gebhart/patrepeval huggingface dataset:
Calculated calibration models for glucose in cutaneous tissue from temperature modulation of localized reflectance measurements (Invited Paper) (2005)

We used a temperature controlled localized reflectance optical probe to test the effect of distance source detector distance, temperature and wavelength on the calibration of localized reflectance signals versus glucose concentration. Successful calibration models were established. The data suggests that the interplay of source-detector distances, wavelengths and temperature may lead to selecting a defined subcutaneous volume, where the signal can correlate better with glucose.
Diazo compounds as highly tunable reactants in 1,3-dipolar cycloaddition reactions with cycloalkynes (2012)

Diazo compounds, which can be accessed directly from azides by deimidogenation, are shown to be extremely versatile dipoles in 1,3-dipolar cycloaddition reactions with a cyclooctyne. The reactivity of a diazo compound can be much greater or much less than its azide analog, and is enhanced markedly in polar-protic solvents. These reactivities are predictable from frontier molecular orbital energies. The most reactive diazo compound exhibited the highest known second-order rate constant to date for a dipolar cycloaddition with a cycloalkyne. These data provide a new modality for effecting chemoselective reactions in a biological context.
CWC: A Companion Write Cache for Energy-Aware Multi-Level Spin-Transfer Torque RAM Cache Design (2015)

Due to its large leakage power and low density, the conventional SARM becomes less appealing to implement the large on-chip cache due to energy issue. Emerging non-volatile memory technologies, such as phase change memory (PCM) and spin-transfer torque RAM (STT-RAM), have advantages of low leakage power and high density, which makes them good candidates for on-chip cache. In particular, STT-RAM has longer endurance and shorter access latency over PCM. There are two kinds of STT-RAM so far: single-level cell (SLC) STT-RAM and multi-level cell (MLC) STT-RAM. Compared to the SLC STT-RAM, the MLC STT-RAM has higher density and lower leakage power, which makes it a even more promising candidate for future on-chip cache. However, MLC STT-RAM improves density at the cost of almost doubled write latency and energy compared to the SLC STT-RAM. These drawbacks degrade the system performance and diminish the energy benefits. To alleviate these problems, we propose a novel cache organization, companion write cache (CWC), which is a small fully associative SRAM cache, working with the main MLC STT-RAM cache in a master-and-servant way. The key function of CWC is to absorb the energy-consuming write updates from the MLC STT-RAM cache. The experimental results are promising that CWC can greatly reduce the write energy and dynamic energy, improve the performance and endurance of MLC STT-RAM cache compared to a baseline.
Polarization inversion via parametric scattering in quasi-one-dimensional microcavities (2005)

Parametric polariton scattering is studied in quasi-one-dimensional microcavities. A polarization splitting of the polariton modes is observed and its origin is discussed. In contrast to planar cavities, here, the large splitting leads to a comprehensive analysis of the polarization dynamics. We demonstrate phase matched intersubbranch parametric polariton scattering at $k=0$ with an inversion of the linear polarization of signal and idler with respect to the pump beam.
CYP4F2 genetic variant alters required warfarin dose (2008)

Warfarin is an effective, commonly prescribed anticoagulant used to treat and prevent thrombotic events. Because of historically high rates of drug-associated adverse events, warfarin remains underprescribed. Further, interindividual variability in therapeutic dose mandates frequent monitoring until target anticoagulation is achieved. Genetic polymorphisms involved in warfarin metabolism and sensitivity have been implicated in variability of dose. Here, we describe a novel variant that influences warfarin requirements. To identify additional genetic variants that contribute to warfarin requirements, screening of DNA variants in additional genes that code for drug-metabolizing enzymes and drug transport proteins was undertaken using the Affymetrix drug-metabolizing enzymes and transporters panel. A DNA variant (rs2108622; V433M) in cytochrome P450 4F2 (CYP4F2) was associated with warfarin dose in 3 independent white cohorts of patients stabilized on warfarin representing diverse geographic regions in the United States and accounted for a difference in warfarin dose of approximately 1 mg/day between CC and TT subjects. Genetic variation of CYP4F2 was associated with a clinically relevant effect on warfarin requirement.
Personality genetics, 2002. (2002)

