gebhart/patrepeval huggingface dataset:
Uridine phosphorylase knockout mice confirm the critical role of this enzyme in fluoropyrimidine activation and reveal its function in mediating host toxicity (2004)

2971 Uridine phosphorylase is widely induced in various human and rodent tumors, compared to matched normal tissues. A majority of studies have indicated that the activity of uridine phosphorylase may correlate with the activation of 5-fluorouracil and 5’-deoxy-5-fluorouridine and ultimately with their antiproliferative activity. In this study, we have generated uridine phosphorylase knockout mice to evaluate the role of uridine phosphorylase in fluoropyrimidine activity in vivo. Our results show that the abrogation of uridine phosphorylase activity led to a 2.5- and 2-fold increase in the maximum tolerated doses of 5-fluorouracil and 5’-deoxy-5-fluorouridine, respectively. The maximum tolerated doses of capecitabine, an oral prodrug of 5-fluorouracil, also increased from 1000 mg/kg in wild-type mice to 1375 mg/kg in uridine phosphorylase knockout mice. Pathological examinations of the gastrointestinal tracts and the hematological analysis of animals exposed to capecitabine revealed a significant reduction of gastrointestinal lesion and bone marrow toxicity following exposure to the fluoropyrimidine in uridine phosphorylase knockouts. This data indicates the critical roles for uridine phosphorylase in the activation of fluoropyrimidines and in mediating host toxicities. To understand the role of uridine phosphorylase in the antitumor activity and tumor selectivity of fluoropyrimidines, we further evaluated the response of colon 38 tumor (expressing wild type uridine phosphorylase), transplanted in uridine phosphorylase null mice, to fluoropyrimidines. The preliminary data indicates that the abrogation of uridine phosphorylase activity in the host tissues does not prevent the antiproliferative activity of 5-fluorouracil in tumors and contributes to an increased therapeutic index. A more detailed evaluation of the antineoplastic activity of several fluoropyrimidines in the uridine phosphorylase knockout model is in progress to determine the tumor selectivity of this new potential therapeutic approach. * This work was supported in part by a grant from the National Cancer Institute CA67035 (GP), the Charlotte Geyer Foundation (GP), and the United Army Medical Research Breast Cancer Research Program (DLC).
Detection of Pathological Myopia by PAMELA with Texture‐Based Features through an SVM Approach (2010)

Pathological myopia is the seventh leading cause of blindness worldwide. Current methods for the detection of pathological myopia are manual and subjective. We have developed a system known as PAMELA (Pathological Myopia Detection Through Peripapillary Atrophy) to automatically assess a retinal fundus image for pathological myopia. This paper focuses on the texture analysis component of PAMELA which uses texture features, clinical image context and support vector machine‐based classification to detect the presence of pathological myopia in a retinal fundus image. Results on a test image set from the Singapore Eye Research Institute show an accuracy of 87.5% and a sensitivity and specificity of 0.85 and 0.90 respectively. The results show good promise for PAMELA to be developed as an automatic tool for pathological myopia detection.
A local proton source in a [Mn(bpy-R)(CO)<sub>3</sub>Br]-type redox catalyst enables CO<sub>2</sub> reduction even in the absence of Brønsted acids (2014)

The effect of a local proton source on the activity of a bromotricarbonyl Mn redox catalyst for CO2 reduction has been investigated. The electrochemical behaviour of the novel complex [fac-Mn(dhbpy)(CO)3Br] (dhbpy = 4-phenyl-6-(1,3-dihydroxybenzen-2-yl) 2,2'-bipyridine), containing two acidic OH groups in the proximity of the metal centre, under a CO2 atmosphere showed a sustained catalysis in homogeneous solution even in the absence of Brønsted acids.
Dynamic Rematerialization: Processing Distributed Queries Using Redundant Data (1983)

In this paper an approach to processing distributed queries that makes explicit use of redundant data is proposed. The basic idea is to focus on the dynamics of materialization, defined as the collection of data and partial results available for processing at any given time, as query processing proceeds. In this framework the role of data redudancy in maximizing parallelism and minimizing data movement is clarified. What results is not only the discovery of new algorithms but an improved framework for their evaluation.
Large flattened-mode optical fiber for reduction of nonlinear effects in optical fiber lasers (2004)

