gebhart/patrepeval huggingface dataset:
CathaCyc, a Metabolic Pathway Database Built from Catharanthus roseus RNA-Seq Data (2013)

The medicinal plant Madagascar periwinkle (Catharanthus roseus) synthesizes numerous terpenoid indole alkaloids (TIAs), such as the anticancer drugs vinblastine and vincristine. The TIA pathway operates in a complex metabolic network that steers plant growth and survival. Pathway databases and metabolic networks reconstructed from 'omics' sequence data can help to discover missing enzymes, study metabolic pathway evolution and, ultimately, engineer metabolic pathways. To date, such databases have mainly been built for model plant species with sequenced genomes. Although genome sequence data are not available for most medicinal plant species, next-generation sequencing is now extensively employed to create comprehensive medicinal plant transcriptome sequence resources. Here we report on the construction of CathaCyc, a detailed metabolic pathway database, from C. roseus RNA-Seq data sets. CathaCyc (version 1.0) contains 390 pathways with 1,347 assigned enzymes and spans primary and secondary metabolism. Curation of the pathways linked with the synthesis of TIAs and triterpenoids, their primary metabolic precursors, and their elicitors, the jasmonate hormones, demonstrated that RNA-Seq resources are suitable for the construction of pathway databases. CathaCyc is accessible online (http://www.cathacyc.org) and offers a range of tools for the visualization and analysis of metabolic networks and 'omics' data. Overlay with expression data from publicly available RNA-Seq resources demonstrated that two well-characterized C. roseus terpenoid pathways, those of TIAs and triterpenoids, are subject to distinct regulation by both developmental and environmental cues. We anticipate that databases such as CathaCyc will become key to the study and exploitation of the metabolism of medicinal plants.
An Architecture for Secure Generation and Verification of Electronic Coupons (2001)

Coupons are very useful mechanism for carrying out different marketing management functions like sales promotion, brand promotion, and inventory management. With the advent of Internet shopping and online stores, there is an immediate need for an electronic equivalent of traditional paper coupons. Security issues such as coupon tampering, exchange, duplication and double spending become very important for electronic coupons. Although the security issues in electronic coupons appear to be similar to those in electronic cash systems, there are signi - cant dierences that require the design of a dierent protocol to carry out secure coupon transactions.
Nanoelectrochemistry of mammalian cells (2008)

There is a significant current interest in development of new techniques for direct characterization of the intracellular redox state and high-resolution imaging of living cells. We used nanometer-sized amperometric probes in combination with the scanning electrochemical microscope (SECM) to carry out spatially resolved electrochemical experiments in cultured human breast cells. With the tip radius approximately 1,000 times smaller than that of a cell, an electrochemical probe can penetrate a cell and travel inside it without apparent damage to the membrane. The data demonstrate the possibility of measuring the rate of transmembrane charge transport and membrane potential and probing redox properties at the subcellular level. The same experimental setup was used for nanoscale electrochemical imaging of the cell surface.
Complement Component C1q Enhances the Biological Activity of Influenza Virus Hemagglutinin-Specific Antibodies Depending on Their Fine Antigen Specificity and Heavy-Chain Isotype (2002)

We have previously observed that selected influenza virus hemagglutinin (HA)-specific monoclonal antibodies (MAbs) with poor virus-neutralizing (VN) activity in vitro exhibited greatly enhanced VN activity in vivo after administration to SCID mice. The same Abs displayed improved VN activity also when tested in vitro in the presence of noninactivated serum from SCID mice. To identify Ab-dependent properties and serum components that contributed to enhancement of Ab activity, we screened a large panel of HA-specific MAbs for hemagglutination inhibition (HI) in the presence of noninactivated serum from naive mice (NMS). We found that HI activity was enhanced by NMS depending on the Ab's fine specificity (antigenic region Cb/E > Ca/A,D > Sa,Sb/B), its heavy-chain isotype (immunoglobulin G2 [IgG2] > IgG3; IgG1 and IgM negative), and to some extent also on its derivation (primary response > memory response). On average, the HI activity of Cb/E-specific MAbs of the IgG2 isotype isolated from the primary response was enhanced by 20-fold. VN activity was enhanced significantly but less strongly than HI activity. Enhancement (i) was destroyed by heat inactivation (30 min, 56 degrees C); (ii) did not require C3, the central complement component; (iii) was abolished by treatment of serum with anti-C1q; and (iv) could be reproduced with purified C1q, the binding moiety of C1, the first complement component. We believe that this is the first description of a direct C1q-mediated enhancement of antiviral Ab activities.
A genomic approach to study down syndrome and cancer inverse comorbidity: untangling the chromosome 21 (2015)

