gebhart/patrepeval huggingface dataset:
Impact o f t he N umber o f T reatment C ourses o n t he Clinical R esponse o f P atients W ho R eceive H igh-Dose Bolus I nterleukin-2 (2008)

Purpose: To determine the impact of treatment with successive courses of high-dose bolus interleukin-2 (IL-2) on the incidence of clinical responses in patients with metastatic melanoma or renal cell cancer. Patients and Methods: A consecutive series of 350 patients with either metastatic melanoma or renal cell cancer who were treated with high-dose bolus IL-2 in the Surgery Branch, National Cancer Institute, between September 1985 and November 1996 was analyzed, with a median potential follow-up of 7.1 years. All patients were treated with 720,000 IU/kg of IL-2 administered by a 15-minute intravenous infusion every 8 hours for up to 5 days, as clinically tolerated per cycle. Patients were retreated according to clinical response and tolerance to the IL-2 therapy. Results: Of the 149 patients with melanoma, 10 achieved complete responses (CRs) and 13 partial responses (PRs), for an overall response rate of 15.4%. Of the 201 patients with renal cell cancer, 18 achieved CRs and 20 PRs, for an overall response rate of 19.0%. Among responding patients, 21 of 23 with melanoma and 34 of 38 with renal cell cancer developed at least PRs after the first course of IL-2. Conclusion: Most patients with metastatic melanoma and renal cell cancer who achieved PRs or CRs to intravenous high-dose bolus IL-2 were identified after the first course of therapy. Those who demonstrated no response after two treatment courses failed to respond to additional IL-2 therapy. Based on this retrospective analysis, we recommend that patients who exhibit objective responses to treatment with high-dose bolus IL-2 receive additional treatment courses until either CR or IL-2 intolerance develops. Patients who do not achieve objective responses after two courses of IL-2 should receive no further treatment with this regimen. J Clin Oncol 18:1954-1959. © 2000 by American Society of Clinical Oncology.
Physics Guided Machine Learning Methods for Hydrology (2020)

Streamflow prediction is one of the key challenges in the field of hydrology due to the complex interplay between multiple non-linear physical mechanisms behind streamflow generation. While physics based models are rooted in rich understanding of the physical processes, a significant performance gap still remains which can be potentially addressed by leveraging the recent advances in machine learning. The goal of this work is to incorporate our understanding of hydrological processes and constraints into machine learning algorithms to improve the predictive performance. Traditional ML models for this problem predict streamflow using weather drivers as input. However there are multiple intermediate processes that interact to generate streamflow from weather drivers. The key idea of the approach is to explicitly model these intermediate processes that connect weather drivers to streamflow using a multi-task learning framework. While our proposed approach requires data about intermediate processes during training, only weather drivers will be needed to predict the streamflow during testing phase. We assess the efficacy of the approach on a simulation dataset generated by the SWAT model for a catchment located in the South Branch of the Root River Watershed in southeast Minnesota. While the focus of this paper is on improving the performance given data from a single catchment, methodology presented here is applicable to ML-based approaches that use data from multiple catchments to improve performance of each individual catchment.
Diabetes and its drivers: the largest epidemic in human history? (2017)

The "Diabesity" epidemic (obesity and type 2 diabetes) is likely to be the biggest epidemic in human history. Diabetes has been seriously underrated as a global public health issue and the world can no longer ignore "the rise and rise" of type 2 diabetes. Currently, most of the national and global diabetes estimates come from the IDF Atlas. These estimates have significant limitations from a public health perspective. It is apparent that the IDF have consistently underestimated the global burden. More reliable estimates of the future burden of diabetes are urgently needed. To prevent type 2 diabetes, a better understanding of the drivers of the epidemic is needed. While for years, there has been comprehensive attention to the "traditional" risk factors for type 2 diabetes i.e., genes, lifestyle and behavioral change, the spotlight is turning to the impact of the intra-uterine environment and epigenetics on future risk in adult life. It highlights the urgency for discovering novel approaches to prevention focusing on maternal and child health. Diabetes risk through epigenetic changes can be transmitted inter-generationally thus creating a vicious cycle that will continue to feed the diabetes epidemic. History provides important lessons and there are lessons to learn from major catastrophic events such as the Dutch Winter Hunger and Chinese famines. The Chinese famine may have been the trigger for what may be viewed as a diabetes "avalanche" many decades later. The drivers of the epidemic are indeed genes and environment but they are now joined by deleterious early life events. Looking to the future there is the potential scenario of future new "hot spots" for type 2 diabetes in regions e.g., the Horn of Africa, now experiencing droughts and famine. This is likely to occur should improved economic and living conditions occur over the next few decades. Type 2 diabetes will remain one of the greatest challenges to human health for many years to come.
Physical mixing of metal acetates: a simple, scalable method to produce active chloride free bimetallic catalysts (2012)

