gebhart/patrepeval huggingface dataset:
Topical Anesthetic EMLA for Postoperative Wound Pain in Stereotactic Gamma Knife Radiosurgery: A Perspective, Randomized, Placebo-Controlled Study (2011)

EMLA when applied 60 min before frame removal has an anesthetic effect of reducing the postoperative wound pain in patients who undergo GKRS.
Synthesizing a predatory search strategy for VLSI layouts (1999)

When searching for prey, many predator species exhibit a remarkable behavior: after prey capture, the predators promptly engage in "area-restricted search", probing for consecutive captures nearby. Biologists have been surprised with the efficiency and adaptability of this search strategy to a great number of habitats and prey distributions. We propose to synthesize a similar search strategy for the massively multimodal problems of combinatorial optimization. The predatory search strategy restricts the search to a small area after each new improving solution is found. Subsequent improvements are often found during area-restricted search. Results of this approach to gate matrix layout, an important problem arising in very large scale integrated (VLSI) architectures, are presented. Compared to established methods over a set of benchmark circuits, predatory search is able to either match or outperform the best-known layouts. Additional remarks address the relation of predatory search to the "big-valley" hypothesis and to the field of artificial life.
Towards the Efficient, Total Glycan Utilization of Biomass (2009)

From biomass to mass transportation: Waste biomass (newspaper, corn stover, straw, and wood) is converted into biofuel precursors and value-added products in excellent yield using a simple, inexpensive process involving concurrent hydrolysis, dehydration, and substitution reactions in a biphasic reactor. The hemicellulose fraction of these substrates is simultaneously converted into furfural, and together these constitute an efficient means for the total exploitation of the carbohydrate content of biomass.
The CXCR4 Score: A New Prognostic Marker in Acute Myelogenous Leukemia. (2004)

Abstract Despite major improvements in the understanding and treatment of certain leukemias during the past years, the overall survival of patients with acute myelogenous leukemia (AML) remains poor and new prognostic markers and therapeutic strategies are urgently needed. The chemokine stromal cell-derived factor-1 (SDF-1) and its receptor CXCR4 play key roles in retention of hematopoietic cells in the marrow microenvironment and release into the circulation. Rambouts and colleagues recently reported that CXCR4 expression on AML cells correlates with Flt3 mutations and prognosis (Blood 104: 550-57, July 2004). The aim of our study is to evaluate the prognostic significance of CXCR4 surface expression by AML blasts. Ninty newly diagnosed patients with AML were were divided into three groups based on expression of CXCR4 by AML blasts (CXCR4 score A–C). Group A contains patients with a mean fluorescence intensity ratio (MFIR) for CXCR4 &amp;lt;5 (n=32), group B: MFIR 5–10 (n=26), and group C: MFIR &amp;gt;10 (n=32). MFIR was calculated by divding the mean flourescence intensity for CXCR4 by that for the non-specific isotype control of the respective sample and indicates the level of CXCR4 expression. The characteristics for each group are summarized in Table 1. Previously, we demonstrated that CXCR4 receptors on AML cells mediate adesion and induce migration beneath marrow stromal cells (Burger JA,et al., Br J Haematol. 122: 579–89, August 2003). Because adhesion to stromal elements can affect survival and induce adhesion-mediated drug resistance, antagonists of the CXCR4/SDF-1 axis may increase the efficacy of current treatments. We conclude that CXCR4 expression at time of diagnosis correlates with leukocytosis, LDH, blast persistence after first therapy, relapse rate, and survival. Therfore, CXCR4 expression in AML may be an important progostic factor for complete remission and survival. As such, CXCR4/SDF-1 interaction may provide the basis for a novel therapeutic approach in AML. Characteristic Score A (N=32) Score B (N=26) Score C (N=32) Median CXCR4 MFIR (range) 2.8 (1.0–4.9) 6.9 (5.1–9.4) 17.2 (10.3–73.4) Median Age (range) 62.0 (21–89) 59.5 (18–80) 65.0 (32–93) Median WBC (range) 2.3 (1.0–14.0) 10.2 (10.2–17) 30.0 (2.7–240) Median PLT (range) 56.0 (8–211) 86.0 (13.6–265) 82.5 (4–218) Median LDH (range) 251.5 (140–2637) 368.0 (187–1489) 357.0 (144–2760) Unfavorable Cytogenetics 4/28 10/24 7/27 blast persistence after first therapy N=6, 22.2% N=13, 65% N=14, 73.7% Relapse Rate 13.8% 52.4% 40% Total Deaths N=7, 21.9% N=13, 50% N=17, 53.1% Mean overall survival (months) 12.4±11.9 10.3±9.8 8.3±7.4 Mean follow-up (months) 12.0±19.7 Median Overall Survival (months) 9.0 (2–52) 6.5 (0–42) 7.0 (0–25) Median follow-up (months) 7.0 (0–52) Table
It's the DNA That Counts (2009)

