gebhart/patrepeval huggingface dataset:
A Comprehensive Immunologic Portrait of Triple-Negative Breast Cancer (2018)

Triple-negative breast cancer (TNBC) is a high-risk malignancy due to its high capacity for invasion and lack of targeted therapy. Immunotherapy continues to demonstrate efficacy in a variety of cancers, and thus may be a promising strategy for TNBC given the limited therapeutic options currently available for TNBC. In this study, we performed an exhaustive analysis of immunogenic signatures in TNBC based on 2 large-scale breast cancer (BC) genomic data. We compared enrichment levels of 26 immune cell activities and pathways among TNBC, non-TNBC, and normal tissue, and within TNBCs of different genotypic or phenotypic features. We found that almost all analyzed immune activities and pathways had significantly higher enrichment levels in TNBC than non-TNBC. Elevated enrichment of these immune activities and pathways was likely to be associated with better survival prognosis in TNBC. This study demonstrated that TNBC likely exhibits the strongest immunogenicity among BC subtypes, and thus warrants the immunotherapeutic option for TNBC.
VirD4‐independent transformation by CloDF13 evidences an unknown factor required for the genetic colonization of plants via <i>Agrobacterium</i> (2003)

Agrobacterium uses a mechanism similar to conjugation for trans-kingdom transfer of its oncogenic T-DNA. A defined VirB/VirD4 Type IV secretion system is responsible for such a genetic transfer. In addition, certain virulence proteins as VirE2 can be mobilized into host cells by the same apparatus. VirE2 is essential to achieve plant but not yeast transformation. We found that the limited host range plasmid CloDF13 can be recruited by the virulence apparatus of Agrobacterium for transfer to eukaryotic hosts. As expected the VirB transport complex was required for such trans-kingdom DNA transfer. However, unexpectedly, the coupling factor VirD4 turned out to be necessary for transfer to plants but not for transport into yeast. The CloDF13 encoded coupling factor (Mob) was essential for transfer to both plants and yeast though. This is interpreted by the different specificities of Mob and VirD4. Hence, Mob being required for the transport of the CloDF13 transferred DNA (to both plants and yeast) and VirD4 being required for transport of virulence proteins such as VirE2. Nevertheless, the presence of the VirE2 protein in the host plant was not sufficient to restore the deficiency for VirD4 in the transforming bacteria. We propose that Mob functions encoded by the plasmid CloDF13 are sufficient for DNA mobilization to eukaryotic cells but that the VirD4-mediated pathway is essential to achieve DNA nuclear establishment specifically in plants. This suggests that other Agrobacterium virulence proteins besides VirE2 are translocated and essential for plant transformation.
Improving search in social networks by agent based mining (2009)

The popularity of social networks have burgeoned in recent years. Users share and access large volumes of information on social networking sites like Facebook, Flickr, del.icio.us, etc. Whereas a few of these sites have generic, impersonal searching mechanisms, we have developed an agent-based framework that mines the social network of a user to improve search results. Our Social Networkbased Item Search (SNIS) system uses agents that utilize the connections of a user in the social network to facilitate the search for items of interest. Our approach generates targeted search results that can improve the precision of the result returned from a user’s query. We have implemented the SNIS agent-based framework in Flickr, a photosharing social network, for searching for photos by using tag lists as search queries. We discuss the architecture of SNIS, motivate the searching scheme used, and demonstrate the effectiveness of the SNIS approach by presenting results. We also show how SNIS can be utilized for expertise location. 1
Chemically Sensitive High Throughput Parallel Analysis of Solid Phase Supported Library Members (2000)

This paper introduces Fourier transform infrared imaging as a powerful spectroscopic tool for the parallel identification of members of resin-supported combinatorial libraries. This technique combines the chemical specificity and high sensitivity of FTIR with the ability to rapidly analyze multiple supported resin beads simultaneously. It is shown here that the chemical identity of ligands on a variety of supported resin beads can be identified in a single experiment without destroying or otherwise perturbing the system.
VALUE OF ELECTROTHERMIC METHODS IN THE TREATMENT OF MALIGNANCY (1925)

