gebhart/patrepeval huggingface dataset:
Society for Immunotherapy of Cancer consensus statement on immunotherapy for the treatment of renal cell carcinoma (2016)

Immunotherapy has produced durable clinical benefit in patients with metastatic renal cell cancer (RCC). In the past, patients treated with interferon-alpha (IFN) and interleukin-2 (IL-2) have achieved complete responses, many of which have lasted for multiple decades. More recently, a large number of new agents have been approved for RCC, several of which attack tumor angiogenesis by inhibiting vascular endothelial growth factors (VEGF) and VEGF receptors (VEGFR), as well as tumor metabolism, inhibiting the mammalian target of rapamycin (mTOR). Additionally, a new class of immunotherapy agents, immune checkpoint inhibitors, is emerging and will play a significant role in the treatment of patients with RCC. Therefore, the Society for Immunotherapy of Cancer (SITC) convened a Task Force, which met to consider the current role of approved immunotherapy agents in RCC, to provide guidance to practicing clinicians by developing consensus recommendations and to set the stage for future immunotherapeutic developments in RCC.
Arteriogenic therapy based on simultaneous delivery of VEGF-A and FGF4 genes improves the recovery from acute limb ischemia (2013)

Synergy between VEGF-A and FGF4 to produce stable and functional blood vessels may be considered a promising option in cardiovascular gene therapy.
Adenovirus-Mediated Transfer of Human Acid Maltase Gene Reduces Glycogen Accumulation in Skeletal Muscle of Japanese Quail with Acid Maltase Deficiency (1998)

Acid maltase deficiency (AMD) causes a lysosomal glycogenosis inherited as an autosomal recessive trait. The infantile type of AMD (Pompe disease) leads to early death due to severe dysfunction of cardiac and respiratory muscles and no effective therapy is available. Replication-defective adenovirus vectors offer a promising tool for in vivo gene delivery and gene therapy. We constructed a recombinant adenovirus containing the human acid maltase (AM) cDNA downstream of the CAG promoter, composed of modified chicken beta-actin promoter and CMV IE enhancer (AxCANAM). Japanese quail with AMD was used for this study as an animal model for human AMD. When cultured fibroblasts from AMD quail were infected with AxCANAM, AM activity in the cells increased in proportion to the multiplicity of infection (MOI). When AxCANAM (4.5 x 10(8) PFU) was injected into unilateral superficial pectoral muscle of AMD quail, PAS staining showed that glycogenosomes disappeared and stainability of acid phosphatase was reduced in the injected area as compared with the contralateral muscle of the same birds. Biochemically, AM activity increased and glycogen content decreased in the injected muscle. Western blot analysis showed that AMD quail muscle injected with AxCANAM expressed human AM protein processed to active forms. These results suggest that the human AM cDNA transferred by an adenovirus vector was sufficiently expressed, leading to a marked reduction of the glycogen accumulation in the skeletal muscle of AMD quail.
VM-based Architecture for Network Monitoring and Analysis (2008)

A single physical machine provides multiple network monitoring and analysis services (e.g., IDS, QoS) which are installed on the same operating system. Isolation between services is weak and it is difficult to decide the optimum allocation of resources for each service. This paper presents a virtual-machine-based architecture for network traffic monitoring and analysis. Through virtualization, a machine under the architecture logically is divided into one host, one virtual machine monitor (VMM) and multiple virtual machines. The host is responsible for capturing network traffic, and multiplexing it to multiple virtual machines. Each virtual machine hosts a service. VMM performs functions such as isolating services and resolving the conflict between services. Compared with Xen, KVM is chosen as a VMM to implement the architecture. Some network optimizations of the architecture are given. Our evaluation results show that these optimizations can multiplex network traffic received by the host to all services, and improve the data receive performance of services by 67% compared to the architecture in which the traffic is directly transferred to virtual machines, instead of the host, and optimized methods are not adopted.
Language models for contextual error detection and correction (2009)

