gebhart/patrepeval huggingface dataset:
Abstract 1755: PEGylated adenosine deaminase (ADA2) prevents adenosine-mediated increase in tumor growth and improves antitumor immune responses (2018)

Abstract Adenosine deaminase 2 (ADA2) is a human serum protein that catalyzes the reaction of deamination of adenosine to inosine. Besides catalytic activity, ADA2 has a heparin-binding domain and a growth factor-like domain. Adenosine accumulates in the tumor microenvironment and suppresses anti-tumor immune responses, while promoting tumor cell metastasis. Previously, we showed that treatment of mice with PEGylated forms of ADA2 (PEG ADA2) can decrease the accumulation of tumor-associated adenosine. Here, we analyzed the TCGA RNA-seq database using OncoLnc tool and observed that high expression of the ADA2 gene (CECR1) in certain immunotherapy responsive tumors correlated with increased survival of patients. We then tested different engineered ADA2 variants, using the inactive enzyme variant as a control, for the reversal of adenosine-mediated responses in human T cells, mouse peritoneal macrophages, and mouse and human tumor cell lines. ADA2 variants with higher catalytic activity were able to reverse adenosine-mediated suppression of human T-cell proliferation, cAMP accumulation in tumors and human T cells, and polarization of macrophages into an immunosuppressive, pro-tumor phenotype, whereas the inactive ADA2 variant failed to cause any of these effects. In addition, the variant that lacks the ability to bind to heparin but has improved catalytic activity (PEG NME8058) showed similar responses to those with the catalytically improved variant with intact heparin-binding domain (PEG NME8062). These results suggest that the improved immune cell activity with ADA2 in the presence of adenosine requires the enzyme activity of this molecule. Next, we assessed PEG NME8062 in MC38 and CT26 colon carcinoma syngeneic tumors in C57BL/6 and Balb/c mice, and observed delayed growth in both tumors. Using the inactive enzyme variant, we have shown that anti-tumor effect of PEG NME8062 depends on enzyme activity. Delayed tumor growth was also associated with increased density of key anti-tumor immune cell populations in both tumor models. These data suggest that PEG ADA2 can reduce tumor growth in an enzyme-activity-dependent manner and promote anti-tumor immune responses in vitro and in vivo. These findings have important implications for targeting purinergic signaling for cancer therapy. Citation Format: Luz Marina Londoño-R, Jessica Cowell, Lin Wang, Qiping Zhao, Lei Huang, Chris Thanos, Michael J. LaBarre, Xiaoming Li, Caglar Cekic. PEGylated adenosine deaminase (ADA2) prevents adenosine-mediated increase in tumor growth and improves antitumor immune responses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1755.
GUIfetch (2018)

A typical way to design and develop a mobile app is to sketch the graphical user interfaces (GUIs) for the different screens in the app and then create actual GUIs from these sketches. Doing so involves identifying which layouts to use, which widgets to add, and how to configure and connect the different pieces of the GUI. To help with this difficult and time-consuming task, we propose GUIFetch, a technique that takes as input the sketch for an app and leverages the growing number of open source apps in public repositories to identify apps with GUIs and transitions that are similar to those in the provided sketch. GUIFetch first searches public repositories to find potential apps using keyword matching. It then builds models of the identified apps' screens and screen transitions using a combination of static and dynamic analyses and computes a similarity metric between the models and the provided sketch. Finally, GUIFetch ranks the identified apps (or parts thereof) based on their computed similarity value and produces a visual ranking of the results together with the code of the corresponding apps. We implemented GUIFetch for Android apps and evaluated it through user studies involving different types of apps.
Pulse detection algorithm for line-of-sight (LOS) UWB ranging applications (2005)

This paper presents an algorithm for precise determination of the distance between a pair of transmitting and receiving antennas using FCC conforming ultra-wideband (UWB) pulses. Indoor line-of-sight (LOS) measurements up to 24 m were conducted at Research Technoplaza, Nanyang Technological University, Singapore. The proposed algorithm is developed using Matlab to post process the captured waveform. Significant improvement of accuracy is observed in determining the time of flight using a combination of match filtering and peak search technique, achieving centimeter level accuracy. Ranging results show a worst case standard deviation of 2 cm for distance up to 8 m and 10.6 cm for distance up to 24 m.
The use of cleavage site specific antibodies to delineate protein processing and breakdown pathways. (1999)

