gebhart/patrepeval huggingface dataset:
An Introduction to ULDBs and the Trio System (2006)

We introduce ULDBs: relational databases that add uncertainty and lineage of the data as first-class concepts. The ULDB model underlies the Trio system under development at Stanford. We describe the ULDB model, then present TriQL, our SQL-based query language for ULDBs. TriQL's semantics over ULDBs is defined both formally and operationally, and TriQL extends SQL with constructs for querying lineage and confidence values. We also briefly describe our initial prototype Trio implementation, which encodes ULDBs in conventional relations and automatically translates TriQL queries into SQL commands over the encoding. We conclude with research directions for ULDBs and the Trio system.
Resistance to vemurafenib resulting from a novel mutation in the <scp>BRAFV</scp>600<scp>E</scp> kinase domain (2013)

Resistance to the BRAF inhibitor vemurafenib poses a significant problem for the treatment of BRAFV600E-positive melanomas. It is therefore critical to prospectively identify all vemurafenib resistance mechanisms prior to their emergence in the clinic. The vemurafenib resistance mechanisms described to date do not result from secondary mutations within BRAFV600E. To search for possible mutations within BRAFV600E that can confer drug resistance, we developed a systematic experimental approach involving targeted saturation mutagenesis, selection of drug-resistant variants, and deep sequencing. We identified a single nucleotide substitution (T1514A, encoding L505H) that greatly increased drug resistance in cultured cells and mouse xenografts. The kinase activity of BRAFV600E/L505H was higher than that of BRAFV600E, resulting in cross-resistance to a MEK inhibitor. However, BRAFV600E/L505H was less resistant to several other BRAF inhibitors whose binding sites were further from L505 than that of PLX4720. Our results identify a novel vemurafenib-resistant mutant and provide insights into the treatment for melanomas bearing this mutation.
A NOVEL DETERMINANT IN THE COMPLEX REGULATION OF RhoB EXPRESSION BY THE MEVALONATE PATHWAY (2002)

Statins improve vascular functions by mechanisms in- dependent from their cholesterol-lowering effect. Rho GTPases are emerging as key targets for the vascular effects of statins. RhoB is a short-lived, early-response inducible protein involved in receptor endocytosis, apo- ptosis, and gene expression. Here we show that statins regulate RhoB expression by acting at multiple levels. Simvastatin increased RhoB protein levels by 8- to 10- fold. This effect was related to a depletion of isoprenoid intermediates, as deduced from the observation that several metabolites of the cholesterol biosynthetic path- way, namely, mevalonate and geranylgeranyl-pyrophos- phate, attenuated simvastatin-induced RhoB up-regula- tion. Moreover, prenyltransferase inhibitors mimicked simvastatin effect. Cholesterol supplementation did not prevent simvastatin-elicited up-regulation but in- creased RhoB levels per se. Simvastatin moderately aug- mented RhoB transcript levels, but markedly impaired the degradation of RhoB protein, which accumulated in the cytosol in its non-isoprenylated form. Inhibition of RhoB isoprenylation was apparently required for simv- astatin-induced up-regulation, because levels of an iso- prenylation-deficient RhoB mutant were not affected by simvastatin. Moreover, this mutant was found to be markedly more stable than the wild-type protein. These results show that RhoB isoprenylation is necessary for rapid turnover of this protein and identify a novel link between the cholesterol biosynthetic pathway and the regulation of G-protein expression.
THE REGULATION OF GROWTH AND GROWTH HORMONE SECRETION IN FISH (1996)

This paper reviews the recent research on the neuroendocrine regulation of growth and growth hormone secretion in fish by the brain(neuroendocrine factor)-pituitary (growth hormone)-liver (insulin-like growth factor) axis; and describes the potential approach in fish culture applications by manipulation of this axis.
Recursive implementation of optimal time VLSi integer multipliers (2018)

Computer Science Department
The Changing Nature of Accountability in Administrative Practice (2010)

