gebhart/patrepeval huggingface dataset:
Live Metric 3D Reconstruction on Mobile Phones (2013)

In this paper, we propose a complete on-device 3D reconstruction pipeline for mobile monocular hand-held devices, which generates dense 3D models with absolute scale on-site while simultaneously supplying the user with real-time interactive feedback. The method fills a gap in current cloud-based mobile reconstruction services as it ensures at capture time that the acquired image set fulfills desired quality and completeness criteria. In contrast to existing systems, the developed framework offers multiple innovative solutions. In particular, we investigate the usability of the available on-device inertial sensors to make the tracking and mapping process more resilient to rapid motions and to estimate the metric scale of the captured scene. Moreover, we propose an efficient and accurate scheme for dense stereo matching which allows to reduce the processing time to interactive speed. We demonstrate the performance of the reconstruction pipeline on multiple challenging indoor and outdoor scenes of different size and depth variability.
Predicting Human Immunodeficiency Virus (HIV) Drug Resistance using Recurrent Neural Networks (2006)

Motivation: Predicting HIV resistance to drugs is one of many problems for which bioinformaticians have implemented and trained machine learning methods, such as neural networks. Predicting HIV resistance would be much easier if we could directly use the three-dimensional (3D) structure of the targeted protein sequences, but unfortunately we rarely have enough structural information available to train a neural network. Furthermore, prediction of the 3D structure of a protein is not straightforward. However, characteristics related to the 3D structure can be used to train a machine learning algorithm as an alternative to take into account the information of the protein folding in the 3D space. Here, starting from this philosophy, we select the amino acid energies as features to predict HIV drug resistance, using a specific topology of a neural network.Results: In this paper, we demonstrate that the amino acid energies are good features to represent the HIV genotype. In addition, it was shown that Bidirectional Recurrent Neural Networks can be used as an efficient classification method for this problem. The prediction performance that was obtained was greater than or at least comparable to results obtained previously. The accuracies vary between 81.3% and 94.7%.
Pathomechanisms of Dextran-Induced Anaphylactoid/Anaphylactic Reactions in Man (1982)

Immune complex-mediated (type III) anaphylaxis is shown to be the pathomechanism of severe dextran-induced anaphylactic reactions in man. Mild reactions may be either antibody-dependent or not. Patients with severe reactions have regularly high titers of preformed, circulating dextran-reactive antibodies and represent a small subpopulation of high responders to dextran. Upon infusion of clinical dextran, noxious immune complexes are formed, leading to mediator release and symptoms of anaphylaxis. Consequently, application of the hapten inhibition principle is recommended for prevention of such reactions.
Recognition and phagocytosis of cells undergoing apoptosis (1997)

In vivo, the normal fate of cells undergoing apoptosis is recognition, uptake and degradation of the intact dying cell by phagocytes. Cell clearance by this mechanism is fast, efficient and injury-limiting, being mediated by macrophages and semi-professional phagocytes. Apoptotic cells are marked for disposal by mechanisms which remain poorly understood, although in some circumstances surface sugar changes and exposure of phosphatidylserine lead to recognition by uncharacterised phagocyte receptors. Furthermore, there is specific evidence in vitro for involvement of phagocyte receptors including the thrombospondin receptors alpha v beta 3 and CD36, scavenger receptors, the 61D3 antigen and the ABC 1 transporter. It is conceivable that recognition mechanisms may be ordered in a hierarchy of 'back ups', each recognising cells at different stages of the death program. Nevertheless, a full understanding of this complexity will require definition of recognition mechanisms which operate in vivo in higher organisms.
LEFLUNOMIDE, A NOVEL IMMUNOSUPPRESSIVE AGENT (1993)