The study of the genetics of personality looks for effects of genetic differences on psychological differences between people. The most replicated associations have been between the dopamine D4 receptor gene and "novelty seeking" and between the serotonin reuptake transporter gene and anxiety. But even these reports are controversial, and their effects are too small to add to existing scientific theories or allow for clinical use in psychological counseling. Simultaneously studying three polymorphisms suggests that gene-gene interactions are partly responsible for these difficulties. Recently a linkage of anxiety-related traits to chromosome 8p21-23 has been replicated, and we may be close to isolating relevant genes in the region. But uncertainty about psychological phenotypes remains, and it is not clear whether future breakthroughs will require studies of thousands of genes in very large samples, or revolutions in the current assumptions and methods of personality genetics.
Quantitative determination of naltrexone, 6 beta-naltrexol and 2-hydroxy-3-methoxy-6 beta-naltrexol (HMN) in human plasma, red blood cells, saliva and urine by gas liquid chromatography. (1981)

Two gas liquid chromatographic methods differing mainly in sensitivity are described for the quantitative determination of naltrexone (NT) and its metabolites in human biofluids. Flame ionization detection of the N,O-bis-(trimethylsilyl) trifluoroacetamide (BSTFA) derivatives provided sufficient separation and sensitivity for quantitative of the bases in urine. However, the thousand times lower levels in serum, red blood cells (RBC) and saliva necessitated the use of more sensitive electron capture detection methods of the pentafluoro derivatives of NT and its metabolites. The 2-hydroxy-3-methoxy-6 beta-naltrexol (HMN) and 6 beta-naltrexol (beta-OL) pentafluoro derivatives had nearly identical gas liquid chromatographic retention times in a number of stationary liquid phases. Thus, their separation had to be achieved prior to chromatography. Differential extraction was based on the different partition characteristics of HMN and 6 beta-naltrexol between aqueous and organic solvents. Applicability of the methods was tested using the biofluids of four subjects taking 2 x 200 mg naltrexone per day chronically. Blood, saliva and urine samples were collected at the same time (prior to drug administration), which was 16 and 24 hours after the doses. In the plasma the relative percentages of the bases were 73.5 beta-OL; 23.1 HMN and 3.4 NT. The same in the urine were 76.6 beta-OL, 14.4 HMN and 9.0 NT. The lipophilic nature of HMN and the hydrophilic property of beta-OL may have influenced their distribution into RBC and saliva. In the RBC 96.1% HMN and only trace amounts of beta-OL distributed and in saliva 92.3% of beta-OL and no HMN was found; the difference in both cases was made up by naltrexone to 100%.
Clinical and biochemical studies on treatment of Lesch-Nyhan syndrome (1974)

The clinical findings in a previously unreported case of the Lesch-Nyhan syndrome are described. Though formal intellectual testing is very difficult because of the severe choreoathetosis and compulsive self mutilation, cognition appears to be less severely damaged than motor functions. It is most important to devise an active education programme for these children, and to control their self mutilation. Extracting all the teeth is strongly recommended from the latter point of view. Replacing the deficient enzyme by means of exchange blood transfusion was associated with only a transient and small decrease of the serum uric acid level; the urinary uric acid excretion was not significantly altered. The blood levels of hypoxanthine-guanine phosphoribosyltransferase (HGPRT) had not decreased to about 10% of the mean normal range until 90 days after the transfusion. The patient9s motor state was not improved by any of the following. (i) Exchange blood transfusion; (ii) oral adenine and allopurinol; (iii) tetrabenazine; (iv) thiopropazate; (v) chlorpromazine. His scores in the Reynell Development Language scale tests improved during the 14-month period of observation, but the present evidence does not justify attributing this to any of the attempted treatments. Some possible reasons for the apparent failure of transfusion to suppress purine synthesis or to improve the neurological disorder are discussed. The present clear evidence that HGPRT-containing cells remain in the circulation in sufficient numbers to keep the HGPRT activity above 10% of the normal value for at least 90 days, suggests that it would still be justifiable to investigate a similar treatment in the neonatal period.
Reliable High-Throughput Genotyping and Loss-of-Heterozygosity Detection in Formalin-Fixed, Paraffin-Embedded Tumors Using Single Nucleotide Polymorphism Arrays (2005)

