gebhart/patrepeval huggingface dataset:
The predictive value of prostate cancer biomarkers depends on age and time to diagnosis: Towards a biologically‐based screening strategy (2007)

Both benign and malignant prostate diseases elevate total prostate-specific antigen (tPSA), and the incidence of benign disease increases markedly with age. There is evidence, however, that free-to-total PSA ratio (%fPSA) and human kallikrein 2 (hK2) more closely reflect the malignant process. We tested the hypothesis that tPSA levels are more strongly predictive of cancer in younger when compared to older men, whereas %fPSA and hK2 are more strongly predictive in men tested closer to diagnosis. The study included 13,676 men age >/= 44 in Sweden, where PSA screening was uncommon during the study period. fPSA, tPSA and hK2 were measured in archived plasma collected during 1974-1986 in 501 men subsequently diagnosed with prostate cancer up to 1999 and in 1,292 matched controls. The predictive value of tPSA was lower in older men (p = 0.003) but was not strongly affected by time to diagnosis (p = 0.3); the predictive value of hK2 was higher closer to diagnosis (p < 0.0005) but was not modified by age (p = 0.7). A model including tPSA, fPSA and hK2 was superior (p = 0.02) to tPSA alone in older (AUC 0.819 vs. 0.794), but not in younger men (0.758 vs. 0.759). Total PSA can be used as a single marker at early middle age to predict long-term risk of prostate cancer and thus to determine intensity of subsequent screening. In contrast, %fPSA and hK2 add important predictive value in older men and much closer to diagnosis. Strategies for prostate cancer screening should be based on thorough understanding of the interaction of kallikrein-related biomarkers with prostate pathobiology.
Semiconductor Nanorod Liquid Crystals (2002)

Rodlike molecules form liquid crystalline phases with orientational order and positional disorder. The great majority of materials in which liquid crystalline phases have been observed comprise organic molecules or polymers, even though there has been continuing and growing interest in inorganic liquid crystals. Recent advances in the control of the sizes and shapes of inorganic nanocrystals allow for the formation of a broad class of new inorganic liquid crystals. Here, we show the formation of liquid crystalline phases of CdSe semiconductor nanorods. These new liquid crystalline phases may have great importance for both application and fundamental study.
Unplanned releases and injuries associated with aerial application of chemicals, 1995-2002. (2005)

For this article, records of the Hazardous Substances Emergency Events Surveillance (HSEES) system were reviewed to identify and describe acute, unplanned releases of agricultural chemicals and associated injuries related to aerial application during 1995-2002. Records of aerial-application accidents from the National Transportation Safety Board were also reviewed. Of the 54,090 events in the HSEES system for 1995-2002, 91 were identified as aerial-application events. The most commonly released substance was malathion. There were 56 victims; 12 died, and 34 required treatment at a hospital. A higher percentage of HSEES aerial-applicator events involved injury and death than did other HSEES transportation events. The relatively high number of injuries and fatalities underscores the need for precautions such as monitoring and limiting pilot cumulative exposures to pesticides, and using appropriate personal protective equipment and decontamination equipment. Emergency responders should be educated about the hazards associated with chemicals at aerial-application crash sites.
NMDA Receptor-Dependent Synaptic Reinforcement as a Crucial Process for Memory Consolidation (2000)

The hippocampal CA1 region is crucial for converting new memories into long-term memories, a process believed to continue for week(s) after initial learning. By developing an inducible, reversible, and CA1-specific knockout technique, we could switch N-methyl-D-aspartate (NMDA) receptor function off or on in CA1 during the consolidation period. Our data indicate that memory consolidation depends on the reactivation of the NMDA receptor, possibly to reinforce site-specific synaptic modifications to consolidate memory traces. Such a synaptic reinforcement process may also serve as a cellular means by which the new memory is transferred from the hippocampus to the cortex for permanent storage.
Pharmacogenetics of Gilbert‘s Syndrome (2008)

