gebhart/patrepeval huggingface dataset:
Using software visualization technology to help genetic algorithm designers (1997)

This work is part of a three year PhD project to examine how Software Visualization(SV) can be applied to support the design and construction of Genetic Algorithms (GAs). A user survey carried out at the start of this project identified a set of key system features required by GA users. A visualization system embodying these features was then designed and a prototype built. This paper describes what genetic algorithms are and how they can be applied. It then reviews some of the survey results and their impact on the design of the visualization system. The paper concludes with an exploration of how the resulting prototype may be evaluated.
Pro- and anti-inflammatory responses in respiratory syncytial virus bronchiolitis (2003)

Respiratory syncytial virus (RSV) bronchiolitis is an important cause of severe respiratory disease in infants. This study aimed to characterise changes in pulmonary pro- and anti-inflammatory responses in infants with RSV bronchiolitis over the course of the illness. On the day of intubation (Day 1) and the day of extubation (Day X), nonbronchoscopic bronchoalveolar lavage was performed on term and preterm infants ventilated for RSV bronchiolitis and on control infants on Day 1. Tumour necrosis factor (TNF)-alpha, soluble TNF receptor (sTNFR) and interleukin (IL)-6 messenger ribonucleic acid (mRNA) and protein were measured. Twenty-four infants, born at term and 23 infants born preterm with RSV bronchiolitis and 10 controls were recruited. TNF-alpha and IL-6 mRNA and protein in infants with bronchiolitis were greater than the control group on Day 1. In preterm infants, who were ventilated for longer than term infants, TNF-alpha and IL-6 proteins decreased between Day 1 and Day X. Concentrations of sTNFRs differed between groups on Day 1, but levels did not change between Day 1 and Day X. Large amounts of tumour necrosis factor-alpha and interleukin-6 in the respiratory syncytial virus-infected lung suggest important roles for these cytokines in the pathogenesis of respiratory syncytial virus bronchiolitis. The decrease in tumour necrosis factor-alpha and interleukin-6 protein in preterm infants may reflect the prolonged clinical course seen in these infants.
Rous sarcoma virus transformed cells are resistant to cyclic AMP (1982)

A nontransformed line of Chinese hamster ovary (CHO) cells (Pollard and Stanners, 1979) has been transformed by the Schmidt-Ruppin subgroup D strain of Rous sarcoma virus (SR-RSV). SR-RSV transformed CHO cells are shown to differ from spontaneously transformed cells in that the virally transformed cells are more resistant to growth inhibition or changes in cell shape by 8-Br-cyclic AMP or cholera toxin. SR-RSV transformed rat (NRK) cells also have a reduced sensitivity to growth inhibition by 8-Br-cyclic AMP. Cyclic AMP-dependent protein kinase was examined in SR-RSV transformed CHO cells, but no differences in enzyme level, activation by cyclic AMP, chromatographic behavior, or its ability to phosphorylate endogenous proteins in whole cells could be detected. It is concluded that transformation of CHO and NRK cells by SR-RSV alters the cells in a manner different from spontaneous transformation, and that this alteration does not affect cAMP-dependent protein kinase activity.
CXXIV.—The bromination of phenols (1904)

J. T. Hewitt, J. Kenner and H. Silk, J. Chem. Soc., Trans., 1904, 85, 1225 DOI: 10.1039/CT9048501225
The Biology Behind mTOR Inhibition in Sarcoma (2007)

Dysregulation of the mammalian target of rapamycin (mTOR) pathway has been found in many human tumors and implicated in the promotion of cancer cell growth and survival. Hence, the mTOR pathway is considered an important target for anticancer drug development. Currently, the mTOR inhibitor rapamycin and its derivatives CCI-779, RAD001, and AP23573 are being evaluated in cancer clinical trials. To date, clinical results have shown good tolerability of treatment with mTOR inhibitors in most reports and varying effectiveness of mTOR inhibitors in a variety of tumors in a subset of patients. For the targeted treatment of sarcomas, AP23573 has shown promising clinical efficacy and low toxicity profiles in patients. Further studies should define the optimal dose/schedule, patient selection, and combination strategies with other biological agents, especially those targeting signaling pathways crucial for cell survival. Disclosure of potential conflicts of interest is found at the end of this article.
Diagnosis of Thin-Capped Fibroatheromas in Intravascular Optical Coherence Tomography Images (2016)