During the last decade, the successful treatment of cancer has been greatly facilitated by improvements in our physical methods; namely, roentgen ray and radium. General surgeons have paid no little attention to heat, a most potent factor in destroying neoplastic cells without serious damage to surrounding healthy tissues, and with a resultant slowly healing, indolent, sclerotic ulceration, although it has not been universally accepted and used. The reason for the apparent general discard of so powerful a therapeutic agent has undoubtedly been the lack of any efficient apparatus and technic to cause penetration of the heat sufficiently deep to kill the cells at a distance from the point of application. Boiling water, superheated steam and aerocauterization have fallen into disuse because accurate and convenient application is impossible and penetration is limited. Other heat producing apparatus, as the Paquelin and electric cauteries, destroy cells at the point of contact and for
Chemical vapor deposition of diamond growth using a chemical precursor (1998)

A nucleation method to form diamond on chemically pretreated silicon (111) surfaces is reported. The nucleation consisted of binding covalently 2,2-divinyladamantane molecules on the silicon substrate. Subsequently, low pressure diamond growth was performed via microwave plasma chemical vapor deposition in a tubular deposition system. The resulting diamond layers presented a good crystallinity and the Raman spectra showed a very sharp peak at 1331 cm−1.
Nonlinear refractive index in erbium doped optical fiber: Theory and experiment (1991)

An intensity-dependent refractive index in erbium doped optical fiber has been observed for the first time. The effect has been observed by an interferometric technique using a two-core fiber. The effect is analyzed theoretically, and the important nonlinear parameters for thin material have been determined and are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Thiopeptin, a New Feed Additive Antibiotic: Microbiological and Chemical Studies (1972)

The thiopeptins are a new group of sulfur-containing peptide antibiotics produced by Streptomyces tateyamensis. The antibiotic consists of a major component (designated as thiopeptin B) and four minor ones (thiopeptins A(1) to A(4)). These components were isolated by solvent extraction from mycelium followed by chromatography on silica gel with various ratios of chloroform and methanol as elution solvents. Acid hydrolysis of each of the thiopeptin components yielded 1 mole of valine, 1 of threonine, 1 of cysteine, and 2 of alanine as amino acids. Each component of the thiopeptin A group has chemical and biological properties closely similar to those of thiopeptin B, but detailed characterization has established that thiopeptins A(1), A(3), and A(4) are new antibiotics. We could not obtain accurate data for determination of the uniqueness of A(2) because of insufficient sample. Thiopeptin has strong antibacterial activity against gram-positive bacteria and Mycoplasma, and exhibits no cross-resistance to major human-use antibiotics.
High-Performance Blue Electroluminescent Devices Based on a Biaryl (2002)

BTP (2,2′-bistriphenylenyl) emits very strong blue light in the solid state and in solution and shows excellent physical properties, such as a very good thermal stability and a high melting point. Electroluminescent devices using BTP as the blue emitter show high brightness, good external quantum and current efficiency, and excellent CIE coordinates.
Tumour markers in pancreatic cancer. (1989)

