gebhart/patrepeval huggingface dataset:
Automatically Extracting Requirements Specifications from Natural Language. (2014)

Natural language (supplemented with diagrams and some mathematical notations) is convenient for succinct communication of technical descriptions between the various stakeholders (e.g., customers, designers, implementers) involved in the design of software systems. However, natural language descriptions can be informal, incomplete, imprecise and ambiguous, and cannot be processed easily by design and analysis tools. Formal languages, on the other hand, formulate design requirements in a precise and unambiguous mathematical notation, but are more difficult to master and use. We propose a methodology for connecting semi-formal requirements with formal descriptions through an intermediate representation. We have implemented this methodology in a research prototype called ARSENAL with the goal of constructing a robust, scalable, and trainable framework for bridging the gap between natural language requirements and formal tools. The main novelty of ARSENAL lies in its automated generation of a fully-specified formal model from natural language requirements. ARSENAL has a modular and flexible architecture that facilitates porting it from one domain to another. ARSENAL has been tested on complex requirements from dependable systems in multiple domains (e.g., requirements from the FAAIsolette and TTEthernet systems), and evaluated its degree of automation and robustness to requirements perturbation. The results provide concrete empirical evidence that it is possible to bridge the gap between stylized natural language requirements and formal specifications with ARSENAL, achieving a promising level of performance and domain independence.
Effect of inositol trisphosphate and calcium on oscillating elevations of intracellular calcium in Xenopus oocytes. (1990)

Stimulation of many nonexcitable cells by Ca2(+)-mobilizing receptor agonists causes oscillating elevations of the intracellular free Ca2+ concentration ((Ca2+]i), rather than a continuous increase. It has been proposed that the frequency at which [Ca2+]i oscillates determines the biological response. Because the occurrence of [Ca2+] oscillations is observed together with endogenous inositol polyphosphate (InsPs) production or following InsPs application, we injected Xenopus laevis oocytes with InsPs and monitored Ca2(+)-activated Cl- currents as an assay of [Ca2+]i. Microinjection of the poorly metabolizable inositol trisphosphate (InsP3) derivatives inositol 2,4,5-trisphosphate (Ins(2,4,5)P3) and inositol 1,4,5-trisphosphorothioate (Ins(1,4,5) P3S3) induced [Ca2+]i oscillations. The frequency at which [Ca2+]i oscillated increased with the injected dose, indicating that the frequency-generating mechanism lies distal to InsP3 production and that generation of oscillations does not require either oscillation of InsP3 levels or InsP3 metabolism. Injections of high doses of Ins(1,4,5)P3 or Ins(2,4,5)P3 inhibited ongoing oscillations, whereas Ca2+ injections decreased the amplitude of Ins(2,4,5)P3-induced oscillations without altering their frequency. Injections of the Ins(1,4,5)P3 metabolite inositol 1,3,4,5-tetrakisphosphate also caused oscillations whose frequency was related to the injected dose, although inositol tetrakisphosphate injection induced an increase in the cellular level of Ins(1,4,5)P3. The results suggest a multicomponent oscillatory system that includes the InsP3 target as well as a Ca2(+)-sensitive step that modulates amplitude.
Prolonged in‐hospital stay and higher mortality after Covid‐19 among patients with non‐Hodgkin lymphoma treated with B‐cell depleting immunotherapy (2021)

