gebhart/patrepeval huggingface dataset:
Spatio-temporal adaptive 3-D Kalman filter for video (1997)

This paper presents three-dimensional (spatio-temporal) Kalman filters for video as the extension of the two-dimensional (2-D) reduced update Kalman filter (RUKF) approach for images. We start out with three-dimensional (3-D) RUKF, a shift-invariant recursive estimator with efficiency advantages over the 3-D Wiener filter. Then, we turn to the motion-compensated extension MC-RUKF, which gives improved performance when coupled with a motion estimator. Since motion compensation sometimes fails, causing severe fluctuations in temporal correlation, we then present multimodel MC-RUKF, to adapt to variation in temporal and spatial correlation, by detecting the local image model out of a class, and using it in MC-RUKF. Finally, we introduce a novel multiscale model detection algorithm for use in high noise environments.
Rapid Spread of Carbapenem-Resistant Klebsiella pneumoniae in New York City (2005)

Carbapenem-resistant K pneumoniae isolates are rapidly emerging in New York City. The spread of a strain that possesses a carbapenem-hydrolyzing beta-lactamase has occurred in regional hospitals. Because these isolates are resistant to virtually all commonly used antibiotics, control of their spread is crucial. However, automated systems used for susceptibility testing may not accurately identify all these isolates, which will severely hamper control efforts.
Development of a Catalytic Enantioselective Conjugate Addition of 1,3-Dicarbonyl Compounds to Nitroalkenes for the Synthesis of Endothelin-A Antagonist ABT-546. Scope, Mechanism, and Further Application to the Synthesis of the Antidepressant Rolipram (2002)

The enantioselective synthesis of endothelin-A antagonist ABT-546 has been accomplished via the discovery and development of a highly selective catalytic asymmetric conjugate addition of ketoesters to nitroolefins. Employing just 4 mol % bis(oxazoline)-Mg(OTf)(2) complex with an amine cocatalyst, we obtained the product nitroketone with 88% selectivity at the aryl-bearing stereocenter and in good yield on scales ranging to 13 mol. The effects of ligand structure, metal salt, and solvent on the reaction are described. Particularly important to the reaction is the water content. While water is necessary during the generation of the catalyst, the water must be then removed to maximize stereoselectivity and reactivity. The reaction has been extended to other dicarbonyl substrates, and a variety of substitution patterns are tolerated on the nitroolefin partner. The reaction has also been employed in the synthesis of the antidepressant rolipram. Investigations relating to the mechanism of the reaction are also described.
Major Depression and Generalized Anxiety Disorder (1992)

Bivariate twin analysis can determine the extent to which two disorders share common genetic, familial environmental, or individual-specific environmental risk factors. We applied this method to lifetime diagnoses of major depression and generalized anxiety disorder as assessed at personal interview in a population-based sample of 1033 pairs of female same-sex twins. Three definitions of generalized anxiety disorder were used that varied in minimum duration (1 vs 6 months) and in the presence or absence of a diagnostic hierarchy. For all definitions of generalized anxiety disorder, the best-fitting twin model was the same. Familial environment played no role in the etiology of either condition. Genetic factors were important for both major depression and generalized anxiety disorder and were completely shared between the two disorders. A modest proportion of the nonfamilial environmental risk factors were shared between major depression and generalized anxiety disorder. Within the limits of our statistical power, our findings suggest that in women, the liability to major depression and generalized anxiety disorder is influenced by the same genetic factors, so that whether a vulnerable woman develops major depression or generalized anxiety disorder is a result of her environmental experiences.
Immunostimulation in mice infected with Sendai virus. (1987)

