gebhart/patrepeval huggingface dataset:
Mechanisms of antibody-mediated insulin-like growth factor I receptor (IGF-IR) down-regulation in MCF-7 breast cancer cells. (2009)

The insulin-like growth factor I receptor (IGF-IR) plays a critical role in cell proliferation and survival. We previously reported that a recombinant anti-IGF-IR antibody, scFv-Fc, consisting of 1H7 monoclonal antibody (mAb)-derived single chain antibody (scFv) and human IgG1 Fc, significantly suppressed breast tumor growth, and we proposed IGFIR down-regulation as a mechanism for tumor growth inhibition (Horm Metab Res. 2003; 35:836, Cancer Res. 2003; 63:627). This study used MCF-7 breast cancer cells to investigate the effects of anti-IGF-IR mAbs with various epitope specificities on IGF-IR downregulation and signaling pathways. Despite their differing effects on IGF-IR signaling, all five mAbs used down-regulated IGF-IR. Inhibitor experiments indicated that anti-IGF-IR mAbs induced internalization of IGF-IR from clathrin coated-pits. Pretreatment of MCF-7 cells with methylamine substantially reduced the antibody-mediated IGF-IR down-regulation while MG115 did not. Ubiquitination of IGF-IR did not occur in MCF-7 cells after mAb treatment. These results suggest that anti-IGF-IR antibodies with different epitope-specificities can cause internalization of IGF-IR from clathrin-coated pits and down-regulation via a lysosome-dependent pathway in an IGF-IR activation-independent manner.
Pre-Virtualization: Slashing the cost of virtualization (2005)

Despite its current popularity, para-virtualization has an enormous cost. Its diversion from the platform architecture abandons many of the benefits that come with pure virtualization (the faithful emulation of the platform API): stable and well-defined platform interfaces, single binaries for kernel and device drivers (and thus lower testing, maintenance, and support cost), and vendor independence. These limitations are accepted as inevitable for significantly better performance and the ability to provide virtualization-like behavior on non-virtualizable hardware, such as x86. We argue that the above limitations are not inevitable, and present pre- virtualization, which preserves the benefits of full virtualization without sacrificing the performance benefits of para-virtualization. In a semi-automatic step an OS is prepared for virtualization. The required modifications are orders of magnitudes smaller than for para-virtualization. A virtualization module, that is collocated with the guest OS, transforms the standard platform API into the respective hypervisor API. The guest OS is still programmed against a common architecture, and the binary remains fully functional on bare hardware. The support of a new hypervisor or updated interface only requires the implementation of a single interface mapping. We validated our approach for a variety of hypervisors, on two very different hardware platforms (x86 and Itanium), with multiple generations of Linux as guests. We found that pre-virtualization achieves essentially the same performance as para-virtualization, at a fraction of the engineering cost.
An automated integrated platform for rapid and sensitive multiplexed protein profiling using human saliva samples (2014)

During the last decade, saliva has emerged as a potentially ideal diagnostic biofluid for noninvasive testing. In this paper, we present an automated, integrated platform useable by minimally trained personnel in the field for the diagnosis of respiratory diseases using human saliva as a sample specimen. In this platform, a saliva sample is loaded onto a disposable microfluidic chip containing all the necessary reagents and components required for saliva analysis. The chip is then inserted into the automated analyzer, the SDReader, where multiple potential protein biomarkers for respiratory diseases are measured simultaneously using a microsphere-based array via fluorescence sandwich immunoassays. The results are read optically, and the images are analyzed by a custom-designed algorithm. The fully automated assay requires as little as 10 μL of saliva sample, and the results are reported in 70 min. The performance of the platform was characterized by testing protein standard solutions, and the results were comparable to those from the 3.5 h lab bench assay that we have previously reported. The device was also deployed in two clinical environments where 273 human saliva samples collected from different subjects were successfully tested, demonstrating the device's potential to assist clinicians with the diagnosis of respiratory diseases by providing timely protein biomarker profiling information. This platform, which combines noninvasive sample collection and fully automated analysis, can also be utilized in point-of-care diagnostics.
Disseminated Granuloma Annulare – Treatment with Fumaric Acid Esters (2005)

