gebhart/patrepeval huggingface dataset:
Efficacy of daratumumab in combination with lenalidomide plus dexamethasone (DRd) or bortezomib plus dexamethasone (DVd) in relapsed or refractory multiple myeloma (RRMM) based on cytogenetic risk status. (2017)

8006 Background: In 2 randomized phase 3 trials of RRMM patients (pts), DRd (POLLUX) or DVd (CASTOR) significantly improved PFS and deepened responses compared with Rd or Vd alone, respectively. The novel mechanism of action of daratumumab (D) may improve the poor prognosis associated with high-risk cytogenetic abnormalities in RRMM. Therefore, we examined the efficacy of DRd and DVd among RRMM pts with standard (std) or high cytogenetic risk status. Methods: Bone marrow aspirates were collected at screening and assessed centrally via next generation sequencing (NGS). Pts with high-risk cytogenetics included those who had ≥1 of the following abnormalities: t(4;14), t(14;16), or del17p; std-risk pts were defined as those confirmed negative for these abnormalities. Efficacy analyses included PFS and ORR. Results: Samples from 311/569 pts in POLLUX and 353/498 pts in CASTOR were assessed via NGS. In POLLUX, the median duration of follow-up was 17.3 months. Significantly longer median PFS and numerically higher ORR were observed with DRd vs Rd among high-risk patients, and significant improvements in these outcomes were observed in std-risk patients (Table). In CASTOR, the median duration of follow-up was 13.0 months. Significantly longer median PFS and higher ORR were observed with DVd vs Vd among both high- and std-risk pts (Table). Concordance rates for t(4;14), t(14;16), and del17p were high (88%-98%) between NGS and FISH. Updated data, including subgroup analyses, will be presented. Conclusions: In RRMM pts, the addition of D to standard-of-care regimens improved outcomes regardless of cytogenetic risk status. Targeting CD38 by combining D with Rd or Vd appears to improve the poor outcomes associated with high-risk cytogenetic status. See table. Clinical trial information: NCT02136134 and NCT02076009. [Table: see text]
Multicenter Review of Preoperative Risk Factors for Endarterectomy for Asymptomatic Carotid Artery Stenosis (1998)

The overall risk of postoperative stroke or death was nearly twice that reported by Asymptomatic Carotid Atherosclerosis Study (ACAS) investigators in the setting of a clinical trial but was within acceptable guidelines. Women were at higher postoperative risk than men, which supported ACAS findings. Additional high-risk groups were those aged 75 years or older, those with a history of congestive heart failure, and those undergoing prophylactic endarterectomy for asymptomatic stenosis in combination with coronary surgery. Knowledge of these rates may help to better assess an individual's postoperative risk and therefore the anticipated benefit of surgery.
Gaussian-product subdivision surfaces (2019)

Probabilistic distribution models like Gaussian mixtures have shown great potential for improving both the quality and speed of several geometric operators. This is largely due to their ability to model large fuzzy data using only a reduced set of atomic distributions, allowing for large compression rates at minimal information loss. We introduce a new surface model that utilizes these qualities of Gaussian mixtures for the definition and control of a parametric smooth surface. Our approach is based on an enriched mesh data structure, which describes the probability distribution of spatial surface locations around each vertex via a Gaussian covariance matrix. By incorporating this additional covariance information, we show how to define a smooth surface via a nonlinear probabilistic subdivision operator based on products of Gaussians, which is able to capture rich details at fixed control mesh resolution. This entails new applications in surface reconstruction, modeling, and geometric compression.
Comparison of zirconocene and hafnocene catalysts for the polymerization of ethylene and 1‐butene (1992)

Abstract In polymerizations with ethylene and copolymerizations with ethylene and 1‐butene the catalyst system rac ‐ethylene(bisindenyl)zirconium dichloride ( rac ‐Et(Ind) 2 ZrCl 2 )/methylaluminoxane (MAO) shows lower activities than the analogous Hafnium catalyst. The polymers obtained with the hafnium‐catalyst have average molar masses up to ten times higher than those synthesized with the zirconium compound. It is remarkable that rac ‐Et(Ind) 2 HfCl 2 is much more able to incorporate the comonomer. This is expressed by the copolymerization parameters. At a polymerization temperature of +30°C, e.g., the r 1 ‐parameter of the hafnium‐catalyst is 5,4, the corresponding parameter of the zirconium catalyst is 19,4. Polymerizations with a catalyst mixture rac ‐Et(Ind) 2 (Hf, Zr)Cl 2 (containing 95% rac ‐Et(Ind) 2 HfCl 2 and 5% rac ‐Et(Ind) 2 ZrCl 2 ) show that each catalyst compound produces its own polymer independently.
Regulation of the Interferon‐indueible Protein Kinase PKR and (2′‐5′)oligo(Adenylate) Synthetase by a Catalytically Inactive PKR Mutant Through Competition for Double‐stranded RNA Binding (1995)

