gebhart/patrepeval huggingface dataset:
Polygenic risk heterogeneity among focal epilepsies (2020)

Focal epilepsy (FE) is clinically highly heterogeneous. It has been shown recently that not only rare but also a subset of common genetic variants confer risk for FE. The relatively modest power of genetic studies in FE suggests a high genetic heterogeneity of FE when grouped as one disorder. We hypothesize that the clinical heterogeneity of FE is correlated with genetic heterogeneity on a common risk variant level. To test the hypothesis, we used an FE polygenic risk score "FE-PRS" that combines small effect sizes of thousands of common variants from the largest FE-GWAS (genome-wide association study) into a single measure. We grouped 414 individuals with FE according to common clinical features into subgroups, either by one feature at a time or by all features combined in a cluster analysis. We examined their association with FE-PRS compared to 20 435 matched population controls and observed heterogeneous FE-PRS burden among the subgroups. The highest phenotypic variance explained by FE-PRS was identified in a cluster analysis-defined FE subgroup where all individuals had unknown etiologies and psychiatric comorbidities, and the majority had early onset seizures. Our results indicate that genetic factors associated with FE have differential burden among FE subtypes. Future studies using better-powered FE-PRS might have clinical utility.
Controllable degradation product migration from biomedical polyester-ethers (2007)

The use of degradable biomedical materials has during the past decades indeed modernized medical science, finding applications in e.g. tissue engineering and drug delivery. The key question is to adapt the material with respect to mechanical properties, surface characteristics and degradation profile to suit the specific application. Degradation products are generally considered non-toxic and they are excreted from the human body. However, large amounts of hydroxy acids may induce a pH decrease and a subsequent inflammatory response at the implantation site. In this study, macromolecular design and a combination of cross-linking and adjusted hydrophilicity are utilized as tools to control and tailor degradation rate and subsequent release of degradation products from biomedical polyester-ethers. A series of different homo- and copolymers of -caprolactone (CL) and 1,5-dioxepan-2-one (DXO) were synthesized and their hydrolytic degradation was monitored in phosphate buffer solution at pH 7.4 and 37 °C for up to 546 days. The various materials comprised linear DXO/CL triblock and multiblock copolymers, PCL linear homopolymer and porous structure, and random cross-linked homo- and copolymers of CL/DXO using 2,2’-bis-(ε-caprolactone-4-yl) propane (BCP) as a cross-linking agent. The results showed that macromolecular engineering and controlled hydrophilicity of cross-linked networks were useful implements for customizing the release rate of acidic degradation products in order to prevent the formation of local acidic environments and thereby reduce the risk of inflammatory responses in the body.
Simultaneous determination of monomeric and oligomeric alkannin and shikonin by HPLC-DAD-APCI-MS (2007)

Alkannin and shikonin (A/S) derivatives possessing a wide spectrum of biological activities have been found in roots of several Boraginaceous species [1,2]. As reviewed in [3], determination of monomeric A/S derivatives in commercial samples, root extracts and tissue cultures by HPLC has been described previously. Although the presence of oligomeric A/S derivatives has been confirmed by size exclusion chromatography, their analysis by HPLC has not been reported. Therefore, in the present study a rapid and simple HPLC-DAD-APCI-MS method was developed to detect and determine monomeric and oligomeric alkannins/shikonins simultaneously for the first time. Commercial samples of alkannin and shikonin were analyzed for the respective compounds and the structures of the oligomeric derivatives were identified based on their MS-spectra.
Methods to Evaluate the Inhibition of TTR Fibrillogenesis Induced by Small Ligands (2012)