This article looks at the subject of accountability in the administration of the human services. The history of accountability over the last four decades is chronicled and discussed. The point is made that during this period, funders have largely determined the nature of accountability. Because funders have been primarily concerned with funding, accountability has tended to be financial in nature. The authors argue that the focus on financial accountability had two major detrimental effects. First, programmatic accountability was reduced to secondary importance. Second, a wedge was driven between macro administrative practice and micro direct practice as social work managers and administrators became almost exclusively concerned with financial accountability to the detriment of programmatic accountability. The authors go on to suggest that the performance measurement movement has united programmatic and financial accountability and has reunited macro administrative practice and micro direct practice.
Synthesis of a Single-Molecule <scp>l</scp>-Rhamnose-Containing Three-Component Vaccine and Evaluation of Antigenicity in the Presence of Anti-<scp>l</scp>-Rhamnose Antibodies (2010)

Carbohydrates are generally considered to be poorly immunogenic. Therefore, new approaches for enhancing their immunogenicity are important for the development of carbohydrates as vaccine components. We hypothesized that conjugation of an l-rhamnose (Rha) moiety to a carbohydrate antigen would enhance the antigenicity of the antigen in mice possessing anti-Rha antibodies via an antibody-dependent antigen uptake mechanism. To explore this hypothesis, we synthesized a single-molecule three-component vaccine containing the GalNAc-O-Thr (Tn) tumor-specific antigen, a 20 amino acid helper T-cell epitope (YAF) derived from an outer-membrane protein of Neisseria meningitides, and a Rha moiety. The vaccine was synthesized by automated Fmoc-based solid-phase peptide synthesis and deacetylated by brief treatment with NaOMe. Groups of female BALB/c mice were immunized and boosted with Rha-ovalbumin (Rha-OVA) formulated with either TiterMax Gold or Sigma Adjuvant System for a period of 35 days in order to determine optimal conditions for generating anti-Rha titers in mice. Anti-Rha antibody titers were >100 fold higher in groups of mice immunized with Rha-OVA than in the control groups. Mice producing anti-Rha were challenged with Rha-YAF-Tn or YAF-Tn. Sera collected from the groups initially immunized with Rha-OVA and later challenged with Rha-YAF-Tn showed a 2-fold increase in anti-Tn titer at 1/100 serum dilution relative to mice not immunized with Rha-OVA. An in vitro T-cell proliferation study using cells primed with either Rha-YAF-Tn or YAF-Tn was done to examine possible differences in antigen uptake and presentation due to anti-Rha antibody and chemical modification. Proliferation of T cells was stimulated by a 10-fold lower antigen concentration in the presence of Rha antibodies. The results strongly suggest that T cells present in the spleen were presented with higher concentrations of Rha-YAF-Tn as a result of the presence of the anti-Rha antibodies.
pH-Responsive Copolymer Films Prepared by Surface-Initiated Polymerization and Simple Modification (2020)

We report the preparation of pH-responsive, ester/carboxylic acid random copolymer films via simple modification of poly(norbornene diacyl chloride) (pNBDAC), prepared via surface-initiated ring-opening metathesis polymerization, with mixtures of water and ethanol to form carboxylic acid and ethyl ester side groups. The pNBDAC film serves as a compositionally versatile platform to controllably obtain copolymers with multiple functionalities. In modifying the pNBDAC to form the copolymer film, ethanol exhibits a significantly higher reactivity with acyl chloride groups within the film than does water. The magnitude and range of the pH-responsive performance are highly dependent on the carboxylic acid content in the copolymer films, which demonstrates the effect of film hydrophilicity on the pH-responsive switching of ionic barrier properties. The resistance of the film against ion transfer can be decreased by a factor of 10<sup>4</sup> through pH change, demonstrating pH-induced switching from hydrophobic and insulating to swollen and ion-permeable films. The interactions of the copolymer films with water at different pH values were also explored. When the copolymer contains 34% carboxylic acids, a 4× greater film thickness is obtained in high pH solution than in low pH solution due to ionically driven water swelling. The reversibility of the pH-responsive performance of these copolymer films is high based on measurements using quartz crystal microbalance with dissipation (QCM-D).
PHENOPSIS Quelles évolutions technologiques du premier automate de phénotypage des plantes? (2016)