Systemic therapy with FAE can be effective in patients suffering from disseminated forms of granuloma annulare, but side-effects of FAE have to be taken into consideration.
Low-complexity bit-parallel canonical and normal basis multipliers for a class of finite fields (1998)

We present a new low-complexity bit-parallel canonical basis multiplier for the field GF(2m) generated by an all-one-polynomial. The proposed canonical basis multiplier requires m/sup 2/-1 XOR gates and m/sup 2/ AND gates. We also extend this canonical basis multiplier to obtain a new bit-parallel normal basis multiplier.
Video skimming and characterization through the combination of image and language understanding (2002)

Digital video is rapidly becoming important for education, entertainment and a host of multimedia applications. With the size of the video collections growing to thousands of hours, technology is needed to effectively browse segments in a short time without losing the content of the video. We propose a method to extract the significant audio and video information and create a skim video which represents a very short synopsis of the original. The goal of this work is to show the utility of integrating language and image understanding techniques for video skimming by extraction of significant information, such as specific objects, audio keywords and relevant video structure. The resulting skim video is much shorter; where compaction is as high as 20:1, and yet retains the essential content of the original segment. We have conducted a user-study to test the content summarization and effectiveness of the skim as a browsing tool.
Phase error free linc modulator (1989)

A new technique for linear amplification with nonlinear components (LINC) is described. LINC implementation is thought to be very difficult because of its sensitivity to phase error caused by the difference in electrical length between two power amplifier branches. The allowable limit of phase error for achieving the 60 dB suppression of the adjacent channel interference (ACI) power is estimated for roll-off bandlimited offset QPSK (OQPSK). Then, a compensating method for this phase error is presented. By using the proposed method, sufficient out-of-band spectrum suppression for mobile radio application is obtained. An output power of 7.5 W and a power efficiency of 21% are experimentally confirmed.
THE MOLECULAR BASIS OF DEHYDRATION TOLERANCE IN PLANTS (1996)

Molecular studies of drought stress in plants use a variety of strategies and include different species subjected to a wide range of water deficits. Initial research has by necessity been largely descriptive, and relevant genes have been identified either by reference to physiological evidence or by differential screening. A large number of genes with a potential role in drought tolerance have been described, and major themes in the molecular response have been established. Particular areas of importance are sugar metabolism and late-embryogenesis-abundant (LEA) proteins. Studies have begun to examine mechanisms that control the gene expression, and putative regulatory pathways have been established. Recent attempts to understand gene function have utilized transgenic plants. These efforts are of clear agronomic importance.
Vasopressin and Shock (2001)

Vasopressin (antidiuretic hormone) is emerging as a potentially major advance in the treatment of a variety of shock states. Increasing interest in the clinical use of vasopressin has resulted from the recognition of its importance in the endogenous response to shock and from advances in understanding of its mechanism of action. From animal models of shock, vasopressin has been shown to produce greater blood flow diversion from non-vital to vital organ beds (particularly the brain) than does adrenaline. Although vasopressin has similar direct actions to the catecholamines, it may uniquely also inhibit some of the pathologic vasodilator processes that occur in shock states. There is current interest in the use of vasopressin in the treatment of shock due to ventricular fibrillation, hypovolaemia, sepsis and cardiopulmonary bypass. This article reviews the physiology and pharmacology of vasopressin and all of the relevant animal and human clinical literature on its use in the treatment of shock following a MEDLINE (1966-2000) search.
Femtosecond laser-induced formation of submicrometer spikes on silicon in water (2004)

We fabricate submicrometer silicon spikes by irradiating a silicon surface that is submerged in water with 400 nm, 100 fs laser pulses. These spikes are less than a micrometer tall and about 200 nm wide—one to two orders of magnitude smaller than the microspikes formed by laser irradiation of silicon in gases or vacuum. Scanning electron micrographs of the surface show that the formation of the spikes involves a combination of capillary waves on the molten silicon surface and laser-induced etching of silicon. Chemical analysis and scanning electron microscopy of the spikes show that they are composed of silicon with a 20-nm-thick surface oxide layer.
A Comparison of Angioplasty with Medical Therapy in the Treatment of Single-Vessel Coronary Artery Disease (1992)

