gebhart/patrepeval huggingface dataset:
An Economic Framework for Evaluating Personalized Medicine (2004)

Individual variation accounts for a wide range of medical and economic consequences, from inefficiencies in drug discovery and development to ineffectiveness of drug treatment to drug-induced morbidity and mortality. Addressing these consequences could benefit patients, health care providers and payers, and the pharmaceutical industry. When appropriate markers are known, diagnostic tests allow precise diagnosis and dosing, prediction of disease progression, prediction of treatment response and prediction of adverse drug reactions for individual patients. There may also be substantial savings realized by eliminating costs associated with failed treatment. We developed an analytical framework for analyzing the potential value of using a diagnostic test in clinical practice. Our framework determines the economic consequences of implementing pharmacogenomics in the clinic using a diagnostic test to predict drug response. We offer an empirical test of these ideas: we calculated the cost offset realized by predicting the likelihood of response to an alternative existing treatment using a hypothetical pharmacogenomic test in an asthma population. Because the diagnostic test is hypothetical, our framework is general and could be applied to other indications where diagnostic tests have not been developed. Our results could potentially guide future economic evaluation of new diagnostic tests. Importantly, they may also influence biomarker discovery strategies to ensure consistency between market priorities and the future stream of product introductions.
ANALYSIS OF CONGESTED TRAFFIC FLOW (1998)

Recent results of investigations of congested traffic flow are presented. It is noted that there are two qualitative different types of phase transitions from free traffic flow: (i) free flow to synchronized traffic flow and (ii) free flow to traffic jam. It is also noted that the flow rate out from a traffic jam qout can be considerably lower than the maximal possible flow rate in free flow q(free)max: q(free)max / qout approximates to 1.5. It is stressed that while traffic jams show characteristic parameters which do not depend on initial conditions, synchronized flow show a very complex spatial-temporal behavior. The properties of traffic flow found can be used for traffic forecasting with the aim of improvement of route guidance systems. For the covering abstract see IRRD E102946.
Fabrication of porous polyvinyl alcohol scaffold for bone tissue engineering via selective laser sintering (2013)

A tetragonal polyvinyl alcohol (PVA) scaffold with 3D orthogonal periodic porous architecture was fabricated via selective laser sintering (SLS) technology. The scaffold was fabricated under the laser power of 8 W, scan speed of 600 mm min(-1), laser spot diameter of 0.8 mm and layer thickness of 0.15 mm. The microstructure analysis showed that the degree of crystallization decreased while the PVA powder melts gradually and fuses together completely with laser power increasing. Thermal decomposition would occur if the laser power was further higher (16 W or higher in the case). The porous architecture was controllable and totally interconnected. The porosity of the fabricated scaffolds was measured to be 67.9 ± 2.7% which satisfies the requirement of micro-pores of the bone scaffolds. Its bioactivity and biocompatibility were also evaluated in vitro as tissue engineering (TE) scaffolds. In vitro adhesion assay showed that the amount of pores increased while the scaffold remains stable and intact after immersion in simulated body fluid for seven days. Moreover, the number of MG-63 cells and the bridge between cells increased with increasing time in cell culture. The present work demonstrates that PVA scaffolds with well-defined porous architectures via SLS technology were designed and fabricated for bone TE.
Translating SQL for database reengineering (1996)

A tool for porting database applications is presented. The tool transforms VMS/Rdb applications written in C and embedded SQL into a portable, database-independent application interface which can be directly installed on a target platform and database management system with a separate customization tool. The converter is based on standard techniques developed for compiling programming languages. The original task of the converter was to port a large administrative system from VMS/Rdb into Oracle, but the tool can be used for other reengineering applications as well.
Lipid mediators of autophagy in stress-induced premature senescence of endothelial cells (2008)

