gebhart/patrepeval huggingface dataset:
Lateral selectivity of ion-induced quantum well intermixing (1998)

Quantum well (QW) intermixing using high-energy ion implantation is a promising technique for laterally selective, post-growth modification of a quantum well structure. In this work, we investigate the lateral selectivity of the technique, which is a function of the ion straggling during implantation and of the lateral diffusion of defects during post-implantation annealing. We have used photoluminescence and a specially designed mask to monitor the intermixing of QWs under masked regions. A significant amount of intermixing, resulting in a blueshift of the QW band-gap energy, was observed when the mask stripe width was less than 5 μm, thus giving a lateral selectivity of 2.5 μm.
In Situ Oxidative Catalysis by Neurofibrillary Tangles and Senile Plaques in Alzheimer’s Disease (2000)

There is a great deal of evidence to support a pathogenic role of oxidative stress in Alzheimer's disease (AD), but the sources of reactive oxygen species have not been directly demonstrated. In this study, using a novel in situ detection system, we show that neurofibrillary tangles and senile plaques are major sites for catalytic redox reactivity. Pretreatment with deferoxamine or diethylenetriaminepentaacetic acid abolishes the ability of the lesions to catalyze the H2O2-dependent oxidation of 3,3'-diaminobenzidine (DAB), strongly suggesting the involvement of associated transition metal ions. Indeed, following chelated removal of metals, incubation with iron or copper salts reestablished lesion-dependent catalytic redox reactivity. Although DAB oxidation can also detect peroxidase activity, this was inactivated by H2O2 pretreatment before use of DAB, as shown by a specific peroxidase detection method. Model studies confirmed the ability of certain copper and iron coordination complexes to catalyze the H2O2-dependent oxidation of DAB. Also, the microtubule-associated protein tau, as an in vitro model for proteins relevant to AD pathology, was found capable of adventitious binding of copper and iron in a redox-competent manner. Our findings suggest that neurofibrillary tangles and senile plaques contain redox-active transition metals and may thereby exert prooxidant or possibly antioxidant activities, depending on the balance among cellular reductants and oxidants in the local microenvironment.
CCL16/LEC powerfully triggers effector and antigen-presenting functions of macrophages and enhances T cell cytotoxicity (2003)

The human CC chemokine CCL16, a liver-expressed chemokine, enhances the killing activity of mouse peritoneal macrophages by triggering their expression of tumor necrosis factor alpha (TNF-alpha) and Fas ligand. Macrophages also respond to CCL16 by enhancing their production of monocyte chemoattractant protein-1, regulated on activation, normal T cells expressed and secreted chemokines, and interleukin (IL)-1 beta, TNF-alpha, and IL-12. The effect of CCL16 is almost as strong as that of lipopolysaccharide and interferon-gamma, two of the best macrophage activators. Moreover, CCL16-activated macrophages overexpress membrane CD80, CD86, and CD40 costimulatory molecules and extensively phagocytose tumor cell debris. On exposure to such debris, they activate a strong, tumor-specific, cytolytic response in virgin T cells. Furthermore, cytolytic T cells generated in the presence of CCL16 display a higher cytotoxicity and activate caspase-8 in tumor target cells. This ability to activate caspase-8 depends on their overexpression of TNF-alpha and Fas ligand induced by CCL16. These data reveal a new function for CCL16 in the immune-response scenario. CCL16 significantly enhances the effector and the antigen-presenting function of macrophages and augments T cell lytic activity.
Anti-AIDS Agents. 37. Synthesis and Structure−Activity Relationships of (3‘R,4‘R)-(+)-cis-Khellactone Derivatives as Novel Potent Anti-HIV Agents (1999)

