gebhart/patrepeval huggingface dataset:
Efficient Synthesis of Aromatic sec-Amides from Esters: Synthetic Utility of Bislithium Amides (1999)

Convenient, efficient preparation of aromatic sec-amides from esters has been accomplished using dilithium amides which are easily prepared by treatment of aromatic amines with 2 equiv of BuLi in THF. This new method allows a facile formation of amide bond even with sterically hindered esters.
Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis (1998)

Populations of surface-attached microorganisms comprising either single or multiple species are commonly referred to as biofilms. Using a simple assay for the initiation of biofilm formation (e.g. attachment to an abiotic surface) by Pseudomonas fluorescens strain WCS365, we have shown that: (i) P. fluorescens can form biofilms on an abiotic surface when grown on a range of nutrients; (ii) protein synthesis is required for the early events of biofilm formation; (iii) one (or more) extracytoplasmic protein plays a role in interactions with an abiotic surface; (iv) the osmolarity of the medium affects the ability of the cell to form biofilms. We have isolated transposon mutants defective for the initiation of biofilm formation, which we term surface attachment defective (sad). Molecular analysis of the sad mutants revealed that the ClpP protein (a component of the cytoplasmic Clp protease) participates in biofilm formation in this organism. Our genetic analyses suggest that biofilm formation can proceed via multiple, convergent signalling pathways, which are regulated by various environmental signals. Finally, of the 24 sad mutants analysed in this study, only three had defects in genes of known function. This result suggests that our screen is uncovering novel aspects of bacterial physiology.
Proposing a framework for crowd-sourced green infrastructure design (2014)

Green stormwater infrastructure (GI) (e.g., rain gardens, bioswales, green roofs, etc.) are decentralized systems that have gained recent attention for their ability to reduce stormwater management problems while significantly benefiting human and ecosystem well-being. Available GI design methodologies lack a participatory framework that considers community-specific social, cultural, economic, and political constraints, critical components for widespread acceptance and effective implementation and maintenance of such systems. A project funded by the U.S. National Science Foundation seeks to develop a novel, computational, GI design framework that integrates interactive, neighborhood-scale, collaborative design by multiple stakeholders ("crowd-sourced" design) with multi- scale models of ecosystem and human impacts. The primary research tasks include: (1) creation of integrated models to predict hydrologic, human, and ecosystem impacts of GI designs from site to catchment scales, (2) development of interactive methods for crowd-sourcing model parameterization and GI design, and (3) implementation of modeling and crowd-sourced design methods in a cyberinfrastructure (CI) framework. The models developed in this project will be among the first to integrate criteria for human well-being with site-and-watershed-scale hydrologic and ecologic processes. Furthermore, by advancing crowd-sourced interactive optimization and model parameterization, this project can influence other design processes where early, diverse input is important for design acceptance.
Opiate modulation of the active and inactive components of the postshock reaction: Parallels between naloxone pretreatment and shock intensity. (1984)

Electric footshock elicited an immediate burst of activity followed by a period of immobility termed freezing. Naloxone, an opiate antagonist, enhanced both of these postshock reactions (Experiment 1). Naloxone's effects on the active and inactive components of the postshock reaction paralleled those of increasing shock intensity (Experiment 2). This finding suggests that the drug caused these results by enhancing the perceived intensity of shock. The facilitatory effects of naloxone on the active and inactive reactions to shock appear to be specific to nociceptive stimuli, as naloxone decreased the activity burst elicited by a nonnociceptive startling stimulus and had no effect on the freezing that followed that nonnociceptive stimulus (Experiment 3). Naloxone could accomplish its alteration of perceived intensity by antagonizing endogenous opioid analgesic systems. However, as hypophysectomy did not block the drug's action, the effects are not mediated by pituitary opioids (Experiment 4).
Multiplexed fiber Bragg grating strain-sensor system with a fiber Fabry–Perot wavelength filter (1993)

The use of a fiber Fabry–Perot filter for detecting the wavelength shift of a fiber Bragg grating sensor or network of sensor elements along a commonfiber path is described. Results obtained by using a system with four sensor elements are presented.
Identification of Acetylcholine Receptor Channel-Lining Residues in the M1 Segment of the .alpha.-Subunit (1995)