Our group (Patschan S, Chen J, Gealekman O, Krupincza K, Wang M, Shu L, Shayman JA, Goligorsky MS; Am J Physiol Renal Physiol 294: F100-F109, 2008) previously observed an accumulation of gangliosides coincident with development of cell senescence and demonstrated lysosomal permeabilization in human umbilical vein endothelial cells exposed to glycated collagen I (GC). Therefore, we investigated whether the lysosome-dependent, caspase-independent or type 2-programmed cell death (autophagy) is involved in development of premature senescence of endothelial cells. The cleaved microtubule-associated protein 1 light-chain 3 (LC3), a marker of autophagosome formation, was overexpressed within 24 h of GC treatment; however, by 4-5 days, it was nearly undetectable. Early induction of autophagosomes was associated with their fusion with lysosomes, a phenomenon that later became subverted. Autophagic cell death can be triggered by the products of damaged plasma membrane, sphingolipids, and ceramide. We observed a clustering of membrane rafts shortly after exposure to GC; later, after 24 h, we observed an internalization, accompanied by an increased acid sphingomyelinase activity and accumulation of ceramide. Pharmacological inhibition of autophagy prevented development of premature senescence but did lead to the enhanced rate of apoptosis in human umbilical vein endothelial cells exposed to GC. Pharmacological induction of autophagy resulted in reciprocal changes. These observations appear to represent a mechanistic molecular cascade whereby advanced glycation end products like GC induce sphingomyelinase activity, accumulation of ceramide, clustering, and later internalization of lipid rafts.
Robotic Mastoidectomy (2010)

To the best of our knowledge, this is the first time that a robot has been used to perform a mastoidectomy. Although significant hurdles remain to translate this technology to clinical use, we have shown that it is feasible. The prospect of reducing surgical time and enhancing patient safety by replacing human hand-eye coordination with machine precision motivates future work toward translating this technique to clinical use.
High-confinement photonic structures for light propagation in the visible range (2004)

Planar integrated photonic devices are typically designed for telecommunications wavelengths in the 1.55 micron range. For strong mode-confinement at these wavelengths, very high index contrasts are required and semiconductor materials are often used for the waveguide core. Recently, planar devices designed for the visible range were demonstrated with relatively large dimensions on the order of 0.5 - 5 mm. Here in contrast we demonstrate micron-size photonic devices with single-mode operation in the visible range. Devices made for light propagation in the visible range are designed for tapping specific wavelengths of light vertically out of the plane of integration. The structures are based on high confinement waveguides with an effective mode size on the order of 0.5 &mu;m<sup>2</sup>.
Sim-to-Real Transfer with Neural-Augmented Robot Simulation (2018)

International audience
A fast GEMM implementation on the cypress GPU (2011)

We present benchmark results of optimized dense matrix multiplication kernels for Cypress GPU. We write general matrix multiply (GEMM) kernels for single (SP), double (DP) and double-double (DDP) precision. Our SGEMM and DGEMM kernels show ~ 2 Top/s and ~ 470 Glop/s, respectively. These results for SP and DP correspond to 73% and 87% of the theoretical performance of the GPU, respectively. Currently, our SGEMM and DGEMM kernels are fastest with one GPU chip to our knowledge. Furthermore, the performance of our matrix multiply kernel in DDP is 31 Gop/s. This performance in DDP is more than 200 times faster than the performance results in DDP on single core of a recent CPU (with mpack version 0.6.5). We describe our GEMM kernels with main focus on the SGEMM implementation since all GEMM kernels share common programming and optimization techniques. While a conventional wisdom of GPU programming recommends us to heavily use shared memory on GPUs, we show that texture cache is very effective on the Cypress architecture.
Linezolid Dampens Neutrophil-Mediated Inflammation in Methicillin-Resistant Staphylococcus aureus-Induced Pneumonia and Protects the Lung of Associated Damages (2014)

Our results indicate that linezolid could be superior to vancomycin for the management of MRSA pneumonia by attenuating an excessive inflammatory reaction and protecting the lung from pathogen-associated damages.
Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells (2017)