National audience
Protection against Aerosolized <i>Yersinia pestis</i> Challenge following Homologous and Heterologous Prime-Boost with Recombinant Plague Antigens (2005)

A Yersinia pestis-derived fusion protein (F1-V) has shown great promise as a protective antigen against aerosol challenge with Y. pestis in murine studies. In the current study, we examined different prime-boost regimens with F1-V and demonstrate that (i) boosting by a route other than the route used for the priming dose (heterologous boosting) protects mice as well as homologous boosting against aerosol challenge with Y. pestis, (ii) parenteral immunization is not required to protect mice against aerosolized plague challenge, (iii) the route of immunization and choice of adjuvant influence the magnitude of the antibody response as well as the immunoglobulin G1 (IgG1)/IgG2a ratio, and (iv) inclusion of an appropriate adjuvant is critical for nonparenteral immunization.
An Analog Approach to Suppressing In-Band Narrow-Band Interference in UWB Receivers (2007)

Due to the huge bandwidth of ultra-wide-band (UWB) systems, in-band narrow-band interference (NBI) may hinder receiver performance. Sources of potential NBI that lie within the IEEE 802.15.3a UWB bandwidth are presented. To combat interference in multi-band orthogonal frequency-division multiplexing (MB-OFDM) UWB systems, an analog notch filter is designed to be included in the UWB receive chain. The filter's architecture is based on feedforward subtraction of the interference, and includes a least-mean-square (LMS) tuning scheme to match amplitudes of the two paths. An 8-bit discrete control is used to adjust the filter's center frequency across the UWB baseband. It was fabricated in TSMC's 0.18-mum process, and experimental results are provided
Mobilisation of neural structures opens up new possibilities for idiopathic scoliosis treatment (2012)

Background Idiopathic Scoliosis (IS) is a progressive disorder with reduced mobility of the spine. This makes corrections difficult or sometimes even inhibits postural changes. Even when correction of frontal or coronal plane deformity seems successful, sagittal correction mostly is not addressed appropriately. This might be due to functional tethering of the spinal cord or even of peripheral neural structures. This explains the lack of success when trying to correct sagittal plane deformity with the help of stretching exercises. Purpose of this study was to test how the release of these structures may relax lordotic tension in the thoracic area.
Coronary pressure measurement and fractional flow reserve (1998)

The shortcomings of coronary arteriography to assess the physiological significance of coronary stenoses have been recognised for decades1 2; therefore, the importance of additional physiological techniques is beyond doubt. One of the currently available physiological techniques is coronary pressure measurement, which has emerged over the past few years as a major step forward in the invasive assessment of coronary artery disease.3-9This was partly owing to major technical progress in developing pressure monitoring guidewires and partly to a theoretical innovation, the concept of coronary pressure derived fractional flow reserve (FFR), which closely relates distal coronary pressure to myocardial blood flow during maximum arteriolar vasodilatation. In the catheterisation laboratory, this new approach enables an “on the spot” diagnosis as to what extent a given epicardial stenosis contributes to reversible myocardial ischaemia and the decision whether revascularisation of the stenosis is warranted. In addition, pressure derived FFR appears to be a useful index to monitor and guide coronary intervention, particularly adequate stent deployment.10 11 

This review aims to provide a short overview of the theoretical and physiological background of this new approach and to focus on its clinical applicability, both for diagnostic and therapeutic catheterisation.

The functional state of a patient with a coronary artery stenosis is determined by the maximum blood flow that can reach the dependent myocardium. As soon as maximum achievable blood flow, at a given level of exercise, is no longer sufficient to match oxygen demand, myocardial ischaemia and angina pectoris will occur. Therefore, fundamentally, it is maximum blood flow that should be studied to establish the physiological significance of a coronary stenosis.