The problem of identifying and correcting confusibles, i.e. context-sensitive spelling errors, in text is typically tackled using specifically trained machine learning classifiers. For each different set of confusibles, a specific classifier is trained and tuned.
Supported atom transfer radical polymerization of methyl methacrylate mediated by CuBr-tetraethyldiethylenetriamine grafted onto silica gel (2001)

Silica-gel particles grafted with tetraethyldiethylenetriamine were synthesized as support for CuBr for the heterogeneous atom transfer radical polymerization of methyl methacrylate (MMA). The immobilized CuBr mediated a living polymerization of MMA, demonstrated by an increase in molecular weight with conversion and low polydispersity. An excessive amount of catalyst (typically, CuBr/initiator = 1.5) was required to achieve a living process because of the limited mobility of the supported catalyst. The silica-gel concentration had a strong effect on the polymerization. The recycled catalyst still mediated a living process but showed a reduced catalytic activity due to the presence of Cu(II). After being regenerated by a reaction with Cu(0), the catalyst regained its activity. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 1051–1059, 2001
Molecular genetic aspects of the citric acid cycle of Escherichia coli. (1987)

The genes encoding all of the citric acid cycle enzymes of Escherichia coli have been cloned and much has been learned about the structure, function and expression of these enzymes from the nucleotide sequences, the mRNA transcripts and site-directed mutagenesis of the corresponding genes. Special features of the expression of the aerobic cycle, and its anaerobic transformation into a branched pathway in a facultative anaerobe, are considered. Aspects of the structure-function relationships of succinate dehydrogenase, succinyl-CoA synthetase, fumarase and related enzymes, and the 2-oxo acid dehydrogenase complexes are reviewed.
Transform Coding Techniques in HEVC (2013)

High Efficiency Video Coding (HEVC) is the most recent jointly developed video coding standard of ITU-T Visual Coding Experts Group (VCEG) and ISO/IEC Moving Picture Experts Group (MPEG). Although its basic architecture is built along the conventional hybrid block-based approach of combining prediction with transform coding, HEVC includes a number of coding tools with greatly enhanced coding-efficiency capabilities relative to those of prior video coding standards. Among these tools are new transform coding techniques that include the support for dyadically increasing transform block sizes ranging from 4 × 4 to 32 × 32, the partitioning of residual blocks into variable block-size transforms by using a quadtree-based partitioning dubbed as residual quadtree (RQT) as well as some properly designed entropy coding techniques for quantized transform coefficients of variable transform block sizes. In this paper, we describe these HEVC techniques for transform coding with a particular focus on the RQT structure and the entropy coding stage and demonstrate their benefit in terms of improved coding efficiency by experimental results.
Coordinate Regulation of the Expression of the Fatty Acid Transport Protein and Acyl-CoA Synthetase Genes by PPARα and PPARγ Activators (1997)

Intracellular fatty acid (FA) concentrations are in part determined by a regulated import/export system that is controlled by two key proteins, i.e. fatty acid transport protein (FATP) and acyl-CoA synthetase (ACS), which respectively facilitate the transport of FAs across the cell membrane and their esterification to prevent their efflux. The aim of this investigation was to analyze the expression pattern of FATP and ACS and to determine whether their expression was altered by agents that affect FA metabolism through the activation of peroxisome proliferator-activated receptors (PPAR) such as the fibrates and thiazolidinediones. FATP mRNA was ubiquitously expressed, with highest levels being detected in adipose tissue, heart, brain, and testis. Fibrate treatment, which is known to preferentially activate PPARalpha, induced FATP mRNA levels in rat liver and intestine and induced ACS mRNA levels in liver and kidney. The antidiabetic thiazolidinedione BRL 49653, which is a high-affinity ligand for the adipocyte-specific PPARgamma form, caused a small induction of muscle but a robust induction of adipose tissue FATP mRNA levels. BRL 49653 did not affect liver FATP and had a tendency to decrease heart FATP mRNA levels. ACS mRNA levels in general showed a similar pattern after BRL 49653 as FATP except for the muscle where ACS mRNA was induced. This regulation of FATP and ACS expression by PPAR activators was shown to be at the transcriptional level and could also be reproduced in vitro in cell culture systems. In the hepatocyte cell lines AML-12 or Fa 32, fenofibric acid, but not BRL 49653, induced FATP and ACS mRNA levels, whereas in the 3T3-L1 preadipocyte cell line, the PPARgamma ligand induced FATP and ACS mRNA levels quicker than fenofibric acid. Inducibility of ACS and FATP mRNA by PPARalpha or gamma activators correlated with the tissue-specific distribution of the respective PPARs and was furthermore associated with a concomitant increase in FA uptake. Most interestingly, thiazolidinedione antidiabetic agents seem to favor adipocyte-specific FA uptake relative to muscle, perhaps underlying in part the beneficial effects of these agents on insulin-mediated glucose disposal.
Flue Gas Desulfurization: The State of the Art (2001)