Most human cancers show genetic instabilities leading to allelic imbalances, including loss of heterozygosity (LOH). Single nucleotide polymorphism (SNP) arrays can be used to detect LOH. Currently, these arrays require intact genomic DNA as obtained from frozen tissue; however, for most cancer cases, only low-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is available. In this study, we tested Illumina BeadArrays to genotype FFPE tissue and detect LOH/allelic imbalances in matched colorectal tumor and normal tissue. Genotypes were compared between leukocyte and FFPE normal tissue as well as between frozen and FFPE tumor tissue. Identical genotypes and LOH profiles were obtained from normal and tumor isolates. LOH was mainly observed on chromosomes 4, 5q, 12q, 14q, 15q, 17p, 18, and 20p, which are commonly detected regions in colorectal cancer. LOH profiles of the BeadArrays were compared with profiles obtained by Affymetrix GeneChip 10K arrays, showing identical LOH patterns. These data show that genome-wide genotyping of FFPE tissue with the BeadArray gives reliable results and is a powerful technique for LOH analysis.
Dynamic management of scratch-pad memory space (2001)

Optimizations aimed at improving the efficiency of on-chip memories are extremely important. We propose a compiler-controlled dynamic on-chip scratch-pad memory (SPM) management framework that uses both loop and data transformations. Experimental results obtained using a generic cost model indicate significant reductions in data transfer activity between SPM and off-chip memory.
Peroxynitrite induces integrin‐dependent adhesion of human neutrophils to endothelial cells via activation of the Raf‐1/MEK/Erk pathway (2000)

Accumulating evidence suggests that enhanced peroxynitrite (ONOO-) formation occurs during inflammation. We have studied the impact and the mechanisms of ONOO- action on expression of adhesion molecules on human neutrophils and coronary artery endothelial cells (HCAEC) and binding of neutrophils to HCAEC. Addition of ONOO- (0.1 to 200 5M) to isolated neutrophils resulted in a concentration-dependent down-regulation of L-selectin expression, and up-regulation of CD11b/CD18 expression. ONOO- stimulation of Erk activity was accompanied by activation of Ras, Raf-1 and MEK (mitogen-activated protein kinase kinase), and was sensitive to the MEK inhibitor PD 98059. We have observed a tight association between Erk activation and changes in CD11b/CD18 expression. ONOO- also evoked activation of neutrophil p38 MAPK. Neither ONOO--induced up-regulation of CD11b/CD18 expression nor Erk activation was affected by SB 203580, a selective inhibitor of p38 MAPK. ONOO- by itself had little effect on expression of ICAM-1 and E-selectin on HCAEC, whereas it markedly enhanced attachment of neutrophils to lipopolysaccharide-activated HCAEC only when it was added together with neutrophils. Increases in neutrophil adhesion evoked by ONOO- were blocked by an anti-CD18 monoclonal antibody. These data suggest that ONOO- activates Erk in neutrophils via the Ras/Raf-1/MEK signal transduction pathway, leading to up-regulation of surface expression of CD11b/CD18 and consequently to increased neutrophil adhesion to endothelial cells.
Generating Wikipedia by Summarizing Long Sequences (2018)

We show that generating English Wikipedia articles can be approached as a multi- document summarization of source documents. We use extractive summarization to coarsely identify salient information and a neural abstractive model to generate the article. For the abstractive model, we introduce a decoder-only architecture that can scalably attend to very long sequences, much longer than typical encoder- decoder architectures used in sequence transduction. We show that this model can generate fluent, coherent multi-sentence paragraphs and even whole Wikipedia articles. When given reference documents, we show it can extract relevant factual information as reflected in perplexity, ROUGE scores and human evaluations.
Penicillin tolerance genes ofStreptococcus pneumoniae: the ABC‐type manganese permease complex Psa (1998)