The muscle-type acetylcholine (ACh) receptor has the composition alpha 2 beta gamma delta. The subunits are arranged quasisymmetrically around a central, ion-conducting, water-filled channel. Each subunit has four membrane-spanning segments, M1-M4, and the channel through the membrane is formed among these segments. Substituting cysteine for each of the residues in and flanking the alpha M2 segment, we previously found that, at 10 of the 21 mutated positions, the cysteine was accessible to a small, positively charged, sulfhydryl-specific reagent, methanethiosulfonate ethylammonium (MTSEA), and inferred that the residues at these positions are exposed in the channel lumen. We have now applied the substituted-cysteine-accessibility method to alpha M1. We analyzed 15 consecutive residues, starting at alpha Pro211 at the extracellular end of M1. Wild-type alpha contains Cys222, which is inaccessible to MTSEA. We mutated each of the other 14 residues to cysteine and expressed the mutant alpha subunits, together with wild-type beta, gamma, and delta subunits, in Xenopus oocytes. Thirteen of the fourteen mutants gave robust ACh-induced currents. MTSEA irreversibly altered the ACh-induced response of seven cysteine-substitution mutants: alpha Y213C was susceptible to MSTEA added in the presence or the absence of ACh, alpha P211C, alpha I215C, alpha V216C, alpha N217C, and alpha I220C were susceptible in the absence of ACh, and alpha V218C was susceptible in the presence of ACh. These results imply that M1 is exposed in the channel, and its exposure changes during gating or desensitization.(ABSTRACT TRUNCATED AT 250 WORDS)
Implementing the data center energy productivity metric (2012)

As data centers proliferate in size and number, the endeavor to improve their energy efficiency and productivity is becoming increasingly important. We discuss the properties of a number of the proposed metrics of energy efficiency and productivity. In particular, we focus on the Data Center Energy Productivity (DCeP) metric, which is the ratio of useful work produced by the data center to the energy consumed performing that work. We describe our approach for using DCeP as the principal outcome of a designed experiment using a highly instrumented, high-performance computing data center. We found that DCeP was successful in clearly distinguishing different operational states in the data center, thereby validating its utility as a metric for identifying configurations of hardware and software that would improve (or even maximize) energy productivity. We also discuss some of the challenges and benefits associated with implementing the DCeP metric, and we examine the efficacy of the metric in making comparisons within a data center and among data centers.
Ex Vivo Gene Transfer for Improvement of Transplanted Pancreatic Islet Viability and Function (2005)

Human pancreatic islet transplantation has recently been shown to be successful in replacing pancreatic endocrine function into type 1 diabetic recipients. A major drawback, however, is the high amount of pancreatic ss cells required to render one single patient insulin-independent. Given the shortage of human beta cell donors, the majority of type 1 diabetic patients remain excluded from this therapeutic option. High number of islets are requested since substantial islet cell death and dysfunction occur within the first few hours and days after islet transplantation. Impaired vascularization of the engraft, the non-specific inflammatory reaction at the site of transplantation, together with the presence of active or memory autoimmune responses to islet autoantigens and allogeneic recognition contribute to apoptosis of ss cells and subsequent early graft function loss. This review will focus on ex vivo engineering of the islet graft by gene transfer to improve islet engraftment. An overview of currently used gene transfer techniques will be given and their potential will be discussed.
Standards-Based Sharable Active Guideline Environment (SAGE): A Project to Develop a Universal Framework for Encoding and Disseminating Electronic Clinical Practice Guidelines (2002)

A collaborative project has been initiated to develop a standards-based, comprehensive technology infrastructure that will enable encoding and dissemination of interoperable, electronic clinical practice guidelines (CPG's). Three key deliverables of this large scale ($18M), 3-year project include: An interoperable guideline model, a guideline authoring/encoding workbench, and a guideline deployment system. Our approach will be to employ and extend existing informatics standards, and to collaborate closely with standards development organizations. The project methodology will build on earlier efforts in this field, and will be driven by requirements specific to supporting active deployment of guideline content within clinical information system (CIS) workflow.
Type-II Quantum Dots:  CdTe/CdSe(Core/Shell) and CdSe/ZnTe(Core/Shell) Heterostructures (2003)