We have prepared supported gold, palladium and gold–palladium bimetallic catalysts by the physical mixing of the acetate salts of the metals followed by a simple heat treatment. The use of the acetates as the metal precursor eliminates chloride from the catalyst preparation step. Extensive characterisation shows the formation of bimetallic alloy particles. These catalysts are extremely active for alcohol oxidations and the direct formation of hydrogen peroxide.
Germinal Center Function in the Spleen during Simian HIV Infection in Rhesus Monkeys (2006)

Infection with HIV-1, SIV, or simian HIV is associated with abnormalities in the number, size, and structure of germinal centers (GCs). To determine whether these histopathologic abnormalities are associated with abnormalities in Ab development, we analyzed nucleotide sequences of Igs from splenic GCs of simian HIV-infected macaques. Virus-specific GCs were identified in frozen splenic tissue sections by inverse immunohistochemistry using rHIV-1 gp120 as a probe. B cells from envelope-specific GCs were isolated from these sections using laser capture microdissection. Their Igs were amplified from cDNA using nested PCR, then cloned and sequenced. Nucleotide sequences were recovered from nine multimember clonal lineages. Within each lineage, sequences had similar V-D-J or V-J junctions but differed by somatic mutations distributed throughout the variable domain. The clones were highly mutated, similar to that previously reported for HIV-1-specific human IgG Abs. The average clone had 37 mutations in the V region, for a frequency of 0.11 mutations/base. The mutational pattern was strikingly nonrandom, with somatic mutations occurring preferentially at RGYW/WRCY hotspots. Transition mutations were favored over transversions, with C-->T and G-->A replacements together accounting for almost one-third of all mutations. Analysis of replacement and silent mutations in the framework and CDRs suggests that the Igs were subjected to affinity selection. These data demonstrate that the process of Ab maturation is not seriously disrupted in GCs during the early stages of immunodeficiency virus infection, and that Env-specific Igs developing in GCs are subject to extensive somatic mutation and profound selection pressures.
A new method of generating multivariate Weibull distributed data (2016)

In order to fully test detector frameworks, it is important to have representative simulated clutter data readily available. While measured clutter data has often been fit to the Weibull distribution, generation of simulated complex multivariate Weibull data with prescribed covariance structure has been a challenging problem. As the multivariate Weibull distribution is admissible as a spherically invariant random vector for a specific range of shape parameter values, it can be decomposed as the product of a modulating random variable and a complex Gaussian random vector. Here we use this representation to compare the traditional method of generating multivariate Weibull data using the Rejection Method to a new approximation of the modulating random variable that lends itself to efficient computer generation.
Injection Enhancement in a Deep-Water Gulf of Mexico Multi Zone Completion Enabled by Downhole Multi-Position Flow Valves (2023)

Abstract The Deep-Water (DW) Gulf of Mexico (GOM) fields have a complex mix of multi-layered reservoirs, with thicknesses and rock properties which can widely differ from layer to layer within the same reservoir. Injection of 25,000 bpd of water from a shallower aquifer B4 sand via a dump flood technique, benefited from a variable and controlled zonal distribution of the injection into two separate layers connected to the producer B6 Sands over life of well. This paper presents the modelling performed to achieve optimal choke selection, specified distributions, job execution and results of utilizing multi-position flow valves as part of the 3 ½" completion with the objective of achieving the optimal injection rates in the upper and lower layers of the BB Sands. Design parameters considered critical by Talos included a controlled and variable distribution of the injection via dump flood of 50%/50% or 25%/75% respectively for the upper and lower layer of the producer B6 Sands, with the option to selective shut-off one of the layers over time, while maintaining the 3 ½" full-bore inner diameter for future interventions. Discussed within this paper : The selection process to meet the required distribution rates with the extensive modelling performed using modeling software for the choke size selection, quantity, and distribution in each of the three open positions of the multi-position flow valve to achieve the total flow area required to distribute the injection at the desired rate in each layer of the producer sand, and CFD (Computational Fluid Dynamics) for the choke design. Field data from the first installment of two multi-position flow valves in a well located in the Tornado project, operational considerations that enabled the manipulation of the flow valves and a summary of the achieved results will be presented and explained. This is the first deployment for the multi-position flow valve with variable chokes in the deep-water Gulf of Mexico well environment. The solution provided controlled injection with variable rates into the two upper and lower producer sands, this technique enables a cost-effective and reliable proven solution which can be applicable to any type of injector well, with the goal to increase the overall NPV of the field, through the increased recoverable using a predictable and safer method of downhole flow control.
Breaking the language barrier: machine assisted diagnosis using the medical speech translator. (2005)