The hydrolysis of peptide bonds is an integral part of most physiological and pathological processes, yet knowledge is often lacking as to which peptide bonds are cleaved, in which protein substrates, in which order, and by which proteolytic enzymes. An increase in our understanding of these processes will enhance understanding of the pathogenesis underlying many diseases and might aid in the recognition of new targets for therapeutic intervention. This article reviews the development, design, and use of antibodies for the detection of specific peptide bond cleavage events, and describes how the application of such antibodies can increase our understanding of the roles played by proteolytic enzymes in physiology and pathology.
Colon and Breast Anti-cancer Effects of Peptide Hydrolysates Derived from Rice Bran (2009)

Rice bran is an economical, under-utilized co-product of rough rice milling. The objective of this study was to produce rice-bran peptides and investigate for anti-cancer activity. Protein hydrolysates were prepared by treating heat stabilized defatted rice-bran with food grade Alcalase enzyme, followed by treatment with simulated gastric and intestinal juices to obtain resistant peptides. Resistant peptides were fractionated into >50, 10-50, 5-10, and <5 kDa sizes, freeze dried, and evaluated for inhibitory and cytotoxicity activities on human colon (HCT-116) and breast (HTB-26) cancer cell lines. The results showed that <5 kDa fraction of rice-bran is a potent anti-cancer agent. The cytotoxicity of the fraction to both cancer cell types was more pronounced after the treatment with 500 µg/mL. The IC 50 of the peptide fraction was approximately 750 µg/mL. These results indicate that the <5 kDa peptide fraction separated from rice bran protein hydrolysate has a potent anti-tumor activity for colon cancer cells. The peptide fractions that demonstrate anti-cancer activities have the potential for use as functional food ingredients for health benefits.
2016 Infectious Diseases Society of America (IDSA) Clinical Practice Guideline for the Treatment of Coccidioidomycosis (2016)

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. Infectious Diseases Society of America considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.Coccidioidomycosis, also known as San Joaquin Valley fever, is a systemic infection endemic to parts of the southwestern United States and elsewhere in the Western Hemisphere. Residence in and recent travel to these areas are critical elements for the accurate recognition of patients who develop this infection. In this practice guideline, we have organized our recommendations to address actionable questions concerning the entire spectrum of clinical syndromes. These can range from initial pulmonary infection, which eventually resolves whether or not antifungal therapy is administered, to a variety of pulmonary and extrapulmonary complications. Additional recommendations address management of coccidioidomycosis occurring for special at-risk populations. Finally, preemptive management strategies are outlined in certain at-risk populations and after unintentional laboratory exposure.
Optimal Reversible Logic Circuit Synthesis Based on a Hybrid DFS-BFS Technique (2010)

Logic synthesis with reversible circuits has received considerable interest in the light of advances recently made in quantum computation. In this paper, we propose an improved technique for synthesizing reversible circuits based on a combined depth-first search (DFS) and breadth-first search (BFS) algorithm. A method based on DFS alone may often take a long time to converge, whereas, a BFS based method requires a large amount of memory for designing a circuit of moderate complexity. To strike a balance between these two approaches, we propose a hybrid DFS-BFS based synthesis algorithm that reduces the computation time compared to the DFS method and requires less space compared to the BFS method, while optimizing the cost of the circuit. Synthesis results on several reversible benchmark circuits have been reported.
Motor and Blood Pressure Effects of Epidural Sustained-Release Bupivacaine from Polymer Microspheres (1995)