Patients with pancreatic cancer usually lack signs and symptoms in the early course of the disease. Even when malignancy is suspected, differential diagnosis between benign and malignant pancreatic disorders may be difficult with current methods. An increasing interest has been focused on the utility of immunological tumour markers. CEA has been widely used since the early seventies, but the results in diagnosis of pancreatic cancer have been disappointing. Tumour marker tests for CA 19-9 and CA 50 are based on monoclonal antibodies to colonic carcinoma cell lines. CA 19-9 and CA 50 are strongly expressed in most tissue specimens from pancreatic carcinomas, but are also found in normal pancreas and benign pancreatic diseases. The CA 19-9 and CA 50 antigens are shed or released into the circulation, and are found in increased concentrations in 70-80% of patients with pancreatic cancer. Also 50-65% of patients with small resectable carcinomas have elevated CA 19-9 and CA 50 levels, although very high serum concentrations usually indicate advanced disease. Slightly elevated serum CA 19-9 and CA 50 levels are seen in some patients with benign pancreatic diseases, more often in acute than in chronic pancreatitis. Elevated values are often observed in patients with benign obstruction of the common bile duct, particularly in patients with cholangitis. In patients with jaundice of hepatocellular origin, the CA 19-9 and CA 50 levels are lower than in extrahepatic cholestasis. CA 19-9 and CA 50 have better diagnostic accuracy for pancreatic cancer than CEA, CA 125, DU-PAN-2, TPA and PSTI/TATI. However, the sensitivities and specificities of CA 19-9 and CA 50 are too low for screening of an asymptomatic population. Nevertheless, CA 19-9 and CA 50 have in our experience shown to be useful complements to other diagnostic methods in symptomatic patients with suspicion of pancreatic cancer. Combinations of different markers improve the sensitivity only slightly compared to the use of CA 19-9 or CA 50 alone. Follow-up using CA 19-9 and CA 50 is a simple and sensitive way of monitoring the postoperative course of patients with pancreatic cancer, and may give a lead time of several months for a recurrence compared to conventional methods.
Design, Modeling, and Optimization for Highly Efficient Ionic Wind-Based Cooling Microfabricated Devices (2010)

The purpose of this work is to re-design, model and optimize a single microfabricated ionic wind pump device [1]. The device could then be employed in a three-dimensional array for use in larger-scale microchip cooling and enhanced thermal spreading applications. The innovative microfabricated air-cooling technology employs an electrohydrodynamic corona discharge (i.e. ionic wind pump) for efficient heat removal from electronic components. Our single ionic wind pump element consists of two parallel collecting electrodes between which a single emitting tip is positioned. The collector electrodes are patterned with a grid structure, which enhances the overall heat transfer coefficient and facilitates a batch and IC compatible process. Various design configurations are explored and modeled computationally to investigate their influence on the cooling phenomenon. In particular, COMSOL Multiphysics™ is employed to computationally explore the effects of collector-emitter configuration on the electrohydrodynamic phenomenon, the flow field and resulting cooling effects. Using both computational and experimental results, we estimate that a two-dimensional array of microfabricated ionic wind pumps covering approximately 2″ square should be able to dissipate greater than 2 W of heat, using about 1/5 the power input as a conventional fan.
High-Throughput Selection of Effective RNAi Probes for Gene Silencing (2003)

RNA interference (RNAi) is a process of sequence-specific posttranscriptional gene silencing mediated by double-stranded RNA. RNAi has recently emerged as a powerful genetic tool to analyze gene function in mammalian cells. The power of this method is limited however, by the uncertainty in predicting the efficacy of small interfering RNAs (siRNAs) in silencing a gene. This has imposed serious limitations not only for small-scale but also for high-throughput RNAi screening initiatives in mammalian systems. We have developed a reliable and quantitative approach for the rapid and efficient identification of the most effective siRNA against any gene. The efficacy of siRNA sequences is monitored by their ability to reduce the expression of cognate target-reporter fusions with easily quantified readouts. Finally, using micro array-based cell transfections, we demonstrate an unlimited potential of this approach in high-throughput screens for identifying effective siRNA probes for silencing genes in mammalian systems. This approach is likely to have implications in the use of RNAi as a reverse genetic tool for analyzing mammalian gene function on a genome-wide scale.
CMOS optical receiver chipset for gigabit Ethernet applications (2003)

This paper describes a 1.25-Gb/s simplified CMOS optical receiver chipset for gigabit Ethernet applications, consisting of a transimpedance amplifier (TIA) and a clock and data recovery (CDR) circuit. The TIA takes a fully differential regulated cascode configuration, demonstrating 700 MHz bandwidth for 1 pF photodiode capacitance, 80 dB/spl Omega/ transimpedance gain, -17 dBm sensitivity for BER of 10/sup -12/, and 27 mW power consumption. In our design, the postamplifier is omitted due to the large voltage swing of the TIA and to the high sensitivity of the proposed CDR. The CDR takes a half-rate clock technique and thus removes the necessity of a 1:2 demultiplexer. It achieves 40 mV/sub pp/ sensitivity due to the high sensitivity phase detector. The RMS clock jitter and data jitter are measured to be 3.9 ps/sub rms/ and 20.2 ps/sub rms/, respectively. Two chips dissipate 127 mW from a single 2.5 V supply.
Review: Poly(vinyl alcohol) Functionalizations and Applications (2015)

