gebhart/patrepeval huggingface dataset:
Organometal Halide Perovskite Quantum Dot Light‐Emitting Diodes (2016)

Organometal halide perovskites quantum dots (OHP‐QDs) with bright, color‐tunable, and narrow‐band photoluminescence have significant advantages in display, lighting, and laser applications. Due to sparse concentrations and difficulties in the enrichment of OHP‐QDs, production of large‐area uniform films of OHP‐QDs is a challenging task, which largely impedes their use in electroluminescence devices. Here, a simple dip‐coating method has been reported to effectively fabricate large‐area uniform films of OHP‐QDs. Using this technique, multicolor OHP‐QDs light‐emitting diodes (OQ‐LEDs) emitting in blue, blue‐green, green, orange, and red color have been successfully produced by simply tuning the halide composition or size of QDs. The blue, green, and red OQ‐LEDs exhibited, respectively, a maximum luminance of 2673, 2398, and 986 cd m −2 at a current efficiency of 4.01, 3.72, and 1.52 cd A −1 , and an external quantum efficiency of 1.38%, 1.06%, and 0.53%, which are much better than most LEDs based on OHP films. The packaged OQ‐LEDs show long‐term stability in air (humidity ≈50%) for at least 7 d. The results demonstrate the great potential of the dip‐coating method to fabricate large‐area uniform films for various QDs. The high‐efficiency OQ‐LEDs also demonstrate the promising potential of OHP‐QDs for low‐cost display, lighting, and optical communication applications.
Collagenolytic Activity of Alkali-Burned Corneas (1969)

Collagenolytic activity of alkali-burned corneas of rabbits was investigated using a tissue-culture assay technique. The technique was standardized, and in every instance, tissues from the immediate vicinity of the ulcers or perforations showed substantial collagenase production, while generally, tissues more than 2 mm away from the lesions were free of enzyme activity.
Regulation of the mouse desmin gene: transactivation by MyoD, myogenin, MRF4 and Myf5 (1993)

Desmin, the muscle specific intermediate filament (IF) protein, is expressed at low levels in myoblasts and at the onset of differentiation its expression increases several fold. In an effort to explore the mechanism involved in the tissue-specific and developmentally regulated expression of desmin, we have isolated the mouse desmin gene. Sequence analysis of 976 bp 5' flanking region revealed several potential cis-acting elements: 1) Three E boxes (MyoD binding sites), namely, E1, E2 and E3, located at -79, -832 and -936, respectively; 2) one MEF2 binding site at -864; 3) a region with homology to M-CAT motif at -587; 4) several GC boxes. Transient transfections with various 5' flank deletion mutants into C2C12 muscle cells have revealed both positive and negative elements that seem to be involved in the expression of desmin. The first 81 bp upstream of the transcription initiation site, including E1 box, were sufficient to confer muscle specific expression of the desmin gene. The maximal level of expression was achieved by the construct containing up to -897 base pairs. The region between -578 to -976 behaves as a classical enhancer in the absence of which the region between -578 and -81 suppresses CAT activity. Gel electrophoretic mobility shift assays using both C2C12 muscle cell nuclear extracts as well as in vitro translated myoD/E12 and myogenin/E12 heterodimers, showed that both myoD and myogenin bind to the proximal E1 and the distal E2 boxes of the desmin promoter and enhancer respectively. Co-transfection of myoD, myogenin, MRF4 and Myf5, with the desmin-CAT construct into 10T-1/2 cells demonstrated that all these factors could transactivate desmin gene expression.
RNA-guided gene drives can efficiently and reversibly bias inheritance in wild yeast (2015)

Inheritance-biasing “gene drives” may be capable of spreading genomic alterations made in laboratory organisms through wild populations. We previously considered the potential for RNA-guided gene drives based on the versatile CRISPR/Cas9 genome editing system to serve as a general method of altering populations. Here we report molecularly contained gene drive constructs in the yeast Saccharomyces cerevisiae that are typically copied at rates above 99% when mated to wild yeast. We successfully targeted both non-essential and essential genes, showed that the inheritance of an unrelated “cargo” gene could be biased by an adjacent drive, and constructed a drive capable of overwriting and reversing changes made by a previous drive. Our results demonstrate that RNA-guided gene drives are capable of efficiently biasing inheritance when mated to wild-type organisms over successive generations.
AIDS, Zinc Deficiency, and Thymic Hormone Failure (1988)