The incorporation of local anesthetics into injectable polymer microspheres can be useful in providing prolonged regional effects.This randomized study was designed to compare the effects of bupivacaine and bupivacaine-loaded microspheres on the time course of motor block in rabbits injected epidurally. Bupivacaine-loaded microspheres and drug-free microspheres 1-10 micro meter in size were devised from poly-d,l-lactic acid by using a solvent evaporation/extraction method. The effects of bupivacaine and of similar amounts of bupivacaine-loaded microspheres were studied in 26 rabbits as follows: 0.9% sodium chloride, followed by drug-free microspheres, then 1.25 mg of bupivacaine and 1.25 mg of bupivacaine-loaded microspheres (Group I; n = 8); 2.5 mg of bupivacaine, then 2.5 mg of bupivacaine-loaded microspheres (Group II; n = 8); and 5 mg of bupivacaine and 5 mg of bupivacaine-loaded microspheres (Group III; n = 10). Motor block was evaluated blindly by observation of walking disturbances, using a scale from 0 (free movements) to 3 (total limb paralysis). A period of 3 days elapsed between each injection. No limitation on movements was observed after 0.9% sodium chloride and drug-free microsphere injection. With 5 mg, both bupivacaine solutions provided complete motor block which was significantly more prolonged (+244% +/- 129%, mean +/- SD) with bupivacaine-loaded microspheres than bupivacaine. With 2.5 and 1.25 mg, block intensity was less marked, and block duration was shorter after administration of bupivacaine-loaded microspheres than after bupivacaine. We concluded that blocks resulting from bupivacaine-loaded microspheres are highly influenced by the amount of drug initially released by the polymer. (Anesth Analg 1995;81:519-24)
Interval Velocities from Seismic Reflection Time Measurements (1980)

“Over the years, ray theory has furnished the exploration geophysicist with most of the working tools for understanding and interpreting events observed on reflection seismic sections. Even today, notwithstanding the pace at which the more powerful acoustic wave theory is introducing its new tools, ray theory, in the hands of the authors, retains its preeminence for providing insights into fundamental problems in reflection seismology. Professor Krey's earlier contributions are part of ray theory's rich heritage. Alongside C. Hewitt Dix and Hans Durbaum, he elucidated relationships between interval velocity and observed reflection moveout.”
Algorithm For Modeling Coordinates Of Corners Of Buildings Determined With RTN GNSS Technology Using Vectors Translation Method (2015)

Abstract The paper presents an innovative solution which increases the reliability of determining the coordinates of corners of building structures in the RTN GNSS mode. Having performed the surveys of the base points in real time, it is proposed to use the method of line-line intersection , which results in capturing the Cartesian coordinates X, Y of the corners of buildings. The coordinates which were obtained in this way, are subjected to an innovative solution called the method of vectors translation . This method involves modeling the coordinates obtained by the algorithm developed by the author. As a result, we obtain the Cartesian coordinates X and Y of the corners of building structures, the accuracy and reliability of determining which is on a very high level.
Intravenous Glucocorticoids for Graves' Orbitopathy: Efficacy and Morbidity (2011)

The current first-line treatment for active, moderate-to-severe GO is a 12-wk course of high-dose iv glucocorticoid pulses. The response rate of this regimen is approximately 80%. Intravenous glucocorticoids have a statistically significant advantage over oral treatment and cause significantly fewer adverse events. However, major side effects related to preexisting diseases, administered dose, and treatment schedule have been reported. The morbidity and mortality of iv glucocorticoid therapy are 6.5 and 0.6%, respectively. Thus, careful patient selection is warranted. Before iv glucocorticoid administration, patients should be screened for recent hepatitis, liver dysfunction, cardiovascular morbidity, severe hypertension, inadequately managed diabetes, and glaucoma. The cumulative dose should not exceed 8 g, and with the exception of sight-threatening GO the single doses preferably should not be administered on consecutive days. Monthly monitoring during subsequent treatment is warranted.
The Learning and Prediction of Application-Level Traffic Data in Cellular Networks (2017)