Memory T cells exhibit transcriptional memory and "remember" their previous pathogenic encounter to increase transcription on re-infection. However, how this transcriptional priming response is regulated is unknown. Here we performed global FAIRE-seq profiling of chromatin accessibility in a human T cell transcriptional memory model. Primary activation induced persistent accessibility changes, and secondary activation induced secondary-specific opening of previously less accessible regions associated with enhanced expression of memory-responsive genes. Increased accessibility occurred largely in distal regulatory regions and was associated with increased histone acetylation and relative H3.3 deposition. The enhanced re-stimulation response was linked to the strength of initial PKC-induced signalling, and PKC-sensitive increases in accessibility upon initial stimulation showed higher accessibility on re-stimulation. While accessibility maintenance was associated with ETS-1, accessibility at re-stimulation-specific regions was linked to NFAT, especially in combination with ETS-1, EGR, GATA, NFkappaB, and NR4A. Furthermore, NFATC1 was directly regulated by ETS-1 at an enhancer region. In contrast to the factors that increased accessibility, signalling from bHLH and ZEB family members enhanced decreased accessibility upon re-stimulation. Interplay between distal regulatory elements, accessibility, and the combined action of sequence-specific transcription factors allows transcriptional memory-responsive genes to "remember" their initial environmental encounter.
ChemInform Abstract: Resolution and Absolute Configuration of 2,3‐Methanopyroglutamic Acid, 3‐Oxo‐2‐azabicyclo(3.1.0)hexane‐1‐carboxylic Acid (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Disc Degeneration/Back Pain and Calcification of the Abdominal Aorta (1997)

Advanced aortic atherosclerosis, presenting as calcific deposits in the posterior wall of the aorta, increases a person's risk for development of disc degeneration and is associated with the occurrence of back pain.
A modular strategy for fabrication of responsive nanocomposites using functionalized oligocaprolactones and hydroxyapatite nanoparticles (2020)

A systematic approach was used to fabricate a modulated supramolecular nanocomposite with a bioactivity characteristic and an exciting self-healing ability.
Clock and Data Recovery-Free Data Communications Enabled by Multi-Core Fiber With Low Thermal Sensitivity of Skew (2020)

Optical switching has the potential to scale the capacity of data center networks (DCN) with a simultaneously reduction in latency and power consumption. One of the main challenges of optically-switched DCNs is the need for fast clock and data recovery (CDR). Because the DCN traffic is dominated by small packets, the CDR locking time is required to be less than one nanosecond for achieving high network throughput. This need for sub-nanosecond CDR locking time has motivated research on optical clock synchronization techniques, which deliver synchronized clock signals through optical fibers such that the CDR modules in each transceiver only need to track the slow change of clock phase, due to change of the time of flight as temperature varies. It is desired to remove the need for clock phase tracking (and thereby the CDR modules) if the temperature-induced clock phase drift can be significantly reduced, which would reduce the power consumption and the cost of transceivers. Previous studies have shown that the temperature-induced skew change between multi-core fiber (MCF) cores can be forty times lower than that of standard single mode fibers. Thus, clock-synchronized transmission maybe possible by using two different MCF cores for clock and data transmission, respectively, enabling the sharing of an optical clock with stable clock phase. To investigate the potential of MCF for CDR-free short-reach communications, we first improve the measurement method of the temperature dependent inter-core skew change by using a modified delay interferometer, achieving a resolution of 3.8 femtoseconds for accurate inter-core skew measurements. Building on the MCF measurement results, we carried out an MCF-based clock-synchronized transmission experiment, demonstrating the feasibility of CDR-free data communications over a temperature range of 43 °C that meets DCN requirements.
Ein großes, neuartiges Polyoxowolframat: [AsW65O217(H2O)7]26− (2001)

