gebhart/patrepeval huggingface dataset:
Core Topics in Neuroanaesthesia and Neurointensive Care (2011)

Core Topics in Neuroanesthesia and Neurointensive Care is an authoritative and practical clinical text that offers clear diagnostic and management guidance for a wide range of neuroanesthesia and neurocritical care problems. With coverage of every aspect of the discipline by outstanding world experts, this should be the first book to which practitioners turn for easily accessible and definitive advice. Initial sections cover relevant anatomy, physiology and pharmacology, intraoperative and critical care monitoring and neuroimaging. These are followed by detailed sections covering all aspects of neuroanesthesia and neurointensive care in both adult and pediatric patients. The final chapter discusses ethical and legal issues. Each chapter delivers a state-of-the art review of clinical practice, including outcome data when available. Enhanced throughout with numerous clinical photographs and line drawings, this practical and accessible text is key reading for trainee and consultant anesthetists and critical care specialists.
New modified nucleoside 5′-triphosphates: synthesis, properties towards DNA polymerases, stability in blood serum and antiviral activity (1999)

A series of new nucleoside 5′-triphosphate mimetics, 2, 3, 5, 6, 8–10, modified at the glycone and all three phosphate residues, have been synthesised and studied. These compounds only bear the enzymatically labile anhydride bond between the α and β phosphorus atoms. The preparative chemistry involved the preparation of phosphonic salts 30, 31 and 32 and coupling of these species to the morpholidate 33. The mechanism of formation of some of the intermediates ‘en route’ to 27 and 28 is discussed. All of the target compounds demonstrated high stability in human blood serum with half lives towards hydrolysis of up to 4.5 days. Some of these nucleoside triphosphonates have been shown to be selective inhibitors of DNA synthesis catalysed by retroviral reverse transcriptases and terminal deoxynucleotidyl transferases. They inhibited replication of the artificial virus containing Moloney murine leukemia virus reverse transcriptase in infected cell culture, probably due to the inhibition of a reverse transcription step of a genomic RNA. Compared to the triphosphonates, the corresponding monophosphonates demonstrated decreased antiviral activity by 1–2 orders of magnitude. This implies that the triphosphonates inhibit virus replication directly, rather than by a two-step mechanism based on their hydrolysis to the monophosphonates and subsequent intracellular diphosphorylation. Being totally independent of the enzymatic phosphorylation pathways of the host cell, the compounds under study may also be able to inhibit retrovirus reproduction both in kinase deficient cell lines and in the intercellular blood media.
Identification of a novel mutation in the paired domain of PAX3 in an Iranian family with Waardenburg syndrome Type I (2000)

Waardenburg syndrome Type I (WS1) is an autosomal dominant disorder that has previously been associated with mutations in the PAX3 gene on the 2q35 region. In this study, we used an Iranian WS1 family with seven affected individuals in three generations. The phenotypic characteristics of the family include sensorineural deafness, dystopia canthorum, hypopigmented skin patches of the upper limbs, congenital white forelock, confluent white eyebrows, nonpigmented iris, poliosis, and hypopigmentation of the retina. Herein, we report a previously unidentified single-base substitution in exon II (C-->T at position 218) that results in a change of serine to leucine (S73L) in this family. This change was not observed in 100 chromosomes of healthy unrelated individuals. This mutation is within the PAX3 paired domain region, a structure that is highly conserved and implicated in DNA binding. This is the first identification of a PAX3 mutation for this phenotype in the Iranian population. This also provides additional confirmation for the involvement of this gene in the etiology of WS1.
Optimization of First-in-Class Dual-Acting FFAR1/FFAR4 Allosteric Modulators with Novel Mode of Action (2022)

The free fatty acid receptors FFAR1 and FFAR4 are considered promising therapeutic targets for management of metabolic and inflammatory diseases. However, there is a need for entirely novel chemical scaffolds, since many of the highly similar lipophilic chemotypes in development have been abandoned by the pharmaceutical industry, due to toxic effects on hepatocytes and β-cells. Our group has recently reported the discovery of a 1,3,5-triazine-2-amine-based compound that acts as an allosteric agonist on FFAR1. Here, we present the synthesis and investigation of the structure-activity relationship of an extensive set of analogues of which many display dual-acting agonist properties for both FFAR1 and FFAR4. In several rounds of optimization, we discovered multiple analogues with single-digit nanomolar potency on FFAR1. Pending additional optimization for metabolic stability, the compounds in this study present novel ways of providing beneficial glycemic control while avoiding the notorious toxicity challenges associated with previously identified chemotypes.
Data from p38γ Promotes Breast Cancer Cell Motility and Metastasis through Regulation of RhoC GTPase, Cytoskeletal Architecture, and a Novel Leading Edge Behavior (2023)