Traffic learning and prediction is at the heart of the evaluation of the performance of telecommunications networks and attracts a lot of attention in wired broadband networks. Now, benefiting from the big data in cellular networks, it becomes possible to make the analyses one step further into the application level. In this paper, we first collect a significant amount of application-level traffic data from cellular network operators. Afterward, with the aid of the traffic “big data,” we make a comprehensive study over the modeling and prediction framework of cellular network traffic. Our results solidly demonstrate that there universally exist some traffic statistical modeling characteristics at a service or application granularity, including α-stable modeled property in the temporal domain and the sparsity in the spatial domain. But, different service types of applications possess distinct parameter settings. Furthermore, we propose a new traffic prediction framework to encompass and explore these aforementioned characteristics and then develop a dictionary learning-based alternating direction method to solve it. Finally, we examine the effectiveness and robustness of the proposed framework for different types of application-level traffic. Our simulation results prove that the proposed framework could offer a unified solution for application-level traffic learning and prediction and significantly contribute to solve the modeling and forecasting issues.
Molecular pathophysiology in Tay-Sachs and Sandhoff diseases as revealed by gene expression profiling (2002)

Tay-Sachs and Sandhoff diseases are lysosomal storage disorders characterized by the absence of beta-hexosaminidase activity and the accumulation of GM2 ganglioside in neurons. In each disorder, a virtually identical course of neurodegeneration begins in infancy and leads to demise generally by 4-6 years of age. Through serial analysis of gene expression (SAGE), we determined gene expression profiles in cerebral cortex from a Tay-Sachs patient, a Sandhoff disease patient and a pediatric control. Examination of genes that showed altered expression in both patients revealed molecular details of the pathophysiology of the disorders relating to neuronal dysfunction and loss. A large fraction of the elevated genes in the patients could be attributed to activated macrophages/microglia and astrocytes, and included class II histocompatability antigens, the pro-inflammatory cytokine osteopontin, complement components, proteinases and inhibitors, galectins, osteonectin/SPARC, and prostaglandin D2 synthase. The results are consistent with a model of neurodegeneration that includes inflammation as a factor leading to the precipitous loss of neurons in individuals with these disorders.
Maternal transmission of immunity to Eimeria maxima: enzyme-linked immunosorbent assay analysis of protective antibodies induced by infection (1994)

Vaccination of broiler chickens against Eimeria infection is problematic because of the need to ensure that birds are protected from the time of hatching. We have therefore investigated the feasibility of protecting hatchling broilers via maternal transfer of protective antibodies from hens to their offspring. Oral infection of broiler breeder hens with 20,000 sporulated Eimeria maxima oocysts caused production of antibodies which were passed into the egg yolk and subsequently to hatchlings. The level of specific antibodies in the yolks to unsporulated oocysts, sporulated oocysts, merozoites, and gametocytes was assessed by enzyme-linked immunosorbent assays. The levels in yolks of antibodies to all developmental stages peaked 3 to 4 weeks after infection of the hens. Groups of 10 hatchlings were challenged at 3 days of age by oral infection with 100 sporulated E. maxima oocysts. In the first experiment, the mean 4-day (days 6 to 9 post-infection) total number of oocysts excreted in the feces of chicks from eggs collected 3 weeks after infection of the hens was (0.6 +/- 0.4) x 10(6) (mean +/- standard error) compared with (9.9 +/- 1.4) x 10(6) for the progeny of uninfected hens, which represents a greater than 90% reduction. However, oocyst excretion by chicks from eggs collected 7 or 8 weeks after infection of the hens was only 47 or 68% lower than control values, reflecting declining levels of protective antibodies. In a second experiment, in which the hens were somewhat older and pretreated by intramuscular injection of saline in the emulsifying agent, Arlacel A, the period for which protective antibodies were transferred to hatchlings was prolonged. Thus, oocyst excretion by challenged hatchlings from eggs collected for an 8-week period after infection of the hens was more than 90% lower than oocyst excretion by control chicks, and even hatchlings of eggs collected 19 weeks after infection of the hens showed a 60% reduction in oocyst output. In both experiments, the levels of immunoglobulin G (IgG) antibodies to all developmental stages in yolks or hatchling sera were very strongly correlated with maternally derived immunity to E. maxima. In contrast, parasite-specific IgM or IgA was not detectable, either in egg yolk or egg white. These results demonstrate the ability of IgG antibodies to protect against E. maxima in poultry, thus raising the possibility of using protective maternally derived IgG antibodies to identify potentially protective parasite antigens and indicating the feasibility of using maternal immunization as a means for parasite control.
High transmission gain inverted-F antenna on low-resistivity Si for wireless interconnect (2006)