We have developed and demonstrated a large flattened mode (LFM) optical fiber, which raises the threshold for non-linear interactions in the fiber core by a factor of 2.5 over conventional large mode area fiber amplifiers. The LFM fiber works by incorporating a raised index ring around the outer edge of the fiber core, which serves to flatten the fundamental fiber mode from a Bessel function to a top hat function. This increases the effective area of the core intersected by the mode by a factor of 2.5 without increasing the physical size of the core. This is because the core is uniformly illuminated by the LFM mode rather than having most of the light confined to the center of the core. We present experimental and theoretical results relating to this fiber and its design.
Statistical Selection and Interpretation of Imagery Features for Computer Vision-Based Pavement Crack–Detection Systems (2017)

This paper aims to explore the statistics of pavement cracks using computer-vision techniques. The knowledge discovered by mining the crack data can be used to avoid subjective crack feature selection for vision-based pavement evaluation systems. Moreover, the statistical evaluation of crack features can be used as fundamental data to justify pavement rehabilitation policies. For this purpose, surface images of flexible pavements in different deterioration stages were analyzed using a novel image-processing technique. Seven imagery features of the detected objects including area, length, width, orientation, intensity, texture roughness, and wheel-path position, which are commonly used in pavement applications, were extracted and analyzed. A comprehensive statistical analysis was performed using filter feature subset selection (FSS) methods to rank crack features based on their significance (relevance and redundancy) for the pavement crack–detection problem. Based on the results, length, intensity, and wheel-path position were identified as the optimal feature-set for the vision-based system. Statistical characteristics of crack features were also analyzed to extract accurate quantitative measures for pavement conditions assessment. The statistical characterization identified longitudinal cracks within the wheel path as the dominant defect of the validation data set. Such information can help management agencies make informed pavement maintenance policies.
Weekly paclitaxel (T) and pegylated liposomal doxorubicin (PLD) as first line treatment in metastatic breast cancer (MBC) patient (2004)

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Cloning of the <i>Arabidopsis WIGGUM</i> gene identifies a role for farnesylation in meristem development (2000)

Control of cellular proliferation in plant meristems is important for maintaining the correct number and position of developing organs. One of the genes identified in the control of floral and apical meristem size and floral organ number in Arabidopsis thaliana is WIGGUM. In wiggum mutants, one of the most striking phenotypes is an increase in floral organ number, particularly in the sepals and petals, correlating with an increase in the width of young floral meristems. Additional phenotypes include reduced and delayed germination, delayed flowering, maturation, and senescence, decreased internode elongation, shortened roots, aberrant phyllotaxy of flowers, aberrant sepal development, floral buds that open precociously, and occasional apical meristem fasciation. As a first step in determining a molecular function for WIGGUM, we used positional cloning to identify the gene. DNA sequencing revealed that WIGGUM is identical to ERA1 (enhanced response to abscisic acid), a previously identified farnesyltransferase beta-subunit gene of Arabidopsis. This finding provides a link between protein modification by farnesylation and the control of meristem size. Using in situ hybridization, we examined the expression of ERA1 throughout development and found it to be nearly ubiquitous. This extensive expression domain is consistent with the pleiotropic nature of wiggum mutants and highlights a broad utility for farnesylation in plant growth and development.
Novel Ru(III), Rh(III), Pd(II) and Pt(II) complexes with ligands incorporating azole and pyrimidine rings. I. Antiproliferative activity in vitro. (2000)

A number of co-ordination compounds of Ru(III), Rh(III), Pd(II) and Pt(II) with ligands incorporating azole and pyrimidine rings has been synthesized. The in vitro cell proliferation-inhibitory activity of these compounds was examined against human cancer cell lines: A 549 (lung carcinoma), LS-180 (colon cancer) and MCF-7 (breast cancer), using SRB technique. Six out of 13 compounds studied revealed cytotoxic activity in vitro. Inhibitory dose 50% (ID50) was lower than 4 microg/ml, which is an activity criterion accepted in conventional in vitro cytotoxic screening tests. Two compounds revealed weak cytotoxic activity with ID50 higher than 4 microg/ml and five compounds were inactive.
A plant‐derived edible vaccine against hepatitis B virus (1999)