Leflunomide is a novel immunomodulating drug that has recently been demonstrated to prevent acute rejection and reverse ongoing rejection of kidney and cardiac allografts in rats. In vitro studies here demonstrate that leflunomide suppresses proliferation of human PBL stimulated with (1) allogeneic PBL in a one-way MLR (50% inhibition with 50-25 microM); (2) anti-CD3 mABs plus PMA (50% inhibition with 70 microM leflunomide); and (3) anti-CD28 mABs plus PMA (50% inhibition with 65 microM leflunomide). In contrast, CsA only inhibited T cell proliferation stimulated by anti-CD3 plus PMA. Leflunomide partially inhibited IL-2 production of T cells stimulated with anti-CD3 plus PMA or anti-CD28 plus PMA, whereas CsA completely inhibited IL-2 production by T cells stimulated by the CD3 pathway and only partially inhibited IL-2 production by T cells stimulated by the CD28 pathway. Because comparable levels of IL-2 were produced by CD28-stimulated T cells treated with either CsA or leflunomide, but no inhibition of proliferation was observed in the CsA-treated cultures, we hypothesized that the lowering of IL-2 levels was not the mechanism by which leflunomide inhibited T cell proliferation. This hypothesis was supported by the observations that exogenous IL-2 failed to restore the T cell proliferation in the presence of leflunomide. Loss of T cell responsiveness to IL-2 in the presence of leflunomide was not due loss of expression of IL-2 receptors. Collectively, our data suggest that inhibition of T cell proliferation by leflunomide occurs via inhibition of responsiveness to IL-2.
Constitutive activation of mitogen-activated protein (MAP) kinases in human renal cell carcinoma. (1995)

Mitogen-activated protein kinases (MAPKs) play a pivotal role in the mitogenic signal transduction pathway and are essential components of the MAPK cascade, which includes MEK (also known as MAP kinase kinase), Raf-1, and Ras. In this study, we examined whether constitutive activation of the MAPK cascade was associated with the carcinogenesis of human renal cell carcinomas in a series of 25 tumors and in corresponding normal kidneys. Constitutive activation of MAPKs in tumor tissue, as determined by the appearance of phosphorylated forms, was found in 12 cases (48%), and this activation was confirmed by a direct in vitro kinase assay of immunoprecipitate using myelin basic protein as the substrate. The phosphorylation of MEK and of Raf-1, as monitored by a mobility shift in SDS-PAGE, which is reportedly associated with the activation of these kinases, occurred in 9 of 18 cases (50%) and in 6 of 11 cases (55%) respectively. The activation of MAPKs was correlated with MEK activation (P = 0.0045) and with Raf-1 activation (P = 0.067). Furthermore, overexpression of MEK was found in 13 of 25 cases (52%) by Western blot analysis, and this overexpression was associated significantly with MAPK activation (P = 0.034). No mutations were noted in H-,K-, or N-ras genes by PCR direct sequencing in any of the 25 tumor samples. Of the patients studied, 8 of 18 (44%) stage pT2 patients and four of six (67%) stage pT3 patients showed MAPK activation. The single stage pT1 patient did not evidence MAPK activation. Furthermore, one of seven (14%) grade 1 patients, 9 of 13 (69%) grade 2 patients, and two of five (40%) grade 3 patients showed MAPK activation (grade 1 versus grades 2 and 3, P = 0.046). Our results suggest that constitutive activation of MAPKs may be associated with the carcinogenesis of human RCCs.
Identification of small molecules that induce apoptosis in a Myc-dependent manner and inhibit Myc-driven transformation (2006)

The Myc transcription factor plays a central role in the regulation of cell cycle progression, apoptosis, angiogenesis, and cellular transformation. Myc is a potent oncoprotein that is deregulated in a wide variety of human tumors and is therefore an attractive target for novel cancer therapies. Using a cellular screening approach, we have identified low-molecular-weight compounds, Myc pathway response agents (MYRAs), that induce apoptosis in a c-Myc-dependent manner and inhibit Myc-driven cellular transformation. MYRA-A inhibits Myc transactivation and interferes with the DNA-binding activity of Myc family proteins but has no effect on the E-box-binding protein USF. In contrast, MYRA-B induces Myc-dependent apoptosis without affecting Myc transactivation or Myc/Max DNA binding. Our data show that cellular screening assays can be a powerful strategy for the identification of candidate substances that modulate the Myc pathway. These compounds can be useful tools for studying Myc function and may also be of therapeutic potential as leads for drug development.
Early cytological events after induction of cell division in egg cells and zygote development following in vitro fertilization with angiosperm gametes (1995)

