gebhart/patrepeval huggingface dataset:
Applications of Polyhydroxyalkanoates (PHA) in Medicine and Pharmacy (2002)

Abstract Introduction Historical Outline PHA Preparation and Properties: A Primer Production Mechanical and Thermal Properties Sterilization of PHA Polymers Biocompatibility Natural Occurrence In vitro Cell Culture Testing In vivo Tissue Responses Biodistribution Bioabsorption In vitro Degradation In vivo Bioabsorption Applications Cardiovascular Dental and Maxillofacial Drug Delivery Prodrugs Nerve Repair Nutritional Uses Orthopedic Urology Wound Management Future Directions Patents
Electrochemical treatment of lung cancer (1997)

A pilot study of electrochemical treatment (ECT) as a therapy for 386 patients with nonsmall cell lung cancer was undertaken. There were 103 stage II cases, 89 stage IIIa cases, 122 stage IIIb cases, and 72 stage IV cases. Two ECT methods were used: For peripherally located lung cancer, platinum electrodes were inserted transcutaneously into the tumor under x-ray or CT guidance. For central type lung cancer or for those inoperable during thoracotomy, electrodes were inserted intraoperatively directly into the cancer. Voltage was 6-8 V, current was 40-100 mA, and electric charge was 100 coulombs per cm of tumor diameter. The number of electrodes was determined from the size of cancer mass, because the diameter of effective area around each electrode is approximately 3 cm. The short-term (6 months after ECT) results of the 386 lung cancer cases were: complete response (CR), 25.6% (99/386); partial response (PR), 46.4% (179/386); no change (NC), 15.3% (59/386); and progressive disease (PD), 12.7% (49/386). The total effective rate (CR + PR) was 72% (278/386). The 1, 3, and 5 year overall survival rates were 86.3% (333/386), 58.8% (227/386), and 29.5% (114/386), respectively. The main complication was traumatic pneumothorax, with an incidence rate of 14.8% (57/386). These clinical results show that ECT is simple, safe, effective, and minimally traumatic. ECT provides an alternative method for treating lung cancers that are conventionally inoperable, that are not responsive to chemotherapy or radiotherapy, or that cannot be resected after thoracotomy. Long-term survival rates suggest that ECT warrants further investigation.
Toward the estimation of the absolute quality of individual protein structure models (2010)

The Z-score calculation has been integrated in the QMEAN server available at: http://swissmodel.expasy.org/qmean.
Increasing fatty acid production in E. coli by simulating the lipid accumulation of oleaginous microorganisms (2010)

Unlike many oleaginous microorganisms, E. coli only maintains a small amount of natural lipids in cells, impeding its utility to overproduce fatty acids. In this study, acetyl-CoA carboxylase (ACC) from Acinetobacter calcoaceticus was expressed in E. coli to redirect the carbon flux to the generation of malonyl-CoA, which resulted in a threefold increase in intracellular lipids. Moreover, providing a high level of NADPH by overexpressing malic enzyme and adding malate to the culture medium resulted in a fourfold increase in intracellular lipids (about 197.74 mg/g). Co-expression of ACC and malic enzyme resulted in 284.56 mg/g intracellular lipids, a 5.6-fold increase compared to the wild-type strain. This study provides some attractive strategies for increasing lipid production in E. coli by simulating the lipid accumulation of oleaginous microorganisms, which could aid the development of a prokaryotic fatty acid producer.
Ionic Conductivity, Capacitance, and Viscoelastic Properties of Block Copolymer-Based Ion Gels (2011)