Gilbert's syndrome is characterized by mild unconjugated nonhemolytic hyperbilirubinemia, which does not lead to hepatic inflammation, fibrosis, chronic liver disease or liver failure. Almost 100 years after its clinical description, it was linked to a genetic variant of the human bilirubin UDP-glucuronosyltransferase (UGT1A1), UGT1A1 (*)28, found in approximately 40% of Caucasoid individuals. Over 113 UGT1A1 variants have since been reported, leading to a continuous spectrum from mild hyperbilirubinemia to life-threatening jaundice. UGT1A variants are evolutionary diverse and occur in the context of haplotypes combining different variants within the promoter, the 5 exons, as well as introns of the UGT1A1 gene, and also in combination with other UGT1A genes expressed in the liver and the extrahepatic gastrointestinal tract. The variation of glucuronidation hidden behind Gilbert's syndrome impacts drug therapy, which includes the well-characterized examples of irinotecan and atazanavir. The prediction of unwanted drug reactions associated with Gilbert's syndrome will improve drug safety, therapeutic individualization and impact the drug-development process.
Great Expectations: Privacy Rights in Automobiles (1979)

The authors examine the history of the standing doctrine as it relates to the ability to contest searches and seizures. After analyzing the cases in this area, the recent Supreme Court case of Rakas v. Illinois is discussed and critiqued in depth. Cases decided after Rakas serve as the backdrop for a discussion of the exclusionary rule and the privacy rights of automobile passengers. Finally, the authors propose an alternative to the Rakas holding.
Signal processing with higher-order spectra (1993)

The strengths and limitations of correlation-based signal processing methods are discussed. The definitions, properties, and computation of higher-order statistics and spectra, with emphasis on the bispectrum and trispectrum are presented. Parametric and nonparametric expressions for polyspectra of linear and nonlinear processes are described. The applications of higher-order spectra in signal processing are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Preliminary Mechanical Characterization of the Small Bowel for In Vivo Robotic Mobility (2011)

In this work we present test methods, devices, and preliminary results for the mechanical characterization of the small bowel for intra luminal robotic mobility. Both active and passive forces that affect mobility are investigated. Four investigative devices and testing methods to characterize the active and passive forces are presented in this work: (1) a novel manometer and a force sensor array that measure force per cm of axial length generated by the migrating motor complex, (2) a biaxial test apparatus and method for characterizing the biomechanical properties of the duodenum, jejunum, and ileum, (3) a novel in vitro device and protocol designed to measure the energy required to overcome the self-adhesivity of the mucosa, and (4) a novel tribometer that measures the in vivo coefficient of friction between the mucus membrane and the robot surface. The four devices are tested on a single porcine model to validate the approach and protocols. Mean force readings per cm of axial length of intestine that occurred over a 15 min interval in vivo were 1.34 ± 0.14 and 1.18 ± 0.22 N cm(-1) in the middle and distal regions, respectively. Based on the biaxial stress/stretch tests, the tissue behaves anisotropically with the circumferential direction being more compliant than the axial direction. The mean work per unit area for mucoseparation of the small bowel is 0.08 ± 0.03 mJ cm(-2). The total energy to overcome mucoadhesion over the entire length of the porcine small bowel is approximately 0.55 J. The mean in vivo coefficient of friction (COF) of a curved 6.97 cm(2) polycarbonate sled on live mucosa traveling at 1 mm s(-1) is 0.016 ± 0.002. This is slightly lower than the COF on excised tissue, given the same input parameters. We have initiated a comprehensive program and suite of test devices and protocols for mechanically characterizing the small bowel for in vivo mobility. Results show that each of the four protocols and associated test devices has successfully gathered preliminary data to confirm the validity of our test approach.
A mouse Chromosome 11 library generated from sorted chromosomes using linker-adapter polymerase chain reaction (1994)

We describe the generation of a mouse whole chromosome library using sequence-independent polymerase chain reaction (PCR) to amplify sequences contained in DNA extracted from flow sorted chromosomes. DNA in sorted chromosomes from a human x mouse hybrid cell line was digested with a frequent four-cutter restriction enzyme, Sau3AI, and the ends were ligated to an adapter oligonucleotide. The ligated DNA fragments were amplified using PCR primers homologous to the linker-adapter oligonucleotide. PCR-generated products were characterized by gel electrophoresis. The size of the amplified DNA ranged from 100 to more than 1,000 bp with a relatively high proportion of products at approximately 400 bp. Biotinylated PCR products used for FISH showed specific hybridization to murine metaphases and no hybridization to human lymphocyte and hamster metaphase cells. Banding analysis indicated that the probes were specific for mouse Chromosome 11. We anticipate that availability of painting probes for specific murine chromosomes will facilitate cytogenetic studies in the mouse.
Raltitrexed plus oxaliplatin as first-line chemotherapy in metastatic colorectal carcinoma: a multicentric phase II trial (2002)