Early events, such as formation of the cell wall, first nuclear division and first unequal division of the zygote, were examined following in vitro fusion of single egg and sperm protoplasts of maize ( Zea mays L.). The time course of these events was determined. The formation of cell wall components was observed 30 sec following egg—sperm fusion and proceeded continuously thereafter. Within 15 h after fusion most of the organelles became more densely grouped around the nucleus of the zygote. In the in vitro produced zygote the location of the cell organelles and of the dividing nucleus showed polarity. Two nucleoli were first observed 18 h after gamete fusion. The zygotic nucleus remained undivided for about 40 h. The first cell division was observed 40–60 h, generally 42–46 h, after egg—sperm fusion. The non‐fused egg cell could be triggered to sporophytic development in vitro by pulses of high amounts of 2,4‐D. Without such a treatment, cultured egg cells of different maize lines did not divide. Although nuclear fusion seemed to occur, fusion products of two egg cells also did not divide. Cell wall formation was incomplete and non‐uniform, showing a polarity of cultured egg cells and fusion products of two egg protoplasts. Cell division was also induced after fusion of maize egg with sperms of genetically remote species, such as Coix, Sorghum, Hordeum or Triticum . These gametic heterologous fusion products developed to microcalli. Moreover, cell division occurred in fusion products of an egg and a diploid somatic cell‐suspension protoplast from maize.
Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics (2002)

The biological control of inorganic crystal formation, morphology, and assembly is of interest to biologists and biotechnologists studying hard tissue growth and regeneration, as well as to materials scientists using biomimetic approaches for the control of inorganic material fabrication and assembly. Biomimetics requires an accurate understanding of natural mechanisms at the molecular level. Such understanding can be derived from the use of metal surfaces to study surface recognition by proteins together with combinatorial genetics techniques for the selection of suitable peptides. Polymerization of these peptides produces engineered polypeptides large enough to encode their own folding information with low structural complexity, while enhancing binding affinity to surfaces. The low complexity of such polypeptides can aid in analyses, leading to modeling and eventual manipulation of the structure of the folded polypeptide. This paper presents structure predictions for gold-binding protein sequences, originally selected by combinatorial techniques. Molecular dynamics simulations lasting 5 ns were carried out using solvated polypeptides at the gold surface to assess the dynamics of the binding process and the effects of surface topography on the specificity of protein binding.
Protein immobilization on the surface of liposomes via carbodiimide activation in the presence of N‐hydroxysulfosuccinimide (1988)

A method of the covalent immobilization of proteins on the surface of liposomes, containing 10% (by mol) of N-glutaryl phosphatidylethanolamine, is described. Carboxylic groups of liposomal N-glutaryl phosphatidylethanolamine were activated in the presence of water-soluble carbodiimide and N-hydroxysulfosuccinimide and reacted subsequently with protein amino groups. The liposome-protein conjugates formed contained up to 5 x 10(-4) mol protein/mol lipid. Lectins (RCA1 and WGA) upon immobilization on liposomes retained saccharide specificity and the ability to agglutinate red blood cells. The immobilization of mouse monoclonal IgG in a ratio of 3.5 x 10(-4) mol IgG/mol lipid was achieved. The liposome activation in the absence of N-hydroxysulfosuccinimide resulted in a 2-fold decrease of protein coupling yields.
The expression of 4-1BBL in different gastric cancer cell lines (2010)

Objective To study the expression of 4-1BBL and its biological function in different human gastric cancer cell lines. Methods The expression of 4-1BBL in different human gastric cancer cell lines was detected by using immunohistochemistry and reverse transcription-polymerase chain reaction (RT-PCR). The killing activity of lymphocytes against gastric cancer cell lines was measured by MTT, and interleukin (IL)-2, IL-10 and tumor necrosis factor (TNF)-ct were determined in the supernatant by en-zyme-linked immunosorbent assay (ELISA). Results The RT-PCR revealed that the 4-1BBL mRNA was expressed in MKN-28 (46. 63% ), SGC-7901 (37. 13% ), BGC-823(20. 43% ) and MGC-803 (14. 14% ) in the sequence from high to low levels. The 4-1BBL protein was expressed in MKN-28, SC, C-7901, BGC-823 and MGC-803 in the sequence from high to low levels. MTF analysis indicated that the killing activity was found from high to low in MKN-28, SGC-7901, BGC-823, MGC-803. ELISA analysis showed that IL-2 and TNF-α were found in MKN-28, SGC-7901, BGC-823 and MGC-803, and IL-10 was found in MGC-803, BGC-823, SGC-7901 and MKN-28 from high to low. Conclusion The four different gastric cancer cell lines all express 4-1BBL at the mRNA and protein level. The expression level of 4-1 BBL is related to dif-ferentiation of gastric cancer cell lines. The killing activity of lymphocytes against gastric cancer cell lines is increases with the increased 4-1BBL expression. Moreover, 4-1BBL can regulate tumor immunity by pro-moting the production of TNF-α, IL-2 and IL-10.