Prolonged Covid-19 is an emerging issue for patients with lymphoma or immune deficiency. We aimed to examine prolonged length of in-hospital stay (LOS) due to Covid-19 among patients with lymphoma and assess its determinants and outcomes. Adult patients with lymphoma admitted for Covid-19 to 16 French hospitals in March and April, 2020 were included. Length of in-hospital stay was analyzed as a competitor vs death. The study included 111 patients. The median age was 65 years (range, 19-92). Ninety-four patients (85%) had B-cell non-Hodgkin lymphoma. Within the 12 months prior to hospitalization for Covid-19, 79 patients (71%) were treated for their lymphoma. Among them, 63 (57%) received an anti-CD20 therapy. Fourteen patients (12%) had relapsed/refractory disease. The median LOS was 14 days (range, 1-235). After a median follow-up of 191 days (3-260), the 6-month overall survival was 69%. In multivariable analyses, recent administration of anti-CD20 therapy was associated with prolonged LOS (subdistribution hazard ratio 2.26, 95% confidence interval 1.42-3.6, p < 0.001) and higher risk of death (hazard ratio 2.17, 95% confidence interval 1.04-4.52, p = 0.039). An age ≥ 70 years and relapsed/refractory lymphoma were also associated with prolonged LOS and decreased overall survival. In conclusion, an age ≥ 70 years, a relapsed/refractory lymphoma and recent administration of anti-CD20 therapy are risk factors for prolonged LOS and death for lymphoma patients hospitalized for Covid-19. These findings may contribute to guide the management of lymphoma during the pandemic, support evaluating specific therapeutic approaches, and raise questions on the efficacy and timing of vaccination of this particular population.
Limitations of Monitoring Wells for the Detection and Quantification of Petroleum Products in Soils and Aquifers (1989)

Abstract Theoretical analysis and laboratory column experiments were carried out to investigate the conditions required for petroleum products (oil) to flow into a well installed through a sandy porous medium contaminated with the oil. The results indicated that oil would flow into a well only after a layer of “free oil” is formed in the adjacent porous medium. Because significant quantities of oil could be stored in the porous medium under the influence of capillary suction prior to the formation of the zone of free oil, the presence of oil in a well would indicate an advanced stage of oil contamination of the subsurface. While monitoring wells could be used to delineate the extent of the free‐oil plume and the plume of dissolved petroleum constituents, they are not useful for delineating the extent of capillary held oil. The experimental results also indicated that the ratio of the oil‐layer thickness in the well to that in the porous medium is not a constant as is sometimes assumed in practice. Further, estimates of the oil thickness in the medium based on the oil thickness in wells and on capillary properties measured in the laboratory were sensitive to the values of the parameters used in these estimates. The measured thickness of the oil layer in a monitoring well alone may not yield reliable estimates of the amount of oil in the subsurface, and assuming that the oil‐thickness ratio is a constant can lead to inadequate site assessments and inappropriate remedial plans.
TRPV4 Agonists and Antagonists (2011)

TRPV4 belongs to the TRPV subfamily of Transient Receptor Potential (TRP) ion channels. This year marks the 10 year anniversary of the discovery of this polymodal ion channel which is activated by a variety of stimuli including warm temperatures, hypotonicity and endogenous lipids. Coupled with a widespread tissue distribution, this activation profile has resulted in a large number of disparate physiological functions for TRPV4. These range from temperature monitoring in skin keratinocytes to osmolarity sensing in kidneys, sheer stress detection in blood vessels and osteoclast differentiation control in bone. As knowledge of its physiological roles has expanded, interest in targeting TRPV4 modulation for therapeutic purposes has arisen and is now focused on several areas. First, as with related TRP channels TRPV1, TRPV3, TRPM8 and TRPA1, TRPV4 antagonism is being considered for inflammatory and neuropathic pain treatment. Recent work conducted using KO mice and agonists 4αPDD and GSK1016790A suggests bladder dysfunctions may also be targeted. Additionally, ventilator-induced lung injury has emerged as another potential indication for TRPV4 antagonists. Herein we review the known small molecule modulators of TRPV4 and relate progress made in identifying potent, selective and bioavailable agonists and antagonists to interrogate this ion channel in vivo.
ChemInform Abstract: Na+‐Glucose Cotransporter Inhibitors as Antidiabetics. Part 1. Synthesis and Pharmacological Properties of 4′‐Dehydroxyphlorizin Derivatives Based on a New Concept. (1996)

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.
Sacramento-Watt Avenue transit priority and mobility enhancement demonstration project: phase III evaluation report (2006)