We demonstrate that IVOCT can exhibit 87% (95% CI, 75%-93%) sensitivity and 92% specificity (95% CI, 86%-96%) to detect all lipid arcs (both obtuse and acute, <1 quadrant) TCFA, and we also propose new mechanisms involving light scattering that explain why other plaque components can masquerade as TCFA and cause low positive predictive value of IVOCT for TCFA detection (47% for obtuse lipid arcs). Disregarding the lipid arc >1 quadrant requirement enhances the ability of IVOCT to detect TCFA.
No pane, no gain (2005)

Windows queries are proving essential to data-stream processing. In this paper, we present an approach for evaluating sliding-window aggregate queries that reduces both space and computation time for query execution. Our approach divides overlapping windows into disjoint panes, computes sub-aggregates over each pane, and "rolls up" the pane-aggregates to computer window-aggregates. Our experimental study shows that using panes has significant performance benefits.
A collagenase gel/physical defect model for controlled induction of superficial digital flexor tendonitis (2011)

This model will allow for objective assessment of therapies for tendon regeneration in the mid-metacarpal SDFT prior to clinical trials and routine clinical application.
Apolipoprotein E (APOE) allele distribution in the world. Is APOE*4 a ‘thrifty’ allele? (1999)

Apolipoprotein E (APOE = gene, apoE = protein) plays a central role in plasma lipoprotein metabolism and in lipid transport within tissues. The APOE shows a genetic polymorphism determined by three common alleles, APOE*2, APOE*3, APOE*4 and the product of the three alleles differs in several functional properties. APOE is involved in the development of certain pathological conditions. In particular, the APOE*4 allele is a risk factor for susceptibility to coronary artery disease (CAD) and Alzheimer's Disease (AD). In the present study we analyzed the APOE allele distribution in the world. The APOE*3 is the most frequent in all the human groups, especially in populations with a long-established agricultural economy like those of the Mediterranean basin (0.849-0.898). The frequency of APOE*4, the ancestral allele, remains higher in populations like Pygmies (0.407) and Khoi San (0.370), aborigines of Malaysia (0.240) and Australia (0.260), Papuans (0.368), some Native Americans (0.280), and Lapps (0.310) where an economy of foraging still exists, or food supply is (or was until the recent past) scarce and sporadically available. The APOE*2 frequency fluctuates with no apparent trend (0.145-0.02) and is absent in Native Americans. We suggest that the APOE*4, based on some functional properties it has and on its distribution among human populations, could be identified as a 'thrifty' allele. The exposure of APOE*4 to the contemporary environmental conditions (Western diet, longer lifespans) could have rendered it a susceptibility allele for CAD and AD. The absence of the association of APOE*4 with CAD and AD in Sub-Saharan Africans, and its presence in African Americans, seems to confirm this hypothesis.
DUET: A Phase 2 Study Evaluating the Efficacy and Safety of Sparsentan in Patients with FSGS (2018)

Patients with FSGS achieved significantly greater reductions in proteinuria after 8 weeks of sparsentan versus irbesartan. Sparsentan was safe and well tolerated.
Lack of persistence of E1- recombinant adenoviral vectors containing a temperature-sensitive E2A mutation in immunocompetent mice and hemophilia B dogs. (1996)

Two recombinant adenoviruses expressing either human alpha 1-antitrypsin (hAAT) or canine factor IX (cFIX) were modified so that they also contained a temperature-sensitive mutation (ts125) in the DNA binding protein encoded within the viral E2A region. The effects of the inclusion of the ts125 mutation on transgene expression in vivo were evaluated in Balb/c mice and hemophilia B dogs by comparison with adenoviral vectors containing the same transgene but lacking the ts125 mutation. No significant differences in the duration of transgene expression were observed in either animal model. Insufficiency of the ts125 mutation in the prolongation of transgene expression in these two animal models suggests that further modification of the vector backbone may be required to achieve long-term gene expression in a wide variety of applications. Additionally, humoral immune response to transgene products has been demonstrated in immunocompetent animal models, which will also need to be surmounted for long-term efficacy in disease treatment by gene therapy.
Relative influence of polymer fiber diameter and surface charge on fibrous capsule thickness and vessel density for single‐fiber implants (2003)