The effect of Sendai virus infection on the splenic primary plaque-forming cell (PFC) response to sheep RBC in 2 strains of mice, with contrasting susceptibility to Sendai viral pneumonia, was examined. Mice were given single inoculations of sheep RBC, which varied relative to time of inoculation with Sendai virus, PFC were counted 6 days later, and were compared with PFC responses from noninfected mice. The IgM- and IgG-PFC responses were augmented in resistant C57BL/6J mice 7 and 9 days after inoculation with Sendai virus (sheep RBC given 1 and 3 days after inoculation with Sendai virus, respectively) and in susceptible DBA/2J mice 7, 9, 10, and 13 days after inoculation with Sendai virus. Augmentation was restricted mainly to IgM-, IgG3-, and IgG2b-PFC. The number of splenic background antitrinitrophenyl sheep RBC PFC in mice of both strains was examined during the course of Sendai virus infection. Only a marginal increase in background PFC was seen in C57BL/6J mice on or after viral inoculation day 11 and no change was seen in DBA/2J mice. Serum of infected mice also was examined sequentially for alpha/beta interferon (IFN). Despite vigorous lung IFN production, infected mice rarely had detectable circulating IFN. Seemingly, Sendai virus infection can induce transient hyperresponsiveness to a nonviral antigen.
Detailed genetic and physical map of the 3p chromosome region surrounding the familial renal cell carcinoma chromosome translocation, t(3;8)(p14.2;q24.1). (1993)

Extensive studies of loss of heterozygosity of 3p markers in renal cell carcinomas (RCCs) have established that there are at least three regions critical in kidney tumorigenesis, one most likely coincident with the von Hippel-Lindau gene at 3p25.3, one in 3p21 which may also be critical in small cell lung carcinomas, and one in 3p13-p14.2, a region which includes the 3p chromosome translocation break of familial RCC with the t(3;8)(p14.2;q24.1) translocation. A panel of rodent-human hybrids carrying portions of 3p, including a hybrid carrying the derivative 8 (der(8)(8pter-->8q24.1::3p14.2-->3pter)) from the RCC family, have been characterized using 3p anchor probes and cytogenetic methods. This 3p panel was then used to map a large number of genetically mapped probes into seven physical intervals between 3p12 and 3pter defined by the hybrid panel. Markers have been physically, and some genetically, placed relative to the t(3;8) break, such that positional cloning of the break is feasible.
c-myc amplification is a better prognostic factor than HER2/neu amplification in primary breast cancer. (1992)

Amplification of the c-myc and HER2/neu genes was found in 20 and 23%, respectively, of primary breast cancer tissues derived from 282 patients (median follow-up, 74 months). c-myc amplification was observed more frequently in larger tumors (P = 0.01) and in lymph node-positive patients (P = 0.01) but was not associated with age, menopausal status, or with differentiation grade or steroid receptor status. c-myc amplification was strongly negatively correlated with HER2/neu amplification (P less than 0.001). In univariate analysis, amplification of c-myc proved to be a significant predictor of reduced relapse-free and overall survival (for both, P less than 0.001). In multivariate analysis for relapse-free survival, c-myc amplification significantly (P = 0.001) added to the prognostic power of tumor size (P less than 0.001), lymph node status (P less than 0.001), and estrogen receptor status (P = 0.003), with the highest relative failure rate (1.8) after lymph node status (2.2). In this pilot study, c-myc amplification was predictive for outcome, especially among patients with node-negative disease or steroid receptor-positive tumors; 51 and 46% differences in actuarial 5-year recurrence rates when compared to patients with tumors with normal c-myc gene copy numbers, respectively. HER2/neu amplification was not associated with relapse-free survival but weakly with shorter overall survival in univariate analysis (P = 0.035). Only in the relatively small subgroup of steroid receptor-negative tumors, HER2/neu amplification may identify those patients with an increased risk of death. In conclusion, amplification of c-myc is an independent powerful prognosticator, particularly in node-negative and steroid receptor-positive breast cancer, whereas HER2/neu amplification may be of limited prognostic value, only in steroid receptor-negative disease.
Immunoaffinity purification of FLAG epitope-tagged bacterial alkaline phosphatase using a novel monoclonal antibody and peptide elution. (1994)

The FLAG epitope is an eight amino acid peptide (AspTyrLysAspAspAspAspLys) that is useful for immunoaffinity purification of fusion proteins. A monoclonal antibody (anti-FLAG M1) that binds the FLAG epitope in a calcium-dependent manner and requires an N-terminal FLAG sequence has been described previously. We describe the use of a second anti-FLAG monoclonal antibody (anti-FLAG M2) in immunoaffinity purification of N-terminal Met-FLAG and C-terminal FLAG fusion to bacterial alkaline phosphatase. Although binding of an anti-FLAG M2 monoclonal antibody to the FLAG epitope is not calcium-dependent, bound fusion proteins can be eluted by competition with FLAG peptide.
Vitamin D Receptor and p21/WAF1 Are Targets of Genistein and 1,25-Dihydroxyvitamin D3 in Human Prostate Cancer Cells (2004)