A simple genetic circuit that counts molecular events may be further developed to program complex cell behaviors.
A dynamic load balancing algorithm for conservative parallel simulations (2002)

Load balancing is an important component in improving the efficiency of distributed systems because it distributes an even workload over all the processors. This paper considers the problem of load-balancing a conservative parallel simulation for execution on a multicomputer. The synchronization protocol makes use of Chandy-Misra (1979) null-messages. An earlier study conducted by Boukerche and Tropper (1994) showed that static load balancing for conservative parallel simulation is effective when the workload can be sufficiently well characterized beforehand. In this paper, we present a dynamic load balancing algorithm which assumes no compile-time knowledge about the workload parameters. It is based upon a process migration mechanism and the notion of CPU-queue length, which indicates the workload at each processor. We discuss the algorithm and its implementation, and report on the performance results of a simulation of FCFS (first-come, first-served) queueing network models on an Intel Paragon A4.
Modeling of Web Robot Navigational Patterns (2000)

In recent years, it is becoming increasingly difficult to ignore the impact of Web robots on both commercial and institutional Web sites. Not only do Web robots consume valuable bandwidth and Web server resources, they are also making it more difficult to apply Web Mining techniques eectively on the Web logs. E-commerce Web sites are also concern about unauthorized deployment of shopbots for the purpose of gathering business intelligence at their Web sites. Ethical robots can be easily detected because they tend to follow most of the guidelines proposed for robot designers. On the other hand, unethical robots are more difficult to identify since they tend to camouage their entries in the Web logs. In this paper, we examine the problem of identifying navigational patterns of Web robots using conventional machine learning techniques. Our goal is to construct a predictive model that will distinguish between the browsing behavior of legitimate Web users from access patterns due to Web robots. Our results show that highly accurate models can be obtained using a small set of access features deduced from the Web logs.
Synthesis of Boron Nanorods by Smelting Non‐Toxic Boron Oxide in Liquid Lithium (2010)

In contrast to the conventional bottom‐up syntheses of boron nanostructures, a unique top‐down and greener synthetic strategy is presented for boron nanorods involving nontoxic boron oxide powders ultrasonically smelted in liquid lithium under milder conditions. The product was thoroughly characterized by energy dispersive X‐ray analysis, atomic emission spectroscopy, thermogravimetric analysis and, UV‐Vis spectroscopy, including structural characterization by transmission electron microscopy (TEM).
Carbon monoxide, but not endothelin-1, plays a major role for the hepatic microcirculation in a murine model of early systemic inflammation (2005)

Objective: Endothelin-1 and carbon monoxide play a major role in the regulation of liver microcirculation in numerous disease states. During sepsis and endotoxemia, elevated formation of endothelin-1 results in reduced sinusoidal blood flow. However, the role of carbon monoxide and endothelin-1 and its receptors endothelin receptor A and endothelin receptor B in the deranged liver microcirculation during early systemic inflammation remains unclear. Design: Prospective, randomized, controlled experiment. Setting: University animal laboratory. Subjects: Male C57/BL6 mice, weighing 23–27 g. Interventions: To induce a systemic inflammation, mice were treated with 1 hr of bilateral hind limb ischemia followed by 3 hrs or 6 hrs of reperfusion. Animals were randomly exposed to the nonselective endothelin receptor antagonist Ro-61-6612 (Tezosentan) and/or a continuous endothelin-1 infusion. Different animals were randomized to methylene chloride gavage or carbon monoxide inhalation during the reperfusion period. Measurements and Main Results: After ischemia/reperfusion, endothelin-1 plasma concentrations, endothelin-1 messenger RNA expression, and endothelin receptor A and B messenger RNA expression revealed no significant changes when compared with sham animals. After 6 hrs of ischemia/reperfusion, hepatic microcirculatory variables (sinusoidal density, sinusoidal diameter, and red blood cell velocity) deteriorated. Tezosentan after 6 hrs of ischemia/reperfusion did not improve the liver microcirculation, whereas the continuous infusion of endothelin-1 after 6 hrs of ischemia/reperfusion further impaired sinusoidal blood flow. Tezosentan treatment did not produce any alterations in hepatocellular injury or hepatic redox status when compared with the untreated animals receiving 6 hrs of ischemia/reperfusion. Animals receiving 6 hrs of ischemia/reperfusion and exposed to methylene chloride gavage or inhaled carbon monoxide during limb reperfusion showed significantly improved microcirculatory variables, hepatic redox status, and attenuated hepatocellular injury. Conclusions: These data suggest that endothelin-1 and the endothelin receptors A and B are not responsible for the observed hepatic microcirculatory and cellular dysfunction during early systemic inflammation, but exposure to exogenous carbon monoxide protected the hepatic microcirculation and improved the impaired hepatic cellular integrity and the hepatocellular redox status.
Mechanistic Studies of Cyclohexanone Monooxygenase:  Chemical Properties of Intermediates Involved in Catalysis (2001)