Single polypropylene microfibers plasma-coated with polymers of different surface charge [N,N-dimethylaminoethyl methacrylate (NN) (positive charge), methacrylic acid (MA) (negative charge), and hexafluoropropylene (HF) (neutral)] were implanted in the subcutaneous dorsum of Sprague-Dawley rats for 5-week intervals. Thee groups of fiber diameters were used: (I) 1.0 to 5.9 microm; (II) 6.0 to 10.9 microm; and (III) 11.0 to 15.9 microm. Fibrous capsule thickness and blood-vessel density (number of vessels within 100 microm of the fiber) were assessed in tissue sections in the planes of microfiber cross-sections. Results from a multifactorial analysis of variance demonstrated statistically significant main effects (p < 0.05) for microfiber diameter but not for surface-charge coating. The mean differences in capsule thickness among the microfiber diameter groups were: between groups II and I: 5.4 microm; between groups III and I: 10.2 microm; and between groups III and II: 4.7 microm. The mean differences in capsule thickness among surface-charge coatings were: between MA and NN: 0.7 microm; between MA and HF: 1.4 microm; and between NN and HF: 0.7 microm. Many of the 1.0 to 5.9 microm-in-diameter fibers had no capsule and no sign of a foreign-body reaction. For the vessel density analysis, neither microfiber diameter nor surface-charge coating had a statistically significant effect. Thus the geometric feature of microfiber diameter was more important than was surface charge relative to fibrous capsule formation but not relative to local vessel density. This ranking of the relative influence of design features in relation to tissue response provides useful information for prioritization in biomaterial design.
A Mutation Altering Auxin Homeostasis and Plant Morphology in Arabidopsis (1995)

Joseph J. King, Dennis P. Stimart, Roxanne H. Fisher, Anthony B. Bleecker, A Mutation Altering Auxin Homeostasis and Plant Morphology in Arabidopsis, The Plant Cell, Vol. 7, No. 12 (Dec., 1995), pp. 2023-2037
Hydrogels in drug delivery: Progress and challenges (2008)

There has been considerable progress in recent years in addressing the clinical and pharmacological limitations of hydrogels for drug delivery applications but substantial challenges remain. Here we discuss recent progress in overcoming these challenges, particularly with regards to effectively delivering hydrogels inside the body without implantation, prolonging the release kinetics of drugs from hydrogels, and expanding the nature of drugs which can be delivered using hydrogel-based approaches.
LEDs based on poly(p‐phenylenevinylene) and polyimide LB films (1995)

Highly ordered organic thin films with well defined film thicknesses produced using the Langmuir‐Blodgett technique can employed in the fabrication of ultra‐thin heterostructure devices. Heterostructure LEDs have been shown to exhibit superior performance characteristics. Recent progress is reviewed.
The retinoblastoma gene is involved in malignant progression of astrocytomas (1994)

Loss of chromosome 13q occurs in up to 50% of human astrocytomas, suggesting the presence of an astrocytoma tumor suppressor gene on that chromosome. To determine whether the retinoblastoma susceptibility gene (Rb) on 13q14 contributes to the formation of astrocytomas, we examined 85 tumors for loss of heterozygosity (LOH) at the intragenic Rb 1.20 locus. LOH was detected in 16 of 54 informative high-grade astrocytomas (30%), but was not detected in 12 low-grade gliomas. Deletion mapping with flanking markers on 13q revealed that the Rb 1.20 region was preferentially targeted by the deletions. Tumors with LOH at Rb 1.20 were examined for mutations in the remaining Rb allele using single-strand conformational polymorphism (SSCP) analysis and direct DNA sequencing. Mutations were detected in exon 8 (1 tumor), exon 24 (2 tumors), and intron 24 (1 tumor). Rb protein expression, as assessed by immunohistochemistry, was altered in 3 of 9 cases with LOH and in 1 tumor without LOH. Our results demonstrate that Rb inactivation contributes to the formation of high-grade astrocytomas, and therefore implicate a second, known tumor suppressor gene in astrocytoma tumorigenesis.
Pre-B cell generation potentiated by soluble factors from a bone marrow stromal cell line. (1988)

