplet bases for SU(N) color space.
BDNF-Live-Exon-Visualization (BLEV) Allows Differential Detection of BDNF Transcripts in vitro and in vivo
2018-09-27

Bdnf exon-IV and exon-VI transcripts are driven by neuronal activity and are involved in pathologies related to sleep, fear or memory disorders. However, how their differential transcription translates activity changes into long-lasting network changes is elusive. Aiming to trace specifically the network controlled by exon-IV and -VI derived BDNF during activity-dependent plasticity changes, we generated a transgenic reporter mouse for BDNF-live-exon-visualization (BLEV), in which expression of Bdnf exon-IV and -VI can be visualized by co-expression of CFP and YFP. CFP and YFP expression was differentially activated and targeted in cell lines, primary cultures and BLEV reporter mice without interfering with BDNF protein synthesis. CFP and YFP expression, moreover, overlapped with BDNF protein expression in defined hippocampal neuronal, glial and vascular locations in vivo. So far, activity-dependent BDNF cannot be explicitly monitored independent of basal BDNF levels. The BLEV reporter mouse therefore provides a new model, which can be used to test whether stimulus-induced activity-dependent changes in BDNF expression are instrumental for long-lasting plasticity modifications.
Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing
2018-09-27

Biological data sets are typically characterized by high dimensionality and low effect sizes. A powerful method for detecting systematic differences between experimental conditions in such multivariate data sets is multivariate pattern analysis (MVPA), particularly pattern classification. However, in virtually all applications, data from the classes that correspond to the conditions of interest are not homogeneous but contain subclasses. Such subclasses can for example arise from individual subjects that contribute multiple data points, or from correlations of items within classes. We show here that in multivariate data that have subclasses nested within its class structure, these subclasses introduce systematic information that improves classifiability beyond what is expected by the size of the class difference. We analytically prove that this subclass bias systematically inflates correct classification rates (CCRs) of linear classifiers depending on the number of subclasses as well as on the portion of variance induced by the subclasses. In simulations, we demonstrate that subclass bias is highest when between-class effect size is low and subclass variance high. This bias can be reduced by increasing the total number of subclasses. However, we can account for the subclass bias by using permutation tests that explicitly consider the subclass structure of the data. We illustrate our result in several experiments that recorded human EEG activity, demonstrating that parametric statistical tests as well as typical trial-wise permutation fail to determine significance of classification outcomes correctly.
Reduced representation characterization of genetic and epigenetic differentiation to oil pollution in the foundation plant Spartina alterniflora
2018-09-27

Abstract Theory predicts that environmental challenges can shape the composition of populations, which is manifest at the molecular level. Previously, we demonstrated that oil pollution affected gene expression patterns and altered genetic variation in natural populations of the foundation salt marsh grass, Spartina alterniflora. Here, we used a reduced representation bisulfite sequencing approach, epigenotyping by sequencing (epiGBS), to examine relationships among DNA sequence, DNA methylation, gene expression, and exposure to oil pollution. We documented genetic and methylation differentiation between oil-exposed and unexposed populations, suggesting that the Deepwater Horizon oil spill may have selected on genetic variation, and either selected on epigenetic variation or induced particular epigenotypes and expression patterns in exposed compared to unexposed populations. In support of the potential for differential response to the Deepwater Horizon oil spill, we demonstrate genotypic differences in response to oil under controlled conditions. Overall, these findings demonstrate genetic variation, epigenetic variation and gene expression are correlated to exposure to oil pollution, which may all contribute to the response to environmental stress.
Alteration of the affective modulation of the startle reflex during antidepressant treatment
2018-09-27

Abstract Whereas the amplitude of the startle reflex varies with stimulus valence in the normal population, a lack of this affective modulation has been reported in patients with major depressive disorder. The present study sought to clarify blunted startle modulation as a feature of depression by comparing 16 patients diagnosed with major depression prior to and after 2 weeks of SSRI treatment, and 16 healthy controls. The affect‐modulated startle reflex paradigm and the Self‐Assessment Manikin were used to probe affective reactivity. In addition, a preliminary analysis of change in affective reactivity pattern was performed with depressed patients who could be assessed in the eighth week of treatment ( n = 13). The control group showed a linear trend in response across valence categories, which was stable over sessions. Blunted affective reactivity was observed only in the patients and persisted after 2 weeks of treatment. Nevertheless, a linear trend could be detected in the eighth week of treatment. These findings confirm that the affective reactivity is blunted in depression and provide initial evidence for the lack of change in the early phase of SSRI antidepressant treatment. Nevertheless, in a small group, the emergence of a linear trend in response was evident later with treatment. Large‐scale studies are required to assess the relation between the treatment response and the change in affective modulation of the startle reflex, as a potential biomarker.
Evaluation of a Wind Farm Parametrization for Mesoscale Atmospheric Flow Models with Aircraft Measurements
2018-09-28