The effects of composition, temperature, and polymer identity on the electrical and viscoelastic properties of block copolymer-based ion gels were investigated. Ion gels were prepared through the self-assembly of poly(styrene-b-ethylene oxide-b-styrene) (SOS) and poly(styrene-b-methyl methacrylate-b-styrene) (SMS) triblock copolymers in a room-temperature ionic liquid, 1-ethyl-3-methylimidazolium bis(trifluoromethylsufonyl)imide ([EMI][TFSI]). The styrene end-blocks associate into micelles, whereas the ethylene oxide and methyl methacrylate midblocks are well-solvated by this ionic liquid. The properties of the ion gels were examined over the composition range of 10−50 wt % polymer and temperature range of 25−160 and 25−200 °C for the SOS- and SMS-based gels, respectively. The response of the ion gels to ac electric fields below 1 MHz can be represented by a resistor and constant phase element (CPE) series circuit, with a characteristic time corresponding to the establishment of stable electrical double layers (EDLs) at the gel/electrode interfaces. The ionic conductivity and specific capacitance were found to range from 3 × 10−5 to 3 × 10−2 S/cm and 0.3 to 10 μF/cm2, respectively. For 1 mm thick gels, the corresponding RC time constants ranged from 2 × 10−5 to 5 × 10−3 s. Notably, at high polymer concentrations, the ionic conductivity is much higher in SOS than SMS due to the higher glass transition of the methyl methacrylate block. Two relaxation modes have been observed in the ion gels under oscillatory mechanical shear. The faster mode corresponds to the relaxation of the midblocks in the ionic liquid, while the slow mode reflects motion of the end-blocks within their micellar cores. The plateau modulus of the gels was found to vary from 0.5 to 100 kPa over the measured composition and temperature ranges. While the ionic conductivity generally decreases as the modulus increases, it is possible to achieve conductivities greater than 0.01 S/cm with moduli above 10 kPa in the SOS system.
Rational Design of CH/π Interaction Sites in a Basic Resolving Agent (2004)

A novel synthetic basic resolving agent, cis-1-aminobenz[f]indan-2-ol (ABI), was rationally designed by introducing effective CH/pi interaction sites to cis-1-aminoindan-2-ol (AI), whose chiral recognition ability has been reported from our laboratory. ABI was applicable to a wide variety of racemic arylalkanoic acids and showed moderate to excellent chiral recognition ability, which was obviously higher than that of AI. The fundamental and important role of CH/pi interactions, such as tunable CH(sp(2))/pi and CH(sp(3))/pi interactions, in the chiral recognition by ABI was revealed by X-ray crystallographic study.
High flux beam source of thermal rare-gas metastable atoms (1980)

A high-flux beam source has been constructed for the production of helium, neon and argon metastable atoms. The source is a DC electric discharge maintained in an expanding gas. A metastable flux of 3.5*1014, and 7.2*1013 atoms s-1 sr-1 has been achieved with most probable energies of 66, 72 and 74 meV for the helium, neon and argon sources, respectively. Time-of-flight measurements showed the widths of the respective velocity distributions to be 45%, 27% and 27%.
Radiation-induced toxicities: the role of radioprotectants. (1998)

Ionizing radiation has been used to treat many malignancies since the turn of the century. Modern radiotherapeutic techniques have led to increased cure rates and improved local regional control, but the potentially severe and debilitating adverse effects of radiation therapy have not been fully eliminated. Managing radiation-induced toxicities often focuses on treating the symptoms as they manifest. However, preventing these complications is clearly more desirable. Radiation-induced toxicities may be ameliorated in several ways. Dose fractionation was one of the earliest methods recognized to decrease radiation-induced toxicities. Another early method was the use of physical shielding to reduce the area of exposure. Pharmacologic approaches to improving the therapeutic index of radiotherapy fall under two categories: radiosensitizers or radioprotectants. Radiosensitizers are compounds that enhance the sensitivity of tumors to the effects of radiation, but not normal tissue. Radioprotectants such as amifostine function by reducing the effects of radiation on normal cells while maintaining tumor sensitivity. Clinical trials have demonstrated that amifostine can reduce both acute and late radiation-induced toxicities. The development of amifostine has thus resulted in greater tumor control without sacrificing patient well-being. Further investigations are necessary to ensure that patients receive the optimum therapeutic benefit.
Partitioning Grammars and Composing Parsers (1995)

GLR parsers have been criticized by various authors for their potentially large sizes. Other parsers also have individual weaknesses and strengths. Our heterogeneous parsing algorithm is based on GLR parsers that handle the size and other problems by partitioning the grammar during compiling and assembling the partitioned sub-grammars during parsing. We discuss different parsers for different grammars and present some intuitive considerations for the partitioning. 1 Introduction Various authors [9, 18, 19, 11] have criticized the size of (G)LR parsers as being too big for programming languages and natural languages. In addition, there exist context-free grammars G whose collection of LR(0) items is exponentially larger than jGj. Other parsers also have their own weaknesses and strengths. A number of attempts have been made to counter these problems[9, 12], and in this paper we present a new approach. The main idea is to look for certain partitions of a grammar. Instead of having compi...
Uptake and intracellular transport of the connective tissue growth factor: a potential mode of action (2001)

