gebhart/patrepeval huggingface dataset:
In vitro mechanisms of action of rituximab on primary non-Hodgkin lymphomas (2003)

To assess the sensitivity of primary non-Hodgkin lymphoma cells to rituximab-mediated cytotoxicity, we compared the potency of several rituximab-mediated killing mechanisms on fresh lymphoma cells. All lymphoma cells tested were equally sensitive to antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-mediated phagocytosis of tumor cells, and rituximab-induced apoptosis. However, they were differentially lysed by complement-dependent cytotoxicity (CDC). We found that taking into account both CD20 and complement regulatory protein expression on tumor cells could predict CDC sensitivity in vitro. Importantly, the sensitivity of lymphoma cells to CDC was consistent with the reported different clinical response rates of lymphomas: rituximab induced high CDC killing of follicular lymphoma cells, whereas mantle cell lymphoma and diffuse large cell lymphoma cells were moderately sensible to CDC, and small lymphocytic lymphoma cells were almost all resistant. We propose that CDC is a determinant mechanism of rituximab-induced killing in vivo. Poor sensitivity to CDC in vitro might predict a poor clinical response, whereas high sensitivity to CDC would only indicate a likelihood of response to rituximab treatment.
Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments (2005)

We present a method to specifically select large sets of DNA sequences for parallel amplification by PCR using target-specific oligonucleotide constructs, so-called selectors. The selectors are oligonucleotide duplexes with single-stranded target-complementary end-sequences that are linked by a general sequence motif. In the selection process, a pool of selectors is combined with denatured restriction digested DNA. Each selector hybridizes to its respective target, forming individual circular complexes that are covalently closed by enzymatic ligation. Non-circularized fragments are removed by exonucleolysis, enriching for the selected fragments. The general sequence that is introduced into the circularized fragments allows them to be amplified in parallel using a universal primer pair. The procedure avoids amplification artifacts associated with conventional multiplex PCR where two primers are used for each target, thereby reducing the number of amplification reactions needed for investigating large sets of DNA sequences. We demonstrate the specificity, reproducibility and flexibility of this process by performing a 96-plex amplification of an arbitrary set of specific DNA sequences, followed by hybridization to a cDNA microarray. Eighty-nine percent of the selectors generated PCR products that hybridized to the expected positions on the array, while little or no amplification artifacts were observed.
Abstract 628: Functional characterization of a diverse set of ERBB3 inhibitory antibodies (2011)

Abstract One important manifestation of the plasticity of cancer is the rapid escape from the effect of anti-cancer agents following initial therapeutic response. ERBB3, a kinase inactive member of the epidermal growth factor (EGFR) receptor family, which also includes EGFR, HER-2 and ERBB-4, has been linked to the development of resistance to multiple cancer therapies. The reactivation of ERBB3 following treatments with EGFR or HER-2 inhibitors has been observed in multiple tumor types following initial responses. The reactivation of ERBB3 signaling is thought to be the consequence of the formation of kinase active heterodimers of ERBB3 with EGFR, HER-2 and c-Met. ERBB3 heterodimer formation is consequence of a conformational change in the ErbB3 ECD (extracellular domain) in response to increased presence of the ERBB3 ligand NRG (neuregulin) or increased membrane concentrations of ERBB3 partners or ERBB3 itself which is often due overexpression or increased membrane localization. To understand the role of NRG dependent and independent ERBB3 activation mechanisms in the development of resistance to EGFR and/or HER-2 inhibitors, we set out to identify a diverse set of ERBB3 specific inhibitory monoclonal antibodies with different mechanisms of action. Immunizations with a mixture of tethered and opened ERBB3 ECD antigens allowed us to identify a large variety of potent ERBB3 inhibitors. Competition binding experiments have identified at least 5 independent binding sites for these antibodies on ERBB3. Some of these antibodies inhibited NRG binding (ligand neutralizers) while others did not interfere with ligand binding. Since a few of these antibodies bound to the dimerization domain (domain II) of ERBB3, we have inferred that they most likely inhibit the formation of ERBB3 heterodimers (dimerization inhibitors). In vivo activity of these antibodies was tested in tumor models driven by ligand independent and dependent activation of ERBB3 to identify the most promising candidate for the development of a highly potent ERBB3 therapeutic antibody with superior activity against both ligand dependent and independent ERBB3 heterodimers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 628. doi:10.1158/1538-7445.AM2011-628
Cyclically permutable codes specified by roots of generator polynomial (2014)