Das größte bisher bekannte Wolframatoarsenat(III), [AsW65O217(H2O)7]26− 1, wurde aus wässriger, saurer Lösung in Form seines Kaliumsalzes in guter Ausbeute isoliert und durch Einkristall-Röntgenstrukturanalyse, 183W-NMR- und FT-IR-Spektroskopie sowie Elementaranalyse charakterisiert. Die kompakte Struktur von 1 mit idealisierter C2h-Symmetrie (siehe Bild) besteht aus vier inneren (β-AsW9O33)- und zwei äußeren (α-AsW9O33)-Fragmenten (rot), die durch insgesamt elf eckenverknüpfte WO6-Oktaeder (grün, gelb) verbunden sind.
Using Transparent Shaping and Web Services to Support Self-Management of Composite Systems (2005)

Increasingly, software systems are constructed by composing multiple existing applications. The resulting complexity increases the need for self-management of the system. However, adding autonomic behavior to composite systems is difficult, especially when the existing components were not originally designed to support such interactions. Moreover, entangling the code for integrated self-management with the code for the business logic of the original applications may actually increase the complexity of the system, counter to the desired goal. In this paper, we propose a technique to enable self-managing behavior to be added to composite systems transparently, that is, without requiring manual modifications to the existing code. The technique uses transparent shaping, developed previously to enable dynamic adaptation in existing programs, to weave self-managing behavior into existing applications, which interact through Web services. A case study demonstrates the use of this technique to construct a fault-tolerant surveillance application from two existing applications, one developed in .NET and the other in CORBA, without the need to modify the source code of the original applications
The Implication of the Connected Net Topology on the Morphology of β-Monoacid Triacylglycerol Crystals (1999)

The crystal morphology of β n.n.n TAGs, still the only triacylglycerol series of which the crystallographic structures have been elucidated, is predicted using a revised version of the Hartman−Perdok theory. In an earlier publication by Bennema et al.1 the morphology was predicted on the basis of attachment energy. The platelike shape of the crystals was predicted well, but the indices for the top faces failed. Second, the experimentally observed crystals are much more elongated. In the present approach, the morphology is not only predicted using the attachment energy but also use is made of roughening temperatures. For faces that grow below the roughening temperature at low supersaturation, the rate-limiting step is the formation of steps on the surface. Therefore, under these growth conditions, the roughening temperatures of the faces determine the morphology rather than the attachment of new growth units to the surfaces. The roughening temperature of a flat face {hkl} can be estimated by the Ising temperatures, which are calculated from substitute nets constructed from all possible step energies found from the connected nets. In some cases, depending on the topology of the connected net, exceptionally low Ising temperatures can be found. In these cases, it is shown that the roughening temperature is not directly determined by the slice energy. If this concept is used for the prediction of the morphology of TAG crystals, a good agreement with the experimentally observed faces is obtained. Moreover, the dependence of the morphology for the various TAGs on the chain length n is explained. Using this concept, however, the presence of the {31l} faces on the morphology cannot be explained. It is shown that this face is probably an F-face that is stabilized by solvent molecules.
Mutations within Sox2/SOX2 are associated with abnormalities in the hypothalamo-pituitary-gonadal axis in mice and humans (2006)

The transcription factor SOX2 is expressed most notably in the developing CNS and placodes, where it plays critical roles in embryogenesis. Heterozygous de novo mutations in SOX2 have previously been associated with bilateral anophthalmia/microphthalmia, developmental delay, short stature, and male genital tract abnormalities. Here we investigated the role of Sox2 in murine pituitary development. Mice heterozygous for a targeted disruption of Sox2 did not manifest eye defects, but showed abnormal anterior pituitary development with reduced levels of growth hormone, luteinizing hormone, and thyroid-stimulating hormone. Consequently, we identified 8 individuals (from a cohort of 235 patients) with heterozygous sequence variations in SOX2. Six of these were de novo mutations, predicted to result in truncated protein products, that exhibited partial or complete loss of function (DNA binding, nuclear translocation, or transactivation). Clinical evaluation revealed that, in addition to bilateral eye defects, SOX2 mutations were associated with anterior pituitary hypoplasia and hypogonadotropic hypogonadism, variable defects affecting the corpus callosum and mesial temporal structures, hypothalamic hamartoma, sensorineural hearing loss, and esophageal atresia. Our data show that SOX2 is necessary for the normal development and function of the hypothalamo-pituitary and reproductive axes in both humans and mice.
Magnetic Susceptibility as a Biosignature (2010)