To explore the structural requirements of (+)-cis-khellactone derivatives as novel anti-HIV agents, 24 monosubstituted 3', 4'-di-O-(S)-camphanoyl-(+)-cis-khellactone (DCK) derivatives were synthesized asymmetrically. These compounds included 4 isomeric monomethoxy analogues (3-6), 4 isomeric monomethyl analogues (7-10), 4 4-alkyl/aryl-substituted analogues (11-14), and 12 4-methyl-(+)-cis-khellactone derivatives (15-26) with varying 3', 4'-substituents. These (+)-cis-khellactone derivatives were screened against HIV-1 replication in acutely infected H9 lymphocytes. The results demonstrated that the (3'R,4'R)-(+)-cis-khellactone skeleton, two (S)-(-)-camphanoyl groups at the 3'- and 4'-positions, and a methyl group on the coumarin ring, except at the 6-position, were optimal structural moieties for anti-HIV activity. 3-Methyl- (7), 4-methyl- (8), and 5-methyl- (9) 3',4'-di-O-(S)-camphanoyl-(3'R, 4'R)-(+)-cis-khellactone showed EC(50) and therapeutic index values of <5.25 x 10(-5) microM and >2.15 x 10(6), respectively, in H9 lymphocytes, which are much better than those of DCK and AZT in the same assay. Furthermore, 8 and 9 also showed potent inhibitory activity against HIV-1 replication in the CEM-SS cell line, and most monosubstituted DCK analogues were less toxic than DCK in both assays.
Characterization of PaxA and Its Operon: a Cohemolytic RTX Toxin Determinant from Pathogenic Pasteurella aerogenes (2000)

Pasteurella aerogenes is known as a commensal bacterium or as an opportunistic pathogen, as well as a primary pathogen found to be involved in abortion cases of humans, swine, and other mammals. Using broad-range DNA probes for bacterial RTX toxin genes, we cloned and subsequently sequenced a new operon named paxCABD encoding the RTX toxin PaxA in P. aerogenes. The pax operon is organized analogous to the classical RTX operons containing the activator gene paxC upstream of the structural toxin gene paxA, which is followed by the secretion protein genes paxB and paxD. The highest sequence similarity of paxA with known RTX toxin genes is found with apxIIIA (82%). PaxA is structurally similar to ApxIIIA and also shows functional analogy to ApxIIIA, since it shows cohemolytic activity with the sphingomyelinase of Staphylococcus aureus, known as the CAMP effect, but is devoid of direct hemolytic activity. In addition, it shows to some extent immunological cross-reactions with ApxIIIA. P. aerogenes isolated from various specimens showed that the pax operon was present in about one-third of the strains. All of the pax-positive strains were specifically related to swine abortion cases or septicemia of newborn piglets. These strains were also shown to produce the PaxA toxin as determined by the CAMP phenomenon, whereas none of the pax-negative strains did. This indicated that the PaxA toxin is involved in the pathogenic potential of P. aerogenes. The examined P. aerogenes isolates were phylogenetically analyzed by 16S rRNA gene (rrs) sequencing in order to confirm their species. Only a small heterogeneity (<0.5%) was observed between the rrs genes of the strains originating from geographically distant farms and isolated at different times.
The Usefulness of a Urinary LH Kit for Ovulation Prediction During Menstrual Cycles of Normal Women (1996)

Urine LH testing every evening is a reliable method of predicting ovulation within the ensuing 48 hours.
Cytomegalovirus (CMV) titers among acquired immunodeficiency syndrome (AIDS) patients with and without a history of Kaposi's sarcoma (KS). (1990)

The relationship between a history of Kaposi's sarcoma (KS) and serum titers to cytomegalovirus (CMV) among homosexual patients with acquired immunodeficiency syndrome (AIDS) was studied. Individuals with a history of AIDS and biopsy-proven or clinically confirmed KS were identified and compared with AIDS patients who did not have a history of KS. By demographic parameters and level of immunosuppression, the two groups were similar. Titers to CMV among the 53 AIDS patients (using an indirect fluorescent antibody [IFA] system) demonstrated a median titer for the first group of 1:512 and 1:2048 for the second. The two groups, however, did not differ in a matched study using a McNemar's test for correlated proportions. Wilcoxon ranked sum test performed on the data also demonstrated that the two groups did not differ with respect to the distribution of CMV titers. Serologic data failed to demonstrate a role for CMV infection in the pathogenesis of KS.
Endoglin gene polymorphism as a risk factor for sporadic intracerebral hemorrhage (1997)