Key words: 
Gastric carcinoma;  Tumor immunity;  4-1BBL
In Situ XRD and Electrochemical Study of the Reaction of Lithium with Amorphous Silicon (2004)

Silicon is a very promising candidate to replace graphite as the anode in Li-ion batteries because of its very high theoretical capacity. It has not yet made its way into commercial cells because of severe problems with the charge and discharge cycling of the material. It seems that amorphous silicon and amorphous silicon-containing alloys exhibit much improved cycling performance. Therefore, it is desirable to fully understand the reaction of Li with a-Si. To this end, an in situ X-ray diffraction study of the reaction of lithium with a-Si has been performed. The results confirm that a new crystalline phase is formed below 30 mV vs. as first reported by Obrovac and Christensen in an article published in Electrochemical and Solid-State Letters. However, the crystalline phase only forms for films of a-Si above a critical thickness of about 2 μm. © 2004 The Electrochemical Society. All rights reserved.
Molecular Diversity in Chemical Databases:  Comparison of Medicinal Chemistry Knowledge Bases and Databases of Commercially Available Compounds (1996)

A molecular descriptor space has been developed which describes structural diversity. Large databases of molecules have been mapped into it and compared. This analysis used five chemical databases, CMC and MDDR, which represent knowledge bases containing active medicinal agents, ACD and SPECS, two databases of commercially available compounds, and finally the Wellcome Registry. Together these databases contained more than 300,000 structures. Topological indices and the free energy of solvation were computed for each compound in the databases. Factor analysis was used to reduce the dimensionality of the descriptor space. Low density observations were deleted as a way of removing outliers, which allowed a further reduction in the descriptor space of interest. The five databases could then be compared on an efficient basis using a metric developed for this purpose. A Riemann gridding scheme was used to subdivide the factor space into subhypercubes to obtain accurate comparisons. Most of the 300,000 structures were highly clustered, but unique structures were found. An analysis of overlap between the biological and commercial databases was carried out. The metric provides a useful algorithm for choosing screening sets of diverse compounds from large databases.
Dual Pillar Spin Transfer Torque MRAM with tilted magnetic anisotropy for fast and error-free switching and near-disturb-free read operations (2011)

We propose a three terminal, dual pillar magnetic tunnel junction (MTJ) with tilted magnetic anisotropy for fast and error-free precessional magnetic switching with near-disturb-free magneto-resistive data sensing.
Regulation by dimethylsulfoxide, insulin, and corticosteroids of hepatitis b virus replication in a transfected human hepatoma cell line (1989)

A human hepatoblastoma cell clone E4 was obtained by transfection of HepG2 cells with a plasmid DNA containing four tandem copies of hepatitis B virus (HBV) genome. Analysis of both intracellular and extracellular viral DNA revealed that this clone exhibited the main steps of the replication process previously found in normal hepatocyte primary cultures experimentally infected in vitro. Indeed, relaxed-circular, covalently closed circular, and single-stranded forms of viral DNA were identified in the cells together with complete virions and immature cores in the medium. Furthermore, the ability of these secreted particles to infect normal human hepatocyte cultures was established. These E4 cells were used to evaluate the effect of various soluble factors on HBV replication. Corticosteroids and, to a greater extent, dimethylsulfoxide (DMSO) increased intracellular viral DNA, whereas insulin reduced it dramatically. Parallel changes in the amounts of viral DNA secreted in the medium were observed. Measurement of the albumin secretion rate indicated that cellular and viral activities could be regulated, at least in part, in a coordinated manner.
Computer-aided diagnosis for pulmonary nodules based on helical CT images (2002)