A condition is proven on the roots of the generator polynomial of a q ‐ary cyclic code of block length n which guarantees full cyclic order for all nonzero codewords. For such cyclic codes having n = q m − 1, a theorem is proven which allows to partition the set of all nonzero codewords into cyclic equivalence classes of order n .
A New Human Lung Adenocarcinoma Cell Line Harboring the EML4-ALK Fusion Gene (2014)

We successfully established a new lung adenocarcinoma cell line harboring the EML4-ALK fusion gene. This cell line could contribute to future research of EML4-ALK-positive lung cancer both in vivo and in vitro.
Low-Density Lipoprotein Size, Pravastatin Treatment, and Coronary Events (2001)

Large LDL size was an independent predictor of coronary events in a typical population with myocardial infarction, but the adverse effect was not present among patients who were treated with pravastatin. Identifying patients on the basis of LDL size may not be useful clinically, since effective treatment for elevated LDL cholesterol concentrations also effectively treats risk associated with large LDL.
Quantum Interference and Ballistic Transmission in Nanotube Electron Waveguides (2001)

The electron transport properties of well-contacted individual single-walled carbon nanotubes are investigated in the ballistic regime. Phase coherent transport and electron interference manifest as conductance fluctuations as a function of Fermi energy. Resonance with standing waves in finite-length tubes and localized states due to imperfections are observed for various Fermi energies. Two units of quantum conductance 2G(0) = 4e(2)/h are measured for the first time, corresponding to the maximum conductance limit for ballistic transport in two channels of a nanotube.
Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins (1991)

The cleavages at the junctions of the flavivirus nonstructural (NS) proteins NS2A/NS2B, NS2B/NS3, NS3/NS4A, and NS4B/NS5 share an amino acid sequence motif and are presumably catalyzed by a virus-encoded protease. We constructed recombinant vaccinia viruses expressing various portions of the NS region of the dengue virus type 4 polyprotein. By analyzing immune precipitates of 35S-labeled lysates of recombinant virus-infected cells, we could monitor the NS2A/NS2B, NS2B/NS3, and NS3/NS4A cleavages. A polyprotein composed of NS2A, NS2B, and the N-terminal 184 amino acids of NS3 was cleaved at the NS2A/NS2B and NS2B/NS3 junctions, whereas a similar polyprotein containing only the first 77 amino acids of NS3 was not cleaved. This finding is consistent with the proposal that the N-terminal 180 amino acids of NS3 constitute a protease domain. Polyproteins containing NS2A and NS3 with large in-frame deletions of NS2B were not cleaved at the NS2A/NS2B or NS2B/NS3 junctions. Coinfection with a recombinant expressing NS2B complemented these NS2B deletions for NS2B/NS3 cleavage and probably also for NS2A/NS2B cleavage. Thus, NS2B is also required for the NS2A/NS2B and NS2B/NS3 cleavages and can act in trans. Other experiments showed that NS2B was needed, apparently in cis, for NS3/NS4A cleavage and for a series of internal cleavages in NS3. Indirect evidence that NS3 can also act in trans was obtained. Models are discussed for a two-component protease activity requiring both NS2B and NS3.
Yeasts associated with algarrobo trees (Prosopis spp.) in northwest Argentina: A preliminary report (1995)

Yeasts were isolated from exudates from trees at three sites in northwest Argentina, two between the towns of Amaicha del Valle and Cafayate and one in the Quebrada de Cafayate, a deep river valley north of Cafayate. The majority of the yeasts were identified asCandida famata andRhodotorula graminis, though isolates of other species ofRhodotorula, Candida boidinii, Pichia membranaefaciens, and occasional isolates of other species were obtained. None of the species was the same as those isolated in Crete, from pods of the carob (European algarrobo). Of 96 cultures investigated, 26 utilized methanol as sole carbon source. The frequency of isolation of methylotrophic yeasts from this habitat may prove to be of considerable scientific and technological interest.
Robust single-view geometry and motion reconstruction (2009)