For patients with single-vessel coronary artery disease, PTCA offers earlier and more complete relief of angina than medical therapy and is associated with better performance on the exercise test. However, PTCA initially costs more than medical treatment and is associated with a higher frequency of complications.
Prometheus's Vulture and the Stem-Cell Promise (2003)

Embryonic stem cells have been the focus of intense study over the past two decades. Embryonic stem cells originate from undetermined early embryos, with no possible history of differentiation, whereas the provenance of adult stem cells found in mature tissues is far less well understood. The possibility that a population of reserve stem cells, perhaps set aside during gestation, might be coerced into renewed regenerative service later in life holds great promise. This review considers the status of stem-cell research.
Isolation and characterization of a MAGE gene family in the Xp21.3 region. (1995)

A human gene with strong homology to the MAGE gene family located in Xq27-qter has been isolated by using exon-trapping of cosmids in the Xp21.3 region. We have mapped and sequenced cDNA and genomic clones corresponding to this gene, MAGE-Xp, and shown that the last exon contains the open reading frame and is present in a minimum of five copies in a 30-kb interval. MAGE-Xp is expressed only in testis and, unlike the Xq27-qter MAGE genes, it is not expressed in any of 12 different tumor tissues tested. However, the gene and predicted protein structure are conserved, suggesting a similar function. MAGE-Xp is located in the 160-kb critical interval defined for the locus involved in sex determination within Xp21 and is 50 kb distal to the DAX-1 gene, which is responsible for X-chromosome-linked adrenal hypoplasia congenita.
T Cell‐Mediated Cytotoxicity Against p53‐Protein Derived Peptides in Bulk and Limiting Dilution Cultures of Healthy Donors (1995)

The p53 tumour suppressor gene product plays an important role in the development of most human cancers. Point mutations in the p53 gene are common in malignant states and results in over-expression of wild type and mutant determinants of the p53 protein. This process might generate MHC-I restricted epitopes for T cell recognition and p53-derived peptides have been suggested as targets for tumour-specific cytotoxic T lymphocytes (CTL). Our primary aim was to estimate the frequencies of p53-peptide reactive CTL precursors (CTLp) in peripheral blood from healthy young individuals. We selected wild type and mutated peptides derived from the p53 sequence with a binding motif for HLA-A2.1 molecules. Peripheral blood mononuclear cells (PBMC) from healthy HLA-A2 donors were stimulated in vitro in bulk cultures as well as in limiting dilution cultures using autologous cells pulsed with p53 peptides as stimulator cells. T cell reactivity was observed towards both wild type and mutated p53 peptide epitopes with CTL precursor frequencies varying from 1:2 x 10(4) to 1:1.5 x 10(5). These results might suggest the presence of an ongoing immune response in normal individuals against cells expressing increased levels of p53 protein.
Activation of pp60c-src protein kinase activity in human colon carcinoma. (1987)

The tyrosine-specific protein kinase activity of pp60c-src molecules obtained from human colon carcinoma tissues and tumor-derived cell lines was found to be elevated over that from normal colon tissues or cultures of normal colon mucosal cells. The elevated pp60c-src protein kinase activity in tumor tissues and in cultured colon carcinoma cells does not appear to result solely from an increase in the abundance of the c-src-encoded protein, suggesting that the specific activity of the pp60c-src tyrosine phosphotransferase is enhanced. These results raise the possibility that activation of the pp60c-src protein kinase may contribute to the genesis of human colon tumors.
Protection from Chemotherapy-Induced Alopecia in a Rat Model (1990)