Coal-fired electricity-generating plants may use SO2 scrubbers to meet the requirements of Phase II of the Acid Rain SO2 Reduction Program. Additionally, the use of scrubbers can result in reduction of Hg and other emissions from combustion sources. It is timely, therefore, to examine the current status of SO2 scrubbing technologies. This paper presents a comprehensive review of the state of the art in flue gas desulfurization (FGD) technologies for coal-fired boilers. Data on worldwide FGD applications reveal that wet FGD technologies, and specifically wet limestone FGD, have been predominantly selected over other FGD technologies. However, lime spray drying (LSD) is being used at the majority of the plants employing dry FGD technologies. Additional review of the U.S. FGD technology applications that began operation in 1991 through 1995 reveals that FGD processes of choice recently in the United States have been wet limestone FGD, magnesium-enhanced lime (MEL), and LSD. Further, of the wet limestone processes, limestone forced oxidation (LSFO) has been used most often in recent applications. The SO2 removal performance of scrubbers has been reviewed. Data reflect that most wet limestone and LSD installations appear to be capable of approximately 90% SO2 removal. Advanced, state-of-the-art wet scrubbers can provide SO2 removal in excess of 95%. Costs associated with state-of-the-art applications of LSFO, MEL, and LSD technologies have been analyzed with appropriate cost models. Analyses indicate that the capital cost of an LSD system is lower than those of same capacity LSFO and MEL systems, reflective of the relatively less complex hardware used in LSD. Analyses also reflect that, based on total annualized cost and SO2 removal requirements: (1) plants up to approximately 250 MWe in size and firing low- to medium-sulfur coals (i.e., coals with a sulfur content of 2% or lower) may use LSD; and (2) plants larger than 250 MWe and firing medium- to high-sulfur coals (i.e., coals with a sulfur content of 2% or higher) may use either LSFO or MEL.
The Mobile Genetic Element "Alu" in the Human Genome (1996)

Genetic material has been traditionally envisioned as relatively static with the exception of occasional, often deleterious mutations. The sequence DNA-to-RNA-to-protein represented for many years the central dogma relating gene structure and function. Recently, the field of molecular genetics has provided revolutionary information on the dynamic role of repetitive elements in the function of the genetic material and the evolution of humans and other organisms. Alu sequences represent the largest family of short interspersed repetitive elements (SINEs) in humans, being present in an excess of 500,000 copies per haploid genome. Alu elements, as well as the other repetitive elements, were once considered to be useless. Today, the biology of Alu transposable elements is being widely examined in order to determine the molecular basis of a growing number of identified diseases and to provide new directions in genome mapping and biomedical research. 66 refs., 5 figs.
Functional PET scanning in the assessment of cerebral arteriovenous malformations (1990)