For advanced colorectal carcinoma, two new drugs, raltitrexed (TOM) and oxaliplatin (L-OHP), have recently shown interesting results. Preclinical and clinical studies suggest that this combination, because of its favorable toxicity profile, high response rate and convenient schedule of administration, can be administered successfully in this disease. In our phase II study, 37 non pre-treated patients with metastatic colorectal carcinoma were treated with TOM (3 mg/m(2)) and L-OHP (130 mg/m(2)) every 3 weeks. In total, 222 cycles were administered; all patients received at least 2 cycles (median 6, range 2-8). There were two complete and 14 partial responses for an overall response rate of 43% (95% CI 27-69%). The median time to response was 2.5 months (range 2-4) and the median duration was 10.3 months (range 5-18). Twelve of the 23 (52%) patients with symptomatic colorectal cancer were classified as clinical benefit responders for at least 4 weeks during the study period. Treatment was well tolerated, and both acute, essentially hematologic, and cumulative hepatic and neurologic toxicities were manageable and reversible. Response rate and toxic effects observed during this study warrant additional studies comparing this TOM-L-OHP regimen with CPT-11 and/or capacitebine-containing regimens in metastatic colorectal carcinoma.
Identification of Neutrophil Gelatinase-Associated Lipocalin as a Novel Early Urinary Biomarker for Ischemic Renal Injury (2003)

Acute renal failure (ARF) secondary to ischemic injury remains a common and potentially devastating problem. A transcriptome-wide interrogation strategy was used to identify renal genes that are induced very early after renal ischemia, whose protein products might serve as novel biomarkers for ARF. Seven genes that are upregulated >10-fold were identified, one of which (Cyr61) has recently been reported to be induced after renal ischemia. Unexpectedly, the induction of the other six transcripts was novel to the ARF field. In this study, one of these previously unrecognized genes was further characterized, namely neutrophil gelatinase-associated lipocalin (NGAL), because it is a small secreted polypeptide that is protease resistant and consequently might be readily detected in the urine. The marked upregulation of NGAL mRNA and protein levels in the early postischemic mouse kidney was confirmed. NGAL protein expression was detected predominantly in proliferating cell nuclear antigen-positive proximal tubule cells, in a punctate cytoplasmic distribution that co-localized with markers of late endosomes. NGAL was easily detected in the urine in the very first urine output after ischemia in both mouse and rat models of ARF. The appearance of NGAL in the urine was related to the dose and duration of renal ischemia and preceded the appearance of other urinary markers such as N-acetyl-beta-D-glucosaminidase and beta2-microglobulin. The origin of NGAL from tubule cells was confirmed in cultured human proximal tubule cells subjected to in vitro ischemic injury, where NGAL mRNA was rapidly induced in the cells and NGAL protein was readily detectable in the culture medium within 1 h of mild ATP depletion. NGAL was also easily detectable in the urine of mice with cisplatin-induced nephrotoxicity, again preceding the appearance of N-acetyl-beta-D-glucosaminidase and beta2-microglobulin. The results indicate that NGAL may represent an early, sensitive, noninvasive urinary biomarker for ischemic and nephrotoxic renal injury.
High-sensitivity x-ray photoelectron spectroscopy characterization of a quantum device structure (2002)

A high-resolution, high-sensitivity VG x-ray photoelectron spectrometer was used to study a semiconductor layer structure grown for the fabrication of resonant tunneling bipolar transistor devices. Depth profiling using argon ion milling, at a rate of 50 Å/min, has allowed the device layers to be identified on the basis of their elemental composition. The measurement system sensitivity was sufficient to identify the elemental components of the 11 Å AlAs barrier layer in quantum tunneling InGaAs/AlAs device layers.
HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data (2012)