Down syndrome (DS), one of the most common birth defects and the most widespread genetic cause of intellectual disabilities, is caused by extra genetic material on chromosome 21 (HSA21). The increased genomic dosage of trisomy 21 is thought to be responsible for the distinct DS phenotypes, including an increased risk of developing some types of childhood leukemia and germ cell tumors. Patients with DS, however, have a strikingly lower incidence of many other solid tumors. We hypothesized that the third copy of genes located in HSA21 may have an important role on the protective effect that DS patients show against most types of solid tumors. Focusing on Copy Number Variation (CNV) array data, we have generated frequencies of deleted regions in HSA21 in four different tumor types from which DS patients have been reported to be protected. We describe three different regions of deletion pointing to a set of candidate genes that could explain the inverse comorbidity phenomenon between DS and solid tumors. In particular we found RCAN1 gene in Wilms tumors and a miRNA cluster containing miR-99A, miR-125B2 and miR-LET7C in lung, breast, and melanoma tumors as the main candidates for explaining the inverse comorbidity observed between solid tumors and DS.
Real-time cancer detection with an integrated lensless fluorescence contact imager (2018)

Microscopic tumor cell foci left in a patient after surgery significantly increase the chance of cancer recurrence. However, fluorescence microscopes used for intraoperative navigation lack the necessary sensitivity for imaging microscopic disease and are too bulky to maneuver within the resection cavity. We have developed a scalable chip-scale fluorescence contact imager for detecting microscopic cancer <i>in vivo</i> and in real-time. The imager has been characterized under simulated <i>in vivo</i> conditions using <i>ex vivo</i> samples, providing strong evidence that our device can be used <i>in vivo</i>. Angle-selective gratings enhance the resolution of the imager without impacting its physical size. We demonstrate detection of cancer cell clusters containing as few as 25 HCC1569 breast cancer cells and 400 LNCaP prostate cancer cells with integration times of only 50 ms and 70 ms, respectively. A cell cluster recognition algorithm is used to achieve both a sensitivity and specificity of 92 % for HCC1569 cell samples, indicating the reliability of the imager. The signal-to-noise ratio (SNR) degradation with increased separation is only 1.5 dB at 250 μm. Blood scattering and absorption reduce the SNR by less than 2 dB for typical concentrations. Moreover, HER2+ breast cancer tissue taken from a patient is distinguished from normal breast tissue with an integration time of only 75 ms.
Visual Detection of Unknown Objects in Video Games Using Qualitative Stability Analysis (2015)

Many current computer vision approaches for object detection can only detect objects that have been learned in advance. In this paper, we present a method that uses qualitative stability analysis to infer the existence of unknown objects in certain areas of the images based on gravity and stability of already detected objects. Our method recursively searches these areas for unknown objects until all detected objects form a stable structure or no new objects can be identified anymore. We evaluate our method using the popular video game Angry Birds. We only start with detecting the green pigs and are able to automatically identify and detect all essential game objects in all 400+ available levels. All objects can be accurately and reliably detected. Our method can be applied to other video games where objects obey gravity and are bound by polygons.
A Privacy-Preserving E-Commerce System Based on the Blockchain Technology (2019)