Downregulation of the major autolysin in Streptococcus pneumoniae leads to penicillin tolerance, a feature that is characterized by the ability to survive but not grow in the presence of antibiotic. Screening a library of mutants in pneumococcal surface proteins for the ability to survive 10x minimum inhibitory concentration (MIC) of penicillin revealed over 10 candidate tolerance genes. One such mutant contained an insertion in the known gene psaA, which is part of the psa locus. This locus encodes an ABC-type Mn permease complex. Sequence analysis of adjacent DNA extended the known genetic organization of the locus to include two new open reading frames (ORFs), psaB, which encodes an ATP-binding protein, and psaC, which encodes a hydrophobic transmembrane protein. Mutagenesis of psaB, psaC, psaA and downstream psaD resulted in penicillin tolerance. Defective adhesion and reduced transformation efficiency, as reported previously for a psaA- mutant, were phenotypes shared by psaB-, psaC- and psaD- knockout mutants. Western blot analysis demonstrated that the set of mutants expressed RecA, but none of them showed translation of the autolysin gene, which is located downstream of recA. The addition of manganese (Mn) failed to correct the abnormal physiology. These results suggest that this ABC-type Mn permease complex has a pleiotropic effect on pneumococcal physiology including adherence and autolysis. These are the first genes suggested as being involved in triggering autolysin. The results raise the possibility that loss of function of PsaA, by vaccine-induced antibody for instance, may promote penicillin tolerance.
“Water-in-salt” electrolyte enables high-voltage aqueous lithium-ion chemistries (2015)

A concentrated effort for battery safety Aqueous electrolytes are limited to run below 1.23 V to avoid degradation. Suo et al. smash through this limit with an aqueous salt solution containing lithium (Li) bis(trifluoromethane sulfonyl)imide to create an electrolyte that has an electrochemical window of 3 V (see the Perspective by Smith and Dunn). They used extremely high-concentration solutions, which suppressed hydrogen evolution and electrode oxidation. At these concentrations, the Li solvation shell changes because there simply is not enough water to neutralize the Li + charge. Thus, flammable organic electrolytes could potentially be replaced with a safer aqueous alternative. Science , this issue p. 938 ; see also p. 918
Immunization with theChlamydia trachomatisMouse Pneumonitis Major Outer Membrane Protein Can Elicit a Protective Immune Response against a Genital Challenge (2001)

Infertility, ectopic pregnancy, and chronic abdominal pain are frequent complications of genital infections with Chlamydia trachomatis. In an attempt to produce a vaccine to protect against this pathogen we purified and refolded the C. trachomatis mouse pneumonitis (MoPn) major outer membrane protein (MOMP). This preparation, mixed with Freund's adjuvant using vortexing or sonication, was used to immunize BALB/c mice that were subsequently challenged in the upper genital tract. Vaginal cultures were taken on a weekly basis, and mice were mated 6 weeks after the challenge. Gels of the vortexed MOMP showed a predominant band with a molecular size of 62 kDa and weaker bands at 42 and 132 kDa, while the sonicated MOMP had a single band with a molecular size of 42 kDa. Following immunization with these two preparations, strong humoral and cell-mediated immune responses were detected in the mice inoculated with the vortexed MOMP. On the other hand, mice immunized with the sonicated MOMP had a strong humoral immune response but a relatively weak cell-mediated immune response, as determined by a T-cell lymphoproliferative assay and level of cytokine production by splenocytes. Vaginal cultures showed that the mice immunized with the vortexed MOMP were significantly protected, as determined by a decrease in the number of animals with positive cultures, the length of time the mice shed viable organisms, and the number of inclusion-forming units recovered per mouse. Animals immunized with the sonicated MOMP, on the other hand, showed a weaker level of protection based on the same three parameters. After mating, the number of fertile animals and number of embryos per mouse were significantly higher for the mice immunized with vortexed MOMP, but not for the mice immunized with sonicated MOMP, compared to those of the control groups. In conclusion, immunization with a purified and refolded preparation of the C. trachomatis MoPn MOMP confers a significant level of protection in mice against a genital challenge.
Growth Factors in Mammalian Cell Culture (1976)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Effect of deletions in adenovirus early region 1 genes upon replication of adeno-associated virus (1982)