A case is presented which represents the first instance of the use of functional positron emission tomography (PET) scanning to precisely localize a structural brain lesion to the precentral gyrus, and the first validation of functional PET scanning by intraoperative cortical mapping. The lesion was a 3-cm arteriovenous malformation (AVM) that had produced a generalized seizure in an otherwise asymptomatic young woman. A first, resting H2(15)O PET scan identified the AVM. A second PET scan, performed during vibrotactile stimulation of the contralateral hand, identified the somatosensory area of the hand region and localized the AVM to that part of the precentral gyrus immediately in front of it. This relationship and localization were confirmed by cortical mapping at the time of craniotomy under local anesthesia. Functional PET scanning may prove to be useful to localize cortical lesions precisely and to help in determining preoperatively the best form of treatment for lesions, especially AVM's, in functionally important cortex.
Tissue Engineering of Bladder Using Vascular Endothelial Growth Factor Gene-Modified Endothelial Progenitor Cells (2011)

VEGF-modified EPCs significantly enhanced neovascularization, compared with BAMG alone. These results indicate that EPCs, combined with VEGF gene therapy, may be a suitable approach for increasing blood supply in the tissue engineering of bladders. Thus, a useful strategy to achieve a tissue-engineered bladder is indicated.
INVARIANT OBJECT RECOGNITION BASED ON A NEURAL NETWORK OF CASCADED RCE NETS (1993)

A neural network of cascaded Restricted Coulomb Energy (RCE) nets is constructed for the recognition of two-dimensional objects. A number of RCE nets are cascaded together to form a classifier where the overlapping decision regions are progressively resolved by a set of cascaded networks. Similarities among objects which have complex decision boundaries in the feature space are resolved by this multi-net approach. The generalization ability of an RCE net recognition system, referring to the ability of the system to correctly recognize a new pattern even when the number of learning exemplars is small, is increased by the proposed coarse-to-fine learning strategy. A feature extraction technique is used to map the geometrical shape information of an object into an ordered feature vector of fixed length. This feature vector is then used as an input to the neural network. The feature vector is invariant to object changes such as positional shift, rotation, scaling, illumination variance, variation of camera setup, perspective distortion, and noise distortion. Experimental results for recognition of several objects are also presented. A correct recognition rate of 100% was achieved for both the training and the testing input patterns.
A New Remote Subsite in Ribonuclease A (1998)

The interaction between bovine pancreatic ribonuclease A (RNase A) and its RNA substrate extends beyond the scissile bond. Enzymic subsites interact with the bases and the phosphoryl groups of a bound substrate. We evaluated the four cationic residues closest to known subsites for their abilities to interact with a bound nucleic acid. Lys-37, Arg-39, Arg-85, and Lys-104 were replaced individually by an alanine residue, and the resulting enzymes were assayed as catalysts of poly(cytidylic acid) (poly(C)) cleavage. The values of Km and kcat/Km for poly(C) cleavage were affected only by replacing Arg-85. Moreover, the contribution of Arg-85 to the binding of the ground state and the transition state was uniform---Km increased by 15-fold and kcat/Km decreased by 10-fold. The contribution of Arg-85 to binding was also apparent in the values of Kd for complexes with oligonucleotides of different length. This contribution was dependent on salt concentration, as expected from a coulombic interaction between a cationic side chain and an anionic phosphoryl group. Together, these data indicate that Arg-85 interacts with a particular phosphoryl group of a bound nucleic acid. We propose that Arg-85 comprises a new distal subsite in RNase A---the P(-1) subsite.
Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints (2019)

Prophylactic interventions such as vaccine allocation are some of the most effective public health policy planning tools. The supply of vaccines, however, is limited and an important challenge is to optimally allocate the vaccines to minimize epidemic impact. This resource allocation question (which we refer to as VaccIntDesign) has multiple dimensions: when, where, to whom, etc. Most of the existing literature in this topic deals with the latter (to whom), proposing policies that prioritize individuals by age and disease risk. However, since seasonal influenza spread has a typical spatial trend, and due to the temporal constraints enforced by the availability schedule, the when and where problems become equally, if not more, relevant. In this paper, we study the VaccIntDesign problem in the context of seasonal influenza spread in the United States. We develop a national scale metapopulation model for influenza that integrates both short and long distance human mobility, along with realistic data on vaccine uptake. We also design GreedyAlloc, a greedy algorithm for allocating the vaccine supply at the state level under temporal constraints and show that such a strategy improves over the current baseline of pro-rata allocation, and the improvement is more pronounced for higher vaccine efficacy and moderate flu season intensity. Further, the resulting strategy resembles a ring vaccination applied spatiallyacross the US.
Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS (2004)