Connective tissue growth factor (CTGF) is a secreted cysteine-rich protein now considered as an important effector molecule in both physiological and pathological processes. An increasing amount of evidence indicates that CTGF plays a key role in the pathogenesis of different fibrotic disorders including diabetic nephropathy. However, the molecular mechanisms by which CTGF exerts its effects are not known. Here we provide the first evidence for the existence of an intracellular transport pathway for the growth factor in human mesangial cells. Our results demonstrate that CTGF is internalized from the cell surface in endosomes and accumulates in a juxtanuclear organelle from which the growth factor is then translocated into the cytosol. In the cytosol CTGF is phosphorylated by protein kinase C and PMA treatment can enhance this phosphorylation. Phosphorylated CTGF may have an important role in the cytosol, but it is also translocated into the nucleus where it may directly affect transcription.
Interferon-gamma prevents graft-versus-host disease after allogeneic bone marrow transplantation in mice. (1993)

Lethally irradiated C3H/Law mice were injected (i.v.) with C57BL/Rij allogeneic bone marrow cells to induce a delayed type graft-vs-host disease (GVHD). Signs of GVHD first became apparent in the third week after transplantation. The disease resulted in a mortality rate of 70% at 80 days. Treatment with IFN-gamma twice weekly, for a period of 6 wk, starting at the time of bone marrow transplantation (BMT), completely prevented overt GVHD, as evidenced by a lack of diarrhea and no mortality during the follow-up period of 100 days after BMT. Also, the histologic GVHD lesions in the gastrointestinal tract were almost completely abrogated by the IFN-gamma treatment. All long term survivors were proven to be chimeras. During the induction phase of GVHD, the number of Con A-induced, IFN-gamma-producing cells in the spleen was significantly reduced in the IFN-gamma-treated mice as compared with control mice. These results suggest that the normally enhanced production of endogenous IFN-gamma in the spleen at the time of hematopoietic reconstitution after BMT is down-regulated by exogenously administered IFN-gamma. This cytokine-mediated strategy to prevent GVHD might be an alternative to the current strategy of in vitro depletion of T cells for allogeneic BMT.
Three baculovirus genes involved in late and very late gene expression: ie-1, ie-n, and lef-2 (1993)

We developed a method to identify baculovirus genes required for late and very late gene expression that is based on subtraction of clones from an Autographa californica nuclear polyhedrosis virus genomic library which is able to trans activate promoters of reporter plasmids in transient expression assays. Using this assay, we found that three genes located between 83.7 and 7.5 map units of the Autographa californica nuclear polyhedrosis virus genome were involved in expression from the late capsid protein (vp39) and very late polyhedrin (polh) gene promoters. Two of these genes, ie-1 and ie-n, trans regulate early genes in transient expression assays. Although ie-1 was necessary and sufficient for expression from the early promoter in our assay, it was necessary but not sufficient for expression from the vp39 and polh promoters. The presence of ie-n increased expression from the early, late, and very late classes of promoters tested. However, a third gene identified in this region was specifically required for expression from the vp39 and polh promoters. This gene, a previously sequenced 630-nucleotide open reading frame, was renamed lef-2 for late expression factor 2. We also found that other genes in the region between 83.7 and 7.5 map units were not required for expression from the promoters used in this assay, although we did not eliminate the possibility that they subtly modify expression. These genes include pe-38 and me53, early genes with zinc finger-like motifs, and the upstream exon of ie-0, which specifies an alternate form of IE-1.
Fast Recurrent Fully Convolutional Networks for Direct Perception in Autonomous Driving (2017)

