gebhart/patrepeval huggingface dataset:
Interaction of orally administered Lactobacillus rhamnosus GG with skin and gut microbiota and humoral immunity in infants with atopic dermatitis (2010)

Specific probiotics may enhance gut barrier function and aid in the development of immune responses. Thus, specific probiotics may afford protection against offending macromolecules in the gut and provide control for future infections by accelerated immunological maturation (ClinicalTrials.gov ID NCT01148667).
A Nanoscale Molecular Switch Triggered by Thermal, Light, and Guest Perturbation (2008)

Abstract Schaltbar : In einem diskreten metallosupramolekularen Nanoball (siehe Bild), der mit dem „Bottom‐up“‐Verfahren hergestellt wurde, tritt ein lösungsmittelabhängiges, physikalisch steuerbares Umklappen des Elektronenspins auf. Das Umklappen lässt sich thermisch, durch Licht oder durch das Lösungsmittel auslösen und kann durch Bestrahlen mit grünem und rotem Laserlicht zwischen „an“ und „aus“ hin und her geschaltet werden. magnified image
Neurodegeneration in Heterozygous Niemann-Pick Type C1 (NPC1) Mouse (2005)

Niemann-Pick type C1 (NPC1) disease is an autosomal recessive, fatal disorder characterized by a defect in cholesterol trafficking and progressive neurodegeneration. The disease is predominantly caused by mutations in the NPC1 gene; however, it has been assumed that heterozygous NPC1 mutations do not cause any symptoms. Here we demonstrate that cholesterol accumulation does not occur in young mouse brains; however, it does in aged (104-106-week-old) NPC1+/- mouse brains. In addition, Purkinje cell loss was observed in aged NPC1+/- mouse cerebellums. Immunoblot analysis using anti-phospho-tau antibodies (AT-8, AT-100, AT-180, AT-270, PHF-1, and SMI-31) demonstrates the site-specific phosphorylation of tau at Ser-199, Ser-202, Ser-212, and Thr-214 in the brains of aged NPC1+/- mice. Mitogen-activated protein kinase, a potential serine kinase known to phosphorylate tau, was activated, whereas other serine kinases, including glycogen synthase kinase 3beta, cyclin-dependent kinase 5, or stress-activated protein kinase/c-Jun N-terminal kinase were not activated. Cholesterol level in the lipid raft isolated from the cerebral cortices, ATP level, and ATP synthase activity in the cerebral cortices significantly decreased in the aged NPC1+/- brains compared with those in the NPC1+/+ brains. All of these changes observed in NPC1+/- brains were determined to be associated with aging and were not observed in the age-matched NPC1+/+ brains. These results clearly demonstrate that heterozygous NPC1 impairs neuronal functions and causes neurodegeneration in aged mouse brains, suggesting that human heterozygous NPC1 mutations may be a risk factor for neurodegenerative disorders, such as tauopathy, in the aged population.
T-ray tomography (2005)

We demonstrate tomographic T-ray imaging, using the timing information present in terahertz (THz) pulses in a ref lection geometry. THz pulses are ref lected from refractive-index discontinuities inside an object, and the time delays of these pulses are used to determine the positions of the discontinuities along the propagation direction. In this fashion a tomographic image can be constructed.  1997 Optical Society of America
Cytotoxic Activity of Dendritic Cells as a Possible Mechanism of Negative Regulation of T Lymphocytes in Pulmonary Tuberculosis (2012)