The interferon-inducible double-stranded RNA-dependent protein kinase PKR has been suggested to function as a tumour suppressor gene product. Catalytically inactive mutants of PKR give rise to a tumorigenic phenotype when overexpressed in NIH-3T3 fibroblasts and this has been attributed to a dominant negative effect on the activity of the wild-type enzyme. Here we show that the mutant with Lys296 replaced by Arg, [K296R]PKR, not only inhibits the protein kinase activity of wild-type PKR but is also inhibitory towards another double-stranded RNA-dependent enzyme, the 40-kDa form of (2'-5')oligo(adenylate) synthetase. Inhibition of both wild-type PKR and (2'-5')oligo(adenylate) synthetase is reversed by adding higher concentrations of double-stranded RNA. These results suggest competition between [K296R]PKR and wild-type PKR or (2'-5')oligo(adenylate) synthetase for limiting amounts of double-stranded RNA. Moreover, the data imply that the tumorigenic effect of this PKR mutant could be due to inhibition of additional pathways requiring low levels of double-stranded RNA for activation and cannot be unambiguously attributed to inhibition of endogenous PKR itself.
JAM2 Interacts with α4β1 (2002)

We have previously reported that junctional adhesion molecule 2 (JAM2) adheres to T cells through heterotypic interactions with JAM3. An examination of the cation dependence of JAM2 adhesion to HSB cells revealed a Mn(2+)-enhanced binding component indicative of integrin involvement. Using neutralizing integrin antibodies, we have defined an interaction between JAM2 and alpha(4)beta(1) in T cells. The interaction is readily amenable to drug intervention as demonstrated by the ability of TBC 772, an alpha(4)-specific inhibitor, to attenuate the Mn(2+)-enhanced component. Intriguingly, the engagement of alpha(4)beta(1) by JAM2 is only enabled following prior adhesion of JAM2 with JAM3 and is not detectable in cells where JAM3 expression is absent. Supporting this observation, we show that neutralizing JAM3 serum and soluble JAM3 ectodomain inhibit not only JAM2 binding to JAM3 but also prevent JAM2/alpha(4)beta(1) interactions in T cells. We further define the first Ig-like fold of JAM2 as being competent in binding both JAM3 and alpha(4)beta(1) counter-receptors. Mutagenesis of the only acidic residue in the C-D loop of this Ig fold, namely Asp-82, has no bearing on alpha(4)beta(1) interactions, and thus JAM2 deviates somewhat from the mechanism used by other immunoglobulin superfamily cell adhesion molecules to engage integrin.
Seribantumab, an Anti-ERBB3 Antibody, Delays the Onset of Resistance and Restores Sensitivity to Letrozole in an Estrogen Receptor–Positive Breast Cancer Model (2015)

Heregulin-driven ERBB3 signaling has been implicated as a mechanism of resistance to cytotoxic and antiendocrine therapies in preclinical breast cancer models. In this study, we evaluated the effects of seribantumab (MM-121), a heregulin-blocking anti-ERBB3 monoclonal antibody, alone and in combination with the aromatase inhibitor letrozole, on cell signaling and tumor growth in a preclinical model of postmenopausal estrogen receptor-positive (ER(+)) breast cancer. In vitro, heregulin treatment induced estrogen receptor phosphorylation in MCF-7Ca cells, and long-term letrozole-treated (LTLT-Ca) cells had increased expression and activation levels of EGFR, HER2, and ERBB3. Treatment with seribantumab, but not letrozole, inhibited basal and heregulin-mediated ERBB receptor phosphorylation and downstream effector activation in letrozole-sensitive (MCF-7Ca) and -refractory (LTLT-Ca) cells. Notably, in MCF-7Ca-derived xenograft tumors, cotreatment with seribantumab and letrozole had increased antitumor activity compared with letrozole alone, which was accompanied by downregulated PI3K/MTOR signaling both prior to and after the development of resistance to letrozole. Moreover, the addition of an MTOR inhibitor to this treatment regimen did not improve antitumor activity and was not well tolerated. Our results demonstrate that heregulin-driven ERBB3 signaling mediates resistance to letrozole in a preclinical model of ER(+) breast cancer, suggesting that heregulin-expressing ER(+) breast cancer patients may benefit from the addition of seribantumab to antiendocrine therapy.
High-Throughput Single-Molecule DNA Screening Based on Electrophoresis (2000)