Large offshore wind farms are usually clustered around transmission grids to minimize the expense of transmission and due to space military zones, pipelines and constrains due to other uses such as nature preserves. However, this close proximity can undermine power production in downwind wind farms due to wakes from upwind wind farms. Therefore, the wind energy industry has great interest in determining the spatial dimensions of offshore wind farm wakes to assess the economical potential of planned wind farms. In this work we use wake measurements conducted by a research aircraft to evaluate the performance of a wind farm parameterization (WFP) in a mesoscale model during stably-stratified atmospheric conditions, in which the wake is expected to be the strongest. The observations were conducted on the 10 September 2016 within the project WIPAFF (Wind PArk Far Field) at the North Sea. The observations allow evaluation of both the horizontal and the vertical dimensions of the wake. The model simulates the length and most of the time the spatial dimensions of the wake. Further, we show that the largest potential for improving the performance of theWFP is rooted in an improvement of the background flow. This is due to the fact that the mesoscale model has problems representing the atmospheric boundary layer in the transition between land to open sea.
Simultaneous Volumetric Segmentation of Vertebral Bodies and Intervertebral Discs on Fat-Water MR Images
2018-09-28

Fat-water magnetic resonance (MR) images allow automated noninvasive analysis of morphological properties and fat fractions of vertebral bodies (VBs) and intervertebral discs (IVDs) that constitute an important part of human biomechanical systems. In this paper, we propose a fully automated approach for simultaneously segmenting multiple VBs and IVDs on fat-water MR images without prior localization or geometry estimation. This method involved a hierarchical random forest (HRF) classifier and a hierarchical conditional random field (HCRF) that encoded a multi-resolution image pyramid based on a set of multiscale local and contextual features. The HRF classifier employed penalized multivariate linear discriminants and SMOTEBagging to handle limited and imbalanced training data with large feature dimension. The HCRF estimated optimum labels according to their spatial and hierarchical consistencies by using the layer-wise significant features determined over the trained HRF classifier. To handle variable sample numbers at different resolutions, resolution-specific hyperparameters were used. This method was trained and evaluated for segmenting 15 thoracic and lumbar VBs and their IVDs on fat-water MR images of a subset of a large cohort data set. It was further evaluated for segmenting seven IVDs of the lower spine on fat-water images of a public grand challenge. These evaluations revealed the comparable accuracy of this method with the state-of-the-art while requiring less computational burden due to a simultaneous localization and segmentation.
Precision of T2 TSE MRI-CT-image fusions based on gold fiducials and repetitive T2 TSE MRI-MRI-fusions for adaptive IGRT of prostate cancer by using phantom and patient data
2018-09-28

<b>Introduction:</b> To increase precision of radiation treatment (RT) delivery in prostate cancer, MRI-based RT as well as the use of fiducials like gold markers (GMs) have shown promising results. Their combined use is currently under investigation in clinical trials. Here, we aimed to evaluate a workflow of image registration based on GMs between CT and MRI as well as weekly MRI-MRI adaption based on T2 TSE sequence. <b>Material and methods:</b> A gel-phantom with two inserted GMs was scanned with CT and three different MR-scanners of 1.5 and 3 T (T2 TSE and T1 VIBE-Dixon, isotropic, voxel size 2 × 2 × 2 mm). After image fusion, deviations for fiducial and gel match were measured and artifacts were evaluated. Additionally, CT-MRI-match deviations and MRI-MRI-match deviations of 10 Patients from the M-basePro study using GMs were assessed. <b>Results:</b> GMs were visible in all imaging modalities. The outer gel contours were matched with &lt;1 mm deviation, contour volumes varied between 0 and 1%. The deviations of the GMs were less than 2 mm in any direction of MRI/CT. Shifts of peripherally or centrally located GMs were randomly distributed. The average MRI-CT-match precision of 10 patients with GMs was 1.9 mm (range 1.1–3.1 mm). <b>Conclusions:</b> Match inaccuracies for GMs between reference CT and voxel-isotropic T2-TSE sequences are small. Spatial deviations of CT- and MR-contoured fiducials were less than 2 mm, i.e., below SLT of the applied modalities. In patients, the average CT-MRI-match precision for GMs was 1.9 mm supporting their use in MR-guided high precision RT. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT02724670.
Short‐Term Glucocorticoid Treatment Normalizes the Microcirculatory Response to Remote Ischemic Conditioning in Early Complex Regional Pain Syndrome
2018-09-30