&lt;div&gt;Abstract&lt;p&gt;Understanding the molecular alterations that confer cancer cells with motile, metastatic properties is needed to improve patient survival. Here, we report that p38γ motogen-activated protein kinase regulates breast cancer cell motility and metastasis, in part, by controlling expression of the metastasis-associated small GTPase RhoC. This p38γ–RhoC regulatory connection was mediated by a novel mechanism of modulating RhoC ubiquitination. This relationship persisted across multiple cell lines and in clinical breast cancer specimens. Using a computational mechanical model based on the finite element method, we showed that p38γ-mediated cytoskeletal changes are sufficient to control cell motility. This model predicted novel dynamics of leading edge actin protrusions, which were experimentally verified and established to be closely related to cell shape and cytoskeletal morphology. Clinical relevance was supported by evidence that elevated expression of p38γ is associated with lower overall survival of patients with breast cancer. Taken together, our results offer a detailed characterization of how p38γ contributes to breast cancer progression. Herein we present a new mechanics-based analysis of cell motility, and report on the discovery of a leading edge behavior in motile cells to accommodate modified cytoskeletal architecture. In summary, these findings not only identify a novel mechanism for regulating RhoC expression but also advance p38γ as a candidate therapeutic target. &lt;i&gt;Cancer Res; 71(20); 6338–49. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Diagnosis of Renal Cancer by Molecular Urinalysis (1999)

These data suggest that microsatellite DNA analysis of urine specimens provides a potentially valuable tool for the early detection of resectable kidney cancer. Furthermore, microsatellite analysis of serum samples reveals evidence of circulating tumor-specific DNA in approximately half of these patients and may reflect the propensity of these tumors to spread to distant sites at an early stage.
High Efficiency SHG in Heterogenous Integrated GaAs Ring Resonators (2018)

We demonstrate the first integrated gallium arsenide (GaAs) ring resonators for second-harmonic generation (SHG). The GaAs-on-insulator platform offers high quality factors exceeding 2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> . We demonstrate 4% absolute internal SHG efficiency with a 61-μW pump coupled to the resonator.
Redirected touching (2013)

In immersive virtual environments, virtual objects cannot be touched. One solution is to use passive haptics—physical props to which virtual objects are registered. The result is compelling; when a user reaches out with a virtual hand to touch a virtual object, her real hand touches and feels a real object. However, for every virtual object to be touched, there must be an analogous physical prop. In the limit, an entire real-world infrastructure would need to be built and changed whenever a virtual scene is changed. 
Virtual objects and passive haptics have historically been mapped one-to-one. I demonstrate that the mapping need not be one-to-one. One can make a single passive real object provide useful haptic feedback for many virtual objects by exploiting human perception. I developed and investigated three categories of such techniques: 1. Move the virtual world to align different virtual objects in turn with the same real object 2. Move a virtual object into alignment with a real object 3. Map real hand motion to different virtual hand motion, e.g., when the real hand traces a real object, the virtual hand traces a differently shaped virtual object. The first two techniques were investigated for feasibility, and the third was explored more deeply. 
The first technique (Redirected Passive Haptics) enables users to touch multiple instances of a virtual object, with haptic feedback provided by a single real object. The second technique (The Haptic Hand) attaches a larger-than-hand virtual user interface to the non-dominant hand, mapping the currently relevant part of the interface onto the palm. 
The third technique (Redirected Touching) warps virtual space to map many differently shaped virtual objects onto a single real object, introducing a discrepancy between real and virtual hand motions. Two studies investigated the technique's effect on task performance and its potential for use in aircraft cockpit procedures training. Users adapt rather quickly to real-virtual discrepancy, and after adaptation, users perform no worse with discrepant virtual objects than with one-to-one virtual objects. Redirected Touching shows promise for training and entertainment applications.
Infectivity of West Nile/Dengue Chimeric Viruses for West Nile and Dengue Mosquito Vectors (2005)