Two bone marrow stromal cell lines isolated from the adherent layer of a Dexter-type long term bone marrow culture differ markedly in their hemopoietic support capacity. S17 supports myelopoiesis and the differentiation of early B cell precursors into B lymphocytes while S10 supports myeloid cell differentiation and not B lymphopoiesis. The identification of a stromal cell line with B cell support capacity prompted an investigation of whether the effects of S17 were mediated via soluble factors. Results presented herein indicate that medium conditioned by S17 but not S10 contains an activity that can induce the expression of the 220,000 m.w. 14.8 antigen and cytoplasmic mu H chain of Ig in B lymphocyte progenitors that have not yet expressed these markers. Bone marrow cells were depleted of 14.8+, cytoplasmic mu+ pre-B cells on antibody-coated petri dishes. After 24-h liquid culture newly generated pre-B cells were enumerated as cells that expressed cytoplasmic mu H chain of Ig but not Ig L chains by immunofluorescence. Expression of Ly5(220) was monitored by 14.8 antibody binding. This pre-B cell differentiation activity was abrogated by digestion with pronase, aminopeptidase, or carboxypeptidase. Isoelectric focusing data revealed the activity to have isoelectric point of 5.9 to 6.2. S17-conditioned medium was fractionated using HPLC and each fraction tested for pre-B cell-generating activity. Fractions collected from a Superose 12 gel filtration column were found to have two peaks of activity associated with molecules of apparent m.w. of approximately 60,000 and 10,000. Virtually identical peaks of activity were observed when medium conditioned by heterogeneous stromal cell cultures was fractionated. Separation of S10-conditioned medium revealed no cryptic activity. S17-conditioned medium was further characterized by anion exchange chromatography and the majority of the pre-B cell generating activity shown to be associated with the void volume that eluted from a MonoQ column. These fractions were rechromatographed on Superose and the activity again found to be associated with two fractions corresponding to apparent m.w. of 60,000 and 10,000. The S17 pre-B cell differentiation activity appears to result from the presence of a novel molecule because other well characterized mediators had no activity in this short-term liquid culture system. No pre-B cell-generating activity was observed when IL-1 or conditioned medium containing IL-2, IL-3, or IL-4 (B cell stimulatory factor 1) were added to cultures.(ABSTRACT TRUNCATED AT 400 WORDS)
Copper-Catalyzed Domino Halide Exchange-Cyanation of Aryl Bromides (2003)

An efficient copper-catalyzed domino halogen exchange-cyanation procedure for aryl bromides was developed utilizing 10 mol % CuI, 20 mol % KI, 1.0 equiv of the inexpensive N,N'-dimethylethylenediamine as ligand, and 1.2 equiv of NaCN in toluene at 110 degrees C. The new method represents a significant improvement over the traditional Rosenmund-von Braun reaction: the reaction conditions are much milder, and the use of stoichiometric amounts of copper(I) cyanide and polar solvents is avoided; therefore the isolation and purification of the aromatic nitrile products is greatly simplified. In addition, the new method exhibits excellent functional group compatibility comparable to that of the analogous Pd-catalyzed cyanation methodology.
Ferrous Iron- and Sulfur-Induced Genes in Sulfolobus metallicus (2007)

Genes of Sulfolobus metallicus that appeared to be upregulated in relation to growth on either ferrous iron or sulfur were identified using subtractive hybridization of cDNAs. The genes upregulated during growth on ferrous iron were found in a cluster, and most were predicted to encode membrane proteins. Quantitative reverse transcription-PCR of cDNA showed upregulation of most of these genes during growth on ferrous iron and pyrite compared to results during growth on sulfur. The highest expression levels observed included those for genes encoding proteins with similarities to cytochrome c oxidase subunits and a CbsA-like cytochrome. The genes identified here that may be involved in oxidation of ferrous iron by S. metallicus are termed fox genes. Of three available genomes of Sulfolobus species (S. tokodaii, S. acidocaldarius, and S. solfataricus), only that of S. tokodaii has a cluster of highly similar open reading frames, and only S. tokodaii of these three species was also able to oxidize ferrous iron. A gene encoding sulfur oxygenase-reductase was identified as the source of the dominant transcript in sulfur-grown cells of S. metallicus, with the predicted protein showing high identities to the previously described examples from S. tokodaii and species of Acidianus.
Wavelength-tunable soliton generation in the 1400 -1600 nm region using an Yb fiber laser (2002)