Alopecia (hair loss) is among the most distressing side effects of cancer chemotherapy. Little progress has been made, however, in its prevention or treatment, partly because of the lack of suitable experimental model. In recent work on the treatment of myelogenous leukemia in the rat, the following observations were made: (i) treatment of 8-day-old rats with cytosine arabinoside consistently produced alopecia, and (ii) ImuVert, a biologic response modifier derived from the bacterium Serratia marcescens, uniformly produced complete protection against the alopecia. In subsequent experiments, both cyclophosphamide and doxorubicin also produced alopecia in this model, and the doxorubicin-induced alopecia was prevented by treatment with ImuVert. The potential relevance of these observations to chemotherapy-induced alopecia in the clinical setting should be examined.
Dendritic cells produce macrophage inflammatory protein-1 γ, a new member of the CC chemokine family (1996)

Langerhans cells (LC) are skin-specific members of the dendritic cell (DC) family. DC are unique among APC for their capacity to activate immunologically naive T cells, but little is known about their chemotactic recruitment of T cells. We now report that LC produce macrophage inflammatory protein-1 gamma (MIP-1 gamma), a newly identified CC chemokine. MIP-1 gamma mRNA was detected in epidermal cells freshly procured from BALB/c mice, and depletion of I-A+ epidermal cells (i.e., LC) abrogated that expression. MIP-1 gamma mRNA was detected in the XS52 LC-like DC line as well as by 4F7+ splenic DC and granulocyte-macrophage CSF-propagated bone marrow DC. XS52 DC culture supernatants contained 9 and 10.5 kDa immunoreactivities with anti-MIP-1 gamma Abs. We observed in Boyden chamber assays that 1) XS52 DC supernatant (added to the lower chambers) induced significant migration by splenic T cells; 2) this migration was blocked by the addition of anti-MIP-1 gamma in the lower chambers or by rMIP-1 gamma in the upper chambers; and 3) comparable migration occurred in both CD4+ and CD8+ T cells and in both activated and nonactivated T cells. We conclude that mouse DC (including LC) have the capacity to elaborate the novel CC chemokine MIP-1 gamma, suggesting the active participation of DC in recruiting T cells before activation.
5-Aminolevulinic Acid-Conjugated Gold Nanoparticles for Photodynamic Therapy of Cancer (2008)

5-ALA-conjugated nanoparticles offer a new modality for selective and efficient destruction of tumor cells, with minimal damage to fibroblasts in the 5-ALA-photodynamic therapy.
Ubiquitous Robot: A New Paradigm for Integrated Services (2007)

This paper presents the components and overall architecture of the ubiquitous robot (Ubibot) system developed to demonstrate ubiquitous robotics, a new paradigm for integrated services. The system has been developed on the basis of the definition of the ubiquitous robot as that of encompassing the software robot Sobot, embedded robot Embot and the mobile robot Mobot. This tripartite partition, which independently manifests intelligence, perception and action, enables the abstraction of intelligence through the standardization of sensory data and motor or action commands. The Ubibot system itself is introduced along with its component subsystems of Embots, the position Embot, vision Embot and sound Embot, the Mobots of Mybot and HSR, the Sobot, Rity, a virtual pet modeled as an artificial creature, and finally the middleware which seamlessly enables interconnection between other components. Three kinds of experiments are devised to demonstrate the fundamental features, of calm sensing, context awareness and seamless service transcending the spatial limitations in the abilities of earlier generation personal robots. The experiments demonstrate the proof of concept of this powerful new paradigm which shows great promise.
Estimation from lossy sensor data (2004)

Due to constraints in cost, power, and communication, losses often arise in large sensor networks. The sensor can be modeled as an output of a linear stochastic system with random losses of the sensor output samples. This paper considers the general problem of state estimation for jump linear systems where the discrete transitions are modeled as a Markov chain. Among other applications, this rich model can be used to analyze sensor networks. The sensor loss events are then modeled as Markov processes. Under the jump linear system model, many types of underlying losses can be easily considered, and the optimal estimator to be performed at the receiver in the presence of missing sensor data samples is given by a standard time-varying Kalman filter.We show that the asymptotic average estimation error variance converges and is given by a Linear Matrix Inequality, which can be easily solved. Under this framework, any arbitrary Markov loss process can be modeled, and its average asymptotic error variance can be directly computed. We include a few illustrative examples including .xed-length burst errors, a two-state model,and partial losses due to multiple SNR states. Our analysis encompasses modeling discrete changes not only in the received data as stated above, but also in the underlying system. In the context of the lossy sensor model, the former allows for variation in sensor positioning, power control, and loss of data communications; the latter could allow for discrete changes in the dynamics of the variable monitored by the sensor. This freedom in modeling yields a tool that is potentially valuable in various scenarios in which entities that share information are subjected to challenging and time-varying network conditions.
Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies. (2002)