<h3>To the Editor.</h3> —It has been proposed that thymic secretory function, as assessed by determining levels of circulating thymulin—like activity,<sup>1</sup>is greatly reduced in patients with acquired immunodeficiency syndrome (AIDS) or AIDS-related complex.<sup>2,3</sup>In fact, in both young<sup>3</sup>and adult<sup>2</sup>patients, levels of circulating thymulin, as measured by the rosette inhibition bioassay, are either undetectable or below the values found in age-matched healthy subjects. These findings have been interpreted as showing human immunodeficiency virus (HIV)—induced injury of the thymic epithelial cells that synthesize and release thymic hormones.<sup>4</sup> Since thymulin is biologically active, and therefore measurable by bioassay only when the nonapeptide thymulin is bound to a zinc ion,<sup>5</sup>a reduced circulating level may depend not only on defective production by the thymus, but also on decreased zinc binding, as might occur in zinc deficiencies.<sup>6</sup>In these conditions, inactive, zinc—unbound thymulin molecules are found
Estimating the probability of malignancy in solitary pulmonary nodules. A Bayesian approach. (1986)

Decisions about managing solitary pulmonary nodules often involve estimates of the likelihood that the nodule is malignant. We used Bayes' theorem to devise a simple scheme for estimating the likelihood that a solitary pulmonary nodule is malignant based on the diameter of the nodule, the patient's age and history of cigarette smoking, and data on the overall prevalence of malignancy in solitary nodules. This method may improve the accuracy of estimating the likelihood of malignancy for individual patients with solitary pulmonary nodules.
Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect (2006)

DTASelect provides a means by which complex SEQUEST results can be filtered, organized, and viewed. A single sample may produce tens of thousands of tandem mass spectra. Manually perusing and selecting SEQUEST matches among such a mass of data carries a risk of inconsistency. DTASelect allows the user to set complex criteria for acceptance or rejection of individual spectrum results. It also features rules for dealing with multiple, identical peptide matches and for removing proteins that are insufficiently evidenced. It provides its sorted and filtered summary as HTML and text documents for easy review and also offers several auxiliary reports. DTASelect is a powerful tool for automatic analysis of complex mixture tandem mass spectrometry.
How Many Loci Does it Take to DNA Barcode a Crocus? (2009)

The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.
Use of lipophilic near-infrared dye in whole-body optical imaging of hematopoietic cell homing (2006)

We develop an optical whole-body imaging technique for monitoring normal and leukemic hematopoietic cell homing in vivo. A recently developed near-infrared (NIR) lipophilic carbocyanine dye 1,1'-dioctadecyl-3,3,3',3'-tetramethylindotricarbocyanine iodide (DiR) is used to safely and directly label the membranes of human leukemic Pre-B ALL G2 cell lines as well as primary murine lymphocytes and erythrocytes. DiR has absorption and fluorescence maxima at 750 and 782 nm, respectively, which corresponds to low light absorption and autofluorescence in living tissues. This allows us to obtain a significant signal with very low background level. A charge-coupled device (CCD)-based imager is used for noninvasive whole-body imaging of DiR-labeled cell homing in intact animals. This powerful technique can potentially visualize any cell type without use of specific antibodies conjugated with NIR fluorescent tag or loading cells with transporter-delivered NIR fluorophores. Thus, in vivo imaging based on NIR lipophilic carbocyanine dyes in combination with advanced optical techniques may serve as a powerful alternative or complementation to other small animal imaging methods.
Radical prostatectomy for high‐risk prostate cancer: Biochemical outcome (2009)

Radical prostatectomy is feasible in high-risk prostate cancer patients, only if they have a pathologically organ-confined disease.
Comparison of Kidney Injury Molecule-1 and Other Nephrotoxicity Biomarkers in Urine and Kidney Following Acute Exposure to Gentamicin, Mercury, and Chromium (2007)