Deep convolutional neural networks (CNNs) have been shown to perform extremely well at a variety of tasks including subtasks of autonomous driving such as image segmentation and object classification. However, networks designed for these tasks typically require vast quantities of training data and long training periods to converge. We investigate the design rationale behind end-to-end driving network designs by proposing and comparing three small and computationally inexpensive deep end-to-end neural network models that generate driving control signals directly from input images. In contrast to prior work that segments the autonomous driving task, our models take on a novel approach to the autonomous driving problem by utilizing deep and thin Fully Convolutional Nets (FCNs) with recurrent neural nets and low parameter counts to tackle a complex end-to-end regression task predicting both steering and acceleration commands. In addition, we include layers optimized for classification to allow the networks to implicitly learn image semantics. We show that the resulting networks use 3x fewer parameters than the most recent comparable end-to-end driving network and 500x fewer parameters than the AlexNet variations and converge both faster and to lower losses while maintaining robustness against overfitting.
High-Temperature Microfluidic Synthesis of CdSe Nanocrystals in Nanoliter Droplets (2005)

The high-temperature synthesis of CdSe nanocrystals in nanoliter-volume droplets flowing in a perfluorinated carrier fluid through a microfabricated reactor is presented. A flow-focusing nanojet structure with a step increase in channel height reproducibly generated octadecene droplets in Fomblin Y 06/6 perfluorinated polyether at capillary numbers up to 0.81 and with a droplet:carrier fluid viscosity ratio of 0.035. Cadmium and selenium precursors flowing in octadecene droplets through a high-temperature (240-300 degrees C) glass microreactor produced high-quality CdSe nanocrystals, as verified by optical spectroscopy and transmission electron microscopy. Isolating the reaction solution in droplets prevented particle deposition and hydrodynamic dispersion, allowing the reproducible synthesis of nanocrystals at three different temperatures and four different residence times in the span of 4 h. Our synthesis of a wide range of nanocrystals at high temperatures, high capillary numbers, and low viscosity ratio illustrates the general utility of droplet-based microfluidic reactors to encapsulate nanoliter volumes of organic or aqueous solutions and to precisely control chemical or biochemical reactions.
Inhibition of tumor necrosis factor ?-induced prostaglandin E2 production by the antiinflammatory cytokines interleukin-4, interleukin-10, and interleukin-13 in osteoarthritic synovial fibroblasts: Distinct targeting in the signaling pathways (1999)

The results indicate that these antiinflammatory cytokines reversed the TNFalpha-induced release of PGE2 by OA synovial fibroblasts, by acting at various levels of the TNFa-dependent signaling cascade. These data shed new light on the mechanisms by which these cytokines reduce inflammatory processes.
Minute carcinoma of the pancreas measuring 1 cm or less in diameter--collective review of Japanese case reports. (1999)

These data lead us to conclude that an elevation of serum pancreatic enzyme levels, glucose intolerance, and duct dilation alone depicted by US/CT should not be overlooked. ERP should be more widely applied to such patients, instead of persisting in delineating the tumor mass by US/CT or follow-up by tumor marker.
Mapping of Effector Binding Sites of Transducin α-Subunit Using Gαt/Gαil Chimeras (1996)

The G protein transducin has been an often-used model for biochemical, structural, and mechanistic studies of G protein function. Experimental studies have been limited, however, by the inability to express quantities of mutants in heterologous systems with ease. In this study we have made a series of G alpha t/G alpha i1 chimeras differing at as few as 11 positions from native G alpha t. Ten chimeras are properly folded, contain GDP, can assume an A1F4(-)-induced activated conformation, and interact with beta gamma t and light-activated rhodopsin. They differ dramatically in their affinity for GDP, from Gi-like (initial rates 225 mumol/mol s) to Gt-like (initial rates 4.9 mumol/mol s). We have used these chimeras to define contact sites on G alpha t with the effector enzyme cGMP phosphodiesterase. G alpha t GTP but not G alpha t GDP activates it by removing the phosphodiesterase (PDE) gamma inhibitory subunit. In solution, G alpha t GTP interacts with PDE gamma (Kd 12 nM), while G alpha t GDP binds PDE gamma more weakly (Kd 0.88 microM). The interaction of G alpha i GDP with PDE gamma is undetectable, but G alpha i GDP-A1F4- interacts weakly with PDE gamma (Kd 2.4 microM). Using defined G alpha t/G alpha i chimeras, we have individuated the regions on G alpha t most important for interaction with PDE gamma in the basal and activated states. The G alpha t sequence encompassing alpha helix 3 and the alpha 3/beta 5 loop contributes most binding energy to interaction with PDE gamma. Another composite P gamma interaction site is the conserved switch, through which the GTP-bound G alpha t as well as G alpha i1 interact with P gamma. Competition studies between PDE gamma and truncated regions of PDE gamma provide evidence for the point-to-point interactions between the two proteins. The amino-terminal 1-45 segment containing the central polycationic region binds to G alpha t's alpha 3 helix and alpha 3/beta 5 loop, while the COOH-terminal region of P gamma, 63-87, binds in concert to the conserved switch regions. The first interaction provides specific interaction with both the GDP- and GTP-liganded G alpha t, while the second one is conserved between G alpha t and G alpha i1 and dependent on the activated conformation.
The Attenuation, with Loss of Oncogenicity, of the Herpes-type Virus of Marek's Disease (Strain hprs-16) on Passage in Cell Culture (1969)