Soliton pulses tunable in the 1400 - 1600 nm region are generated in standard telecom fiber seeded with a continuum produced in a fiber taper using an Yb fiber laser. Here we demonstrate supercontinuum generation in the 500 nm - 1600 nm wavelength region using a compact ultrafast Yb fiber laser as a systems-compatible pump source for the first time. Moreover, by injecting the supercontinuum into a length of standard telecommunications fiber, we can induce Raman-soliton generation to produce near bandwidth-limited pulses tunable in the 1400 - 1600 nm wavelength region. The required pulse energy for supercontinuum and Raman-soliton generation is only of the order of 1 nJ, which demonstrates that this technique is compatible with fiber sources operating at GHz repetition rates.
Maturation-Dependent Vulnerability of Oligodendrocytes to Oxidative Stress-Induced Death Caused by Glutathione Depletion (1998)

Death of oligodendrocyte (OL) precursors can be triggered in vitro by cystine deprivation, a form of oxidative stress that involves depletion of intracellular glutathione. We report here that OLs demonstrate maturation-dependent differences in survival when subjected to free radical-mediated injury induced by glutathione depletion. Using immunopanning to isolate rat preoligodendrocytes (preOLs), we generated highly enriched populations of preOLs and mature OLs under chemically defined conditions. Cystine deprivation caused a similar decrease in glutathione levels in OLs at both stages. However, preOLs were completely killed by cystine deprivation, whereas mature OLs remained viable. Although the glutathione-depleting agents buthionine sulfoximine and diethylmaleate were more potent in depleting glutathione in mature OLs, both agents were significantly more toxic to preOLs. Glutathione depletion markedly increased intracellular free radical generation in preOLs, but not in mature OLs, as indicated by oxidation of the redox-sensitive probe dihydrorhodamine 123. The antioxidants alpha-tocopherol, idebenone, and glutathione monoethylester prevented the oxidation of dihydrorhodamine in cystine-depleted preOLs and markedly protected against cell death. When the intracellular glutathione level was not manipulated, preOLs were also more vulnerable than mature OLs to exogenous free radical toxicity generated by a xanthine-xanthine oxidase system. Ultrastructural features of free radical-mediated injury in glutathione-depleted preOLs included nuclear condensation, margination of chromatin, and mitochondrial swelling. These observations indicate that preOLs are significantly more sensitive to the toxic effects of glutathione depletion and that oligodendroglial maturation is associated with decreased susceptibility to oxidative stress.
Allogeneic Lymphocytes Induce Tumor Regression of Advanced Metastatic Breast Cancer (2004)

Allogeneic lymphocytes can induce regression of advanced metastatic breast cancer. These results indicate that an immunological GVT effect from allogeneic lymphocytes exists against metastatic breast cancer and provide rationale for further development of allogeneic cellular therapy for this largely incurable disease.
Prefilter design using the singular value decomposition for MIMO equalization (2002)

This paper describes a new prefilter design method for MIMO communication channels with equalizers. The prefilter is designed in the frequency domain to make the channel easier to equalize. We apply the singular value decomposition (SVD) of the channel frequency response to design the prefilter. The new prefilter achieves a performance improvement at high signal to noise ratio (SNR) while keeping the performance at low SNR. We also show the advantage of transmitter diversity.
An Assessment of Radical Prostatectomy (1993)

Objectives. —To examine temporal trends and geographic variation in radical prostatectomy rates and short-term outcomes. Design. —Population-based study of radical prostatectomy for the years 1984 through 1990. Poisson regression was used to estimate temporal and regional effects. Setting. —The 50 states and the District of Columbia. Participants. —A 20% national sample of male Medicare beneficiaries aged 65 years or older. Main Outcome Measures. —Rate of radical prostatectomy; 30-day mortality; and major cardiopulmonary complications, vascular complications, or surgical repairs within 30 days of radical prostatectomy. Results. —A total of 10598 radical prostatectomies were identified. The adjusted rate of radical prostatectomy in 1990 was 5.75 times that in 1984. The relative increase was similar in all age groups. Substantial geographic variation existed in rates from 1988 through 1990: all states in the New England and Mid-Atlantic regions had rates equal to or below 60 per 100 000 male Medicare beneficiaries, while all states in the Pacific and Mountain regions had rates equal to or above 130 per 100 000. The mortality and morbidity after radical prostatectomy are not trivial for older men (aged 75 years and older)—almost 2% died and nearly 8% suffered major cardiopulmonary complications within 30 days of the operation. Conclusion. —The sharp increase and wide geographic variation in radical prostatectomy rates make the evaluation of this surgical procedure a pressing issue. The rising rate of radical prostatectomy among men aged 75 years and older merits special attention. ( JAMA . 1993;269:2633-2636)