Functionalizations of poly(vinyl alcohol) congruent with the desired applications are discussed inthis article. The chemical modifications of poly(vinyl alcohol) with different molecular weights and hydrolysis degrees via conventional chemistries, namely esterification, carbamation, and etherification, and via the modern ones such as click chemistry, led to finished materials with a wide range of applications and uses: membrane fuel cells, biologicals and biomedicals, adsorption of heavy metals and other contaminants, molecular sensing or chemosensor for detection of some useful molecules or toxic ones, separation of mixtures, and catalysis in organic and inorganic syntheses. Different forms of the duly modified poly(vinyl alcohol)s were used in such applications, including hydrogels, films, membranes, and nanoparticles. The incorporated modifying agents onto poly(vinyl alcohol) matrixes brought some changes that were in tune with the projected applications. These modifying agents were not confined to molecular compounds but also to macromolecular ones which are graphene, hyaluronic acid, β-cylcodextrin, polystyrene, poly(4-vinylpyridine), and poly(L-lactic acid).
Study of Pt Bottom Electrodes using High-Temperature Sputtering for Ferroelectric Memories with SrBi<sub>2</sub>Ta<sub>2</sub>O<sub>9</sub> (SBTO) Film (1998)

Pt bottom electrodes for SrBi 2 Ta 2 O 9 (SBTO) capacitors have been investigated for use in nonvolatile memories. A Pt thin film which is sputtered at a temperature of 300°C consists of enlarged columnar grains, while a film sputtered at room temperature consists of fibrous columnar grains. The formation mechanism of enlarged grains of the Pt film sputtered at 300°C is due to the fact that the film structure changes with substrate temperature based on the structure-zone model. The Pt bottom electrode which consists of the enlarged grains results in a decrease in the Ti diffusion path, leading to effective adhesion of Pt to a SiO 2 film.
Analgesic effects of dextromethorphan and morphine in patients with chronic pain (2002)

N-methyl-aspartate (NMDA) receptor antagonists have been shown to improve opioid analgesia in the animal model. The cough suppressant dextromethorphan is a clinically available NMDA-receptor antagonist. In this randomised, double-blind, placebo-controlled study 20 patients with chronic pain of several years duration were given 100 mg of oral dextromethorphan or matching placebo 4 h prior to an intravenous infusion of morphine 15 mg. Pain intensity and adverse effects were assessed at 0, 4, 5 and 7 h. Dextromethorphan had no effect on morphine analgesia: the mean (+/-SEM) visual analogue scores for pain relief (VAS, 0-100 mm) at the end of the morphine infusion were 38 (+/-6) for dextromethorphan+morphine and 38 (+/-7) for placebo+morphine. VAS scores for pain intensity were comparable both at rest and at movement at all time points. The most common adverse effects reported were dizziness, nausea and sedation. There were no significant differences in either the incidence or severity of adverse effects. In conclusion, oral dextromethorphan 100 mg had no effect on pain relief by intravenous morphine 15 mg in patients with chronic pain.
Surveillance and Tracking System with Collaboration of Robots, Sensor Nodes, and RFID Tags (2009)

In this paper, we propose a divide and conquer based surveillance framework, in which a large surveillance area is divided into small areas by critical points and critical lines. Sensor nodes, sinks, robots, and RFID tags are all used. We deploy sensor nodes along critical lines only instead of all over the region. Our aim is to do surveillance with efficient deployment of sensor nodes and sinks, and to detect then track and even capture targets, e.g., an intrusion tank or forest fire, with the collaboration of robots and sensor nodes.
A blood stage antigen of Plasmodium falciparum shares determinants with the sporozoite coat protein. (1985)