Genome assembly methods produce haplotype phase ambiguous assemblies due to limitations in current sequencing technologies. Determining the haplotype phase of an individual is computationally challenging and experimentally expensive. However, haplotype phase information is crucial in many bioinformatics workflows such as genetic association studies and genomic imputation. Current computational methods of determining haplotype phase from sequence data--known as haplotype assembly--have difficulties producing accurate results for large (1000 genomes-type) data or operate on restricted optimizations that are unrealistic considering modern high-throughput sequencing technologies. We present a novel algorithm, HapCompass, for haplotype assembly of densely sequenced human genome data. The HapCompass algorithm operates on a graph where single nucleotide polymorphisms (SNPs) are nodes and edges are defined by sequence reads and viewed as supporting evidence of co-occurring SNP alleles in a haplotype. In our graph model, haplotype phasings correspond to spanning trees. We define the minimum weighted edge removal optimization on this graph and develop an algorithm based on cycle basis local optimizations for resolving conflicting evidence. We then estimate the amount of sequencing required to produce a complete haplotype assembly of a chromosome. Using these estimates together with metrics borrowed from genome assembly and haplotype phasing, we compare the accuracy of HapCompass, the Genome Analysis ToolKit, and HapCut for 1000 Genomes Project and simulated data. We show that HapCompass performs significantly better for a variety of data and metrics. HapCompass is freely available for download (www.brown.edu/Research/Istrail_Lab/).
Direct in-gel hybridization, without blotting, using nick-translated cloned DNA probe. (1991)

Hybridization of DNA and RNA to labeled probes is central to molecular biology. A method is described here for hybridization of cloned DNA probes directly to DNA in agarose gels. This in-gel hybridization method has several advantages over conventional techniques using transfer to membranes. It is extremely rapid, highly sensitive, less expensive and particularly suited for high molecular weight genomic DNA analysis.
Fibrinogen standards. (1990)

Necrotising lymphadenitis without granulocytic infiltration: case from Western Samoa Kikuchi's disease (necrotising lymphaden- itis) was first reported by Kikuchi' and Fujimoto et aP in Japan in 1972.It is charac- terised by cervical lymphadenitis in young patients, and may simulate malignancy both clinically and histopathologically.Patients
Tyrosine Phosphorylation of the Nuclear Receptor Coactivator AIB1/SRC-3 Is Enhanced by Abl Kinase and Is Required for Its Activity in Cancer Cells (2008)

Overexpression and activation of the steroid receptor coactivator amplified in breast cancer 1 (AIB1)/steroid receptor coactivator-3 (SRC-3) have been shown to have a critical role in oncogenesis and are required for both steroid and growth factor signaling in epithelial tumors. Here, we report a new mechanism for activation of SRC coactivators. We demonstrate regulated tyrosine phosphorylation of AIB1/SRC-3 at a C-terminal tyrosine residue (Y1357) that is phosphorylated after insulin-like growth factor 1, epidermal growth factor, or estrogen treatment of breast cancer cells. Phosphorylated Y1357 is increased in HER2/neu (v-erb-b2 erythroblastic leukemia viral oncogene homolog 2) mammary tumor epithelia and is required to modulate AIB1/SRC-3 coactivation of estrogen receptor alpha (ERalpha), progesterone receptor B, NF-kappaB, and AP-1-dependent promoters. c-Abl (v-Abl Abelson murine leukemia viral oncogene homolog 1) tyrosine kinase directly phosphorylates AIB1/SRC-3 at Y1357 and modulates the association of AIB1 with c-Abl, ERalpha, the transcriptional cofactor p300, and the methyltransferase coactivator-associated arginine methyltransferase 1, CARM1. AIB1/SRC-3-dependent transcription and phenotypic changes, such as cell growth and focus formation, can be reversed by an Abl kinase inhibitor, imatinib. Thus, the phosphorylation state of Y1357 can function as a molecular on/off switch and facilitates the cross talk between hormone, growth factor, and intracellular kinase signaling pathways in cancer.
Surface Cross-Linking of ZIF-8/Polyimide Mixed Matrix Membranes (MMMs) for Gas Separation (2013)

The demand for cost-efficient separations requires membranes with high gas flux and high selectivity which opens the path for further improvements. Mixed matrix membranes (MMMs) made from 33.3 wt % ZIF-8 in 6FDA-durene were tested at 35 °C and 3.5 atm. At 33.3 wt % loading of ZIF-8, H2, N2, O2, and CH4 gas permeabilities increased approximately 400%. Cross-linking the surface of this MMM, by reacting with ethylenediamine vapor, yielded a 10-fold increase in H2/CO2, H2/N2, and H2/CH4 selectivities with respect to 6FDA-durene, preserving 55% of the H2 permeability of 6FDA-durene. The permselective properties of the cross-linked skin of the MMM fall above the most recent permeability–selectivity trade-off lines (2008 Robeson upper bounds) for H2/CO2, H2/N2, and H2/CH4 separations. To the best of our knowledge, this is the first example of a cross-linked ZIF/polymer MMM for gas separation.
Optoelectronic characterization of transmission lines and waveguides by terahertz time-domain spectroscopy (2000)