Fractional flow reserve is defined as maximum myocardial blood flow in the presence of a stenosis divided by the theoretical maximum flow in the absence of the stenosis—that is, maximum flow …
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection (2011)

We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent hidden Markov model (HMM) framework. We find ILS present in ∼1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9-13 million years ago (Mya; contingent on the calibration point). The analyses provide further support for a recent speciation of human and chimpanzee at ∼4 Mya and a diverse ancestor of human and chimpanzee with an effective population size of about 50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome, and we use this to deduce patterns of selection in the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS was found to be reduced in exons and gene-dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny.
Phase III Study of Belatacept Versus Cyclosporine in Kidney Transplants from Extended Criteria Donors (BENEFIT‐EXT Study) (2010)

Recipients of extended criteria donor (ECD) kidneys are at increased risk for graft dysfunction/loss, and may benefit from immunosuppression that avoids calcineurin inhibitor (CNI) nephrotoxicity. Belatacept, a selective costimulation blocker, may preserve renal function and improve long-term outcomes versus CNIs. BENEFIT-EXT (Belatacept Evaluation of Nephroprotection and Efficacy as First-line Immunosuppression Trial-EXTended criteria donors) is a 3-year, Phase III study that assessed a more (MI) or less intensive (LI) regimen of belatacept versus cyclosporine in adult ECD kidney transplant recipients. The co-primary endpoints at 12 months were composite patient/graft survival and a composite renal impairment endpoint. Patient/graft survival with belatacept was similar to cyclosporine (86% MI, 89% LI, 85% cyclosporine) at 12 months. Fewer belatacept patients reached the composite renal impairment endpoint versus cyclosporine (71% MI, 77% LI, 85% cyclosporine; p = 0.002 MI vs. cyclosporine; p = 0.06 LI vs. cyclosporine). The mean measured glomerular filtration rate was 4-7 mL/min higher on belatacept versus cyclosporine (p = 0.008 MI vs. cyclosporine; p = 0.1039 LI vs. cyclosporine), and the overall cardiovascular/metabolic profile was better on belatacept versus cyclosporine. The incidence of acute rejection was similar across groups (18% MI; 18% LI; 14% cyclosporine). Overall rates of infection and malignancy were similar between groups; however, more cases of posttransplant lymphoproliferative disorder (PTLD) occurred in the CNS on belatacept. ECD kidney transplant recipients treated with belatacept-based immunosuppression achieved similar patient/graft survival, better renal function, had an increased incidence of PTLD, and exhibited improvement in the cardiovascular/metabolic risk profile versus cyclosporine-treated patients.
Coal Desulfurization (1977)

The microstructure of coal is of interest in understanding coal properties. Microstructural features may affect the selection of coal beneficiation methods for removing impurities. For example, in planning sulfur removal schemes it is useful to understand the proportionment of inorganic sulfur compared with that of organic sulfur. Details of size, shape, orientation, and distribution factors for pyrite, certain pyrite and maceral groupings or fields, or other coal constituents (macerals and other inorganic components) are of importance in supporting rational designs of sulfur removal processes. Recent scanning electron microscope (SEM) investigations help to show the interrelations between macerals and inorganic phases such as pyrite (FeS2, the primary inorganic source of sulfur in coal) (1,2,3,4). This form of characterization complements optical microscope studies (5,6,7,8) and conventional transmission electron microscope (TEM) studies (9-15) which have been used to classify and to 'study coal constituents. SEM offers a way to visualize features hundreds and
Concise Review: Guidance in Developing Commercializable Autologous/Patient-Specific Cell Therapy Manufacturing (2013)

Cell therapy is poised to play an enormous role in regenerative medicine. However, little guidance is being made available to academic and industrial entities in the start-up phase. In this technical review, members of the International Society for Cell Therapy provide guidance in developing commercializable autologous and patient-specific manufacturing strategies from the perspective of process development. Special emphasis is placed on providing guidance to small academic or biotech researchers as to what simple questions can be addressed or answered at the bench in order to make their cell therapy products more feasible for commercial-scale production. We discuss the processes that are required for scale-out at the manufacturing level, and how many questions can be addressed at the bench level. The goal of this review is to provide guidance in the form of topics that can be addressed early in the process of development to better the chances of the product being successful for future commercialization.
Enrichment of extracellular vesicles with lipid nanoprobe functionalized nanostructured silica (2019)