This report presents the results of the national evaluation of the Sacramento-Watt Avenue Transit Signal Priority Project, a cooperative project between Sacramento County and the Sacramento Regional Transit District (RT) to deploy transit signal priority (TSP) along a highly congested section of Watt Avenue just east of downtown Sacramento. The evaluation approach was to collect data to assess the impact of the transit signal priority on transit travel times and travel time reliability, and to determine if the addition of the system had an impact on traffic on either Watt Avenue or its cross-streets. Bus travel time data was manually collected on-board buses operating on the corridor before and after deployment of TSP, data from automated vehicle location devices on buses operating with and without TSP emitters was obtained, and travel time runs were conducted on Watt Avenue and its cross-streets before and after deployment of TSP. Data were compared to determine the impact of TSP. The results of the transit mobility and performance analysis showed that the average travel time for TSP equipped buses was between 14 and 71 seconds less than for non-TSP buses traveling over the same segments. For the control intersections (i.e., those without TSP), the travel times for TSP and non-TSP buses were similar, indicating that this difference can be attributed to the TSP. The results of the travel time reliability analysis showed that TSP did not significantly improve travel time reliability. For the segments of the corridor with TSP, TSP buses experienced better travel time reliability than non-TSP buses in two of the six time periods (as compared to one out of the six time periods) when looking at non-TSP intersections. The results of the traveler mobility analysis was inconclusive. Although difficult to state with much certainty, the results indicated that the addition of TSP on Watt Avenue had somewhat of a positive impact on Watt Avenue traffic and somewhat of a negative impact on cross-street traffic.
Evaluation of fault tolerance latency from real-time application's perspectives (2000)

Information on Fault Tolerance Latency (FTL), which is defined as the total time required by all sequential steps taken to recover from an error, is important to the design and evaluation of fault-tolerant computers used in safety-critical real-time control systems with deadline information. In this paper, we evaluate FTL in terms of several random and deterministic variables accounting for fault behaviors and/or the capability and performance of error-handling mechanisms, while considering various fault tolerance mechanisms based on the trade-off between temporal and spatial redundancy, and use the evaluated FTL to check if an error-handling policy can meet the Control System Deadline (CSD) for a given real-time application.
Incremental Information Objects and Progressive Barcodes (2012)

In the fast-changing world of actionable printing, there has recently been a huge increase in the adoption of 2D barcodes for enterprise and consumer applications. The Data Matrix 2D barcode has become a primary carrier of supply chain information, most notably for track and trace. The QR (Quick Response) 2D barcode, meanwhile, has spread from Japan to the rest of the world, and is a standard means of connecting a barcode to a URL. We have previously developed a 3D (color + 2D) barcode that increases the barcode data capacity and provides branding possibilities. In this paper, we introduce the 4D barcode (color + 2D + time) as a means of using the same barcode location for multiple barcodes through time. This supports many enterprise workflows, including document lifecycles. In this paper, we consider the theory behind incremental information objects (IIOs), of which progressive barcodes are a key incarnation. We show that the set of progressive barcodes comprising a lifecycle can contain up to twice the data of the associated single-time 3D color barcode.
Kinetics of Difructose Dianhydrides Formation under Fructose Crystallization Conditions (1990)

Abstract Fructose undergoes dehydration reactions to form difructose dianhydrides during crystallization. Difructose dianhydrides can be incorporated into fructose crystals and inhibit the crystal growth. In this study, the kinetics of difructose dianhydrides formation under industrial crystallization conditions were investigated. Four difructose dianhydrides were detected by HPLC analysis. An empirical second‐order irreversible kinetic model was proposed for the reaction. The extent of reaction increased with increasing temperature and decreasing pH value of the solution. The amount of two of the difructose dianhydrides stopped increasing when the fructose concentration was about 70% or less. On the other hand, the formation of all dimers were retarded when the initial fructose concentration was higher than 80%.
Cyproheptadine Treatment in Neuroleptic-Induced Akathisia (1995)

Cyproheptadine may be useful in neuroleptic-induced akathisia.
CDK4 phosphorylation status and rational use for combining CDK4/6 and BRAF/MEK inhibition in advanced thyroid carcinomas (2023)