An overview is presented of an experimental search for an ultrawide-band transmission channel with low dispersion and loss. Such a terahertz (THz) interconnect will soon be required by the insatiable demand for higher speed devices and wider bandwidth communication. Starting with the early optoelectronic generation and detection of single-mode, subpicosecond electrical pulses on coplanar transmission lines, their complete characterization by THz time-domain spectroscopy (THz-TDS) is described. The consequent discovery of phase-coherent Cherenkov radiation in the form of an electromagnetic shock wave from these propagating electrical pulses is discussed together with its dominant role in the large measured propagation loss of these pulses. Various techniques to reduce this radiation are presented. The importance of dielectric materials characterization is explained and illustrated by THz-TDS measurements of high T/sub c/ substrates. Newly obtained THz waveguide results are presented and compared to the performance of coplanar transmission lines.
Crystallization of Nucleic Acids and Proteins: A practical Approach (1998)

International audience
Monoclonal Antibodies against Human β‐Glucocerebrosidase (1983)

Monoclonal antibodies were obtained against the membrane-bound lysosomal enzyme beta-glucocerebrosidase (acid beta-glucosidase), which is deficient in Gaucher's disease. BALB/c mice were immunized with homogeneous enzyme protein extracted from a sodium dodecyl sulphate/polyacrylamide gel. The mice were subsequently hyperimmunized with partially purified enzyme prior to fusion of spleen cells with myeloma cells. After fusion, 32 primary hybrid cell populations were obtained which continued to produce antibodies against beta-glucocerebrosidase after prolonged time of culture. All antibodies reacted with both native and denatured enzyme. Four primary cell populations were subcloned and the antibodies produced were characterized. The antibodies were all four of the IgG1 subclass. Three of these antibodies bind to protein A whereas one does not. The results of binding assays indicated that three of the antibodies react with the same antigenic domain (epitope 1), but the fourth with a different one (epitope 2). Probably two antigenic determinants are present in epitope 1 since one of the antibodies with specificity for epitope 1 is inactivated after iodination by the chloramine-T procedure whereas a second one is not.
Double-stranded DNA analysis by matrix assisted laser desorption/ionization (1994)

Matrix assisted laser desorption/ionization time-of-flight mass spectrometry was used to analyze double-stranded DNA fragments digested with restricted enzymes. As previously reported, only denatured single strands were detected and the resolution of TOFMS was not good enough to distinguish the mass difference between the complementary strands. To prove denaturation occurred rather than detecting doubly charged ds-DNA fragments, new DNA segments and restriction enzyme cleavage sites were searched. A 246 bp DNA designated as pLB129 was used. This segment contains part of the human immunoglobulin V{sub {lambda}} germline gene. It has several restriction sites that provide fragments with sticky ends. The 246 bp DNA was amplified by polyermase chain reaction (PCR), and digested with three kinds of restriction enzymes. The final products were purified with phenol/chloroform extraction and alcohol precipitation. MALDI-MS results clearly indicated that denaturation did happen as the mass peak corresponding to each individual was registered. 3-hydroxypicolinic acid (3-HPA) was used as the matrix. Analysis of double stranded DNA by MALDI-MS will have significant impacts in molecular biology. As coupled with PCR technique, MALDI-MS has great potential in fast screening tests for biomedical applications.
Diastereoselective Magnesium Halide-Catalyzed anti-Aldol Reactions of Chiral N-Acyloxazolidinones (2001)

A chiral auxilliary-based direct aldol reaction is reported. The reactions are catalytic in magnesium salts and are facilitated by silylation with chlorotrimethylsilane. The adducts isolated are in high diastereoselectivity (up to 32:1 dr) and favor the anti-aldol diastereomer B. Reactions are operationally simple and can be run under ambient atmosphere without rigorous exclusion of water. Many of the adducts are highly crystalline and a single diastereomer can be isolated without chromatography.