West Nile virus (WN), an agent of significant human and veterinary disease, is endemic in the Old World and rapidly spreading throughout the Americas. Vaccines are needed to halt the geographic expansion of this virus and prevent disease where it is established. However, to preclude introduction of a vaccine virus into the environment, a live attenuated WN vaccine should have low potential for transmission by mosquitoes. A chimeric WN vaccine candidate was previously generated by replacing the membrane and envelope structural protein genes of recombinant dengue type 4 virus (rDEN4) with those of WN; a derivative of this virus, WN/DEN4-3'delta30, contains a 30-nucleotide deletion in the 3' untranslated region. To assess the potential for transmission by mosquitoes of these vaccine candidates, the ability of each chimeric virus to infect the mosquito midgut, disseminate to the head, and pass into the saliva was compared to that of their wild-type parental WN and DEN4 viruses in three vector species. The WN/DEN4 chimeric viruses were significantly attenuated in both Culex tarsalis, a vector able to transmit WN but not dengue, and in Ae. aegypti, a vector able to transmit dengue but not WN. However, the chimeric viruses were as infectious as either wild-type virus for Ae. albopictus, a vector able to transmit both dengue and WN. These results indicate that chimerization caused a contraction in vector host range rather than universal attenuation for mosquitoes per se. This restriction in potential vectors renders it less likely that WN/DEN4 and WN/DEN4-3'delta30 would be transmitted from vaccinees to mosquitoes.
Design and Application of a Pulsed Cavity Ring-Down Aerosol Extinction Spectrometer for Field Measurements (2007)

This paper describes the design and application of a pulsed cavity ring-down aerosol extinction spectrometer (CRD-AES) for in-situ atmospheric measurement of the aerosol extinction coefficient and its relative humidity dependence. This CRD-AES measures the aerosol extinction coefficient (σ ep) at 355 nm, 532 nm, 683 nm, and 1064 nm with a minimal size dependent bias for particles with diameter less than 10 μm. The σ ep at 532 nm is measured with an accuracy of 1% when extinction is ≥ 10 Mm −1 . The precision is limited by statistical fluctuations within the small optical volume and the time resolution of extinction at 2% uncertainty for various air mass types is evaluated. The CRD-AES is configured with two separate cavity ring-down cells for measurement of the extinction coefficient at 532 nm. This allows the determination of the RH dependence of extinction at 532 nm through independent RH control of the sample for each measurement. Gas phase absorption and minimization of potential interferences is also considered.
Tightly integrated board level free space optical interconnects (2002)

Free-space optical interconnects that use integrated VCSEL/MSM detector arrays can move data faster with lower power dissipation at the board level, and therefore have the potential to impact future router/switch and computer back-plane implementations. This paper summarizes some of the demonstration systems that were built by the 3-d OESP consortium to investigate experimentally the validity of these potentials.
Hepatoprotective Tetrahydrobenzocyclooctabenzofuranone Lignans from Kadsura longipedunculata (2019)

Three new tetrahydrobenzocyclooctabenzofuranone lignan glucosides, longipedunculatins A-C (<b>1</b>-<b>3</b>), a new dibenzocyclooctadiene lignan glucoside, longipedunculatin D (<b>4</b>), a new dibenzocyclooctadiene lignan (<b>5</b>), five new tetrahydrobenzocyclooctabenzofuranone lignans (<b>6</b>-<b>10</b>), and two new simple lignans (<b>11</b>, <b>12</b>) were isolated from the roots of <i>Kadsura longipedunculata.</i> Their structures and absolute configurations were established using a combination of MS, NMR, and experimental and calculated electronic circular dichroism data. Compound <b>7</b> showed moderate hepatoprotective activity against <i>N</i>-acetyl-<i>p</i>-aminophenol-induced toxicity in HepG2 cells with a cell survival rate at 10 μM of 50.8%. Compounds <b>2</b>, <b>7</b>, and <b>12</b> showed significant in vitro inhibitory effects with an inhibition rate of 55.1%, 74.9%, and 89.8% on nitric oxide production assays at 10 μM.
Polarization-Induced Local Pore-Wall Functionalization for Biosensing: From Micropore to Nanopore (2012)