Crystallographic efforts often fail to produce suitably diffracting protein crystals. Unstructured regions of proteins play an important role in this problem and considerable advantage can be gained in removing them. We have developed a number of enhancements to amide hydrogen/high-throughput and high-resolution deuterium exchange MS (DXMS) technology that allow rapid identification of unstructured regions in proteins. To demonstrate the utility of this approach for improving crystallization success, DXMS analysis was attempted on 24 Thermotoga maritima proteins with varying crystallization and diffraction characteristics. Data acquisition and analysis for 21 of these proteins was completed in 2 weeks and resulted in the localization and prediction of several unstructured regions within the proteins. When compared with those targets of known structure, the DXMS method correctly localized even small regions of disorder. DXMS analysis was then correlated with the propensity of such targets to crystallize and was further used to define truncations that improved crystallization. Truncations that were defined solely on DXMS analysis demonstrated greatly improved crystallization and have been used for structure determination. This approach represents a rapid and generalized method that can be applied to structural genomics or other targets in a high-throughput manner.
A symbolic-simulation approach to the timing verification of interacting FSMs (2002)

A timing verifier that scales to verify complex sequential circuits, modeled in terms of interacting FSMs, while rejecting false sequential and combinational paths has, so far, not been developed. We present an algorithm for this purpose. The inherently modular nature of interactions among FSMs, allow a highly efficient symbolic simulation verification methodology. Experimental results illustrate this methodology's ability to scale, while providing accurate timing verification results.
Potential therapeutic applications of PHA-L4, the mitogenic isolectin of phytohemagglutinin. (1990)

Assuming that the attributes of the mitogenic-leukoaggglutinating (L4) isolectin of phytohemagglutinin as a proposed ideal biologic response modifier can be confirmed, it could prove to be a highly versatile agent with broad therapeutic potential for several areas of management including cancer and cancer surgery adjuvant, critical infections (including that with the human immunodeficiency viruses), vaccine adjuvant, allograft transplantations, aplastic anemias, and extensive burns. The isolectin is predictably more likely to be effective as an adjuvant or adjunctive agent than as an induction agent. Initial evaluation in dogs would serve the double purpose of establishing a presumptive key role in veterinary medicine and expediting the development of its use in humans.
Digital Halftoning of Images (1982)

Most printers and some display devices are bilevel (black or white) and therefore not capable of reproducing continuous tone pictures. Digital halftoning algorithms transform digital gray scale images into bilevel ones which give the appearance of containing various shades of gray. A halftoning algorithm is presented in which novel concepts are combined resulting in an output image in which moiré patterns are suppressed and, at the same time, the edges are enhanced. Various other artifacts associated with the halftoning process, such as contouring due to coarse quantization or to textural changes, are also absent from the output images in the proposed scheme. The algorithm separates the image into many small clusters which are processed independently and, therefore, it is capable of parallel implementation.
LSI signal processor development for communications equipment (2005)

A single chip, versatile digital signal processor has been developed, which enables compact and low cost telecommunications equipment realization. The processor architecture has been optimized for real time voiceband signal processing by adopting efficient micro-program control and by integrating a 16 × 16 bit parallel multiplier on a single chip. The processor is fabricated with N-channel MOS technology, and operates at a clock speed up to more than 8 MHz. Any instruction, including multiplication, can be performed within a 250 nanosecond interval. The paper also describes applications to actual voiceband communications equipment to prove the processor effectiveness.
Synthesis of urea oligomers and their antibacterial activity (2005)

Facially amphiphilic urea oligomers were successfully prepared in a one-pot reaction by carbonyl diimidazole (CDI) coupling and showed greater antibacterial activity against both Gram-negative Escherichia coli and Gram-positive Bacillus subtilis than MSI-78.