With the increasing popularity of online shopping, privacy concerns in E-commerce are attracting more and more attention. Existing E-commerce models are trapped in a dilemma between the proof of ownership and privacy protection. To address this issue, in this paper we design a privacy-preserving business protocol by employing private smart contracts in the negotiation phase. The protocol allows counterparties make deals without the disclosure of private information such as identities, addresses, and phone numbers. Moreover, we employ the zero-knowledge proof to guarantee the ownership. To understand the feasibility for implementing the proposed model, we also conduct extensive experiments to evaluate the performance of existing blockchain development platforms, Ethereum Quorum and SERO.
Minimizing the surface effect of PDMS–glass microchip on polymerase chain reaction by dynamic polymer passivation (2006)

Abstract Polydimethyl siloxane (PDMS)–glass microchip has a very strong surface effect on polymerase chain reaction (PCR), leading to a very poor PCR yield. In the work reported here, practical dynamic passivation of surfaces of PDMS–glass microchip using polyethylene glycol (PEG) or polyvinylpyrrolidone (PVP) was achieved using a conventional thermocycler. The passivation procedure was cost‐effective and easy to conduct. The effects of polymer molecular weight and polymer concentration on tube PCR efficiency were investigated primarily to prescreen out suitable polymers and polymer concentrations in the PCR mixture. The result from tube PCR indicated that both PEG and PVP could affect the performance of Taq polymerase. A final concentration of 0.025% (w/v) or 0.4% (w/v) polymer in the PCR mixture can enhance the tube PCR, while 1% (w/v) polymer was found to inhibit the reaction. PEG was more effective in tube PCR, although PVP performed better in chip PCR. Instead of employing the polymer directly in the PCR mixture, i.e. the conventional in situ passivation approach, another approach of dynamic passivation by pre‐injecting polymers into the microchip achieved better performance. The efficiency of pre‐passivation was found to follow the order: PVP10000>PVP55000, PEG8000> PEG10000>PEG400. After pre‐passivation with PVP10000, PVP55000 and PEG8000, the PCR efficiency can recover to 93%, 86% and 83%, respectively, of that obtained from tube PCR. Copyright © 2006 Society of Chemical Industry
Single-mode glass waveguide platform for DWDM chip-to-chip interconnects (2012)

Due to high bandwidth potential, optical single-mode signal transmission is superior to electrical as well as optical multimode signal transmission. For years, optical single-mode fiber cables have been used in telecommunication networks. However, there is a lack of photonic system integration based on optical single-mode interconnects in printed circuit boards and modules for signal transmission between electro-optical components and optical fibers. Therefore, a thin glass-based photonic integration concept for single-mode signal transmission was developed. Optical waveguides and optical free space interconnects are integrated in a single or a stack of thin glass sheets for module and printed circuit board packaging. For light routing inside a thin glass sheet, a singlemode waveguide technology on wafer level (150 mm) was developed promising for scaling up on panel size (45 × 60 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ). The waveguides show single-mode behavior, low propagation (0.05 dB/cm) and fiber coupling (- 0.3 dB) losses at wavelength of 1550 nm. Different waveguide structures such as 180°-bends, S-bends, splitters and crosses have been integrated in thin glass and characterized in detail. Coupling mechanism and misalignment loss has also been studied. Technologies for fiber laser joining on glass as well as laser structuring of an optical mirror are introduced and first results are presented. Generic module and board-based photonic packaging solutions can be put into practice by applying all introduced technologies and will be demonstrated for a chip-to-fiber module package platform.
Aggregation of Hyperion hyperspectral spectral bands into Landsat-&ETM+ spectral bands (2002)