Type-II band engineered quantum dots (CdTe/CdSe(core/shell) and CdSe/ZnTe(core/shell) heterostructures) are described. The optical properties of these type-II quantum dots are studied in parallel with their type-I counterparts. We demonstrate that the spatial distribution of carriers can be controlled within the type-II quantum dots, which makes their properties strongly governed by the band offset of the comprising materials. This allows access to optical transition energies that are not restricted to band gap energies. The type-II quantum dots reported here can emit at lower energies than the band gaps of comprising materials. The type-II emission can be tailored by the shell thickness as well as the core size. The enhanced control over carrier distribution afforded by these type-II materials may prove useful for many applications, such as photovoltaics and photoconduction devices.
Genetic and Pathogenic Characterization of H6N1 Avian Influenza Viruses Isolated in Taiwan Between 1972 and 2005 (2006)

This article reports the genetic and pathogenic characteristics of 34 isolates of H6N1 avian influenza viruses isolated in Taiwan between 1972 and 2005. Genetic analyses showed that a unique lineage of H6N1 viruses has been established in domestic chickens in Taiwan since 1997, and this lineage of viruses differs from the H6N1 viruses circulating in Hong Kong and Southeastern China. Pathogenicity tests showed that all Taiwanese H6N1 viruses were of low pathogenicity but might lead to economic loss when associated with other diseases. Hemagglutination inhibition tests showed that antigenic drift has occurred in Taiwanese H6N1 viruses, and sequence comparison has identified a total of five possible antigenic sites on the hemagglutinin molecule of the H6N1 viruses. Some Taiwanese H6N 1 viruses could replicate in mice without preadaptation, indicating that these viruses have the potential to cause cross-species infection into mammals.
Impact of Sequential Ammonia Fiber Expansion (AFEX) Pretreatment and Pelletization on the Moisture Sorption Properties of Corn Stover (2015)

Combining ammonia fiber expansion (AFEX™) pretreatment with a depot processing facility is a promising option for delivering high-value densified biomass to the emerging bioenergy industry. However, because the pretreatment process results in a high moisture material unsuitable for pelleting or storage (40% wet basis), the biomass must be immediately dried. If AFEX pretreatment results in a material that is difficult to dry, the economics of this already costly operation would be at risk. This work tests the nature of moisture sorption isotherms and thin-layer drying behavior of corn (Zea mays L.) stover at 20°C to 60°C before and after sequential AFEX pretreatment and pelletization to determine whether any negative impacts to material drying or storage may result from the AFEX process. The equilibrium moisture content to equilibrium relative humidity relationship for each of the materials was determined using dynamic vapor sorption isotherms and modeled with modified Chung-Pfost, modified Halsey, and modified Henderson temperature-dependent models as well as the Double Log Polynomial (DLP), Peleg, and Guggenheim Anderson de Boer (GAB) temperature-independent models. Drying kinetics were quantified under thin-layer laboratory testing and modeled using the Modified Page's equation. Water activity isotherms for non-pelleted biomass were best modeled with the Peleg temperature-independent equation while isotherms for the pelleted biomass were best modeled with the Double Log Polynomial equation. Thin-layer drying results were accurately modeled with the Modified Page's equation. The results of this work indicate that AFEX pretreatment results in drying properties more favorable than or equal to that of raw corn stover, and pellets of superior physical stability in storage.
Synchrony dual-optic accommodating intraocular lens (2006)

A dual-optic design linked by spring haptics increases the accommodative effect of axial optic displacement with minimal magnification effect and has promise for improving the performance of accommodative intraocular lenses.
Montreal's Experience with Cyranose Heat and Moisture Exchanger Use in 15 Laryngectomized Patients (2007)

Laryngectomized patients from the Montreal area could benefit from Cyranose artificial nose following an adaptation period during our cold winter.
Capacity enhancement and BER in a combined SDMA/TDMA system (2002)