Abstract Background The early phase of complex regional pain syndrome ( CRPS ) is characterized by an inflammatory state and therefore often treated with anti‐inflammatory acting glucocorticoids. Recently, we demonstrated that remote ischemic conditioning ( RIC ), a cyclic application of nondamaging ischemia on a remote extremity, reduces blood flow and increases oxygen extraction in the CRPS ‐affected extremity. Aim The aim of the presented study was to analyze the effect of short‐term pain treatment including glucocorticoid pulse treatment on the RIC ‐induced perfusion parameters. Method Independently from the study, pain treatment was started with an oral glucocorticoid pulse (180 to 360 mg prednisolone) in 12 patients with CRPS (disease duration &lt; 1 year). RIC was conducted before and after pulse treatment. Three cycles of 5 minutes ischemia and 10 minutes reperfusion were applied to the contralateral limb. Blood flow, tissue oxygenation, and oxygen extraction fraction were assessed ipsilateral before and during RIC . Current pain was assessed on the numeric rating scale (0 to 10), and finger–palm distance was measured. Results Pain level (5.8 ± 1.5 vs. 3.1 ± 1.1) and finger–palm distance (5 ± 1.9 cm vs. 3.7 ± 1.9 cm) were decreased significantly by the treatment. RIC decreased blood flow by 32.8% ± 42.8% ( P &lt; 0.05) and increased oxygen extraction fraction by 8.5% ± 10.3% ( P &lt; 0.05) solely before the treatment. After treatment, all parameters remained unchanged after RIC ( P &lt; 0.05 vs. before), comparable to healthy subjects. Conclusion Confirming previous results, RIC presumably unmasks luxury perfusion in untreated CRPS patients. In accordance with the clinical improvement, the short‐term pain treatment with glucocorticoids as major component normalizes impaired perfusion. These results might underline the rationale for anti‐inflammatory treatment in early‐phase CRPS .
Drought losses in China might double between the 1.5 °C and 2.0 °C warming
2018-10-01

Significance We project drought losses in China under global warming of 1.5 °C and 2.0 °C. To assess future drought losses, we project the regional gross domestic product under shared socioeconomic pathways instead of using a static socioeconomic scenario. We identify increasing precipitation and evapotranspiration patterns. With increasing drought intensity and areal coverage across China, drought losses will increase considerably. The estimated losses in a sustainable development pathway at 1.5 °C warming will be 10 times higher than in the reference period 1986–2005 and three times higher than in 2006–2015. Yet, climate change mitigation, limiting the temperature increase to 1.5 °C, can considerably reduce the annual drought losses in China, compared with 2.0 °C warming.
Influence of unplanned excisions on the outcomes of patients with stage III extremity soft‐tissue sarcoma
2018-10-01

BACKGROUND Soft‐tissue sarcomas (STSs) are a heterogeneous group of malignant tumors that can be difficult to treat. This is particularly true after incomplete or unplanned excisions and especially for patients with American Joint Committee on Cancer stage III tumors, who are at high risk for relapse. Numerous studies have shown that an inadequate sarcoma excision is associated with a worse prognosis. However, other reports have suggested an improved prognosis for patients with an initial unplanned excision and subsequent re‐excision in comparison with patients who undergo planned primary surgery. The purpose of this study was to determine the impact of an unplanned excision on treatment and subsequent oncologic and functional outcomes for patients with stage III extremity STS. METHODS From the prospectively collected database at a tertiary‐referral sarcoma center, all patients with stage III STS of the extremities treated between 1989 and 2010 were identified. Patient records were reviewed to identify patient demographics, tumor details, treatments, complications, and functional and oncologic outcomes. RESULTS Five hundred patients with stage III STSs of the extremities were identified, and 94 of these patients (18.8%) were referred after inadequate excisions had been performed elsewhere. All 94 patients with unplanned excisions underwent re‐excision in an attempt to achieve clear margins, and 83% of these patients had residual tumor in the re‐excision specimen. In the re‐excision group, the rates of plastic reconstruction (eg, skin grafts and rotational or free flaps) and amputation were significantly higher in comparison with the rates for patients who underwent a primary planned resection ( P = .023 and P = .03, respectively). The rates of local recurrence, metastasis‐free survival, and overall survival were not significantly different between the 2 groups, nor were the functional outcomes. CONCLUSIONS Unplanned excision of stage III STS leads to an unfavorable clinical course and necessitates more extensive surgery. As a result of aggressive re‐excision and multidisciplinary treatment, a negative effect on oncologic outcomes cannot be confirmed.