In this paper, we describe and evaluate an Open Source medical speech translation system (MedSLT) intended for safety-critical applications. The aim of this system is to eliminate the language barriers in emergency situation. It translates spoken questions from English into French, Japanese and Finnish in three medical subdomains (headache, chest pain and abdominal pain), using a vocabulary of about 250-400 words per sub-domain. The architecture is a compromise between fixed-phrase translation on one hand and complex linguistically-based systems on the other. Recognition is guided by a Context Free Grammar Language Model compiled from a general unification grammar, automatically specialised for the domain. We present an evaluation of this initial prototype that shows the advantages of this grammar-based approach for this particular translation task in term of both reliability and use.
Supplemental File 2 from Cell Line–Specific Network Models of ER<sup>+</sup> Breast Cancer Identify Potential PI3Kα Inhibitor Resistance Mechanisms and Drug Combinations (2023)

&lt;p&gt;Supplemental File 2. Excel file with the cbioportal data the genomic data analysis is based on.&lt;/p&gt;
Autonomous tracking of vehicle taillights from a mobile platform using an embedded smart camera (2012)

The detection and tracking of vehicle taillights is an important aspect of collision avoidance systems and autonomous vehicle applications. In this paper, we present a novel and efficient algorithm for tracking the vehicle taillights from a mobile platform, under both daytime and nighttime conditions, which is entirely implemented on a CITRIC embedded smart camera. The algorithm uses a Kalman filter and a codebook to achieve a high level of robustness. On the microprocessor of the camera, it takes about 177 ms to process one frame of live camera data (which translates to approximately 6 fps). We demonstrate lightweight and reliable tracking of vehicle taillights, despite foreign objects appearing in view, blocking the view, or the vehicle changing lanes. In all of these cases, the algorithm is able to gracefully recover and resume normal operation. We will use this system as an initial platform for implementing other functionality, such as the detection of vehicle alert signals (brakes, turn signals, emergency flashers), which is also discussed. Compared to most existing work that focuses only on nighttime detection, the proposed algorithm provides daytime tracking of taillights, which is inherently more challenging.
The Untimely and the Messianic (2013)

This chapter demonstrates the structural connection between ideas of the unexpected and ideas of the future perfect in political philosophy, especially in the writing of Elizabeth Grosz and Derrida. It examines Grosz's concept of the untimely as it is developed in relation to Nietzsche and evolutionary theory. It the follows an argument about the similarity of Derrida's early writings on the future anterior and his later writings about the messianic arrival, or a future that cannot be predicted. It follows an argument about Derrida's philosophy of time in the work of Joanna Hodge to show that the two conceptions of time, named by Hodge as the genetic and the structural, are either secret sharers, or aspects of the same structure. The chapter concludes with some reasons to doubt that the notions of the untimely and the messianic can be invoked on behalf of any specific political programme.
Clock synchronization for packet networks using a weighted least‐squares error filtering technique and enabling circuit emulation service (2006)

Abstract Circuit emulation service (CES) allows time‐division multiplexing (TDM) services (T1/E1 and T3/E3 circuits) to be transparently extended across a packet network. With circuit emulation over IP, for instance, TDM data received from an external device at the edge of an IP network is converted to IP packets, sent through the IP network, passed out of the IP network to its destination, and reassembled into TDM bit stream. Clock synchronization is very important for CES. This paper presents a clock synchronization scheme based on a double exponential filtering technique and a linear process model. The linear process model is used to describe the behaviour of clock synchronization errors between a transmitter and a receiver. In the clock synchronization scheme, the transmitter periodically sends explicit time indications or timestamps to a receiver to enable the receiver to synchronize its local clock to the transmitter's clock. A phase‐locked loop (PLL) at the receiver processes the transmitted timestamps to generate timing signal for the receiver. The PLL has a simple implementation and provides both fast responsiveness (i.e. fast acquisition of transmitter frequency at a receiver) and significant jitter reduction in the locked state. Copyright © 2006 John Wiley &amp; Sons, Ltd.
Knowledge Representation and Ontology Mapping Methods for Product Data in Engineering Applications (2010)

This paper presents a semantic approach that uses ontologies to share knowledge related to product data in CAD/CAE applications and for integrating the design evaluation information that these applications individually provide. Our overall approach is the ontology-based adaptive design evaluation, also coined as OADE. This paper reports a piece of our ongoing work in the area of knowledge representation and ontology mapping methods. Here we design ontologies for representing product design and analysis, instantiate a source ontology with the product data, create formal ontology mapping methods, and then apply these methods to transfer the product data from the source ontology to the target one. A prototype implementation has been created using technologies such as OWL (representation language), JENA (ontology API), and PROTÉGÉ (ontology editor) to demonstrate the approach for integrating product design and assembly simulation analysis applications. This work is significant because heuristic methods based on geometry attributes, composition, and inheritance for determining mapped concepts in engineering ontologies is still very new, and not much work has been done in this area. This work will lead to the ability to create, share, and exchange knowledge for solving design evaluation challenges involving multiple applications and viewpoints.
Monodentate Chiral Ferrocenyl Ligands (2009)