International audience
Recovery of proteins and other biological compounds using fibrous materials: II. Flocculation by polyelectrolyte addition (1999)

Polyelectrolytes have been used in wastewater treatment processes to destabilize colloidal suspensions of proteins, cells and other biological compounds, resulting in flocculation. When a solution containing a single model protein, bovine serum albumin (BSA), is treated with a polyelectrolyte, carboxymethyl cellulose (CMC), large and strong flocs are formed, which are easily retained by a 20 µm pore size filter. However, when a mixture of proteins, cells, and fats from an actual wastewater sample is treated in the same manner, smaller and weaker flocs are observed. An adsorption and filtration process for the recovery of valuable biological compounds using cellulose-based fibrous materials has been developed. When used simultaneously with CMC, cellulose acetate and triacetate fibrets (CAF and CTF) resulted in high recovery of biomolecules from solution at very low dosages of both polyelectrolyte and fibrets. CMC interacts with biomolecules by electrostatic interactions and polymer bridging, while CTF/CAF facilitate floc growth by adsorption and bridging of primary particles and by entrapment of small aggregates within their highly fibrillated microstructure. © 1999 Society of Chemical Industry
Exercise and Extracorporeal Blood Cooling During Hemodialysis (1998)

Intradialytic exercise may improve hemodialysis efficiency. Because exercise interferes with thermal energy and fluid balance, relative blood volume changes (deltaBV%), arterial blood temperatures (T(art)), mean arterial blood pressures, and heart rates (HR) were measured using different dialysate temperatures (Tdia). Four stable patients (age, 49.9 +/- 7.7 years) were studied during 22 treatments that either maintained Tdia at 35.9 degrees C +/- 0.1 degrees C (standard) or provided maximum extracorporeal cooling (cool, Tdia = 34.8 degrees C +/- 0.8 degrees C) in attempts to maintain a constant T(art). Patients exercised for 1 hr at a resistance of 21 +/- 5 W on a stationary bicycle ergometer. Energy expenditure monitored by indirect calorimetry increased from 117 +/- 38 W (baseline) to 338 +/- 116 W (exercise). Mean arterial blood pressures increased by 7 +/- 7 mmHg with cool Tdia, but remained unchanged (-1 +/- 4 mmHg) with standard Tdia (p < 0.05). However, the increase in T(art) was smaller with cool (0.1 degrees C +/- 0.3 degrees C) than with standard (0.3 degrees C +/- 0.2 degrees C) Tdia (p < 0.05). The larger increase in O2 uptake per change in HR (68 +/- 56 vs 38 +/- 17 ml/beat) indicated an increase in stroke volume when cool dialysate was used (p = NS). Exercise produced a small (0.95% +/- 0.95%), but significant, decrease in deltaBV% that reversed at the end of exercise. Intradialytic exercise was well tolerated, especially when Tdia was lowered such that hemodynamic stress to dissipate excess heat through the cutaneous circulation was reduced and blood pressure stability was improved.
A Review of Data Analysis Techniques for Application in Automated Quantitative Accuracy Assessments (2000)

A survey of data conditioning and analysis techniques has been undertaken which focuses on their relevance to nuclear reactor systems (NRS) code accuracy and uncertainty assessment. A number of methods are considered for their applicability to the automated assessment of the accuracy of NRS code simulations, through direct comparisons with experimental measurements or other simulations. A variety of data types and computational modeling methods are considered from a spectrum of mathematical and engineering disciplines. The goal of the survey is to identify issues and techniques to be considered in the development of an automated code assessment procedure, to be used in United States Nuclear Regulatory Commission (USNRC) advanced T/H code consolidation efforts. The motivation for the present work is first provided by background discussion that summarizes the relevance of this subject matter to the nuclear reactor industry. Next, the spectrum of NRS data types are classified into categories, in order to provide a basis for assessing individual comparison methods. The main body of the paper then summarizes the survey undertaken. There, each of the relevant issues and techniques considered are addressed. Several of the methods have been coded and/or applied to relevant NRS code-data comparisons. Results of these demonstration calculations are included.
Abstract only (2011)