We selected 10 transmembrane (TM) prediction methods (KKD, TMpred, TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0 and HMMTOP 2.0) and re-assessed its prediction performance using a reliable dataset with 122 entries of experimentally-characterized TM topologies. Then, we improved prediction performance by a consensus prediction method. Prediction performance during re-assessment and consensus prediction were based on four attributes: (i) the number of transmembrane segments (TMSs), (ii) the number of TMSs plus TMS-position, (iii) N-tail location and (iv) TM topology. We noted that hidden Markov model-based methods dominate over other methods by individual prediction performance for all four attributes. In addition, all top-performing methods generally were model-based. Among prokaryotic sequences, HMMTOP 2.0 solely topped among other methods with prediction accuracies ranging from 64% to 86% across all attributes. However, among eukaryotic sequences, prediction performance for all the attributes was relatively poor compared with prokaryotic ones. On the other hand, our results showed that our proposed consensus prediction method significantly improved prediction performance by, at least, an additional nine percentage points particularly among prokaryotic sequences for the number of TMS (84%), number of TMS and position (80%), and TM topology attributes (74%). Although our consensus prediction method improved also the prediction performance among eukaryotic sequences, the obtained accuracies for all attributes were relatively lower than that obtained by prokaryotic counterparts particularly for TM topology.
Investigation of the Influence of Cytosine Methylation on DNA Flexibility (1995)

To test the influence of pyrimidine methyl groups on DNA flexibility and helix repeat, two sets of 14 mixed sequence DNA molecules, spanning a range of lengths from 158 to 180 base pairs, were cyclized with T4 DNA ligase. The two sets differed only in that the Cyt-5 positions of all cytosines (80-90 cytosine residues per molecule) were fully methylated in the members of one set. Determination of the molar cyclization factors, persistence lengths, helix repeats, and torsional elastic constants revealed no significant differences between the two sets. These results imply that, at least for mixed sequence DNA, the biological consequences of cytosine methylation are likely to derive from either local structural distortions in the helix, which do not propagate as altered twist, or from direct protein-methyl cytosine interactions.
Inhibition of Endostatin/Collagen XVIII Deteriorates Left Ventricular Remodeling and Heart Failure in Rat Myocardial Infarction Model (2009)

Neutralization of endostatin worsens the symptoms and outcomes of MI in a rat model. The results imply that endogenous endostatin/collagen XVIII may suppress aberrant LV remodeling and heart failure after MI. (Circ J 2010; 74: 109 - 119).
Molecular cloning and nucleotide sequence of full-length of cDNA coding for porcine gastrin. (1982)

We have cloned in EScherichia coli a cDNA copy of mRNA coding for the porcine antral mucosal hormone preprogastrin. Full-length double-stranded cDNA was synthesized and inserted into the Pst I endonuclease site in plasmid pBR322 by using a homopolymeric extension technique. A partial cDNA clone was used as a probe to identify a complete cDNA clone in a cDNA library by colony hybridization. Four positive clones were isolated, one of which corresponded to porcine preprogastrin mRNA. The nucleotide sequence of the cDNA insert (602 nucleotides) revealed 312 nucleotides in the entire mRNA coding region, 61 nucleotides in the 5' untranslated region, 86 nucleotides in the 3'untranslated region, and a poly(A) tail of 86 nucleotides. Gastrin is located near the carboxyl end of preprogastrin and is flanked at both its amino and carboxyl ends by a pair of basic amino acid residues. The presence of glycine and a pair of basic amino acid residues adjacent in the carboxyl-terminal phenylalanine of gastrin indicates that the glycine and a pair of basic amino acid residues may be required for the enzymatic amidation of phenylalanine to phenylalanine amide.