We present a framework and algorithms for robust geometry and motion reconstruction of complex deforming shapes. Our method makes use of a smooth template that provides a crude approximation of the scanned object and serves as a geometric and topological prior for reconstruction. Large-scale motion of the acquired object is recovered using a novel space-time adaptive, non-rigid registration method. Fine-scale details such as wrinkles and folds are synthesized with an efficient linear mesh deformation algorithm. Subsequent spatial and temporal filtering of detail coefficients allows transfer of persistent geometric detail to regions not observed by the scanner. We show how this two-scale process allows faithful recovery of small-scale shape and motion features leading to a high-quality reconstruction. We illustrate the robustness and generality of our algorithm on a variety of examples composed of different materials and exhibiting a large range of dynamic deformations.
Prostate Specific Membrane Antigen (PSMA) Regulates Angiogenesis Independently of VEGF during Ocular Neovascularization (2012)

Our data indicate that PSMA plays a VEGF-independent role in retinal angiogenesis and that the lack of or inhibition of PSMA may represent a novel therapeutic strategy for treatment of angiogenesis-based ocular diseases.
Inhibition of inositol phosphate second messenger formation by intracellular loop one of a human calcitonin receptor. Expression and mutational analysis of synthetic receptor genes. (1994)

Receptors for calcitonin (CTRs) have been cloned from several species, and two isoforms have been found to be expressed in human tissue. One human CTR isoform (hCTR-1) contains a 16-amino acid insertion in its first intracellular (I1) loop that is not present in porcine CTR (pCTR), rat CTR, or the other human CTR (hCTR-2). To facilitate the study of CTRs by mutational analysis, we have constructed synthetic hCTR-1 and hCTR-2 genes. Activation of hCTR-1 expressed transiently in COS-1 cells stimulates the formation of cAMP but not of inositol phosphates (IPs) whereas pCTR, a chimeric CTR in which the I1 loop of pCTR was substituted for the I1 loop of hCTR-1, and hCTR-2 stimulate cAMP and IP formation. A series of chimeric CTRs in which intracellular loops 1, 2, and 3 and the carboxyl tail of pCTR were substituted individually or in combination for those of hCTR-1 were constructed. All chimeras stimulated cAMP formation whereas chimeras containing the I1 loop of hCTR-1 with its 16-amino acid insertion were incapable of stimulating IP formation. There was no correlation between maximal stimulation of cAMP and IP formation by these CTRs. Thus, an inserted sequence in the I1 loop of hCTR-1 abolishes stimulation of the IP signal transduction pathway while allowing stimulation of the cAMP pathway.
Synthesis of a Class of Non-linear Systems† (1965)

ABSTRACT A problem in the practical application of the Volterra series to nonlinear theory is the synthesis of systems with a given set of Volterra kernels. In this article we present a method of determining whether a given Volterra kernel can be synthesized exactly by using only a finite number of multipliers. A method for the synthesis of such kernels is also presented. The use of the techniques discussed here is illustrated by examples. Notes † Communicated by Dr. Helen L. Thomas. The results presented in this Paper were reported in preliminary form by the author in an article, “The Synthesis of a Class of Non-linear Systems”, Quarterly Progress Report No. 6S, Research Laboratory of Electronics, Massachusetts Institute,of Technology, January 15, 1963; pp. 122–130.
Multi-modal Variational Encoder-Decoders (2017)