Transthyretin is an amyloidogenic protein associated with several amyloidosis, namely familial amyloidotic polyneuropathy, familial amyloidotic cardiomyopathy, and central nervous system selective amyloidosis, familial rare diseases caused by single point mutants, and senile systemic amyloidosis associated with wild-type TTR. The current model for amyloid fibril formation involves initial dissociation of the native TTR tetramer into non-native monomers which associate into soluble oligomers and protofibrils that evolve to mature amyloid deposits. A number of efforts are addressed to identify small molecules targeting the formation, clearance, or assembly of toxic aggregates as a promising therapeutic strategy to treat amyloidosis. This review classifies and summarizes the different strategies and assays that have been developed in vitro, ex vivo, and in vivo as tools to screen libraries of compounds or to test compounds from rational design in the search of drug candidates for the treatment of TTR-associated amyloidosis. Depending on the property they measure, the assays are classified as: a) in vitro assays that monitor protein aggregation and/or fibril formation, b) in vitro assays that monitor binding to native protein, c) ex vivo TTR plasma selectivity assays, d) in vitro assays for tetrameric TTR stabilization, e) cellular assays, and f) animal models to evaluate amyloidosis inhibitors.
Scanning x-ray fluorescence microscopy and principal component analysis (1992)

A relatively new entry, in the field of microscopy, is the Scanning X-Ray Fluorescence Microscope (SXRFM). Using this type of instrument (e.g. Kevex Omicron X-ray Microprobe), one can obtain multiple elemental x-ray images, from the analysis of materials which show heterogeneity. The SXRFM obtains images by collimating an x-ray beam (e.g. 100 μm diameter), and then scanning the sample with a high-speed x-y stage. To speed up the image acquisition, data is acquired "on-the-fly" by slew-scanning the stage along the x-axis, like a TV or SEM scan. To reduce the overhead from "fly-back," the images can be acquired by bi-directional scanning of the x-axis. This results in very little overhead with the re-positioning of the sample stage. The image acquisition rate is dominated by the x-ray acquisition rate. Therefore, the total x-ray image acquisition rate, using the SXRFM, is very comparable to an SEM. Although the x-ray spatial resolution of the SXRFM is worse than an SEM (say 100 vs. 2 μm), there are several other advantages.
Glucose consumption and alpha-glucosidase inhibitory activities of aqueous root extract of Helicteres angustifolia. (2016)

The findings from this study indicate that aqueous root extract of Helicteres angustifolia possesses significant alpha-glucosidase inhibitory activity and moderate enhanced glucose consumption activity, while with low cytotoxic and acute toxicity.
Statistical Uncertainty Estimation Using Random Forests and Its Application to Drought Forecast (2012)

Drought is part of natural climate variability and ranks the first natural disaster in the world. Drought forecasting plays an important role in mitigating impacts on agriculture and water resources. In this study, a drought forecast model based on the random forest method is proposed to predict the time series of monthly standardized precipitation index (SPI). We demonstrate model application by four stations in the Haihe river basin, China. The random‐forest‐ (RF‐) based forecast model has consistently shown better predictive skills than the ARIMA model for both long and short drought forecasting. The confidence intervals derived from the proposed model generally have good coverage, but still tend to be conservative to predict some extreme drought events.
Engineered sensor bacteria evolve master-level gameplay through accelerated adaptation (2022)

Abstract Gene circuits enable cells to make decisions by controlling the expression of genes in reaction to specific environmental factors 1 . These circuits can be designed to encode logical operations 2–7 , but implementation of more complex algorithms has proved more challenging. Directed evolution optimizes gene circuits 8 without the need for design knowledge 9 , but adjusting multiple genes and conditions 10 in genotype searches poses challenges 11 . Here we show a multicellular sensor system, AdaptoCells, in Escherichia coli, that can evolve complex behavior through an accelerated adaptation to chemical environments. AdaptoCells recognize chemical patterns and act as a decision-making system. Using an iterative improvement method, we demonstrate that the AdaptoCells can evolve to achieve mastery in the game of tic-tac-toe, demonstrating an unprecedented level of complexity for engineered living cells. We provide an effective and straightforward way to encode complexity in gene circuits, allowing for fast adaptation in response to dynamic environments and leading to optimal decisions.
IaaS Cloud Security (2013)