In this paper, the authors present a computer assisted automatic diagnostic system for lung cancer that detects nodule candidates at an early stage from helical CT images of the thorax. The diagnostic system consists of analytic and diagnostic procedures. In the analysis procedure, the authors extract the lung and the blood vessel regions using a fuzzy clustering algorithm, then they analyze the features of these regions. In the diagnosis procedure, the authors define diagnostic rules utilizing the extracted features which support the determination of the candidate nodule locations.
Computational augmented reality eyeglasses (2013)

In this paper we discuss the design of an optical see-through head-worn display supporting a wide field of view, selective occlusion, and multiple simultaneous focal depths that can be constructed in a compact eyeglasses-like form factor. Building on recent developments in multilayer desktop 3D displays, our approach requires no reflective, refractive, or diffractive components, but instead relies on a set of optimized patterns to produce a focused image when displayed on a stack of spatial light modulators positioned closer than the eye accommodation distance. We extend existing multilayer display ray constraint and optimization formulations while also purposing the spatial light modulators both as a display and as a selective occlusion mask. We verify the design on an experimental prototype and discuss challenges to building a practical display.
Power spectral analysis of heart rate and arterial pressure variabilities as a marker of sympatho-vagal interaction in man and conscious dog. (1986)

In 57 normal subjects (age 20-60 years), we analyzed the spontaneous beat-to-beat oscillation in R-R interval during control recumbent position, 90 degrees upright tilt, controlled respiration (n = 16) and acute (n = 10) and chronic (n = 12) beta-adrenergic receptor blockade. Automatic computer analysis provided the autoregressive power spectral density, as well as the number and relative power of the individual components. The power spectral density of R-R interval variability contained two major components in power, a high frequency at approximately 0.25 Hz and a low frequency at approximately 0.1 Hz, with a normalized low frequency:high frequency ratio of 3.6 +/- 0.7. With tilt, the low-frequency component became largely predominant (90 +/- 1%) with a low frequency:high frequency ratio of 21 +/- 4. Acute beta-adrenergic receptor blockade (0.2 mg/kg IV propranolol) increased variance at rest and markedly blunted the increase in low frequency and low frequency:high frequency ratio induced by tilt. Chronic beta-adrenergic receptor blockade (0.6 mg/kg p.o. propranolol, t.i.d.), in addition, reduced low frequency and increased high frequency at rest, while limiting the low frequency:high frequency ratio increase produced by tilt. Controlled respiration produced at rest a marked increase in the high-frequency component, with a reduction of the low-frequency component and of the low frequency:high frequency ratio (0.7 +/- 0.1); during tilt, the increase in the low frequency:high frequency ratio (8.3 +/- 1.6) was significantly smaller. In seven additional subjects in whom direct high-fidelity arterial pressure was recorded, simultaneous R-R interval and arterial pressure variabilities were examined at rest and during tilt. Also, the power spectral density of arterial pressure variability contained two major components, with a relative low frequency:high frequency ratio at rest of 2.8 +/- 0.7, which became 17 +/- 5 with tilt. These power spectral density components were numerically similar to those observed in R-R variability. Thus, invasive and noninvasive studies provided similar results. More direct information on the role of cardiac sympathetic nerves on R-R and arterial pressure variabilities was derived from a group of experiments in conscious dogs before and after bilateral stellectomy. Under control conditions, high frequency was predominant and low frequency was very small or absent, owing to a predominant vagal tone. During a 9% decrease in arterial pressure obtained with IV nitroglycerin, there was a marked increase in low frequency, as a result of reflex sympathetic activation.(ABSTRACT TRUNCATED AT 400 WORDS)
Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia (2004)

Gene-expression profiling allows a comprehensive classification of AML that includes previously identified genetically defined subgroups and a novel cluster with an adverse prognosis.
Comparative Analysis of Viral Gene Expression Programs during Poxvirus Infection: A Transcriptional Map of the Vaccinia and Monkeypox Genomes (2008)

The results provide a temporal map of the transcriptome of each virus during infection, enabling us to compare viral gene expression across species, and classify expression patterns of previously uncharacterized ORFs.