The PD-1/B7-H1-mediated induction of T cell apoptosis/anergy as a possible mechanism of immune response failure was studied in 76 patients with pulmonary tuberculosis (TB) with normal and low-proliferative response to antigens of M. tuberculosis (purified protein derivative (PPD)). It was revealed that dendritic cells (DCs), generated in vitro from patient blood monocytes with GM-CSF + IFN-α, were characterized by increased B7-H1 expression, upproduction of IL-10, and reducing of allostimulatory activity in mixed lymphocyte culture (MLC). Moreover, DCs of patients with TB were able to enhance T cell apoptosis and to block T-cell division in MLC. It was shown that neutralizing anti-PD1 antibodies significantly decreased the proapoptogenic/tolerogenic effect of DCs. Correlation analysis revealed a direct relationship between IL-10 production and level of B7-H1 expression in the general group of investigated patients. It was demonstrated that generation of healthy donor DCs in the presence of IL-10 led to an increase in the number of DCs-expressed B7-H1 molecule, DC proapoptogenic activity, and a decrease in their allostimulatory activity. Obviously, the revealed phenomenon of the PD-1/B7-H1-mediated pro-apoptogenic activity of DCs is clinically significant since the cytotoxic/tolerogenic potential of DCs is more pronounced in patients with PPD anergy.
PHOTOFRIN II PHOTOSENSITIZATION IS MUTAGENIC AT THE tk LOCUS IN MOUSE L5178Y CELLS (1992)

Photosensitization mediated by Photofrin II (PFII) was found to be mutagenic at the heterozygous thymidine kinase (tk) locus in mouse L5178Y lymphoma strains LY-S1 and LY-R16 but not in strain LY-R83 which is hemizygous at the tk locus. After treatments yielding 37% survival, the mutagenicity of photosensitization with PFII in strain LY-S1 was similar to that of other mutagenic agents including x-radiation, ethyl methanesulfonate, and photosensitization with chloroaluminum phthalocyanine (AlPcCl). Although both strain LY-S1 and strain LY-R16 were mutagenized by photosensitization with PFII, only strain LY-S1 was mutagenized by photosensitization with AlPcCl. The non-mutability of strain LY-R83 following photodynamic treatment with either sensitizer may be because of the poor recovery of mutants with intergenic mutations in this TK+/0 hemizygous strain, whereas the non-mutability of strain LY-R16 subjected to photodynamic treatment with AlPcCl may be because LY-R16 cells sustaining mutagenic damage do not survive for reasons other than the loss of an essential gene.
PENSA study for the prevention of cognitive decline in APOE‐ɛ4 carriers with subjective cognitive decline: Baseline preliminary demographic and neuropsychological description of the study population (2021)

Abstract Background In the absence of effective treatments to reverse cognitive deterioration related to Alzheimer's disease (AD), nonpharmacological secondary prevention interventions at early preclinical stages have been found to be a promising strategy to prevent cognitive decline. In this context, the PENSA study, framed within the WW‐FINGERS consortium, is a randomized clinical trial involving cognitively normal elderly individuals with an increased risk of developing AD (meeting subjective cognitive decline, SCD‐plus criteria and being APOE‐ɛ4 carriers). The aim of the study is to evaluate the efficacy of a multimodal personalized lifestyle intervention (dietary and physical activity counseling and cognitive training) combined with a dietary supplement, epigallocatechin gallate (EGCG) in slowing down cognitive decline. Method In this work we present the baseline sociodemographic, mood and cognitive characteristics of the already enrolled sample. Cognitive function was measured with the Alzheimer Disease Cooperative Study Preclinical Alzheimer Cognitive Composite (ADCS‐PACC) and adding to this original version the interference score from the Stroop Color and Word Test and the Five Digit Test (ADCS‐PACC‐Plus‐exe). Additionally, the Digit Span, the Boston Naming Test and the Animal Fluency Test were administered. Psychological distress was measured with the Hospital Anxiety and Depression Scale. Result On January 2021 the study had enrolled 68 individuals (62% women) with a mean (SD) age of 67.4 (4.6) years and the following APOE genotype: 83% ɛ3/ɛ4, 13% ɛ4/ɛ4 and 4% ɛ2/ɛ4. Most had higher education (66.2%) and 84% were retired (Table 1). Mild and moderate symptoms of psychological distress were present in 14.7% and 23.5% of participants, respectively. The mean (SD) number of cognitive domains affected (memory, concentration, language, visuospatial skills), measured by an ad‐hoc SCD questionnaire, were 2.54 (±0.9). 77.3% of participants referred memory centered complaints. Considering the different domains, participants reported alterations on memory (97.1%), concentration (73.5%), language (67.6%) and visuospatial skills (11.8%). SCD profiles are shown in Figure 1. Table 2 shows the ADCS‐PACC‐Plus‐exe scores. Conclusion The PENSA study will provide valuable information on the effect of a lifestyle intervention supplemented with EGCG to prevent cognitive decline and will aid to share light on the benefit of these strategies in people at‐risk of developing AD.
Low-temperature-processable amorphous-oxide-semiconductor-based phosphors for durable light-emitting diodes (2022)