Abstract Despite overall good prognosis associated to thyroid cancer (TC), poorly differentiated carcinomas (PDTC) and anaplastic carcinomas (ATC, one of the most lethal human malignancies) represent major clinical challenges. We have shown that the presence of active T172-phosphorylated CDK4 predicts sensitivity to CDK4/6 inhibitory drugs (CDK4/6i) including palbociclib. Here, CDK4 phosphorylation was detected in all well-differentiated TC (n=29), 19/20 PDTC, 16/23 ATC, and 18/21 TC cell lines including 11 ATC-derived ones. The cell lines lacking CDK4 phosphorylation were insensitive to CDK4/6i. RNA-sequencing and immunohistochemistry revealed that tumors and cell lines without phosphorylated CDK4 presented very high p16 CDKN2A levels that were associated with proliferative activity. No RB1 mutations were found in 5 of these 7 tumors. p16/KI67 immunohistochemistry and a previously developed 11-gene signature identified the likely insensitive tumors lacking CDK4 phosphorylation. In cell lines, palbociclib synergized with dabrafenib/trametinib, completely and irreversibly arresting proliferation. The combined drugs prevented resistance mechanisms induced by palbociclib, most notably Cyclin E1-CDK2 activation and a paradoxical stabilization of phosphorylated CDK4 complexes. Our study supports the evaluation of CDK4/6i for ATC/PDTC treatment, including in combination with MEK/BRAF inhibitors.
Reproducibility Using VisTrails (2018)

Science has long placed an emphasis on revisiting and reusing past results: reproducibility is a core component of the scientific process. Testing and extending published results are standard activities that lead to practical progress: science moves forward using past work and allowing scientists to “stand on the shoulders of giants.” In natural science, long tradition requires experiments to be described in enough detail so that they can be reproduced 34by other researchers. This standard, however, has not been widely applied for computational experiments. Researchers often have to rely on tables, plots, and figure captions included in papers. Consequently, it is difficult to verify and reproduce many published results [43], and this has led to a credibility crisis in computational science [17].
Reliability analysis of aeroplane tyres (1996)

Aeroplanes are repairable systems consisting of several non‐repairable parts; tyres are one of these. Proper record of failure data is valuable in interpreting the failure pattern, for comparative evaluation of the quality of tyres of various manufacturers, and for prediction of the future needs in a specified planning horizon or for specified operational hours. Analyses failure data of several aeroplane tyres in an aviation set‐up, and interprets these in a reliability framework. Three parameters Weibull model is found to be quite appropriate for reliability characterization of tyres. These reliability models can be effectively integrated into a computerized material requirement planning system of the aviation facility to forecast the number of tyres needed for a given planning horizon.
Energetic Control of Redox-Active Polymers Towards Safe Organic Bioelectronic Materials (2019)

Avoiding faradaic side reactions during the operation of electrochemical devices is important to enhance the device stability, to achieve low power consumption, and to prevent the formation of reactive side‑products. This is particularly important for bioelectronic devices which are designed to operate in biological systems. While redox‑active materials based on conducting and semiconducting polymers represent an exciting class of materials for bioelectronic devices, they are susceptible to electrochemical side‑reactions with molecular oxygen during device operation. We show that this electrochemical side reaction yields hydrogen peroxide (H2O2), a reactive side‑product, which may be harmful to the local biological environment and may also accelerate device degradation. We report a design strategy for the development of redox-active organic semiconductors based on donor-acceptor copolymers that prevent the formation of H2O2 during device operation. This study elucidates the previously overlooked side-reactions between redox-active conjugated polymers and molecular oxygen in electrochemical devices for bioelectronics, which is critical for the operation of electrolyte‑gated devices in application-relevant environments.
Single-agent docetacel (D) versus docetaxel alternating with single-agent gemcitabine (G) as treatments of patients (pts) with advanced breast cancer (ABC): Final analysis of a randomized trial (2008)