In electrophoresis, the migration velocity is used for sizing DNA and proteins or for distinguishing molecules based on charge and hydrodynamic radius. Many protein and DNA assays relevant to disease diagnosis are based on such separations. However, standard protocols are not only slow (minutes to hours) but also insensitive (many molecules in a detectable band). We successfully demonstrated a high-throughput imaging approach that allows determination of the individual electrophoretic mobilities of many molecules at a time. Each measurement only requires a few milliseconds to complete. This opens up the possibility of screening single copies of DNA or proteins within single biological cells for disease markers without performing polymerase chain reaction or other biological amplification. The purpose is not to separate the DNA molecules but to identify each one on the basis of the measured electrophoretic mobility. We developed three different procedures to measure the individual molecular mobilities. The results correlate well with capillary electrophoresis (CE) experiments for the same samples (2-49 kb dsDNA) under identical separation conditions. The implication is that any electrophoresis protocols from slab gels to CE should be adaptable to single-molecule screening for disease diagnosis.
Notizen: Fast Pulsed Laser Induced Electron Generation for Electron Impact Mass Spectrometry (1988)

A new ultra fast electron impact (El) ion source is pre­sented that produces a very short, high intensity electron beam, allowing medium resolution mass spectra to be re­corded without pulsing the ion accelerating voltages in a time-of-flight mass spectrometer (TOF-MS). The ion source requires minimum modification of any TOF-MS equipped with an electrostatic ion reflector and UV-laser. El-spectra are presented for comparison with literature spectra.
PROBING PHYCOBILISOME STRUCTURE BY IMMUNO‐ELECTRON MICROSCOPY1 (1977)

ABSTRACT By immuno‐electron microscopy it was shown that phycoerythrin is located on the outer surface of the phycobilisome and allophycocyanin is on the inside near the photosynthetic membrane in the red alga Porphyridium purpureum (Bory) Drew &amp; Ross (P. cruentum). These findings are consistent with the idea that the phycobilisome junctions as a light harvesting antenna and energy sink, which directs the energy to chlorophyll in the photosynthetic membrane. A technique was devised in which unfixed phycobilisomes, attached to thylakoid vesicles, were separately reacted with three monospecific antisera (to B‐phycoerythrin, R‐phycocyanin and allophycocyanin) and the reaction products were secondarily marked by reaction with ferritin‐conjugated goat‐antirabbit gamma globulin fraction. This was subsequently followed by glutaraldehyde fixation and staining with phosphotungstic acid. The entire procedure was carried out on an electron microscope grid. The results confirm the previously proposed phycobilisome structural model.
Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-Flight Mass Spectrometry (2009)

Most cancer cells predominantly produce energy by glycolysis rather than oxidative phosphorylation via the tricarboxylic acid (TCA) cycle, even in the presence of an adequate oxygen supply (Warburg effect). However, little has been reported regarding the direct measurements of global metabolites in clinical tumor tissues. Here, we applied capillary electrophoresis time-of-flight mass spectrometry, which enables comprehensive and quantitative analysis of charged metabolites, to simultaneously measure their levels in tumor and grossly normal tissues obtained from 16 colon and 12 stomach cancer patients. Quantification of 94 metabolites in colon and 95 metabolites in stomach involved in glycolysis, the pentose phosphate pathway, the TCA and urea cycles, and amino acid and nucleotide metabolisms resulted in the identification of several cancer-specific metabolic traits. Extremely low glucose and high lactate and glycolytic intermediate concentrations were found in both colon and stomach tumor tissues, which indicated enhanced glycolysis and thus confirmed the Warburg effect. Significant accumulation of all amino acids except glutamine in the tumors implied autophagic degradation of proteins and active glutamine breakdown for energy production, i.e., glutaminolysis. In addition, significant organ-specific differences were found in the levels of TCA cycle intermediates, which reflected the dependency of each tissue on aerobic respiration according to oxygen availability. The results uncovered unexpectedly poor nutritional conditions in the actual tumor microenvironment and showed that capillary electrophoresis coupled to mass spectrometry-based metabolomics, which is capable of quantifying the levels of energy metabolites in tissues, could be a powerful tool for the development of novel anticancer agents that target cancer-specific metabolism.
Space shuttle flight (STS‐90) enhances degradation of rat myosin heavy chain in association with activation of ubiquitin‐proteasome pathway (2001)