The Landsat 7 ETM+ spectral bands centered at 479 nm, 561 nm, 661 nm and 834 mn (Bands 1, 2, 3, and 4) fall nicely across the Hyperion VNIR hyperspectral response region. They have bandwidths of 67 nm, 78 nm, 60 nm and 120 nm, respectively. The Hyperion spectral bandwidth of 10.2 nm results in 10 to 15 Hyperion spectral samples across each Landsat band in the VNIR. When the Hyperion spectral responses in the 10.2 nm bands are properly weighted to aggregate to a given Landsat band, the radiometric response of the Landsat band can be reproduced by Hyperion. This is done for Bands 2, 3 and 4 on the scene 7 of Lake Frome, Australia collected simultaneously by Hyperion and Landsat on January 21, 2001. The initial comparison of the radiances from Hyperion synthesized into the ETM+ bands with the Landsat-7 ETM+ radiances showed differences of 15-23%, with ETM+ being higher. Prior to launch a laboratory standard comparison showed differences of 10-13% in the same direction.
Albumin-binding function is reduced in patients with decompensated cirrhosis and correlates inversely with severity of liver disease assessed by model for end-stage liver disease (2007)

An impaired albumin-binding function of a site II-specific marker in decompensated liver cirrhosis was found to be correlated to the severity of the liver disease.
Theoretical Basic Span Loading Characteristics of Wings with Arbitrary Sweep, Aspect Ratio, and Taper Ratio (1948)

A procedure based on the Weissinger method has been devised so that the basic span loading and associated aerodynamic characteristics can be rapidly predicted for wings having arbitrary values of sweep, aspect ratio, taper ratio, and twist. A method for correcting for the effects of compressibility is given. A comparison of the results of this method with that of lifting-line and lifting-surface method indicates that the accuracy is much better than that obtained with lifting-line methods and is comparable to that obtained with lifting-surface methods. This report, together with NACA TN No. 1491, allows a simple and rapid prediction of both the basic and additional loading characteristics for wings of arbitrary plan form. It is believed the predicted values are valid at all subcritical Mach numbers and for all lift coefficients where viscous and stall effects are negligible. To establish the effects of sweep, aspect ratio, and taper ratio on the basic loading characteristics produced by uniform twist, the method presented in this report was applied to a few representative wing configurations and the results discussed.
Pepstatins: Aspartic proteinase inhibitors having potential therapeutic applications (1993)

Cathepsin D (EC 3.4.23.5) is a lysomal aspartie proteinase that is involved, under normal phusiologycal conditions, ...
The safety and efficacy of bevacizumab therapy in recurrent ovarian carcinoma (2008)

16528 Background: To evaluate the safety and efficacy of bevacizumab alone or in combination therapy in heavily pretreated patients with ovarian cancer. Methods: We identified patients not participating in an ongoing clinical trial who received bevacizumab. Response was retrospectively assessed by CA125 criteria. Complete response (CR) was defined as normalization of serum levels to ≤ 35 U/mL. Partial response (PR) was defined as a ≥50% decrease after initiation of treatment confirmed 28 days apart. Adverse events were prospectively categorized using the common terminology criteria version 3.0. Progression-free and overall survival (PFS and OS) was estimated using Kaplan-Meier method with log-rank test where indicated. Results: Forty-nine patients were identified. The patients were pretreated with a median of 6 (range 1–15) prior chemotherapy regimens including a median of 2 (range 1–6) platinum based regimens. Twenty-two (45%) patients received bevacizumab alone and 27 (55%) received varied combination cytotoxic chemotherapy. Patients received bevacizumab therapy for a median 4.6 months (range 0–27 months). Twenty-two (45%) patients received 10 mg/kg every 2 weeks, while 16 (33%) patients received 15 mg/kg every 3 weeks. Eleven (22%) received both dosing schedules. CTC grade 3 and 4 toxicities occurred in 7 (14.3%) different patients. Toxicities included: 2 (4%) gastrointestinal (GI) perforation, 3 (6%) grade 3 HTN, 1 (2%) transient ischemic attack, and 1 (2%) subarachnoid hemorrhage, Thirty-four patients were evaluable for overall CA-125 response rate (ORR), which included both CR and PR. The ORR for this cohort was 47.1%. The ORR for those who received bevacizumab alone was 30% compared to 65% for those treated with bevacizumab in combination with cytotoxic chemotherapy (P = 0.04). The median PFS for the entire group was 4.6 months (95% CI: 1.1, 8.2 months). The median OS was 11.0 months (95% CI: 3.9, 18.0 months). Conclusions: Bevacizumab alone or in combination therapy is well tolerated and demonstrates activity in heavily pretreated patients with recurrent ovarian cancer. The GI perforation rate in our study is similar to previously reported. Further study of bev alone or in combination therapy is warranted. No significant financial relationships to disclose.
Public Response To Air Pollution In Sheffield, England (1973)