Cyclohexanone monooxygenase (CHMO), a bacterial flavoenzyme, carries out an oxygen insertion reaction on cyclohexanone to form a seven-membered cyclic product, epsilon-caprolactone. The reaction catalyzed involves the four-electron reduction of O2 at the expense of a two-electron oxidation of NADPH and a two-electron oxidation of cyclohexanone to form epsilon-caprolactone. Previous studies suggested the participation of either a flavin C4a-hydroperoxide or a flavin C4a-peroxide intermediate during the enzymatic catalysis [Ryerson, C. C., Ballou, D. P., and Walsh, C. (1982) Biochemistry 21, 2644-2655]. However, there was no kinetic or spectral evidence to distinguish between these two possibilities. In the present work we used double-mixing stopped-flow techniques to show that the C4a-flavin-oxygen adduct, which is formed rapidly from the reaction of oxygen with reduced enzyme in the presence of NADP, can exist in two states. When the reaction is carried out at pH 7.2, the first intermediate is a flavin C4a-peroxide with maximum absorbance at 366 nm; this intermediate becomes protonated at about 3 s(-1) to form what is believed to be the flavin C4a-hydroperoxide with maximum absorbance at 383 nm. These two intermediates can be interconverted by altering the pH, with a pK(a) of 8.4. Thus, at pH 9.0 the flavin C4a-peroxide persists mainly in the deprotonated form. Further kinetic studies also demonstrated that only the flavin C4a-peroxide intermediate could oxygenate the substrate, cyclohexanone. The requirement in catalysis of the deprotonated flavin C4a-peroxide, a nucleophile, is consistent with a Baeyer-Villiger rearrangement mechanism for the enzymatic oxygenation of cyclohexanone. In the course of these studies, the Kd for cyclohexanone to the C4a-peroxyflavin form of CHMO was determined to be approximately 1 microM. The rate-determining step in catalysis was shown to be the release of NADP from the oxidized enzyme.
Procalcitonin in children admitted to hospital with community acquired pneumonia (2001)

PCT concentration, with a threshold of 1 microg/l is more sensitive and specific and has greater positive and negative predictive values than CRP, IL-6, or white blood cell count for differentiating bacterial and viral causes of community pneumonia in untreated children admitted to hospital as emergency cases.
Directed evolution of the peroxidase activity of a de novo-designed protein (2012)

Collections of de novo-designed proteins provide a unique opportunity to probe the functional potential of sequences that are stably folded, but were neither explicitly designed nor evolutionarily selected to perform any particular type of activity. A combinatorial library of folded proteins was designed previously using a strategy that exploits the binary patterning of polar and non-polar amino acids to drive sequences to fold into four-helix bundles. Although these novel four-helix bundles were not explicitly designed for function, previous characterization of several hundred arbitrarily chosen sequences showed that many of them bound the heme cofactor, and several of these novel heme proteins catalyzed peroxidase activity at levels substantially above background. Here, we show that these moderately active de novo heme proteins can serve as non-natural starting points for laboratory-based evolution: Random mutagenesis followed by color-based screening of a relatively small number (hundreds or thousands) of variants yielded novel sequences with improved peroxidase activity. Biochemical characterization of the purified proteins showed that the evolved variants were nearly 3-fold more active than the parental sequence. These results demonstrate that de novo-designed proteins can be utilized as a novel feedstock for the evolution of enzyme activity.
A conserved RNA structure ( thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria (2001)