Summary The herpes-type virus of Marek’s disease showed a gradual increase in the rate of development of cytopathic effect on passage in cell culture. By the 60th passage macroscopic plaques were produced after 6 days under fluid overlay, but no cell-free virus could be recovered after filtration of culture medium. A loss of pathogenicity for chicks was noticed in the virus after 33 passages in cell culture. Furthermore, an antigenic change occurred between the 20th and 30th passage which was characterized by the loss of an antigen which could normally be found in the supernatant medium of cultures infected with low passage virus. The possible origin of the attenuated virus is discussed.
The Residual-Excited Linear Prediction Vocoder with Transmission Rate Below 9.6 kbits/s (1975)

In this paper we present a new vocoder called the residual-excited linear prediction (RELP) vocoder. The concept of the RELP vocoder combines the advantages of linear predictive coding (LPC) and voice-excited vocoding. In the RELP system, vocal tract modeling is done by the LPC technique, and the LPC residual signal is used as the excitation signal. After low-pass filtering the residual signal is coded by adaptive delta modulation and is spectrally flattened before being fed in the LPC synthesizer. The range of the transmission rate is typically between 6 and 9.6 kbits/s; the synthetic speech in this range is quite good. As the transmission rate is lowered, the synthetic speech quality degrades very gradually. Since no pitch extraction is required, the vocoder is robust in any operating environment.
Spectroscopy of Molecular Monolayers by Resonant Second-Harmonic Generation (1982)

Spectra of the ${S}_{0}\ensuremath{\rightarrow}{S}_{2}$ electronic transition of rhodamine dyes adsorbed at submonolayer coverages on a fused silica substrate have been obtained by resonant second-harmonic generation. Polarization dependences of the second-harmonic signal have been studied and are used in the construction of a model for the orientation of the adsorbates. A value for the molecular second-order nonlinear polarizability at resonance is deduced.
Improving the start-up behavior of a congestion control scheme for TCP (1996)

Based on experiments conducted in a network simulator and over real networks, this paper proposes changes to the congestion control scheme in current TCP implementations to improve its behavior during the start-up period of a TCP connection.The scheme, which includes Slow-start, Fast Retransmit, and Fast Recovery algorithms, uses acknowledgments from a receiver to dynamically calculate reasonable operating values for a sender's TCP parameters governing when and how much a sender can pump into the network. During the start-up period, because a TCP sender starts with default parameters, it often ends up sending too many packets and too fast, leading to multiple losses of packets from the same window. This paper shows that recovery from losses during this start-up period is often unnecessarily time-consuming.In particular, using the current Fast Retransmit algorithm, when multiple packets in the same window are lost, only one of the packet losses may be recovered by each Fast Retransmit; the rest are often recovered by Slow-start after a usually lengthy retransmission timeout. Thus, this paper proposes changes to the Fast Retransmit algorithm so that it can quickly recover from multiple packet losses without waiting unnecessarily for the timeout. These changes, tested in the simulator and on the real networks, show significant performance improvements, especially for short TCP transfers. The paper also proposes other changes to help minimize the number of packets lost during the start-up period.