Abstract This paper discusses the attitudes of Sheffield residents to atmospheric pollution and the Clean Air Act, 1956. The majority are aware of air pollution but it is an issue which is low in their problem hierarchy. The magnitude of concentrations of gaseous pollutants is overlooked, and declining levels of participate pollution, the existence of legislation, and press reports have reduced public concern for atmospheric pollution.
Changes in Antigen-specific IgG1 Fc N-glycosylation Upon Influenza and Tetanus Vaccination (2011)

Antibody effector functions have been shown to be influenced by the structure of the Fc N-glycans. Here we studied the changes in plasma or serum IgG Fc N-glycosylation upon vaccination of 10 Caucasian adults and 10 African children. Serum/plasma IgG was purified by affinity chromatography prior to and at two time points after vaccination. Fc N-glycosylation profiles of individual IgG subclasses were determined for both total IgG and affinity-purified anti-vaccine IgG using a recently developed fast nanoliquid chromatography-electrospray ionization MS (LC-ESI-MS) method. While vaccination had no effect on the glycosylation of total IgG, anti-vaccine IgG showed increased levels of galactosylation and sialylation upon active immunization. Interestingly, the number of sialic acids per galactose increased during the vaccination time course, suggesting a distinct regulation of galactosylation and sialylation. In addition we observed a decrease in the level of IgG1 bisecting N-acetylglucosamine whereas no significant changes were observed for the level of fucosylation. Our data indicate that dependent on the vaccination time point the infectious agent will encounter IgGs with different glycosylation profiles, which are expected to influence the antibody effector functions relevant in immunity.
A Theoretical Model for Bubble Formation at a Frit Surface in a Shear Field (1982)

Abstract Engineers, meteorologists, and oceanographers all have an interest in the behavior of small air bubbles in water. Studies that are concerned with the separation of dissolved and particulate species, aerosol formation, and oceanic particle production require a means for the generation of large numbers of small bubbles. A device that produces populations of small bubbles (between 15 and 100 μm in radius) with predictable size distributions has been developed and is described. A model based upon an analysis of the form drag on a bubble emerging from a submerged orifice in a shear field successfully predicts the number-size distribution of bubbles produced by the bubble generator.
How to Plan for Career of Undergraduates of Traditional Chinese Medicine (2010)

The actual state and social need of Chinese material medical modernization were analyzed.And then,the professional knowledge structure of undergraduate student of traditional Chinese medicine was discussed.Based on these analysis,this paper pointed out that 7P including GAP,GEP,GMP,GLP,GCP,GSP and GUP,which deal with all the processes of drug is very important.As a result the education program for Chinese Traditional Medicine College Students should be established by the request of 7P.Then the human resource of Traditional Chinese Medicine will meet the development of Chinese medicine modernization.
Reducing Channel Zapping Time in IPTV Based on User's Channel Selection Behaviors (2010)

Channel zapping time is a crucial issue in Internet Protocol Television (IPTV) Quality of Experience (QoE) performance. One way to reduce channel zapping time is a predictive tuning method, which reduces channel zapping time by prejoining channels that are likely to be selected next, in addition to the currently watched channel. This paper presents an improved predictive tuning method that satisfies required channel zapping time with minimized bandwidth usage. Unlike existing methods, the proposed method determines the most efficient number of prejoining channels in a surfing period and in a viewing period differently by estimating expected channel zapping time and expected bandwidth usage with a Semi-Markov Process. We also propose a prejoining channel selection method according to the combined button and channel preference. Mathematical model and simulation show that the proposed method achieves the required channel zapping time with less bandwidth consumption and a more stable network than previous works.