We investigated mechanisms by which genistein and 1,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)] act synergistically to inhibit the growth of the human prostate cancer cell line LNCaP. We demonstrate that 1,25(OH)(2)D(3) and genistein cooperate to up-regulate the vitamin D receptor protein by increasing the stability of the vitamin D receptor. Genistein and 1,25(OH)(2)D(3) also cooperate to up-regulate the levels of p21/WAF1 (p21). Small interfering RNA-mediated knockdown of p21 expression showed that p21 is essential for significant growth inhibition of LNCaP cells in response to either compound or their combination. We conclude that one mechanism of synergism between genistein and 1,25(OH)(2)D(3) is through genistein modulation of vitamin D signaling.
Severe cytokine release syndrome in a patient receiving PD‐1‐directed therapy (2017)

Cytokine release syndrome (CRS) is a phenomenon of immune hyperactivation described in the setting of cellular and bispecific T-cell engaging immunotherapy. Checkpoint blockade using anti-programmed cell death 1 (anti-PD-1) inhibitors is an approach to antitumor immune system stimulation. A 29-year-old female with alveolar soft part sarcoma developed severe CRS after treatment with anti-PD-1 therapy. CRS was characterized by high fevers, encephalopathy, hypotension, hypoxia, hepatic dysfunction, and evidence of coagulopathy, and resolved after infusion of the interleukin-6 inhibitor tocilizumab and corticosteroids.
Periostin expression and epithelial-mesenchymal transition in cancer: a review and an update (2011)

Periostin, also called osteoblast-specific factor 2, is a secreted cell adhesion protein, which shares a homology with the insect cell adhesion molecule fasciclin I. It has been shown to be an important regulator of bone and tooth formation and maintenance, and of cardiac development and healing. Recent studies revealed that periostin plays an important role in tumor development and is upregulated in a wide variety of cancers such as colon, pancreatic, ovarian, breast, head and neck, thyroid, and gastric cancer as well as in neuroblastoma. Periostin binding to the integrins activates the Akt/PKB- and FAK-mediated signaling pathways which lead to increased cell survival, angiogenesis, invasion, metastasis, and importantly, epithelial-mesenchymal transition of carcinoma cells. In this review we summarize recent clinicopathological studies that have investigated periostin expression in lung, kidney, prostate, liver cancer, and malignant pleural mesothelioma and discuss the role of periostin isoforms in tumorigenesis and their potential as targets for stroma-targeted anticancer therapy.
History of Discovery (2011)

A growth-promoting activity released from activated platelets, the platelet-derived growth factor, was discovered and characterized while the cellular and molecular mechanisms underlying the formation of the lesions of atherosclerosis were being investigated. This review provides a personal account of the different challenges we faced 3 decades ago in this undertaking and describes how our path was influenced by our focus on a disease process and by the evolving general understanding of the molecular effectors of cell proliferation.
GENETIC ANALYSIS OF STAPHYLOCOCCAL NUCLEASE: IDENTIFICATION OF THREE INTRAGENIC "GLOBAL" SUPPRESSORS OF NUCLEASE-MINUS MUTATIONS (1985)

A collection of 77 unique missense mutations distributed across the gene encoding staphylococcal nuclease (nuc) has been assembled. These mutations were induced by random gap misrepair mutagenesis of the cloned gene and were identified in E. coli transformants expressing reduced levels of nuclease activity. Four nuc- mutations which alter amino acid residues at positions outside of the active site region of the enzyme were submitted to a second round of mutagenesis, and characterization of several independent NUC+ isolates lead to the identification of three second-site suppressor mutations within the protein-coding sequence of the nuc gene. On separation from the mutation originally suppressed and recombination with a number of other nuc- mutations, all three suppressors displayed the property of "global" suppression, i.e., phenotypic suppression of the nuclease-minus character of multiple different alleles. A simple and generally applicable strategy was used to obtain efficient homologous recombination between plasmids for purposes of mapping nuc- mutations, mapping second-site suppressors and constructing double mutant combinations from pairs of single mutations.
Intergrain magnetic coupling and microstructure in CoPtCr, CoPtCrTa, and CoPtCrB alloys (1998)