This paper considers the performance of a TDMA system employing smart antennas at the base station. Two adaptation schemes are analyzed-the switched beam approach and an adaptive array based on an adaptation algorithm to maximize the Signal-to-Interference and Noise ratio. For an SDMA system the switched beam approach performs worse than the adaptive array. Adaptive arrays based on gradient-vector estimation (e.g. LMS) are not suitable for mobile radio. The class of Least Squares (LS, RLS, SQRLS) algorithms shows satisfactory performance. For a linear array with 8 elements a minimum angular separation of 10/spl deg/ between two users is sufficient for the adaptive array to achieve as good performance as a system serving one user per traffic channel.
The anatomy and physiology of cortical mechanisms of cardiac control. (1993)

For nearly fifty years, attention has repeatedly been drawn to electrocardiographic changes accompanying acute stroke. The mechanism was unknown. These alterations, which are more frequent after hemisphere than brain stem infarction, are not solely due to concomitant myocardial ischemia. Recently, cardiac chronotropic organization has been shown within the posterior rat insular cortex. Stimulation of that site mimics both the electrocardiographic changes and the cardiac pathology accompanying acute stroke. These effects are attended by increased sympathetic activity. In addition, stimulation of the human right insula increases sympathetic cardiovascular tone, whereas parasympathetic increases are more frequent during left insula stimulation. It is suggested that right middle cerebral artery infarction disinhibits insular function, resulting in increased sympathetic cardiovascular tone and the cardiac consequences of stroke.
Beneficial Effects of Biventricular Pacing in Patients with a “Narrow” QRS (2003)

Congestive heart failure (CHF) patients with LBBB and QRS duration > 150 ms are considered the best candidates to biventricular pacing (Biv-P). However, patients with a narrow (120-150 ms) QRS may also benefit from Biv-P since true ventricular dyssynchrony may be underestimated by considering only QRS enlargement. From October 1999 to April 2002, 158 CHF patients (121 men, mean age 65 years, mean LVEF 0.29, mean QRS width 174 ms) underwent successful Biv-P implantation and were then followed for a mean time of 11.2 months. According to basal QRS duration, patients were divided in two groups, with wide QRS (> or = 150 ms, 128 patients, 81%) and with narrow QRS (< 150 ms, 30 patients, 19%). In the wide QRS group, LVEF improved from 29% to 39% (P < 0.0001), 6-minute walk test from 311 to 463 m (P < 0.0001), while NYHA Class III-IV patients decreased from 86% to 8% (P < 0.0001). In the narrow QRS group LVEF improved from 30% to 38% (P < 0.0001), 6-minute walk test from 370 to 506 m (P < 0.0001), and NYHA Class III-IV patients decreased from 60% to 0% (P < 0.0001). The data showed that in wide and narrow QRS patients, Biv-P significantly improved clinical parameters (NYHA class, 6-minute walk test, quality-of-life, and hospitalization rate) and main echocardiographic indicators. Furthermore, narrow QRS patients had a better survival rate, rapidly regained left ventricular function, and only a few patients remained in a higher NYHA class during follow-up. These patients should not be excluded "a priori" from cardiac resynchronization therapy.
Collagen repair not improved by fibrin adhesive: Cruciate ligament ruptures studied in dogs (1993)

The anterior cruciate ligament in 30 dogs was transected and repaired by simple suture. In every other dog, fibrin adhesive (Tisseel Kit, Immuno AG, Vienna, Austria) was applied to the transection area before suturing. The proportion of organized versus unorganized and inflammatory tissue formation was assessed histologically. At 3 weeks, the amount of normal organized collagenous tissue was reduced to 20 percent both without and with fibrin adhesive. After 6 weeks, a substantial increase of organized collagenous tissue was observed after suture only, which at 12 weeks reached about 70 percent of the total area. In contrast, repair with fibrin adhesive had at 12 weeks only 30 percent of normal collagenous tissue.
Composing specifications (1993)

A rigorous modular specification method requires a proof rule asserting that if each component behaves correctly in isolation, then it behaves correctly in concert with other components. Such a rule is subtle because a component need behave correctly only when its environment does, and each component is part of the others' environments. We examine the precise distinction between a system and its environment, and provide the requisite proof rule when modules are specified with safety and liveness properties.
Expression of lectin binding in oral submucous fibrosis. (1999)