In the last few years, cloud computing has grown from being a promising business concept to one of the fastest growing segments of the IT industry. Now, recession-hit companies are increasingly realizing that simply by tapping into the cloud they can gain fast access to best-of-breed business applications or drastically boost their infrastructure resources, all at negligible cost. Securing our digital assets has become increasingly challenging as our reliance on rapidly evolving technologies continues to grow. The security perimeter in computing has changed from a well-defined boundary that was relatively easy to identify and defend, to an elastic boundary that is constantly changing and for which the threats are constantly evolving. This paper investigates the complex security challenges that are introduced by the trend towards Infrastructure as a Service (IaaS)-based cloud computing. Availability, Authenticity, and Privacy are essential concerns for both Cloud providers and consumers as well. Infrastructure as a Service (IaaS) serves as the foundation layer for the other delivery models, and a lack of security in this layer will certainly affect the other delivery models, i.e., PaaS, and SaaS that are built upon IaaS layer. This paper presents an elaborated study of IaaS components' security and determines vulnerabilities and countermeasures. Finally, as a result of this research, we propose a Security Model for IaaS (SMI) to guide security assessment and enhancement in IaaS layer.
Rate-Distortion-Optimized Video Transmission Using Pyramid Vector Quantization (2012)

Conventional video compression relies on interframe prediction (motion estimation), intra frame prediction and variable-length entropy encoding to achieve high compression ratios but, as a consequence, produces an encoded bitstream that is inherently sensitive to channel errors. In order to ensure reliable delivery over lossy channels, it is necessary to invoke various additional error detection and correction methods. In contrast, techniques such as Pyramid Vector Quantisation have the ability to prevent error propagation through the use of fixed length codewords. This paper introduces an efficient rate distortion optimisation algorithm for intra-mode PVQ which offers similar compression performance to intra H.264/AVC and Motion JPEG 2000 while offering inherent error resilience. The performance of our enhanced codec is evaluated for HD content in the context of a realistic (IEEE 802.11n) wireless environment. We show that PVQ provides high tolerance to corrupted data compared to the state of the art while obviating the need for complex encoding tools.
[Value and limitations of sport in cardiac patients]. (2006)

Regular physical exercise increases effort capacity, the quality of life, and improves symptoms in all cardiac patients. In addition, and much more importantly, all studies show a close correlation between exercise and the reduction of mortality and morbidity with a beneficial effect on the progression of atherosclerosis. This relationship is particularly well documented in patients with coronary artery disease. Exercise has a beneficial effect due to its action on all the principal coronary risk factors, an endothelial dysfunction, coagulability and prevention of thrombosis and an autonomic nervous system tone. All forms of physical activity and some sports may therefore be considered by these patients. In some cases, competitive sport may be permitted, in accordance with popular social custom. In order to obtain these cardiocirculatory protection, physical exercise and sporting activities should be the object of a personalised therapeutic prescription which takes into account the intensity, the type of effort, its duration and frequency. Indeed, if the intensity of the exercise is too low, these patients may not obtain the desired benefits. On the other hand, excessively intensive exercise could trigger serious adverse effects such as severe arrhythmias, sudden death or an acute coronary syndrome. It is, therefore, essential before "prescribing" exercise to perform a preliminary evaluation to stratify the patient's risk and in order to recommend appropriate and well adapted exercise programs.
RobustDistiller: Compressing Universal Speech Representations for Enhanced Environment Robustness (2023)

Self-supervised speech pre-training enables deep neural network models to capture meaningful and disentangled factors from raw waveform signals. The learned universal speech representations can then be used across numerous downstream tasks. These representations, however, are sensitive to distribution shifts caused by environmental factors, such as noise and/or room reverberation. Their large sizes, in turn, make them unfeasible for edge applications. In this work, we propose a knowledge distillation methodology termed RobustDistiller which compresses universal representations while making them more robust against environmental artifacts via a multi-task learning objective. The proposed layer-wise distillation recipe is evaluated on top of three well-established universal representations, as well as with three downstream tasks. Experimental results show the proposed methodology applied on top of the WavLM Base+ teacher model outperforming all other benchmarks across noise types and levels, as well as reverberation times. Oftentimes, the obtained results with the student model (24M parameters) achieved results inline with those of the teacher model (95M).
IMS2014 Student Paper Competition (2014)