This chapter contains sections titled: Introduction Nickel-Catalyzed Asymmetric Reductive Coupling Reactions Copper(I)-Catalyzed Asymmetric Allylic Alkylation Reactions Asymmetric Suzuki–Miyaura Reactions Addition of Organoaluminum to Aldehydes and Enones Asymmetric Nucleophilic Catalysis Conclusion and Perspectives References
A Thymine-PNA Monomer as New Isocyanide Component in the Ugi Reaction: A Direct Entry to PNA Dimers (2004)

A new PNA monomer was synthesized for use as the ­isocyanide component in a Ugi condensation in order to produce peptide nucleic acid (PNA) dimers also labelled with Cr(CO)3.
Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide (2020)

<i>Pseudomonas aeruginosa</i> is an ubiquitous gram-negative opportunistic human pathogen which is not considered part of the human commensal gut microbiota. However, depletion of the intestinal microbiota (Dysbiosis) following antibiotic treatment facilitates the colonization of the intestinal tract by Multidrug-Resistant <i>P. aeruginosa</i>. One possible strategy is based on the use of functional foods with prebiotic activity. The bifidogenic effect of the prebiotic inulin and its hydrolyzed form (fructooligosaccharide: FOS) is well established since they promote the growth of specific beneficial (probiotic) gut bacteria such as bifidobacteria. Previous studies of the opportunistic nosocomial pathogen <i>Pseudomonas aeruginosa</i> PAO1 have shown that inulin and to a greater extent FOS reduce growth and biofilm formation, which was found to be due to a decrease in motility and exotoxin secretion. However, the transcriptional basis for these phenotypic alterations remains unclear. To address this question we conducted RNA-sequence analysis. Changes in the transcript level induced by inulin and FOS were similar, but a set of transcript levels were increased in response to inulin and reduced in the presence of FOS. In the presence of inulin or FOS, 260 and 217 transcript levels, respectively, were altered compared to the control to which no polysaccharide was added. Importantly, changes in transcript levels of 57 and 83 genes were found to be specific for either inulin or FOS, respectively, indicating that both compounds trigger different changes. Gene pathway analyses of differentially expressed genes (DEG) revealed a specific FOS-mediated reduction in transcript levels of genes that participate in several canonical pathways involved in metabolism and growth, motility, biofilm formation, β-lactamase resistance, and in the modulation of type III and VI secretion systems; results that have been partially verified by real time quantitative PCR measurements. Moreover, we have identified a genomic island formed by a cluster of 15 genes, encoding uncharacterized proteins, which were repressed in the presence of FOS. The analysis of isogenic mutants has shown that genes of this genomic island encode proteins involved in growth, biofilm formation and motility. These results indicate that FOS selectively modulates bacterial pathogenicity by interfering with different signaling pathways.
Second-order TDTL with initialization process (2012)

This paper proposes an improved time delay digital tanlock loop (TDTL) system in which a feedforward loop is used to initialize the loop filter memory so as to enhance the acquisition speed of the system. The feedforward loop is used to estimate the value of the steady-state frequency of the input signal which is subsequently loaded into the memory of the loop filter. The system was simulated and tested using Simulink/Matalb using frequency step and FSK modulation. Further, the system was implemented using an FPGA and testing results indicate an ample improvement in the acquisition speed over the original TDTL system.
A Case Study on Improving Capacity Delivery of Battery Packs via Reconfiguration (2017)

Cell imbalance in large battery packs degrades their capacity delivery, especially for cells connected in series where the weakest cell dominates their overall capacity. In this article, we present a case study of exploiting system reconfigurations to mitigate the cell imbalance in battery packs. Specifically, instead of using all the cells in a battery pack to support the load, selectively skipping cells to be discharged may actually enhance the pack’s capacity delivery. Based on this observation, we propose CSR, a Cell Skipping-assisted Reconfiguration algorithm that identifies the system configuration with (near)-optimal capacity delivery. We evaluate CSR using large-scale emulation based on empirically collected discharge traces of 40 lithium-ion cells. CSR achieves close-to-optimal capacity delivery when the cell imbalance in the battery pack is low and improves the capacity delivery by about 20% and up to 1x in the case of a high imbalance.