Sensitive biomarkers are needed to detect kidney injury at the earliest stages. The objective of this study was to determine whether the appearance of kidney injury molecule-1 (Kim-1) protein ectodomain in urine and kidney injury molecule-1/hepatitis A viral cellular receptor-1 (Kim-1/Havcr1) gene expression in kidney tissue may be more predictive of renal injury after exposure to nephrotoxicants when compared to traditionally used biomarkers. Male Sprague-Dawley rats were injected with a range of doses of gentamicin, mercury (Hg; HgCl2), or chromium (Cr; K2Cr2O7). The results showed that increases in urinary Kim-1 and kidney Kim-1/Havcr1 gene expression paralleled the degree of severity of renal histopathology and were detected at lower doses of nephrotoxicants when compared to blood urea nitrogen (BUN), serum creatinine, and urinary N-acetyl-beta-D-glucosaminidase (NAG). In a time course study, urinary Kim-1 was elevated within 24 h after exposure to gentamicin (100 mg/kg), Hg (0.25 mg/kg), or Cr (5 mg/kg) and remained elevated through 72 h. NAG responses were nephrotoxicant dependent with elevations occurring early (gentamicin), late (Cr), or no change (Hg). At 72 h, after treatment with any of the three nephrotoxicants, there was increased Kim-1 immunoreactivity and necrosis involving approximately 50% of the proximal tubules; however, only urinary Kim-1 was significantly increased, while BUN, serum creatinine, and NAG were not different from controls. In rats treated with the hepatotoxicant galactosamine (1.1 mg/kg), serum alanine aminotransferase was increased, but no increase in urinary Kim-1 was observed. Urinary Kim-1 and kidney Kim-1/Havcr1 expression appear to be sensitive and tissue-specific biomarkers that will improve detection of early acute kidney injury following exposure to nephrotoxic chemicals and drugs.
Expression of tumour necrosis factor‐α in cryptogenic fibrosing alveolitis (1993)

We have studied 15 cases of cryptogenic fibrosing alveolitis stained with a monoclonal antibody reactive with human tumour necrosis factor-alpha (TNF alpha), a cytokine that has been implicated in inflammation and fibrosis. Seven were examples of lone cryptogenic fibrosing alveolitis and eight were examples of cryptogenic fibrosing alveolitis in patients with systemic sclerosis. There was widespread staining of epithelial cells, particularly hyperplastic type II pneumocytes. Macrophages stained only weakly. In a control group of 10 patients dying of unrelated conditions, staining for TNF alpha was weak and, in the alveolar epithelium, was confined to a very occasional type II pneumocyte. The strong expression of TNF alpha in hyperplastic type II pneumocytes suggests that TNF alpha produced during alveolar epithelial regeneration may play a part in the fibrosis seen in this disease.
A Fischer rat substrain deficient in dipeptidyl peptidase IV activity makes normal steady-state RNA levels and an altered protein. Use as a liver-cell transplantation model (1991)

Dipeptidyl peptidase IV (DPPIV) is a serine exoproteinase expressed at high levels in epithelial cells of kidney, liver and small intestine. Recently Watanabe, Kohima &amp; Fujimoto [(1987) Experientia 43, 400-401] and Gossrau et al. [(1990) Histochem. J. 22, 172-173] reported that Fischer 344 rats are deficient in this enzyme. We have examined DPPIV expression in Fischer 344 rats available from U.S. and German suppliers and find that livers of the U.S. Fischer rats, in contrast with their German counterparts, express active DPPIV (D+). Northern analysis of liver RNA showed comparable levels of 3.4 kb and 5.6 kb DPPIV transcripts in both D+ rats from the U.S. and German (D-) rats. Monoclonal antibody (MAb) 236.3 to DPPIV immunoprecipitated at 150 kDa enzymically active (105 kDa, denatured) protein from surface-labelled D+ hepatocytes and reacted with canalicular and sinusoidal membranes (as shown by immunofluorescence microscopy). MAb 236.3 failed to immunoprecipitate a labelled peptide from D- cell extract or to stain D- liver sections. Polyclonal antibody (PAb) specific for DPPIV immunoprecipitated an enzymically active peptide from D+ hepatocyte extracts and a smaller, inactive peptide from D- hepatocyte extracts. Peptide maps of DPPIV immunoprecipitated from D+ extracts with MAb 236.3 and PAb were identical, but differed from that of the D- hepatocyte component recognized by PAb. The molecular basis of the DPPIV deficiency in the D- rats thus appears to be the translation of an enzymically inactive protein missing the epitope recognized by MAb 236.3. We have exploited these D- rats as hosts for syngeneic transplantation of liver cells from D+ Fischer rats. DPPIV expression is stable in the transplanted cells and allows them to be readily distinguished from the surrounding D- tissue.
Tyrosine Phosphoproteomics Identifies Both Codrivers and Cotargeting Strategies for T790M-Related EGFR-TKI Resistance in Non–Small Cell Lung Cancer (2014)