We have investigated intergrain magnetic interactions in three types of Co-based alloys of interest for longitudinal magnetic recording: CoPtCr, CoPtCrTa, and CoPtCrB. The goal is to quantify how intergranular exchange interactions in CoPtCr alloys are modified by doping said alloys with additives such as Ta and B. These 20-nm-thick alloys were grown under identical deposition conditions on AlMg/NiP substrates and a comprehensive study of their microstructural and magnetic properties was conducted to evaluate the degree of intergranular exchange coupling and the manner how the coupling depends on the corresponding microstructural properties. We find that the ternary alloy exhibits the strongest intergrain coupling. In the case of the quaternary alloys, the degree of exchange interactions is virtually the same. Consequently, any significant difference pertaining recording performance in these quaternary alloys must be dominated by the inherent differences in grain microstructure and the spatial distribution of the alloy constituent elements.
Quantitative simulation of image correction for astronomy with a segmented active mirror (1988)

Correction by active mirror systems of image distortion due to atmospheric turbulence promises to improve the quality of ground-based astronomical observations. Although the ideal of fully correcting average-to-poor seeing to the diffraction limit of a large telescope cannot be easily realized with current technology, it has been demonstrated that partial correction of severe seeing disturbances can significantly improve image resolution. This paper describes a computer simulation of partial seeing correction by the Lockheed Active Mirror. Quantitative evaluation of the effects of partial correction on simulated wavefronts indicates that, even with a modest number of mirror actuators, one can achieve a diffraction-limited image superimposed on a background of scattered light.
One-way Accumulators: A Decentralized Alternative to Digital Signatures (Extended Abstract) (1993)

Josh Benaloh t and Michael de Mare 2 Clarkson University 2 Giordano Automation Abstract. This paper describes a simple candidate one-way hash function which satisfies a quasi-commutative property that allows it to be used as an accumulator. This property allows protocols to be developed in which the need for a trusted central authority can be eliminated. Spaceefficient distributed protocols are given for document time stamping and for membership testing, and many other applications are possible.
Northern Border Pipeline Logistics Simulation (1990)

A simulation model in GPSS analyzed whether pipe for the Northern Border Pipeline could be delivered within the planned nine months. This analysis led to a 20-percent reduction in railcars needed for transporting the pipe, saving $4.5 million in railcar hiring costs. The reduced number of railcars were hired and the pipeline was completed on schedule as predicted. The model also led to considerable insight regarding meshing factory operations with train loading, transit, unloading, and welding. It was detailed enough to consider the arrival of pipe from abroad, construction of pipe in domestic factories, train transportation including breakdowns, barge transportation, unloading pipe, inspection and subsequent welding.
Characterization and expression of the gene for the human Fc receptor gamma subunit. Definition of a new gene family. (1990)

The high affinity IgE receptor, Fc epsilon RI, is one of the key molecules involved in allergic reactions. It is a tetrameric complex (alpha beta gamma 2). The gamma chains from Fc epsilon RI are also subunits of other Fc receptors. We have isolated, characterized, and sequenced the gene for the human gamma chain of Fc epsilon RI. It consists of five exons and spans 4 kilobases. The leader sequence is encoded by two exons, the second of which also contains the short extracellular domain, the hydrophobic transmembrane region, and the beginning of the cytoplasmic tail. Three short exons encode the remaining of the polypeptide and the 3'-untranslated flanking sequence. The transcription initiation sites have been mapped. Comparison between the gene structures of the gamma chain of the Fc receptor and of the zeta chain of the T-cell receptor indicates that these genes have evolved from a common ancestor by duplication and that they define a new gene family. In addition to being localized on the same chromosome, both genes show an analogous organization of their exons. A high level of homology is found in three of their respective exons, and the splice sites between them are identical. Furthermore, gamma and zeta chains are essential for surface expression of their respective receptors. Therefore, gamma chains of Fc receptors and zeta chains of T-cell receptors may also define a new family of functionally related polypeptides. Expression studies in COS cells show that the human gamma chain alone is sufficient to achieve expression of the human alpha chain on the cell surface, whereas both beta and gamma chains are required for the surface expression of the rodent alpha chain.
Detection of a new mutant α‐1‐antichymotrypsin in patients with occlusive‐cerebrovascular disease (1992)