The infectious hepatitis B virus represents 42 nm spherical double-shelled particles. However, analysis of blood from hepatitis B virus carriers revealed the presence of smaller 22 nm particles consisting of a viral envelope surface protein. These particles are highly immunogenic and have been used in the design of hepatitis B virus vaccine produced in yeast. Upon expression in yeast, these proteins form virus-like particles that are used for parenteral immunization. Therefore, the DNA fragment encoding hepatitis B virus surface antigen was introduced into Agrobacterium tumerifacience LBA4404 and used to obtain transgenic lupin (Lupinus luteus L.) and lettuce (Lactuca sativa L.) cv. Burpee Bibb expressing envelope surface protein. Mice that were fed the transgenic lupin tissue developed significant levels of hepatitis B virus-specific antibodies. Human volunteers, fed with transgenic lettuce plants expressing hepatitis B virus surface antigen, developed specific serum-IgG response to plant produced protein.
Multi-view Reconstruction of Highly Specular Surfaces in Uncontrolled Environments (2015)

Reconstructing the surface of highly specular objects is a challenging task. The shapes of diffuse and rough specular objects can be captured in an uncontrolled setting using consumer equipment. In contrast, highly specular objects have previously deterred capture in uncontrolled environments and have only been reconstructed using tailor-made hardware. We propose a method to reconstruct such objects in uncontrolled environments using only commodity hardware. As input, our method expects multi-view photographs of the specular object, its silhouettes and an environment map of its surroundings. We compare the reflected colors in the photographs with the ones in the environment to form probability distributions over the surface normals. As the effect of inter-reflections cannot be ignored for highly specular objects, we explicitly model them when forming the probability distributions. We recover the shape of the object in an iterative process where we alternate between estimating normals and updating the shape of the object to better explain these normals. We run experiments on both synthetic and real-world data, that show our method is robust and produces accurate reconstructions with as few as 25 input photographs.
Siderophore production by Pasteurella multocida (1986)

Pasteurella multocida grown under conditions of iron deprivation secreted into the culture medium a growth-enhancing factor which functioned as a siderophore. The siderophore was found to be neither a phenolate nor a hydroxamate by chemical tests and bioassays and was given the trivial name multocidin. Multocidin was partially purified and found to be a highly polar, nonaromatic, and dialyzable compound. This is the first report demonstrating the production of a siderophore by P. multocida.
Isomeric Replacement of a Single Aspartic Acid Induces a Marked Change in Protein Function: The Example of Ribonuclease A (2017)

lα-Aspartic acid (Asp) residues in proteins are nonenzymatically isomerized to abnormal lβ-, dα-, and dβ-Asp isomers under physiological conditions. Such an isomerization of Asp residues is considered to be a trigger of protein denaturation because it either elongates the main chain or induces a different orientation of the side chain within the protein structure or both. However, previous studies have found no direct evidence of the effects of Asp isomers on protein function. Therefore, the production of Asp-isomer-containing proteins is required to verify the effects of Asp isomerization. Here, we describe the production of an Asp-isomer-containing protein using the expressed protein ligation. As a model protein, bovine pancreatic ribonuclease A (RNase A, EC 3.1.27.5), which catalyzes the cleavage of phosphodiester bonds in RNA, was used. In this study, lα-Asp at position 121 in RNase A was replaced by lβ-, dα-, and dβ-Asp. The objective aspartic acid at position 121 is located near the active site and related to RNA cleavage. The RNase A with lα-Asp at position 121 showed a normal activity. By contrast, the catalytic activity of lβ-, dα-, and dβ-Asp-containing RNase A was markedly decreased. This study represents the first synthesis and analysis of a protein containing four different Asp isomers.
Laboratory Diagnostic Techniques for Patients with Early Lyme Disease Associated with Erythema Migrans: A Comparison of Different Techniques (2001)