In this study, we fabricated light-emitting diodes (LEDs) on glass substrates at a maximum process temperature of 200 °C using amorphous oxide semiconductor (AOS) materials as emission layers. Amorphous gallium oxide films doped with rare-earth elements (Eu, Pr, and Tb) were employed as AOS emission layers, and the LEDs emitted clear red, green, and pink luminescence upon direct-current application even in the ambient environment. Resonance photoelectron spectroscopy revealed the difference in the electronic structure of the films for each rare-earth dopant, suggesting different emission mechanisms, viz., electron–hole recombination and impact excitation. Although it is widely believed that amorphous materials are unsuitable for use as emission layers of LEDs because of their high concentrations of mid-gap states and defects, the developed rare-earth-doped AOS materials show good performance as emission layers. This study provides opportunities for the advancement of flexible display technologies operating in harsh environments.
Edge die focus-exposure monitoring and compensation to improve CD distributions (2004)

As design rules shrink and process windows become smaller, it is increasingly important to monitor exposure tool focus and exposure in order to maximize device yield. Economic considerations are forcing us to consider nearly all methods to improve yield across the wafer. For example, it is not uncommon in the industry that chips around the edge of the wafer have lower yield or device speed. These effects are typically due to process and exposure tool errors at the edge of the wafer. In order to improve yield and chip performance, we must characterize and correct for changes in the effective focus and exposure at the edge. Monitoring focus and exposure on product wafers is the most effective means for correction, since product wafers provide the most realistic view of exposure tool interactions with the process. In this work, on-product monitoring and correction is based on optical measurement using a compact line end shortening (LES) target that provides a unique separation of exposure and focus on product wafers. Our ultimate objective is indirect CD control, with maximum yield and little or no impact on productivity.
Highly Potent and Selective Phenylmorphan-Based Inverse Agonists of the Opioid δ Receptor (2006)

We recently reported the discovery of (+)-5-(3-hydroxyphenyl)-4-methyl-2-(3-phenylpropyl)-2-azabicyclo[3.3.1]non-7-yl-(1-phenyl-1-cyclopentane)carboxamide [(+)-KF4, (+)-5] as a novel chemotype possessing potent antagonist activity at the delta opioid receptor. Additional SAR studies involving changes to both the 2-amino and 7-amido N-substituents using this same (+)-morphan scaffold have revealed compounds with improved potency and selectivity for the delta opioid receptor. The highly potent and selective 2,2-dimethylphenylacetamide analogue (+)-N-[(1S,4R,5R,7S)-5-(3-hydroxyphenyl)-4-methyl-2-(3-phenylpropyl)-2-azabicyclo[3.3.1]non-7-yl]-2-methyl-2-phenylpropanamide (13d, delmorphan-A) showed picomolar inhibitory potency (Ke = 0.1 nM) in the [35S]GTPgammaS functional assay with delta opioid receptor selectivity ratios of 103- and 132-fold versus the mu and kappa opioid receptors, respectively. The compounds showed no agonist activity at any of the three opioid receptors; however, measurements of delta inverse agonist activity within this series illustrated a broad range of negative efficacy and IC50 values 650-fold more potent than the prototypical delta opioid receptor inverse agonist ICI 174,864 (22).
ImAxes (2017)

We introduce ImAxes immersive system for exploring multivariate data using fluid, modeless interaction. The basic interface element is an embodied data axis. The user can manipulate these axes like physical objects in the immersive environment and combine them into sophisticated visualisations. The type of visualisation that appears depends on the proximity and relative orientation of the axes with respect to one another, which we describe with a formal grammar. This straight-forward composability leads to a number of emergent visualisations and interactions, which we review, and then demonstrate with a detailed multivariate data analysis use case.
Software internationalisation in the large at Oracle (2004)