The thiCOGE genes of Rhizobium etli code for enzymes involved in thiamin biosynthesis. These genes are transcribed with a 211-base untranslated leader that contains the thi box, a 38-base sequence highly conserved in the 5' regions of thiamin biosynthetic and transport genes of Gram-positive and Gram-negative organisms. A deletion analysis of thiC-lacZ fusions revealed an unexpected relationship between the degree of repression shown by the deleted derivatives and the length of the thiC sequences present in the transcript. Three regions were found to be important for regulation: (i) the thi box sequence, which is absolutely necessary for high-level expression of thiC; (ii) the region immediately upstream to the translation start codon of thiC, which can be folded into a stem-loop structure that would mask the Shine-Dalgarno sequence; and (iii) the proximal part of the coding region of thiC, which was shown to contain a putative Rho-independent terminator. A comparative phylogenetic analysis revealed a possible folding of the thi box sequence into a hairpin structure composed of a hairpin loop, two helices, and an interior loop. Our results show that thiamin regulation of gene expression involves a complex posttranscriptional mechanism and that the thi box RNA structure is indispensable for thiCOGE expression.
Improved spelling recognition using a tree-based fast lexical match (1999)

This paper addresses the problem of selecting a name from a very large list using spelling recognition. In order to greatly reduce the computational resources required, we propose a tree-based lexical fast match scheme to select a short list of candidate names. Our system consists of a free letter recognizer, a fast matcher, and a rescoring stage. The letter recognizer uses n-grams to generate an n-best list of letter hypotheses. The fast matcher is a tree that is based on confusion classes, where a confusion class is a group of acoustically similar letters such as the e-set. The fast matcher reduces over 100,000 unique last names to tens or hundreds of candidates. Then the rescoring stage picks the best name using either letter alignment or a constrained grammar. The fast matcher retained the correct name 99.6% of the time and the system retrieved the correct name 97.6% of the time.
Inductance Measurement of Microconnectors for Josephson Packaging Using a Resonance Method (1986)

The inductances of microconnectors for Josephson computer packaging have been measured. Evaluation of the microconnector inductances is very important in order to design fast Josephson signal propagation paths. The inductances are measured by a resonance method which gives accurately sub-nil inductances by means of simple resonance circuits introducing known capacitances. Partial inductances without ground pins and loop inductances with a ground pin-to-signal pin ratio of one are measured. The measured partial inductances are compared with the calculated values using the cylinder model and the agreement is good in most cases. The measured loop inductances agree well with the calculated values of the net inductances consisting of the partial inductances. Inductance influences on signal propagation characteristics, such as reflection, delay, and crosstalk are also discussed.
Adaptive edge image enhancement based on maximum fuzzy entropy (2006)

基于最大的模糊的熵原则，有低对比的边图象最佳地适应地被分类进二个类，在概率分区和模糊分区的条件下面。最佳的阀值被用作分类阀值价值，和一个本地人参量灰色级，转变被用于获得的班。借助于代表的二个参数，在边图象的区域的同质被改进。建议技术的优秀表演通过一套测试图象上的模拟结果是可实行的。提取并且提高的边怎么提供图象的有效边表示，被显示出。这被显示出建议技术 prossesses 在通过一套测试图象上的模拟的同质的优秀性能，和提取并且提高的边提供图象的有效边表示。CLC 数字 TN911。73 文件代码 A
The Cardioprotection of Rutaecarpine is Mediated by Endogenous Calcitonin Related-Gene Peptide Through Activation of Vanilloid Receptors in Guinea-Pig Hearts (2002)