Recently, a number of refinements in diagnostic modalities for detection of Borrelia burgdorferi infection have been developed. These include large-volume blood cultures, quantitative polymerase chain reaction (PCR) techniques, and 2-stage serologic testing. In the present study, we compared 6 diagnostic modalities in 47 adult patients who had a clinical diagnosis of erythema migrans. Quantitative PCR on skin biopsy-derived material was the most sensitive diagnostic method (80.9%), followed by 2-stage serologic testing of convalescent-phase samples (66.0%), conventional nested PCR (63.8%), skin culture (51.1%), blood culture (44.7%), and serologic testing of acute-phase samples (40.4%). Results of all assays were negative for 3 patients (6.4%). We conclude that the clinical diagnosis of erythema migrans is highly accurate in an area where B. burgdorferi is endemic if it is made by experienced health care personnel, but some patients with this diagnosis may not have B. burgdorferi infection. No single diagnostic modality is suitable for detection of B. burgdorferi in every patient with erythema migrans.
Characterization of rat brain stathmin isoforms by two‐dimensional gel electrophoresis‐matrix assisted laser desorption/ionization and electrospray ionizationion trap mass spectrometry (1998)

Stathmin is a regulatory phosphoprotein that is a target for both cell cycle and cell surface receptor-regulated phosphorylation events. There are at least 14 isoforms of stathmin that migrate on two-dimensional electrophoresis (2-DE): two unphosphorylated, and 12 increasingly phosphorylated proteins. Following extracellular stimuli, stathmin is phosphorylated on four serines (Ser16, Ser25, Ser38, and Ser63) by several kinases, such as mitogen-activated protein (MAP), cdc2 kinase, protein kinase A, and Ca2+/calmodulin-dependent kinase-Gr. While all forms of stathmin are derived from the same protein encoded by a single mRNA, the precise nature of the post-translational modifications has not been clear. In this study we have characterized three rat brain stathmin isoforms, #1, #3 and #4, which electrophorese on 2-DE with apparent molecular weight (Mr)/isoelectric point (pI) values of 15,500/6.2, 15,000/6.1, and 15,000/6.0, respectively. The phosphorylation status of these isoforms was determined using a combination of peptide mapping, matrix-assisted laser desorption/ionization mass spectrometry and electrospray-ionization ion trap mass spectrometry. Stathmin isoform #1 was not phosphorylated, stathmin isoform #3 was phosphorylated on Ser38 only, and stathmin isoform #4 was phosphorylated on Ser38; however, the phosphorylation status of Ser63 could not be determined. In addition, three proteins which electrophorese near stathmin were identified in order to more accurately define the Mr/pI locus of this region of the 2-DE gel map. These include: phosphatidyl ethanolamine binding protein (Mr approximately 18,000/pI 6.0), synuclein forms 2 and 3 (Mr approximately 14,000/pI 5.4), and synuclein form 2 (Mr approximately 15,000/pI 5.0).
Vanadium‐Catalyzed Enantioselective Sulfoxidation and Concomitant, Highly Efficient Kinetic Resolution Provide High Enantioselectivity and Acceptable Yields of Sulfoxides (2005)

Abstract Simple, inexpensive, preformed vanadium‐Schiff base complexes were facilely prepared and used in enantioselective sulfoxidation. Both the amount of aqueous H 2 O 2 and reaction time greatly influenced the ee values and yields of chiral sulfoxides. High enantioselectivities (up to 99% ee) and reasonable yields (&gt;40%) for various chiral sulfoxides were achieved by combining enantioselective sulfoxidation and appropriate concomitant kinetic resolution.
Functional Expression of IL-9 Receptor by Human Neutrophils from Asthmatic Donors: Role in IL-8 Release (2001)

Human polymorphonuclear neutrophils (PMNs) express surface receptors for various inflammatory mediators, including IgE and IL-4. Recently, the IL-9R locus has been genetically linked to asthma and bronchial hyperresponsiveness in humans. In this study, we evaluated expression of the IL-9R and the effect of IL-9 on human PMNs. RT-PCR analysis showed the presence of IL-9Ralpha-chain mRNA in PMN RNA preparations from asthmatic patients. Using FACS analysis, surface expression of IL-9Ralpha was detected on PMNs freshly isolated from asthmatics, and to a lesser extent on normal controls. In addition, protein expression of IL-9Ralpha was also detected in peripheral blood and bronchoalveolar lavage PMNs. Furthermore, functional studies showed that IL-9 stimulation of PMNs results in the release of IL-8 in a concentration-dependent manner. The anti-IL-9 neutralizing Ab suppressed this effect, but had no effect on GM-CSF-induced IL-8 release from PMNs. Taken together, these findings suggest a novel role for PMNs in allergic disease through the expression and activation of the IL-9R.
Degradative enzymes modulate airway responses to intravenous neurokinins A and B (1989)