Inverted-F antennas of 2-mm axial length are designed and fabricated on a low-resistivity silicon substrate (10 /spl Omega//spl middot/cm) using a post back-end-of-line process. For the first time, their performances are measured up to 110 GHz for wireless interconnects. Results show that a sharp resonance can be seen at 61 GHz for the antenna, and a high transmission gain of -46.3 dB at 61 GHz is achieved from the pair of inverted-F antennas at a separation of 10 mm on a standard 10 /spl Omega//spl middot/cm silicon wafer of 750-μm thickness.
INTRACELLULAR DIMETHYLSULFOXIDE (DMSO) IN UNICELLULAR MARINE ALGAE: SPECULATIONS ON ITS ORIGIN AND POSSIBLE BIOLOGICAL ROLE (1999)

Recent studies have established that aqueous phase concentrations of dimethylsulfoxide (DMSO) often exceed those of dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS). Yet, in comparison to DMSP and DMS, DMSO remains a poorly understood component of the marine sulfur cycle. Much of what is known about the mechanisms for the formation and loss for DMSO is inferred from laboratory experiments, and no explanation exists to rationalize how a large pool of DMSO is maintained. One formation pathway that, until very recently, has been ignored involves the direct synthesis of DMSO by marine phytoplankton. This review examines some of the circumstantial evidence for DMSO in marine particulate material and recent reports containing preliminary data for particulate DMSO (DMSO p ) in the marine environment. Drawing on literature from a range of scientific disciplines, speculations on the possible origins and biological functions of intracellular DMSO are also made. On the basis of its physicochemical properties, intracellular DMSO could have a potential role as a cryoprotectant, a specialist cryo‐osmoregulator in extreme environments, an intracellular electrolyte modifier, and a free‐radical scavenger. The review also assesses the impact of DMSO p at both the organism and the global level. Consideration is given to the marine biogeochemical cycling of sulfur and potential links to climate control.
Multimedia event-based video indexing using time intervals (2005)

We propose the time interval multimedia event (TIME) framework as a robust approach for classification of semantic events in multimodal video documents. The representation used in TIME extends the Allen temporal interval relations and allows for proper inclusion of context and synchronization of the heterogeneous information sources involved in multimodal video analysis. To demonstrate the viability of our approach, it was evaluated on the domains of soccer and news broadcasts. For automatic classification of semantic events, we compare three different machine learning techniques, i.c. C4.5 decision tree, maximum entropy, and support vector machine. The results show that semantic video indexing results significantly benefit from using the TIME framework.
Genome and Transcriptome Analysis of the Fungal Pathogen Fusarium oxysporum f. sp. cubense Causing Banana Vascular Wilt Disease (2014)

Foc genome sequences will facilitate us to identify pathogenicity mechanism involved in the banana vascular wilt disease development. These will thus advance us develop effective methods for managing the banana vascular wilt disease, including improvement of disease resistance in banana.
Effect of indomethacin-coated posterior chamber intraocular lenses on postoperative inflammation and posterior capsule opacification (1995)

We implanted indomethacin-coated intraocular lenses (IOLs) in rabbit eyes to ascertain how the sustained release of the drug affects postoperative inflammation and posterior capsule opacification (PCO). A preoperative resolution test showed that 1% indomethacin-coated IOLs placed in balanced salt solution released a mean 14.0 +/- 0.6 micrograms of the drug within 24 hours. Postoperatively, aqueous flare intensity in eyes with 0.1% indomethacin-coated IOLs and in eyes with 1.0% indomethacin-coated IOLs was significantly less at day 2 and at days 2 and 3, respectively, than in control eyes with uncoated lenses. In another group of eyes, histopathological examination showed that those with 1.0% indomethacin-coated lenses had significantly less PCO than the contralateral control eyes with uncoated IOLs.