The growth of adeno-associated virus (AAV) is dependent upon helper functions provided by adenovirus. We investigated the role of adenovirus early gene region 1 in the AAV helper function by using six adenovirus type 5 (Ad5) host range mutants having deletions in early region 1. These mutants do not grow in human KB cells but are complemented by and grow in a line of adenovirus-transformed human embryonic kidney cells (293 cells); 293 cells contain and express the Ad5 early region 1 genes. Mutants having extensive deletions of adenovirus early region 1a (dl312) or regions 1a and 1b (dl313) helped AAV as efficiently as wild-type adenovirus in 293 cells, but neither mutant helped in KB cells. No AAV DNA, RNA, or protein synthesis was detected in KB cells in the presence of the mutant adenoviruses. Quantitative blotting experiments showed that at 20 h after infection with AAV and either dl312 or dl313 there was less than one AAV genome per cell. In KB cells infected with AAV alone, the unreplicated AAV genomes were detected readily. Apparently, infection with adenovirus mutant dl312 or dl313 results in degradation of most of the infecting AAV genomes. We suggest that at least an adenovirus region 1b product (and perhaps a region 1a product also) is required for AAV DNA replication. This putative region 1b function appears to protect AAV DNA from degradation by an adenovirus-induced DNase. We also tested additional Ad5 mutants (dl311, dl314, sub315, and sub316). All of these mutants were inefficient helpers, and they showed varying degrees of multiplicity leakiness. dl312 and dl313 complemented each other for the AAV helper function, and each was complemented by Ad5ts125 at the nonpermissive temperature. The defect in region 1 mutants for AAV helper function acts at a different stage of the AAV growth cycle than the defect in the region 2 mutant ts125.
Expert Guidelines for the Management of Alport Syndrome and Thin Basement Membrane Nephropathy (2013)

Few prospective, randomized controlled clinical trials address the diagnosis and management of patients with Alport syndrome or thin basement membrane nephropathy. Adult and pediatric nephrologists and geneticists from four continents whose clinical practice focuses on these conditions have developed the following guidelines. The 18 recommendations are based on Level D (Expert opinion without explicit critical appraisal, or based on physiology, bench research, or first principles-National Health Service category) or Level III (Opinions of respected authorities, based on clinical experience, descriptive studies, or reports of expert committees-U.S. Preventive Services Task Force) evidence. The recommendations include the use of genetic testing as the gold standard for the diagnosis of Alport syndrome and the demonstration of its mode of inheritance; the need to identify and follow all affected members of a family with X-linked Alport syndrome, including most mothers of affected males; the treatment of males with X-linked Alport syndrome and individuals with autosomal recessive disease with renin-angiotensin system blockade, possibly even before the onset of proteinuria; discouraging the affected mothers of males with X-linked Alport syndrome from renal donation because of their own risk of kidney failure; and consideration of genetic testing to exclude X-linked Alport syndrome in some individuals with thin basement membrane nephropathy. The authors recognize that as evidence emerges, including data from patient registries, these guidelines will evolve further.
Cadherin Switch in Tumor Progression (2004)

The loss of E-cadherin expression or function in epithelial carcinomas has long been thought as a primary reason for disruption of tight epithelial cell-cell contacts and release of invasive tumor cells from the primary tumor. Indeed, E-cadherin serves as a widely acting suppressor of invasion and growth of epithelial cancers, and its functional elimination represents a key step in the acquisition of the invasive phenotype for many tumors. Recent evidence indicates, however, that in addition to the loss of the "invasion-suppressor" E-cadherin, another adhesion molecule, N-cadherin, becomes upregulated in invasive tumor cell lines. N-cadherin was shown to be present in the most invasive and dedifferentiated breast cancer cell lines, and its exogenous expression in tumor cells induces a scattered morphology and heightened motility, invasion, and metastasis. N-cadherin cooperates with the FGF receptor, resulting in signals that lead to the up-modulation of MMP-9 and, hence, cellular invasion. In addition to a signaling function in metastasis, N-cadherin probably also supports the systemic dissemination of tumor cells by enabling circulating tumor cells to associate with the stroma and the endothelium at distant sites. Here, we summarize the various aspects of the E- to N-cadherin switching in epithelial carcinomas and its potential impact on metastatic progression.