Summary form only given. The IEEE Microwave Theory and Techniques Society (MTTS) will hold its annual Student Paper Competition at the 2014 International Microwave Symposium (IMS2014). The purpose of the competition is to recognize outstanding technical contribution of individual students and to encourage student involvement in research and development in the technical areas of MTT-S. All papers submitted online to the conference by 9 December 2014 that are denoted as student papers are considered for the competition. At least one finalist is recommended by each technical subcommittee. The student finalists are invited to present their work in a special competition session held separate from their regular paper presentation. The student finalists and their advisors are also invited to attend the Student Awards Luncheon held on Thursday of the conference. The winners of the competition are announced and presented with awards at the Student Awards Luncheon. For more information and instructions about the competition guidelines and logistics, please visit http://www.ims2014.org/students/student-paper-competition.
Scalable Super-Resolution Synthesis of Core-Vest Composites Assisted by Surface Plasmons (2018)

The behavior of composite nanostructures depends on both size and elemental composition. Accordingly, concurrent control of size, shape, and composition of nanoparticles is key to tuning their functionality. In typical core-shell nanoparticles, the high degree of symmetry during shell formation results in fully encapsulated cores with severed access to the surroundings. We commingle light parameters (wavelength, intensity, and pulse duration) with the physical properties of nanoparticles (size, shape, and composition) to form hitherto unrealized core-vest composite nanostructures (CVNs). Unlike typical core-shells, the plasmonic core of the resulting CVNs selectively maintains physical access to its surrounding. Tunable variations in local temperature profiles ≳50 °C are plasmonically induced over starburst-shaped nanoparticles as small as 50-100 nm. These temperature variations result in CVNs where the shell coverage mirrors the temperature variations. The precision thus offered individually tailors access pathways of the core and the shell.
Endothelin Type A Receptor Blockade Attenuates the Hypertension in Response to Chronic Reductions in Uterine Perfusion Pressure (2001)

A chronic reduction in uterine perfusion pressure in pregnant rats is associated with a significant elevation in mean arterial pressure (MAP) and reduction in kidney function. The purpose of this study was to examine the role of endothelin in mediating the hypertension in response to chronic reductions in uterine perfusion pressure in conscious, chronically instrumented, pregnant rats. MAP in pregnant rats with chronic reductions in uterine perfusion pressure (123.0+/-1.8 mm Hg) was significantly higher than that in control pregnant rats (101.3+/-4.0 mm Hg). Renal expression of preproendothelin mRNA as determined by ribonuclease protection assay was also significantly elevated in the medulla (>45%, P<0.05) and in the cortex (>22%, P:<0.05) of the pregnant rats with chronic reductions in uterine perfusion pressure compared with control pregnant rats. Chronic administration of the selective endothelin type A receptor antagonist (ABT-627, 5 mg/kg per day for 10 days) markedly attenuated the increase in MAP observed in the pregnant rats with chronic reductions in uterine perfusion pressure (103.3+/-5.6 mm Hg, plus endothelin antagonist; P<0.05). However, endothelin type A receptor blockade had no significant effect on blood pressure in the normal pregnant animals (96.0+/-2.7 mm Hg, plus endothelin antagonist). These findings suggest that endothelin plays a major role in mediating the hypertension produced by chronic reductions in uterine perfusion pressure in pregnant rats.
Randomized phase I trial HIV-CORE 003: Depletion of serum amyloid P component and immunogenicity of DNA vaccination against HIV-1 (2018)

Clinicaltrials.gov NCT02425241.
Pellet System Description (2006)

The description logic SHOIN (D) has attracted considerable interest as the foundation of the W3C standard Web Ontology Language variant, OWL-DL. Pellet is a sound and complete tableau reasoner for SHOIN (D) and incorporates a number of key features such as conjunctive ABox query, axiom pinpointing, rules, E-connection reasoning, and novel optimizations for nominals. In this paper we summarize Pellet’s features and special capabilities.
Trajectories from Snapshots: Integrated proteomic and metabolic single-cell assays reveal multiple independent adaptive responses to drug tolerance in a BRAF-mutant melanoma cell line (2019)