1035 Background: Alternating use of single agents has not been compared with single-agent taxane as treatment of ABC. Methods: The key eligibility criteria for this open-label, prospective, randomized, multicenter, phase II trial were female gender, age <70, WHO performance status <2, and no prior chemotherapy for ABC. Pts were allocated to receive either D (80 or 100 mg/m2, d. 1 of a 3-wk cycle; D-D-D-D… Group A) or D alternating with G (1,000 mg/m2, d. 1 and 8 of a 3-wk cycle; D-G-D-G… Group B). G was scheduled to be given after treatment failure in Group A, in Group B second-line therapy was not defined. Trastuzumab was allowed for HER2+ disease. The primary endpoint was time to treatment failure (TTTF). Pts were stratified for performance status, prior taxane exposure and center at randomization. The planned sample size was 240 pts, α 0.05, 1-β 0.80, 2- sided log-rank test. Results: 240 pts were entered between Mar 2002 and Sep 2006, of whom 237 were assigned to treatment (Group A, 115; Group B, 122). The groups were balanced with main prognostic factors (ER+, A 71%, B 74%; HER2+, A 24%, B 19%). In May 2007 166 pts (70%) had failed treatment (A, 74%; B, 66%). The median TTTF was 5.6 months in Group A and 6.2 months in Group B (hazard ratio 0.85, 95% CI 0.63–1.16; P=0.31); a median of 8 cycles were given in both groups before failure. There was no statistical difference in time to progression (HR 1.05, P=0.72), survival (HR 1.11, P=0.60), response rate (76% in both groups) or response duration between the groups. When adverse events were evaluated per cycle using generalized estimating equations for repeated measurements, both hematologic (P=0.014) and nonhematologic (P=0.007) grade 3 or 4 events were less frequent in Group B than in Group A. Conclusions: D alternating with G is an effective and generally well tolerated treatment for ABC. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Eli Lilly sanofi-aventis sanofi-aventis Eli Lilly, sanofi-aventis
An Ensemble Approach to Link Prediction (2017)

A network with n nodes contains O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) possible links. Even for networks of modest size, it is often difficult to evaluate all pairwise possibilities for links in a meaningful way. Further, even though link prediction is closely related to missing value estimation problems, it is often difficult to use sophisticated models such as latent factor methods because of their computational complexity on large networks. Hence, most known link prediction methods are designed for evaluating the link propensity on a specified subset of links, rather than on the entire networks. In practice, however, it is essential to perform an exhaustive search over the entire networks. In this article, we propose an ensemble enabled approach to scaling up link prediction, by decomposing traditional link prediction problems into subproblems of smaller size. These subproblems are each solved with latent factor models, which can be effectively implemented on networks of modest size. By incorporating with the characteristics of link prediction, the ensemble approach further reduces the sizes of subproblems without sacrificing its prediction accuracy. The ensemble enabled approach has several advantages in terms of performance, and our experimental results demonstrate the effectiveness and scalability of our approach.
Improving the error-floor performance of binary half-product codes (2016)

Recently, a new type of product-like codes, known as half-product codes, has been studied for OTN applications. Binary half-product codes show excellent bit-error-rate performance under iterative hard-decision decoding in the waterfall region. To further improve the performance in the error floor region, a novel post-processor algorithm is proposed that relies on conditional bit flipping. For a class of important practical half-product codes, the error floor after post-processing is characterized.
Phonon-Mode Calculation, Far- and Mid-Infrared, and Raman Spectra of an ε-Ga0.5Fe1.5O3 Magnet (2017)

Gallium-substituted epsilon iron oxide (ε-Ga0.5Fe1.5O3) has drawn attention because its millimeter wave absorption frequency meets the millimeter wave radar frequency for automobiles. We report the phonon modes of ε-Ga0.5Fe1.5O3, which has an orthorhombic structure in the Pna21 space group. First-principles phonon-mode calculations show that ε-Ga0.5Fe1.5O3 has 117 optical phonon modes (fundamental vibrations) with symmetries of A1, A2, B1, and B2 as well as three acoustic phonon modes. The phonon density of states demonstrates that the movements of Fe and Ga contribute to the phonon modes in the lower energy region of 20–370 cm–1, while the movements of O contribute to the phonon modes in the higher energy region of 370–720 cm–1. We directly measure the optical phonon modes of ε-Ga0.48Fe1.52O3 nanoparticles using far- and mid-infrared (IR) and Raman spectroscopies, which agree well with those obtained by first-principles phonon-mode calculations. Additionally, the thermodynamic parameters of the internal energy (U), the vibrational entropy (Svib), and the Helmholtz energy (A) are calculated and understood through the investigation of the phonon modes. Heat capacity measurements confirm that the observed thermodynamic parameters are consistent with the predicted values.