A new mutant α‐1‐antichymotrypsin (variant ACT) was found by direct sequencing and PCR‐single strand conformation polymorphism (PCR‐SSCP). This variant ACT was a point mutation of exon V of ACT, with the substitution of Met by Val. Four out of six individuals with this variant ACT had occlusive‐cerebrovascular disease, leading to one hypothesis that there might be an association between this mutation and occlusive‐cerebrovascular disease.
THE ROLE OF THE REVERSE-TRANSCRIPTASE POLYMERASE CHAIN REACTION ASSAY FOR PROSTATE-SPECIFIC ANTIGEN IN THE SELECTION OF PATIENTS FOR RADICAL PROSTATECTOMY (1996)

Prostate cells present in the peripheral circulation can be detected using an enhanced reverse-transcriptase polymerase chain reaction (RT-PCR) for prostate-specific antigen (PSA) assay. In one study, preoperative enhanced RT-PCR for PSA status was a significant predictor of surgical pathology and postoperative biomechanical recurrence. The use of RT-PCR may enhance the urologist's ability to stage potential candidates for radical prostatectomy, as the assay is a more sensitive and specific predictor of microscopic extracapsular extension than conventional staging modalities. This highly adaptable assay also may have roles in screening for recurrence and in staging other solid tumors.
Electrospray Ionization Mass Spectrometry for Structural Characterization of the Lipid A Component in Bacterial Endotoxins (1996)

Electrospray ionization mass spectrometry (ESMS) represents a recently developed technology for the direct analysis of glycolipids at high sensitivity. This report investigates phosphoglycolipids known as 'lipid A', originating from lipopolysaccharides of the gram-negative bacteria Enterobacter agglomerans (EA) and Salmonella minnesota (SM). Lipid A is the lipophilic component of the outermost bacterial cell wall. ESMS was found to be more than one order of magnitude more sensitive for lipid A analysis in the positive ion mode, and more than two orders of magnitude more sensitive in the negative ion mode as compared to plasma desorption mass spectrometry (PDMS). Due to the extremely "soft" nature of the ionization process, negative ion ESMS readily produces a profile of the heterogeneity of a crude lipid A preparation by displaying singly charged deprotonated molecules of the various monophosphoryl lipid A forms, and singly or doubly deprotonated molecules corresponding to diphosphoryl forms. Lipid A samples from chemically dephosphorylated lipopolysaccharides produced "distal adduct ions" in the positive ion mode which appear in the form of sodium cations attached to the non-reducing monoglucosamine. These ions are analogs of oxonium ions observed in PDMS. Although fragmentation of ions generated via ESMS is typically quite low, to augment obtained structural information, formed ions can be subjected to collision-induced dissociations (CID), either "pre-analyzer" (in-source) on a single analyzer instrument or in the collision cell of a tandem mass spectrometer. Among the CID processes which can occur are dehydrations, acylium cleavages, carboxylic acid eliminations, and glycosidic cleavages. ESMS has been used to characterize the structures of lipid A species which have undergone hydrolysis either by acid or base treatment. Both acid and base treatments are known to reduce the 'endotoxin level' of bacterial species as measured by the Limulus amebocyte lysate (LAL) assay. Base treatment is effective at eliminating pulmonary toxicity.
Polyclonal human immunoglobulin G labeled with polymeric iron oxide: antibody MR imaging. (1991)

Human polyclonal immunoglobulin (Ig) G was attached to a monocrystalline iron oxide nanocompound (MION), a small superparamagnetic probe developed for receptor and antibody magnetic resonance (MR) imaging. The resulting complex, MION-IgG, had a slightly negative surface charge, a molecular weight of 150-180 kDa, and 0.36 microgram of IgG attached per milligram of iron. After intravenous administration of MION-IgG to normal rats, most of the compound localized in liver, spleen, and bone marrow. In an animal model of myositis, MION-IgG caused reduced signal intensity (most apparent on T2-weighted spin-echo and gradient-echo images) at the site of inflammation. No change in signal intensity existed after an injection of unlabeled MION. Site-specific localization of MION-IgG was corroborated with scintigraphic imaging with indium-111 IgG and MION-In-111-IgG and was confirmed histologically with iron staining. These results indicate that antibody MR imaging is feasible in vivo. Target-specific and antibody MR imaging could be easily extended to other applications, including detection of cancer, infarction, and degenerative diseases.