We studied the effects of the neutral endopeptidase (NEP) inhibitor thiorphan (1.7 mg/kg iv) and the angiotensin-converting enzyme (ACE) inhibitor captopril (5.7 mg/kg iv) on airway responses to rapid intravenous infusions of neurokinin A (NKA) and neurokinin B (NKB) in anesthetized, mechanically ventilated guinea pigs. The dose of NKA required to decrease pulmonary conductance to 50% of its base-line value (ED50GL) was fivefold less (P less than 0.0001) in animals treated with thiorphan compared with controls. NKA1-8, a product resulting from cleavage of NKA by NEP, had no bronchoconstrictor activity. Similar results were obtained by using NKB as the bronchoconstricting agent. Captopril had no significant effect on airway responses to NKA or NKB. In contrast, both thiorphan and captopril decrease the ED50GL for substance P (SP). We also compared the relative bronchoconstrictor potency of NKA, NKB, and SP. In control animals, the rank order of ED50GL values was NKA much less than NKB = SP. NKA also caused a more prolonged bronchoconstriction than SP or NKB. Thiorphan had no effect on the rank order of bronchoconstrictor potency, but in animals treated with captopril, the rank order of ED50GL values was altered to NKA less than SP less than NKB. These results suggest that degradation of NKA and NKB by NEP but not by ACE is an important determinant of the bronchoconstriction induced by these peptides. The degradation by ACE of SP but not NKA or NKB influences the observed relative potency of the three tachykinins as bronchoactive agents.
An inductive detector for time‐of‐flight mass spectrometry (1994)

Abstract In this paper we describe the underlying principles of, and demonstrate some of the attributes of, an inductive detector for use in time‐of‐flight mass spectrometry. Unlike a microchannel plate detector, the detection efficiency of the inductive detector is not dependent on ion velocity. Also, the inductive detector cannot be saturated in the same manner as a microchannel plate detector. Because the inductive detector detects only charged species, the neutral species normally observed in linear time‐of‐flight matrix‐assisted laser desorption/ionization spectra do not appear in spectra obtained with the inductive detector. Further, price and availability of the material needed to fabricate an inductive detector are virtually independent of detector size. Perhaps one of the most important features of the inductive detector is that it is a largely non‐destructive detector.
Server-based traffic shaping for stabilizing oscillating adaptive streaming players (2013)

Prior work has shown that two or more adaptive streaming players can be unstable when they compete for bandwidth. The root cause of the instability problem is that, in Steady-State, a player goes through an ON-OFF activity pattern in which it overestimates the available bandwidth. We propose a server-based traffic shaping method that can significantly reduce such oscillations without significant (or any) loss in bandwidth utilization. The shaper is only activated when oscillations are detected, and it dynamically adjusts the shaping rate so that the player should ideally receive the highest available video profile while being stable. We evaluate the proposed method experimentally in terms of instability and utilization comparing with the unshaped case, under several scenarios.
Digital mobile communication system designed for nationwide police activities-WIDE system (1996)

In 1991, the National Police Agency (NPA) of Japan introduced a new type of digital mobile communication system, called the WIDE system, as a countermeasure against nationwide criminal cases. The WIDE system uses an exclusive radio network for police use. This enables police officers to communicate with each other at any time, even if the public network channels are all in use. The WIDE system has both press-to-talk (simplex) radio and telephone (duplex) functions, and it has such original features as (1) a nationwide communication link and contiguous coverage for broadcasting commands to all the WIDE system terminals in a investigation group (press-to-talk), (2) functioning as a mobile telephone which is connected to both the police and the public telephone network, (3) a function to establish a hotline (non-dialling), and (4) a function to connect a prior terminal call by interrupting an ordinary call when all radio channels are in use. Furthermore, the NPA have introduced new facilities and equipment to improve the service features of the WIDE system. For example, (1) we have developed and introduced a handy WIDE system terminal, which is small and similar to a cellular-phone, for high mobility (for walking policemen), (2) we have set up many radio relay stations, not only on the ground but also under the ground (in blind zones), such as in subway station yards, and (3) we have developed and introduced new data communication equipment and facsimile machines for the WIDE system; using this system, the policemen can transmit and receive image data