Our results identified both codrivers of resistance along with T790M and support further studies of irreversible or T790M-selective EGFR inhibitors combined with dasatinib in patients with NSCLC with acquired T790M.
A double‐blind, placebo‐controlled study of vortioxetine in the treatment of binge‐eating disorder (2019)

Vortioxetine was not more effective than placebo in the treatment of BED. The ability to detect pharmacological treatment benefit may have been hindered by the relatively high placebo response and drop out. Future work should seek to better understand and predict placebo response in BED, with a view to more targeted treatment interventions and, potentially, sample enrichment.
Intracranial branch atheromatous disease (1989)

5-Ethoxydihydro-2(3H)-furanone (4-ethoxy-4-hydroxybutyric acid gamma lactone), a trace component recently isolated from wines, when injected intraperitoneally in rats depressed ambulation, rearing, and defecation in the open-field test. Ethanol injected in conjunction with this ethoxy furanone intensified depression of ambulation. The furanone was lethal at about 600 mg/kg (IP in rats), and ethanol shortened time to death. This ethoxy furanone decomposes at pH 2 - 3; thus passage through the stomach renders it harmless to man.
Genetic Analyses ofSchizosaccharomyces pombe dna2+ Reveal That Dna2 Plays an Essential Role in Okazaki Fragment Metabolism (2000)

In this report, we investigated the phenotypes caused by temperature-sensitive (ts) mutant alleles of dna2(+) of Schizosaccharomyces pombe, a homologue of DNA2 of budding yeast, in an attempt to further define its function in vivo with respect to lagging-strand synthesis during the S-phase of the cell cycle. At the restrictive temperature, dna2 (ts) cells arrested at late S-phase but were unaffected in bulk DNA synthesis. Moreover, they exhibited aberrant mitosis when combined with checkpoint mutations, in keeping with a role for Dna2 in Okazaki fragment maturation. Similarly, spores in which dna2(+) was disrupted duplicated their DNA content during germination and also arrested at late S-phase. Inactivation of dna2(+) led to chromosome fragmentation strikingly similar to that seen when cdc17(+), the DNA ligase I gene, is inactivated. The temperature-dependent lethality of dna2 (ts) mutants was suppressed by overexpression of genes encoding subunits of polymerase delta (cdc1(+) and cdc27(+)), DNA ligase I (cdc17(+)), and Fen-1 (rad2(+)). Each of these gene products plays a role in the elongation or maturation of Okazaki fragments. Moreover, they all interacted with S. pombe Dna2 in a yeast two-hybrid assay, albeit to different extents. On the basis of these results, we conclude that dna2(+) plays a direct role in the Okazaki fragment elongation and maturation. We propose that dna2(+) acts as a central protein to form a complex with other proteins required to coordinate the multienzyme process for Okazaki fragment elongation and maturation.
Molecular analysis and expression of a Borrelia burgdorferi gene encoding a 22kDa protein (pC) in Escherichia coli (1992)

Summary We describe the cloning and expression of the pc gene which encodes a major immunodominant protein of Borrelia burgdorferi , the causative agent of Lyme borreliosis. The pC protein was purified from lysates of B. burgdorferi strain PKo. After tryptic digestion of the pC protein the resulting oligopeptides were applied to a gas‐phase sequenator. Thus partial amino acid sequences were obtained. The deduced oligonucleotides were used as hybridization probes. After Southern blotting a reactive band in the 3 kb range of PstI ‐digested genomic DNA was detected. The insertion of these fragments into pUC vectors finally resulted in pc ‐positive Escherichia coli clones. The gene (encoding a protein with 212 amino acids) was expressed in E. coli with varying deletions at the 5′ end. A sequence comparison with other outer membrane proteins of B. burgdorferi indicates a processing of pC that is similar to that of lipoproteins.
Floating resistivity detector for microchip electrophoresis (2007)