A cDNA clone expressing a Plasmodium falciparum blood-stage antigen in Escherichia coli was identified by colony immunoassay using immune human sera. Antibodies affinity-purified on extracts of this clone reacted with both asexual blood stages and sporozoites of P. falciparum, recognizing a Mr23,000 protein in the blood stages. The nucleotide sequence of the cDNA revealed a signal peptide and an internal hydrophobic sequence typical of transmembrane anchor sequences. Located 3' to the putative anchor are two tetramers, Asn-Ala-Asn-Pro and Asn-Ala-Asp-Pro, which are closely related to the repeats of the circumsporozoite protein of P. falciparum. The blood stage protein is conserved amongst several isolates of P. falciparum, and antibodies against it are common in the sera of individuals living in the area where the parasite is endemic.
Reinforcement Learning for Energy-Efficient Delay-Sensitive CSMA/CA Scheduling (2016)

We study learning-based energy-efficient multi- user scheduling of delay-sensitive data over fading channels. To tradeoff energy and delay, we combine adaptive rate transmission at the physical layer with a rate-adaptive medium access control (MAC) protocol based on carrier sense multiple access with collision avoidance (CSMA/CA). We formulate the multi-user scheduling problem as a constrained Markov decision process (CMDP). We show that the multi-user problem is intractable and propose to decompose it into multiple (coupled) single-user problems. We design a reinforcement learning algorithm to solve the single-user problems online so that users can achieve energy-efficient operation while meeting their delay constraints, even though the channel, traffic, and multi-user dynamics are unknown a priori. Our proposed MAC protocol enables users to meet significantly tighter delay constraints while also consuming less energy than under the 802.11 Distributed Coordination Function (DCF). Moreover, the proposed learning algorithm converges significantly faster than a state-of-the-art solution.
Longitudinal assessment of DNA methylation changes during HPVE6E7-induced immortalization of primary keratinocytes (2015)

High-risk human papillomavirus (hrHPV)-induced immortalization and malignant transformation are accompanied by DNA methylation of host genes. To determine when methylation is established during cell immortalization and whether it is hrHPV-type dependent, DNA methylation was studied in a large panel of HPVE6E7-immortalized keratinocyte cell lines. These cell lines displayed different growth behaviors, i.e., continuous growth versus crisis period prior to immortalization, reflecting differential immortalization capacities of the 7 HPV-types (16/18/31/33/45/66/70) studied. In this study, cells were monitored for hypermethylation of 14 host genes (APC, CADM1, CYGB, FAM19A4, hTERT, mir124-1, mir124-2, mir124-3, MAL, PHACTR3, PRDM14, RASSF1A, ROBO3, and SFRP2) at 4 different stages during immortalization. A significant increase in overall methylation levels was seen with progression through each stage of immortalization. At stage 1 (pre-immortalization), a significant increase in methylation of hTERT, mir124-2, and PRDM14 was already apparent, which continued over time. Methylation of ROBO3 was significantly increased at stage 2 (early immortal), followed by CYGB (stage 3) and FAM19A4, MAL, PHACTR3, and SFRP2 (stage 4). Methylation patterns were mostly growth behavior independent. Yet, hTERT methylation levels were significantly increased in cells that just escaped from crisis. Bisulfite sequencing of hTERT confirmed increased methylation in immortal cells compared to controls, with the transcription core and known repressor sites remaining largely unmethylated. In conclusion, HPV-induced immortalization is associated with a sequential and progressive increase in promoter methylation of a subset of genes, which is mostly independent of the viral immortalization capacity.
GPS Sun tracking Solar Panel (2015)

Overview The concept of our project is based on the Global Positioning System (GPS) controlled Sun Tracking System and the name of our model is GPS CONTROLLED SUN TRACKING SYSTEM. The solar panel will directed towards sun in order to maximize the tracking of solar energy. The tracking of solar energy from the sun will be guided by Global Positioning system. The GPS will regulate the orientation of solar panel to capture the maximum solar energy from the sun. The installed GPS will be equipped with longitude and latitude that correlated with time, therefore in such case the solar panel will actually know where it is and at what angle it should face the sun.