Abstract The determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge, with relevance towards understanding biological changes ranging from cellular differentiation to epigenetic (adaptive) responses of diseased cells to drugging. We report on a combined experimental and theoretic method for determining the trajectories that specific highly plastic BRAF V600E mutant patient-derived melanoma cancer cells take between drug-naïve and drug-tolerant states. Recent studies have implicated non-genetic, fast-acting resistance mechanisms are activated in these cells following BRAF inhibition. While single-cell highly multiplex omics tools can yield snapshots of the cell state space landscape sampled at any given time point, individual cell trajectories must be inferred from a kinetic series of snapshots, and that inference can be confounded by stochastic cell state switching. Using a microfludic-based single-cell integrated proteomic and metabolic assay, we assayed for a panel of signaling, phenotypic, and metabolic regulators at four time points during the first five days of drug treatment. Dimensional reduction of the resultant data set, coupled with information theoretic analysis, uncovered a complex cell state landscape and identified two distinct paths connecting drug-naïve and drug-tolerant states. Cells are shown to exclusively traverse one of the two pathways depending on the level of the lineage restricted transcription factor MITF in the drug-naïve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities, and are independently druggable. Our results update the paradigm of adaptive resistance development in an isogenic cell population and offer insight into the design of more effective combination therapies.
A framework for similarity-based classification methods (2000)

Abstract. A general framework for similarity-based (SB) classification methods is presented. Neural networks, such as the Radial Basis Function (RBF) and the Multilayer Perceptrons (MLPs) models, are special cases of SB methods. Many new versions of minimal distance methods are derived from this framework.
Cobalt PCP Pincer Complexes via an Unexpected Sequence of Ortho Metalations (2014)

The cobalt PCP pincer complexes [Co{2,6-(CH2PPh2-κP)2C6H3-κC1}(L)2], where L = PMe3 (1), CO (2), have been prepared. Complex 1 is obtained by a transmetalation reaction between 1-lithio-2,6-bis((diphenylphosphino)methyl)benzene and [CoCl(PMe3)3]. Subsequent exposure of 1 to CO gave complex 2. Complexes 1 and 2 can also be obtained from 1,3-bis((diphenylphosphino)methyl)benzene and [CoMe(PMe3)4]. Instead of ortho metalation occurring directly at the C2 (pincer) position of the diphosphine, ortho metalation first occurs at the C4 position to form [Co{2-(CH2PPh2-κP)-4-(CH2PPh2)-C6H3-κC1}(PMe3)3] (4). After reflux of the reaction mixture for 24 h, a rearrangement of 4 occurs to give pincer complex 1 with loss of PMe3 in ca. 50% yield; this rearrangement was accompanied by some decomposition. The mechanism for the conversion of 4 to 1 has been probed using 1-deuterio-2,6-bis((diphenylphosphino)methyl)benzene. Unexpectedly, the labeled ligand led to 15% deuterium enrichment of an ortho CH of the terminal PPh2 group in the product complex 1, and the proposed mechanism for this rearrangement involves a four-membered cobaltacyclic intermediate.
Explicit Calculation of Pipe‐Network Parameters (1990)

An explicit algorithm is presented for directly determining a variety of design, operating, and calibration parameters for pipe networks. The problem solution is based on the reformulation of the steady‐state network equilibrium equations in terms of specified pipe‐system parameters. Since these equations are nonlinear, the incremental Newton‐Raphson method is used as the basic solution procedure. A continuous variable space is assumed for the various parameters, which are selected to exactly satisfy stated pressure and flow requirements at critical nodes and pipes throughout the pipeline systems for a range of operating conditions. This approach offers a basis for determining the optimum values for the various design, operating, and calibration parameters in the sense that the parameters can be calculated to exactly meet the specified pressure and flow constraints. All types of pipe distribution systems can be considered. The solution space is secured through a well‐arranged interaction between network topology, boundary constraints, and network parameters. The feasibility and flexibility of the proposed approach are demonstrated using an example network.