A newly developed conductivity detector, the floating resistivity detector (FRD), for microchip electrophoresis was introduced in this work. The detector design permits decoupling of the detection circuit from the high separation voltage without compromising separation efficiency. This greatly simplifies the integration of microchip electrophoresis systems. Its method of detection relies on platinum electrodes being dipped in two buffer-filled branched detection probe reservoirs on the microchip device. In this way, analytes passing through the detection window will not pass through and subsequently adsorb onto the electrodes, alleviating problems of electrode fouling due to analyte contamination and surface reactions. A customized microchip design was proposed and optimized stepwise for the new FRD system. Each branched detection probe was determined to be 4.50 mm long with a 0.075 mm detection window gap between them. The distance between the detection window and buffer waste reservoir was determined to be 1.50 mm. The optimized microchip design was subsequently used in the analysis of four groups of analytes - inorganic cations, amino acids, aminoglycosides antibiotics, and biomarkers. Based on the preliminary results obtained, the detection limits were in the range of 0.4-0.7 mg/L for the inorganic cations and 1.5-15 mg/L for the amino compounds.
Anti‐nucleosome antibodies in the diagnosis of systemic lupus erythematosus (2005)

The anti-nucleosome antibody assay does not offer additional information compared to conventionally used anti-dsDNA tests in the differential diagnosis of SLE.
Sildenafil Citrate Therapy for Pulmonary Arterial Hypertension (2005)

Sildenafil improves exercise capacity, WHO functional class, and hemodynamics in patients with symptomatic pulmonary arterial hypertension.
Vigorous Allograft Rejection in the Absence of Danger (2000)

Tolerance to self is a necessary attribute of the immune system. It is thought that most autoreactive T cells are deleted in the thymus during the process of negative selection. However, peripheral tolerance mechanisms also exist to prevent development of autoimmune diseases against peripheral self-Ags. It has been proposed that T cells develop tolerance to peripheral self-Ags encountered in the absence of inflammation or "danger" signals. We have used immunodeficient Rag 1-/- mice to study the response of T cells to neo-self peripheral Ags in the form of well-healed skin and vascularized cardiac allografts. In this paper we report that skin and cardiac allografts without evidence of inflammation are vigorously rejected by transferred T cells or when recipients are reconstituted with T cells at a physiologic rate by nude bone graft transplantation. These results provide new insights into the role of inflammation or "danger" in the initiation of T cell-dependent immune responses. These findings also have profound implications in organ transplantation and suggest that in the absence of central deletional tolerance, peripheral tolerance mechanisms are not sufficient to inhibit alloimmune responses even in the absence of inflammation or danger.
Eosinophil Viability-Enhancing Activity in Sputum from Patients with Bronchial Asthma, Contributions of Interleukin-5 and Granulocyte/Macrophage Colony-Stimulating Factor (1995)

To investigate the mechanisms of eosinophil activation in the airways of patients with asthma, we attempted to detect eosinophil-activating cytokines in sputum extracts obtained from asthmatic patients during acute attacks or in remission by eosinophil survival assay. Purified guinea pig eosinophils were cultured in the presence or absence of sputum extracts, and the eosinophil viability was measured on Day 4. Eosinophil viability in the presence of sputum extracts derived from patients during moderate or severe attacks was significantly higher than that for sputum obtained from patients in remission or during mild attacks or from those with other respiratory diseases, including bronchiectasis and diffuse panbronchiolitis (p < 0.05). The total symptom score during the week prior to sputum collection correlated with the eosinophil viability (rs = 0.79, p < 0.01). Eosinophil viability-enhancing activity (EVEA) in the sputum of asthmatic patients with moderate or severe attacks was neutralized by anti-IL-5 antibody and by anti-GM-CSF antibody by 19.9 +/- 13.7% and 76.9 +/- 8.2% (mean +/- SEM, n = 7), respectively. EVEA was completely neutralized by a combination of anti-IL-5 and anti-GM-CSF antibodies. There was a significant correlation between the concentration of eosinophil cationic protein (ECP) in sputum extracts and the eosinophil viability (rs = 0.54, p < 0.05). These findings suggest that IL-5 and GM-CSF are present in the sputum during asthma attacks and that these cytokines are at least partially responsible for eosinophil activation in asthma.