Nanoscale extracellular vesicles (nEVs) have recently demonstrated potential value in cancer diagnostics and treatment monitoring, but translation has been limited by technical challenges in nEV isolation. Thus, we have developed a one-step nEV isolation platform that utilizes nEV size-matched silica nanostructures and a surface-conjugated lipid nanoprobe with an integrated microfluidic mixer. The reported platform has 28.8% capture efficiency from pancreatic cancer plasma and can sufficiently enrich nEVs for simpler positive identification of point mutations, particularly KRAS, in nEV DNA from the plasma of pancreatic cancer patients.
cw double cross pumping of the 5<i>I</i>7–5<i>I</i>8 laser transition in Ho3+-doped garnets (1986)

We obtained for the first time efficient room-temperature cw lasing at 2.086 μm in Cr,Tm,Ho:YScAl-garnet and Cr,Tm,Ho:YScGa-garnet crystals. Double cross pumping via Cr3+ and Tm3+ with a krypton pump laser yields threshold pump powers of 25 mW and slope efficiencies up to 13%. Broad band pumping can also be expected.
Assessing Cerebrovascular Reactivity Abnormality by Comparison to a Reference Atlas (2014)

Attribution of vascular pathophysiology to reductions in cerebrovascular reactivity (CVR) is confounded by subjective assessment and the normal variation between anatomic regions. This study aimed to develop an objective scoring assessment of abnormality. CVR was measured as the ratio of the blood-oxygen-level-dependent magnetic resonance signal response divided by an increase in CO2, standardized to eliminate variability. A reference normal atlas was generated by coregistering the CVR maps from 46 healthy subjects into a standard space and calculating the mean and standard deviation (s.d.) of CVR for each voxel. Example CVR studies from 10 patients with cerebral vasculopathy were assessed for abnormality, by normalizing each patient's CVR to the same standard space as the atlas, and assigning a z-score to each voxel relative to the mean and s.d. of the corresponding atlas voxel. Z-scores were color coded and superimposed on their anatomic scans to form CVR z-maps. We found the CVR z-maps provided an objective evaluation of abnormality, enhancing our appreciation of the extent and distribution of pathophysiology compared with CVR maps alone. We concluded that CVR z-maps provide an objective, improved form of evaluation for comparisons of voxel-specific CVR between subjects, and across tests sites.
SNOMED-CT: The advanced terminology and coding system for eHealth. (2006)

A clinical terminology is essential for Electronic Health records. It represents clinical information input into clinical IT systems by clinicians in a machine-readable manner. Use of a Clinical Terminology, implemented within a clinical information system, will enable the delivery of many patient health benefits including electronic clinical decision support, disease screening and enhanced patient safety. For example, it will help reduce medication-prescribing errors, which are currently known to kill or injure many citizens. It will also reduce clinical administration effort and the overall costs of healthcare.
Synthesis, Characterization and Application of Nano Lepidocrocite and Magnetite in the Degradation of Carbon Tetrachloride (2011)

Degradation of halogenated organic compounds using nanoparticles is one of the innovative technologies in environmental remediation. In the present study, the synthesis, characterization and application of lepidocrocite (FeOOH) and magnetite (Fe 3 O 4 ) nanoparticles for the remediation of water contaminated with carbon tetrachloride (CCl 4 ) has been investigated. The synthesized nanoparticles were characterized by using advanced instrumental techniques such as field emission scanning electron microscopy (FESEM) and X-ray diffraction (XRD). The synthesized FeOOH and Fe 3 O 4 nanoparticles were found to have an average crystallite size of 10.94 nm and 18.10 nm, respectively. Batch degradation experiments for the degradation of CCl 4 were carried out separately using both of the above synthesized nanoparticles. The degradation reactions were found to be first-order while using Fe 3 O 4 and second-order while using FeOOH nanoparticles. Moreover, the reactivity of freshly synthesized Fe 3 O 4  nanoparticles was found to be much higher than that of FeOOH nanoparticles. Keywords:  Nanoparticles, magnetite, lepidocrocite, carbon tetrachloride, degradation kinetics