ABSTRACT To elucidate the mechanisms of microgravity‐induced muscle atrophy, we focused on fast‐type myosin heavy chain (MHC) degradation and expression of proteases in atrophied gastrocnemius muscles of neonatal rats exposed to 16‐d spaceflight (STS‐90). The spaceflight stimulated ubiquitination of proteins, including a MHC molecule, and accumulation of MHC degradation fragments in the muscles. Semiquantitative reverse transcriptase‐polymerase chain reaction revealed that the spaceflight significantly increased mRNA levels of cathepsin L, proteasome components (RC2 and RC9), polyubiquitin, and ubiquitin‐conjugating enzyme in the muscles, compared with those of ground control rats. The levels of μ‐calpain, m‐calpain, cathepsin B, and cathepsin H mRNAs were not changed by the spaceflight. We also found that tail‐suspension of rats for 10 d or longer caused the ubiquitination and degradation of MHC in gastrocnemius muscle, as was observed in the spaceflight rats. In the muscle of suspended rats, these changes were closely associated with activation of proteasome and up‐regulation of expression of mRNA for the proteasome components and polyubiquitin. Administration of a cysteine protease inhibitor, E‐64, to the suspended rats did not prevent the MHC degradation. Our results suggest that spaceflight induces the degradation of muscle contractile proteins, including MHC, possibly through a ubiquitin‐dependent proteolytic pathway.
Identification of 12p as a region of frequent deletion in advanced prostate cancer. (1998)

The identification of homozygous deletions in malignant tissue has been a powerful tool for the localization of tumor suppressor genes. Representational difference analysis (RDA) uses selective hybridization and the PCR to isolate regions of chromosomal loss and has facilitated the identification of tumor suppressor genes such as BRCA2 and PTEN. Twenty RDA clones were generated by comparing genomic DNA from a prostate cancer xenograft to the same patient's normal kidney DNA. Southern blot analysis of the tester and driver and of normal and xenograft DNA, using the differential products as probes, showed the homozygous deletion in 16 of 20 RDA clones. The sequence of one of the differential products overlapped HSU59962, a genomic GenBank sequence on chromosome 12p12-13. Multiplex PCR of the xenograft DNA using polymorphic repeats mapped the deletion to a 1-5-cM region on 12p. Genomic DNA isolated from a panel of cryostat microdissected metastatic prostate adenocarcinomas/normal pairs was screened for loss of heterozygosity using the same polymorphic repeats. Loss of heterozygosity was demonstrated in 9 (47%) of 19 patients. This region may contain, or lie in close proximity to, tumor suppressor genes important in the progression and/or initiation of prostate cancer.
Increased levels of spliced RNA account for augmented expression from the MFG retroviral vector in hematopoietic cells. (1996)

A persistent obstacle in the use of vector systems for gene therapy has been the inability to attain high-level expression of the target gene in primary cells in vivo. The MFG retroviral vector was designed to yield improved expression over the widely used N2 or LN vectors; however, the molecular basis for this effect has not been examined. Using the human glucocerebrosidase (GC) enzyme as a reporter, we compared expression from the MFG and N2 vector backbones in transduced murine hematopoietic cells after syngeneic bone marrow transplantation. Reporter enzyme activities in primary spleen colonies of transplanted mice were seven-fold higher per vector copy in cells transduced with the (MFG-based) MGC vector than in cells bearing the (N2-based) G2 vector. In spleen colonies harboring the MGC vector, the ratio of spliced to unspliced vector RNA was increased four-fold relative to the G2 vector transcripts in Northern blot analyses. Further analyses indicated that MGC-transduced cells contained five-fold higher levels of spliced RNA per vector copy. Since translation of spliced RNA species (in which the complex secondary structure of the packaging signal has been excised) is likely to proceed with enhanced efficiency, the augmented levels of spliced RNA produced by MFG may represent the key element of increased protein expression from this vector. These findings suggest that the MFG retroviral vector may provide higher level expression of target genes used in human gene therapy.
Refinement of TF-IDF schemes for web pages using their hyperlinked neighboring pages (2003)