Recent advances in neural variational inference have facilitated efficient training of powerful directed graphical models with continuous latent variables, such as variational autoencoders. However, these models usually assume simple, uni-modal priors — such as the multivariate Gaussian distribution — yet many real-world data distributions are highly complex and multi-modal. Examples of complex and multi-modal distributions range from topics in newswire text to conversational dialogue responses. When such latent variable models are applied to these domains, the restriction of the simple, uni-modal prior hinders the overall expressivity of the learned model as it cannot possibly capture more complex aspects of the data distribution. To overcome this critical restriction, we propose a flexible, simple prior distribution which can be learned efficiently and potentially capture an exponential number of modes of a target distribution. We develop the multi-modal variational encoder-decoder framework and investigate the effectiveness of the proposed prior in several natural language processing modeling tasks, including document modeling and dialogue modeling.
Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine (2008)

A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoadenine (nA) and 2-thiothymine (sT) to generate structure-free DNA that is fully accessible to complementary probes. The analogs, which included bioactive bases such as 6-thioguanine (sG), 5-nitrocytosine (NitroC), 2-pyrimidinone (P; the free base of zebularine) and 6-methylfuranopyrimidinone (MefP), were prepared as dNTPs and evaluated as substrates for T7 and Phi29 DNA polymerases that lacked editor function. Pairing properties of the analogs were characterized by solution hybridization assays using modified oligonucleotides or primer extension products. P and MeP did not support robust primer extension whereas sG and NitroC did. In hybridization assays, however, sG lacked discrimination and NitroC paired too strongly to C. The dNTPs of two other base analogs, 7-nitro-7-deazahypoxanthine (NitrocH) and 2-thiocytosine (sC), exhibited the greatest promise. Either analog could be used with nA and sT to generate DNA that was nearly structure-free. Hybridization of probes to these modified DNAs will require the development of base analogs that pair strongly to NitrocH or sC.
Efficacy and Safety of Retreatment in Patients with Rheumatoid Arthritis with Previous Inadequate Response to Tumor Necrosis Factor Inhibitors: Results from the SUNRISE Trial (2010)

Two courses of rituximab about 6 months apart resulted in improved and sustained efficacy at 1 year, compared with 1 course, with a similar safety profile.
Repurposing CRISPR/Cas9 for in situ functional assays (2013)

RNAi combined with next-generation sequencing has proven to be a powerful and cost-effective genetic screening platform in mammalian cells. Still, this technology has its limitations and is incompatible with in situ mutagenesis screens on a genome-wide scale. Using p53 as a proof-of-principle target, we readapted the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR associated 9) genome-editing system to demonstrate the feasibility of this methodology for targeted gene disruption positive selection assays. By using novel "all-in-one" lentiviral and retroviral delivery vectors heterologously expressing both a codon-optimized Cas9 and its synthetic guide RNA (sgRNA), we show robust selection for the CRISPR-modified Trp53 locus following drug treatment. Furthermore, by linking Cas9 expression to GFP fluorescence, we use an "all-in-one" system to track disrupted Trp53 in chemoresistant lymphomas in the Eμ-myc mouse model. Deep sequencing analysis of the tumor-derived endogenous Cas9-modified Trp53 locus revealed a wide spectrum of mutants that were enriched with seemingly limited off-target effects. Taken together, these results establish Cas9 genome editing as a powerful and practical approach for positive in situ genetic screens.
<title>Absolute orientation of photo pairs using GPS and laser profiles</title> (1993)

The determination of absolute orientation of image pairs is a central task in aerial photogrammetry. The usual way in photogrammetry to determine the absolute orientation is using control points. Acquisition of control points (i.e. the signalization of control points and the preservations over a longer period) is a very time and cost intensive task. Using new sensors as combined systems, the effort for the acquisition of control points to determine the absolute orientation could be minimized or even avoided. Beside the airborne camera, GPS, two laser profilers and an inertial system are used as additional sensors. The laser profilers are looking sidewards, so that during the stripewise flight over the photogrammetric block laser profiles at the upper and lower border of the strip are recorded. GPS- and INS-Data are registered during the whole time of the flight. Using this method there is following additional information for each image pair: (1) GPS determined coordinates of the projection centers of each image, (2) INS determined attitude angles for the absolute orientation of the laser profile, and (3) GPS and INS supported (i.e. absolute oriented) laser profiles at the upper and lower border of each image pair. Using an iterating method utilizing the additional laser profile and GPS information, the absolute orientation of an image pair could be performed without using additional control points.
The Development of Aortic Insufficiency in Left Ventricular Assist Device-Supported Patients (2010)