INTRODUCTION One of the goals of geobiology is to understand the early evolution of life by examining the nature of the most primitive organisms, the environment in which they evolved, and the way in which they influenced that environment. Such endeavors assume that it is easy to differentiate the biotic from the abiotic, whether in ancient rocks on Earth or elsewhere in our solar system. But what constitutes a robust biosignature? What may seem straightforward in theory is difficult in practice. Therefore, determining what is, or is not, a biosignature represents one of the most significant challenges in geobiology today. The focus of this research is on developing a new biosignature, based on magnetic susceptibility of microbialites, taking advantage of recent technological advances applied in a novel way to geobiological questions. Microbialites are macroscopic sedimentary structures built by or influenced by microorganisms— stromatolites, presumed to constitute some of the oldest evidence for life on Earth (Allwood et al., 2006; Hoffman et al., 1999)—are probably the “celebrity” of the microbialite world. Stromatolites are most commonly defined as laminated organo-sedimentary structures built by the trapping and binding and/or precipitation of minerals by microbial mats (Riding and Awramik, 2000; Walter et al., 1976). By this
Preferential gain photonic-crystal fiber for mode stabilization at high average powers (2011)

We report on the design and experimental investigation of a preferential gain photonic-crystal fiber with a mode-field diameter of 47 µm. This few-mode fiber design confines the doping of Ytterbium-ions just to the center of the core and, therefore, promotes fundamental mode operation. In a chirped-pulse amplification system we extracted up to 303 W of average power from this fiber with a measured M2 value of 1.4.
Multi-stream product modal audio-visual integration strategy for robust adaptive speech recognition (2002)

In this paper, we extend an existing audio-only automatic speech recognizer to implement a multi-stream audio-visual automatic speech recognition (AV-ASR) system. Our method forms a multi-stream feature vector from audio-visual speech data, computes the statistical modal parameters probabilities on the basis of multi-stream audio-visual features, and performs dynamic programming jointly on the multi-stream product modal Hidden Markov Models (MS-PM-HMMs) by utilizing a noise type and signal-to-noise ratio (SNR) based stream-weighting value. Experimental results are presented for an isolated word recognition task for eight different noise types from the NOISEX data base for several SNR values. The proposed system reduces the word error rate (WER), averaged over several SNR and noise types, from 55.9% With the audio-only recognizer and 7.9% with the late-integration audio-visual recognizer to 2.6% WER in the validation set.
Optimization of electrolysis in the cylindrical electrochemical cell rotating in the magnetic field (2010)

The relationships between the rotational rate of electrochemical cell, its ohmic resistance, a ratio between the radii of inner and outer cylindrical electrodes, a sum of cathodic and anodic potentials, and the mechanical energy, which is consumed for passing a prescribed current and overcoming friction forces, are analyzed. It is shown that the relationships can be used to optimize the operation of rotating electrochemical cell.
Project Phidisa: development of clinical research capacity within the South African National Defence Force (2007)

In December 2002, a decision was reached between the South African Military Health Service of the South African National Defence Force and the US Ambassador to South Africa that the USA and the Republic of South Africa would explore the possibility of initiating a collaborative effort to build the capacity to conduct clinical research within the South African military environment and that the area of initial focus would be HIV/AIDS. Three and a half years later, a clinical research program now known as Project Phidisa has enrolled over 4000 patients on Institutional Review Board-approved protocols, and provided antiretroviral therapy to approximately 1400 members of the South African National Defence Force and their dependents. The purpose of this article is to present some of the challenges faced in the development of this program and provide the lessons learned as these challenges were and continue to be addressed.