In IR (information retrieval) systems based on the vector space model, the TF-IDF scheme is widely used to characterize documents. However, in the case of documents with hyperlink structures such as Web pages, it is necessary to develop a technique for representing the contents of Web pages more accurately by exploiting the contents of their hyperlinked neighboring pages. In this paper, we first propose several approaches to refining the TF-IDF scheme for a target Web page by using the contents of its hyperlinked neighboring pages, and then compare the retrieval accuracy of our proposed approaches. Experimental results show that, generally, more accurate feature vectors of a target Web page can be generated in the case of utilizing the contents of its hyperlinked neighboring pages at levels up to second in the backward direction from the target page.
TbetaR-I(6A) is a candidate tumor susceptibility allele. (1999)

We have previously described a type I transforming growth factor (TGF)-beta receptor (TbetaR-I) polymorphic allele, TbetaR-I(6A), that has a deletion of three alanines from a nine-alanine stretch. We observed a higher than expected number of TbetaR-I(6A) homozygotes among tumor and nontumor DNA from patients with a diagnosis of cancer. To test the hypothesis that TbetaR-I(6A) homozygosity is associated with cancer, we performed a case-control study in patients with a diagnosis of cancer and matched healthy individuals with no history of cancer and who were identical in their gender and their geographical and ethnic background to determine the relative germ-line frequencies of this allele. We found nine TbetaR-I(6A) homozygotes among 851 patients with cancer. In comparison, there were no TbetaR-I(6A) homozygotes among 735 healthy volunteers (P < 0.01). We also observed an excess of TbetaR-I(6A) heterozygotes in cancer cases compared to controls (14.6% versus 10.6%; P = 0.02, Fisher's exact test). A subset analysis revealed that 4 of 112 patients with colorectal cancer were TbetaR-I(6A) homozygotes (P < 0.01). Using mink lung epithelial cell lines devoid of TbetaR-I, we established stably transfected TbetaR-I and TbetaR-I(6A) cell lines. We found that, compared to TbetaR-I, TbetaR-I(6A) was impaired as a mediator of TGF-beta antiproliferative signals. We conclude that TbetaR-I(6A) acts as a tumor susceptibility allele that may contribute to the development of cancer, especially colon cancer, by means of reduced TGF-beta-mediated growth inhibition.
Dynamics of TCP traffic over ATM networks (1994)

We investigate the performance of TCP connections over ATM networks without ATM-level congestion control, and compare it to the performance of TCP over packet-based networks. For simulations of congested networks, the effective throughput of TCP over ATM can be quite low when cells are dropped at the congested ATM switch. The low throughput is due to wasted bandwidth as the congested link transmits cells from “corrupted” packets, i.e., packets in which at least one cell is dropped by the switch. This fragmentation effect can be corrected and high throughput can be achieved if the switch drops whole packets prior to buffer overflow; we call this strategy Early Packet Discard. We also discuss general issues of congestion avoidance for best-effort traffic in ATM networks.
Preventing Noise Induced Otoacoustic Emission Loss by Increasing Magnesium (Mg2+) Intake in Guinea-Pigs (2003)

This study aimed to explore the effects of increased Mg2+ intake on the activity of the outer hair cells as manifested in Click and Distortion Evoked Otoacoustic Emissions (CEOAEs; DPOAEs) in 25 animals. Thirteen animals were fed with high Mg2+ intake (39 mmol Mg2+/l in drinking water) and 12 without the Mg2+ additive. The OAE amplitudes and frequency ranges as well as the DPOAE thresholds were affected significantly less by noise exposure in the animals fed Mg2+-enriched water. Following the exposure, the auditory recovery was faster in the high than the low Mg2+ animals (controls). In addition, a relationship was found between the Mg2+ level and the emission loss. The post-exposure measures may result from the effect of Mg2+ on cochlear metabolic processes and vascular microcirculation. The results demonstrate that pre-existing low Mg2+ levels will exacerbate noise induced hearing loss (NIHL), and increased Mg2+ intake provides a significant biological cochlear protective effect.