AI progresses over time in LVAD-supported patients. As we move toward an era of long-term cardiac support, more studies are needed to determine the clinical significance of these findings.
hnRNP A1 Recruited to an Exon In Vivo Can Function as an Exon Splicing Silencer (1999)

Some exons contain exon splicing silencers. Their activity is frequently balanced by that of splicing enhancers, and this is important to ensure correct relative levels of alternatively spliced mRNAs. Using an immunoprecipitation and UV-cross-linking assay, we show that RNA molecules containing splicing silencers from the human immunodeficiency virus type 1 tat exon 2 or the human fibroblast growth factor receptor 2 K-SAM exon bind to hnRNP A1 in HeLa cell nuclear extracts better than the corresponding RNA molecule without a silencer. Two different point mutations which abolish the K-SAM exon splicing silencer's activity reduce hnRNP A1 binding twofold. Recruitment of hnRNP A1 in the form of a fusion with bacteriophage MS2 coat protein to a K-SAM exon whose exon splicing silencer has been replaced by a coat binding site efficiently represses splicing of the exon in vivo. Recruitment of only the glycine-rich C-terminal domain of hnRNP A1, which is capable of interactions with other proteins, is sufficient to repress exon splicing. Our results show that hnRNP A1 can function to repress splicing, and they suggest that at least some exon splicing silencers could work by recruiting hnRNP A1.
A Schistosoma mansoni fatty acid-binding protein, Sm14, is the potential basis of a dual-purpose anti-helminth vaccine. (1996)

Molecular cloning of components of protective antigenic preparations has suggested that related parasite fatty acid-binding proteins could form the basis of the protective immune crossreactivity between the parasitic trematode worms Fasciola hepatica and Schistosoma mansoni. Molecular models of the two parasite proteins showed that both molecules adopt the same basic three-dimensional structure, consisting of a barrel-shaped molecule formed by 10 antiparallel beta-pleated strands joined by short loops, and revealed the likely presence of crossreactive, discontinuous epitopes principally derived from amino acids in the C-terminal portions of the molecules. A recombinant form of the S. mansoni antigen, rSm14, protected outbred Swiss mice by up to 67% against challenge with S. mansoni cercariae in the absence of adjuvant and without provoking any observable autoimmune response. The same antigen also provided complete protection against challenge with F. hepatica metacercariae in the same animal model. The results suggest that it may be possible to produce a single vaccine that would be effective against at least two parasites, F. hepatica and S. mansoni, of veterinary and human importance, respectively.
Margin notes (2000)

Both the Human Computer Interaction and Information Retrieval fields have developed techniques to allow a searcher to find the information they seek quickly. However, these techniques are designed to augment one's direct-recall memory, where the searcher is actively trying to find information. Associative memory, in contrast, happens automatically and continuously, triggering memories that relate to the observed world. This paper presents design techniques and heuristics for building “remembrance agents,” applications that watch a user's context and proactively suggest information that may be of use. General design issues are discussed and illuminated by a description of Margin Notes, an automatic just-in-time information system for the Web.
Immunohistochemical Study of Annexin V Expression in Placentae of Preeclampsia (2000)

We investigated the clinical significance of annexin V in the placentae with preeclampsia and found: (1) annexin V was detected on trophoblasts in the placentae and the staining intensity of annexin V in the placentae from such patients was reduced when compared to normal placentae; (2) as expression of annexin V was reduced, the gestosis index from patients with preeclampsia was elevated and the standard deviation value in the infant's standard weight was decreased; plasma level of the fibrin degradation products and thrombin-antithrombin III complex from patients were elevated as the expression of anexin V was reduced. These results suggest that the reduced expression of annexin V in the placentae from patients with preeclampsia may lead to a hypercoagulable state in the intervillous space and may be associated with the development of intrauterine growth restriction.