This presentation is focused upon the most significant problems of software internationalisation which we have confronted at Oracle over the past decade, as the core database and application suites have been deployed in as many as twenty-eight different languages, with numerous additional locale variations. While some of this material is necessarily historical, it provides a critical industry backdrop to the substantial technical progress which has been made in recent years, and some opportunity to reflect on some of the more useful and enduring of the approaches adopted.Nevertheless, in spite of our success in addressing these initial issues, the increasing complexity of modern applications and the more demanding business environment have introduced additional challenges, and the remainder of the talk is devoted to two of the more important:• Simultaneous shipping of applications to multiple target locales -- with reference to the Oracle SimShip project; and• The difficulty of internationalising applications to take account of locale-specific business rules.The presentation will conclude with some attempt at a wish-list for tool support in these and other areas of the problem domain.
Quantitative Brain Morphometry of Portable Low-Field-Strength MRI Using Super-Resolution Machine Learning (2022)

Background Portable, low-field-strength (0.064-T) MRI has the potential to transform neuroimaging but is limited by low spatial resolution and low signal-to-noise ratio. Purpose To implement a machine learning super-resolution algorithm that synthesizes higher spatial resolution images (1-mm isotropic) from lower resolution T1-weighted and T2-weighted portable brain MRI scans, making them amenable to automated quantitative morphometry. Materials and Methods An external high-field-strength MRI data set (1-mm isotropic scans from the Open Access Series of Imaging Studies data set) and segmentations for 39 regions of interest (ROIs) in the brain were used to train a super-resolution convolutional neural network (CNN). Secondary analysis of an internal test set of 24 paired low- and high-field-strength clinical MRI scans in participants with neurologic symptoms was performed. These were part of a prospective observational study (August 2020 to December 2021) at Massachusetts General Hospital (exclusion criteria: inability to lay flat, body habitus preventing low-field-strength MRI, presence of MRI contraindications). Three well-established automated segmentation tools were applied to three sets of scans: high-field-strength (1.5-3 T, reference standard), low-field-strength (0.064 T), and synthetic high-field-strength images generated from the low-field-strength data with the CNN. Statistical significance of correlations was assessed with Student <i>t</i> tests. Correlation coefficients were compared with Steiger <i>Z</i> tests. Results Eleven participants (mean age, 50 years ± 14; seven men) had full cerebrum coverage in the images without motion artifacts or large stroke lesion with distortion from mass effect. Direct segmentation of low-field-strength MRI yielded nonsignificant correlations with volumetric measurements from high field strength for most ROIs (<i>P</i> > .05). Correlations largely improved when segmenting the synthetic images: <i>P</i> values were less than .05 for all ROIs (eg, for the hippocampus [<i>r</i> = 0.85; <i>P</i> < .001], thalamus [<i>r</i> = 0.84; <i>P</i> = .001], and whole cerebrum [<i>r</i> = 0.92; <i>P</i> < .001]). Deviations from the model (<i>z</i> score maps) visually correlated with pathologic abnormalities. Conclusion This work demonstrated proof-of-principle augmentation of portable MRI with a machine learning super-resolution algorithm, which yielded highly correlated brain morphometric measurements to real higher resolution images. © RSNA, 2022 <i>Online supplemental material is available for this article.</i> See also the editorial by Ertl-Wagner amd Wagner in this issue. <i>An earlier incorrect version appeared online. This article was corrected on February 1, 2023.</i>
doepipeline : a systematic approach to optimizing multi-level and multi-step data processing workflows (2018)