Previous investigations have shown that calcitonin gene-related peptide (CGRP) protects against myocardial ischemia-reperfusion injury and that rutaecarpine activates vanilloid receptors to evoke CGRP release. In the present study, we examined whether rutaecarpine enhances preservation with cardioplegia in guinea-pig hearts, and whether the protective effects of rutaecarpine are related to stimulation of endogenous CGRP release via activating vanilloid receptors. The isolated guinea-pig heart was arrested using St. Thomas Hospital solution, and then reperfused with normothermic Krebs-Henseleit solution for 30 min after a 4-h hypothermic ischemic period. Hypothermic ischemia caused a decline in cardiac function (left ventricular pressure, +/-dp/dt(max), heart rate and coronary flow) and an increased release of creatine kinase during reperfusion. Rutaecarpine at the concentration of 1.0 microM significantly improved the recovery of cardiac function and reduced the release of creatine kinase during reperfusion after hypothermic ischemia. Rutaecarpine at the concentration of 3.0 microM significantly reduced the release of creatine kinase and increased the coronary flow, but only caused a slight improvement of left ventricular pressure, +/-dp/dt(max), heart rate during reperfusion. The cardioprotective effects of rutaecarpine were abolished by capsazepine, a competitive vanilloid receptor antagonist, or by CGRP (8-37), a selective CGRP receptor antagonist. Rutaecarpine at the concentration of 1.0 or 3.0 microM significantly increased the release of CGRP, which was also abolished by capsazepine. These results suggest that rutaecarpine enhances preservation with cardioplegia in guinea-pig hearts and that the protective effects of rutaecarpine are due to stimulation of endogenous CGRP release via activating vanilloid receptors.
Discovery and development of sorafenib: a multikinase inhibitor for treating cancer (2006)

Since the molecular revolution of the 1980s, knowledge of the aetiology of cancer has increased considerably, which has led to the discovery and development of targeted therapies tailored to inhibit cancer-specific pathways. The introduction and refinement of rapid, high-throughput screening technologies over the past decade has greatly facilitated this targeted discovery and development process. Here, we describe the discovery and continuing development of sorafenib (previously known as BAY 43-9006), the first oral multikinase inhibitor that targets Raf and affects tumour signalling and the tumour vasculature. The discovery cycle of sorafenib (Nexavar; Bayer Pharmaceuticals) - from initial screening for a lead compound to FDA approval for the treatment of advanced renal cell carcinoma in December 2005 - was completed in just 11 years, with approval being received approximately 5 years after the initiation of the first Phase I trial.
Performance evaluation of Low-PAPR transmit filter for single-carrier transmission (2012)

Single-carrier transmission is a promising transmission technique due to its low peak-to-average power ratio (PAPR) property compared to multicarrier transmission, and using frequency-domain equalization (FDE) at the receiving side also mitigate the adverse effect of channel frequency-selectivity. An introduction of transmit filter can improve the system performance in terms of either PAPR or error probability. In this paper, we focus on the transmit filter aiming to reduce PAPR by employing the minimization of variance of instantaneous transmit power. Filter roll-off factor is also considered in order to provide excess-bandwidth transmission. With a combination of an FDE and spectrum combining at the receiver, excess-bandwidth transmission inherits additional frequency diversity gain, and therefore improves error probability. Performance evaluation of the proposed filtering algorithm is done by computer simulation, while the PAPR and bit-error rate (BER) performance of proposed algorithm are compared with conventional square-root Nyquist filter.
The GroES homolog of Helicobacter pylori confers protective immunity against mucosal infection in mice. (1995)

Helicobacter pylori is an important etiologic agent of gastroduodenal disease. In common with other organisms, H. pylori bacteria express heat shock proteins that share homologies with the GroES-GroEL class of proteins from Escherichia coli. We have assessed the heat shock proteins of H. pylori as potential protective antigens in a murine model of gastric Helicobacter infection. Orogastric immunization of mice with recombinant H. pylori GroES- and GroEL-like proteins protected 80% (n = 20) and 70% (n = 10) of animals, respectively, from a challenge dose of 10(4) Helicobacter felis bacteria (compared to control mice, P = 0.0042 and P = 0.0904, respectively). All mice (n = 19) that were immunized with a dual antigen preparation, consisting of H. pylori GroES-like protein and the B subunit of H. pylori urease, were protected against infection. This represented a level of protection equivalent to that provided by a sonicated Helicobacter extract (P = 0.955). Antibodies directed against the recombinant H. pylori antigens were predominantly of the IgG1 class, suggesting that a type 2 T-helper cell response was involved in protection. This work reports a protein belonging to the GroES class of heat shock proteins that was shown to induce protective immunity. In conclusion, GroES-like and urease B-subunit proteins have been identified as potential components of a future H. pylori subunit vaccine.