Lectins are a group of specific glycoproteins present in cells, particularly cell membrane. Recently, lectin binding studies have been used as a diagnostic as well as prognostic indicator of neoplasm's. Oral submucous fibrosis (OSMF) is a potential premalignant condition predominantly seen in Indian subcontinent. A comparison of expression of lectin binding was studied in normal tissue, OSMF cases and oral squamous cell carcinoma. The OSMF cases were grouped into early and advanced conditions as per the histopathologic criteria. Patterns of lectin binding observed with advanced OSMF cases were comparable with that of Oral squamous cell carcinoma. The role of lectin binding studies in assessing the malignant potential of a pre-malignant condition is discussed.
Gentest: an automatic test-generation system for sequential circuits (1989)

A description is given of Gentest, with emphasis on STG2, a sequential test generator that uses the Back test-generation algorithm and the Split value model. The performance of STG2 on a Convex C-1 computer is compared with that of its predecessor, STG1 and STG1.5. Results are also presented for another set of experiments for Gentest on a Sun 3/60 workstation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Activated ALK signals through the ERK–ETV5–RET pathway to drive neuroblastoma oncogenesis (2018)

Activating mutations of the ALK receptor occur in a subset of neuroblastoma tumors. We previously demonstrated that Alk mutations cooperate with MYCN overexpression to induce neuroblastoma in mice and identified Ret as being strongly upregulated in MYCN/Alk<sup>mut</sup> tumors. By a genetic approach in vivo, we now document an oncogenic cooperation between activated Ret and MYCN overexpression in neuroblastoma formation. We show that MYCN/Ret<sup>M919T</sup> tumors exhibit histological features and expression profiles close to MYCN/Alk<sup>mut</sup> tumors. We show that RET transcript levels decrease precedes RET protein levels decrease upon ALK inhibition in neuroblastoma cell lines. Etv5 was identified as a candidate transcription factor regulating Ret expression from murine MYCN/Alk<sup>mut</sup> tumor transcriptomic data. We demonstrate that ETV5 is regulated both at the protein and mRNA levels upon ALK activation or inhibition in neuroblastoma cell lines and that this regulation precedes RET modulation. We document that ALK activation induces ETV5 protein upregulation through stabilization in a MEK/ERK-dependent manner. We show that RNAi-mediated inhibition of ETV5 decreases RET expression. Reporter assays indicate that ETV5 is able to drive RET gene transcription. ChIP-seq analysis confirmed ETV5 binding on the RET promoter and identified an enhancer upstream of the promoter. Finally, we demonstrate that combining RET and ALK inhibitors reduces tumor growth more efficiently than each single agent in MYCN and Alk<sup>F1178L</sup>-driven murine neuroblastoma. Altogether, these results define the ERK-ETV5-RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK.
A viral vaccine vector that expresses foreign genes in lymph nodes and protects against mucosal challenge (1996)

A candidate live-virus vaccine strain of Venezuelan equine encephalitis virus (VEE) was configured as a replication-competent vector for in vivo expression of heterologous immunogens. Three features of VEE recommend it for use as a vaccine vector. (i) Most human and animal populations are not already immune to VEE, so preexisting immunity to the vector would not limit expression of the heterologous antigen. (ii) VEE replicates first in local lymphoid tissue, a site favoring the induction of an effective immune response. (iii) Parenteral immunization of rodents and humans with live, attenuated VEE vaccines protects against mucosal challenge, suggesting that VEE vaccine vectors might be used successfully to protect against mucosal pathogens. Upon subcutaneous (s.c.) inoculation into the footpad of mice, a VEE vector containing the complete influenza virus hemagglutinin (HA) gene expressed HA in the draining lymph node and induced anti-HA immunoglobulin G (IgG) and IgA serum antibodies, the levels of which could be increased by s.c. booster inoculation. When immunized mice were challenged intranasally with a virulent strain of influenza virus, replication of challenge virus in their lungs was restricted, and they were completely protected from signs of disease. Significant reduction of influenza virus replication in the nasal epithelia of HA vector-immunized mice suggested an effective immunity at the mucosal surface. VEE vaccine vectors represent an alternative vaccination strategy when killed or subunit vaccines are ineffective or when the use of a live attenuated vaccine might be unsafe.