Abstract Background Selecting the proper parameter settings for bioinformatic software tools is challenging. Not only will each parameter have an individual effect on the outcome, but there are also potential interaction effects between parameters. Both of these effects may be difficult to predict. To make the situation even more complex, multiple tools may be run in a sequential pipeline where the final output depends on the parameter configuration for each tool in the pipeline. Because of the complexity and difficulty of predicting outcomes, in practice parameters are often left at default settings or set based on personal or peer experience obtained in a trial and error fashion. To allow for the reliable and efficient selection of parameters for bioinformatic pipelines, a systematic approach is needed. Results We present doepipeline , a novel approach to optimizing bioinformatic software parameters, based on core concepts of the Design of Experiments methodology and recent advances in subset designs. Optimal parameter settings are first approximated in a screening phase using a subset design that efficiently spans the entire search space, then optimized in the subsequent phase using response surface designs and OLS modeling. doepipeline was used to optimize parameters in four use cases; 1) de-novo assembly, 2) scaffolding of a fragmented genome assembly, 3) k-mer taxonomic classification of Oxford Nanopore Technologies MinION reads, and 4) genetic variant calling. In all four cases, doepipeline found parameter settings that produced a better outcome with respect to the characteristic measured when compared to using default values. Our approach is implemented and available in the Python package doepipeline . Conclusions Our proposed methodology provides a systematic and robust framework for optimizing software parameter settings, in contrast to labor- and time-intensive manual parameter tweaking. Implementation in doepipeline makes our methodology accessible and user-friendly, and allows for automatic optimization of tools in a wide range of cases. The source code of doepipeline is available at https://github.com/clicumu/doepipeline and it can be installed through conda-forge.
Effects of Collateral Status on Infarct Distribution Following Endovascular Therapy in Large Vessel Occlusion Stroke (2020)

In this cohort of patients with large vessel occlusion stroke, both the collateral status and endovascular reperfusion were strongly associated with middle cerebral artery territory final infarct volumes. Our findings suggesting that baseline collateral status predominantly affected middle cerebral artery border zones infarction, whereas higher mTICI preserved deep white matter and internal capsule from infarction; may explain why reperfusion success-but not collateral status-was among the independent predictors of favorable outcome at discharge. Infarction of the lentiform nuclei was observed regardless of collateral status or reperfusion success.
Understanding users: a prerequisite for developing new technologies (2004)

The LEADERS Project has sought to develop innovative methods of delivering archive material to users via the Internet. In practice, this has been achieved through the development of open‐source tools that can be used by Archivists to build on‐line applications where transcripts and images of archive documents are delivered alongside contextual information from finding aids and authority records. This article explains how and why archive users have been placed at the centre of the LEADERS Project. It focuses on our preliminary research into who is currently visiting archive repositories and introduces our segmentation model for profiling types of users, as well as the results of our user survey, which we based on this model. This research was a prerequisite for the project: it has given us a broad understanding of the market for our product and has provided us with the background data necessary to ensure that we can go on to engage a representative sample of users to give us feedback on our work.
Sex differences in survival, functional outcomes and health-related quality of life are mostly due to women's greater age, more severe stroke and pre-stroke health compared to men: the INternational STRoke oUtComes sTudy (INSTRUCT) (2017)

Sex in survival, functional outcomes and health-related quality of life are mostly due to women's greater age, more severe stroke and pre-stroke health compared to men: the INternational STRoke oUtComes sTudy (INSTRUCT)Background: The sex differences in stroke outcome may be due to confounding.We established an individual participant data meta-analysis to establish the causes of sex differences in outcome after stroke.Methods: We obtained data on strokes ) from 13 population-based studies including socio-demographics, stroke-related factors, pre-stroke health and 1-year outcomes (mortality, functional outcome, health-related quality of life [HRQoL]).For women compared to men, we estimated the relative risk of mortality and poor functional outcome using log binomial regression and the mean differences in HRQoL using linear regression.Study-specific adjusted models were combined using random effects meta-analysis.Results: There were 16,957 participants followed up at 1 year.Women were 35% more likely to be deceased (RR 1.35 95% CI 1.24-1.47)and 32% more likely to have a poor functional outcome (RR 1.32 95% CI 1.18-1.48)than men.Women had lower mean HRQoL than men: EQ5D -0.064 (95% CI -0.094, -0.035) and AQoL -0.135 (95% CI -0.196, -0.074).For mortality, these differences were explained by age, stroke severity and atrial fibrillation; whereas for functional outcomes the differences were mostly attenuated by age, stroke severity and pre-stroke function.The sex differences in HRQoL remained after accounting for a range of confounders including age, severity, pre-stroke function and vascular risk factors. Conclusion:The worse outcome after stroke in women compared to men is mostly due to their advanced age and more severe strokes.Ensuring equal access to acute care and primary and secondary prevention, particularly for the elderly, should make outcomes more equitable.