Most of the existing WCET estimation methods directly estimate execution time, ET, in cycles. We propose to study ET as a product of two factors, ET = IC * CPI, where IC is instruction count and CPI is cycles per instruction. Considering directly the estimation of ET may lead to a highly pessimistic estimate since implicitly these methods may be using worst case IC and worst case CPI. We hypothesize that there exists a functional relationship between CPI and IC such that CPI=f(IC). This is ascertained by computing the covariance matrix and studying the scatter plots of CPI versus IC. IC and CPI values are obtained by running benchmarks with a large number of inputs using the cycle accurate architectural simulator, Simplescalar on two different architectures. It is shown that the benchmarks can be grouped into different classes based on the CPI versus IC relationship. For some benchmarks like FFT, FIR etc., both IC and CPI are almost a constant irrespective of the input. There are other benchmarks that exhibit a direct or an inverse relationship between CPI and IC. In such a case, one can predict CPI for a given IC as CPI=f(IC). We derive the theoretical worst case IC for a program, denoted as SWIC, using integer linear programming(ILP) and estimate WCET as SWIC*f(SWIC). However, if CPI decreases sharply with IC then measured maximum cycles is observed to be a better estimate. For certain other benchmarks, it is observed that the CPI versus IC relationship is either random or CPI remains constant with varying IC. In such cases, WCET is estimated as the product of SWIC and measured maximum CPI. It is observed that use of the proposed method results in tighter WCET estimates than Chronos, a static WCET analyzer, for most benchmarks for the two architectures considered in this paper.
Hybrid generalized approximate message passing with applications to structured sparsity (2012)

Gaussian and quadratic approximations of message passing algorithms on graphs have attracted considerable attention due to their computational simplicity, analytic tractability, and wide applicability in optimization and statistical inference problems. This paper summarizes a systematic framework for incorporating such approximate message passing (AMP) methods in general graphical models. The key concept is a partition of dependencies of a general graphical model into strong and weak edges, with each weak edge representing a small, linearizable coupling of variables. AMP approximations based on the central limit theorem can be applied to the weak edges and integrated with standard message passing updates on the strong edges. The resulting algorithm, which we call hybrid generalized approximate message passing (Hybrid-GAMP), can yield significantly simpler implementations of sum-product and max-sum loopy belief propagation. By varying the partition between strong and weak edges, a performance-complexity trade-off can be achieved. Structured sparsity problems are studied as an example of this general methodology where there is a natural partition of edges.
Geometric Attributes of Retaining Glycosyltransferase Enzymes Favor an Orthogonal Mechanism (2013)

Retaining glycosyltransferase enzymes retain the stereochemistry of the donor glycosidic linkage after transfer to an acceptor molecule. The mechanism these enzymes utilize to achieve retention of the anomeric stereochemistry has been a matter of much debate. Re-analysis of previously released structural data from retaining and inverting glycosyltransferases allows competing mechanistic proposals to be evaluated. The binding of metal-nucleotide-sugars between inverting and retaining enzymes is conformationally unique and requires the donor substrate to occupy two different orientations in the two types of glycosyltransferases. The available structures of retaining glycosyltransferases lack appropriately positioned enzymatic dipolar residues to initiate or stabilize the intermediates of a dissociative mechanism. Further, available structures show that the acceptor nucleophile and anomeric carbon of the donor sugar are in close proximity. Structural features support orthogonal (front-side) attack from a position lying ≤ 90° from the C1-O phosphate bond for retaining enzymes. These structural conclusions are consistent with the geometric conclusions of recent kinetic and computational studies.
Throughput Optimization Via Adaptive MIMO Communications (2006)

Abstract : A MIMO-OFDM system for aircraft to urban ground non-line-of-sight communications that supports programmable bandwidth efficiency between 0.25 bps/Hz and 20 bps/Hz has been designed. The system supports the whole range of MIMO techniques, namely spatial multiplexing, beamforming, space-time coding, and diversity processing. The system is, on a packet by packet basis, configurable in terms of number of antennas, MIMO techniques, modulation order, channel coding type, channel coding rate, channel training length, and channel tracking overhead. The feasibility and performance has been verified in the developed Matlab end-to-end simulation system and on the Silvus DSP MIMO Testbed.