Intracerebral hemorrhage (ICH) is a common and serious type of stroke. Recent studies have shown that inherited factors that affect the development of the vessel wall can increase the risk of ICH. We studied endoglin as a candidate gene in patients with sporadic ICH, since mutations in this gene can cause telangiectasia formation. One hundred three patients with sporadic ICH and 202 controls were studied. The polymerase chain reaction and single-strand conformational polymorphism analysis were used to screen for mutations in exon 7 of the endoglin gene. No coding mutations in exon 7 were identified in the ICH patients or controls. A 6-base intronic insertion was found 26 bases beyond the 3' end of exon 7. The homozygous form of the insertion was present in 9 of 103 (8.7%) ICH patients compared with 4 of 202 (2.0%) controls, p = 0.012 (odds ratio 4.8 [95% confidence interval, 1.28, 21.60]). Analysis of the endoglin transcript around the insertion did not reveal any changes in the RNA sequence. There were no obvious clinical features that distinguished the ICH patients with the homozygous insertion from the other patients. The pathophysiologic mechanism underlying this association remains to be determined.
Cyclopropane ring formation in membrane lipids of bacteria (1997)

It has been known for several decades that cyclopropane fatty acids (CFAs) occur in the phospholipids of many species of bacteria. CFAs are formed by the addition of a methylene group, derived from the methyl group of S-adenosylmethionine, across the carbon-carbon double bond of unsaturated fatty acids (UFAs). The C1 transfer does not involve free fatty acids or intermediates of phospholipid biosynthesis but, rather, mature phospholipid molecules already incorporated into membrane bilayers. Furthermore, CFAs are typically produced at the onset of the stationary phase in bacterial cultures. CFA formation can thus be considered a conditional, postsynthetic modification of bacterial membrane lipid bilayers. This modification is noteworthy in several respects. It is catalyzed by a soluble enzyme, although one of the substrates, the UFA double bond, is normally sequestered deep within the hydrophobic interior of the phospholipid bilayer. The enzyme, CFA synthase, discriminates between phospholipid vesicles containing only saturated fatty acids and those containing UFAs; it exhibits no affinity for vesicles of the former composition. These and other properties imply that topologically novel protein-lipid interactions occur in the biosynthesis of CFAs. The timing and extent of the UFA-to-CFA conversion in batch cultures and the widespread distribution of CFA synthesis among bacteria would seem to suggest an important physiological role for this phenomenon, yet its rationale remains unclear despite experimental tests of a variety of hypotheses. Manipulation of the CFA synthase of Escherichia coli by genetic methods has nevertheless provided valuable insight into the physiology of CFA formation. It has identified the CFA synthase gene as one of several rpoS-regulated genes of E. coli and has provided for the construction of strains in which proposed cellular functions of CFAs can be properly evaluated. Cloning and manipulation of the CFA synthase structural gene have also enabled this novel but extremely unstable enzyme to be purified and analyzed in molecular terms and have led to the identification of mechanistically related enzymes in clinically important bacterial pathogens.
SMIL 3.0 (2008)

This specification defines the third version of the Synchronized Multimedia Integration Language (SMIL, pronounced smile). SMIL 3.0 has the following design goals:
(1) Define an XML-based language that allows authors to write interactive multimedia presentations. Using SMIL 3.0, an author may describe the temporal behavior of a multimedia presentation, associate hyperlinks with media objects and describe the layout of the presentation on a screen.
(2) Allow reusing of SMIL 3.0 syntax and semantics in other XML-based languages, in particular those who need to represent timing and synchronization. For example, SMIL 3.0 components are used for integrating timing into XHTML and into SVG.
(3) Extend the functionalities contained in the SMIL 2.1 into new or revised SMIL 3.0 modules.
(4) Define new SMIL 3.0 Mobile Profiles incorporating features useful within the industry.

SMIL 3.0 is defined as a set of markup modules, which define the semantics and an XML syntax for certain areas of SMIL functionality.
Quantum cascade laser–based hyperspectral imaging of biological tissue (2014)

The spectroscopy of analyte-specific molecular vibrations in tissue thin sections has opened up a path toward histopathology without the need for tissue staining. However, biomedical vibrational imaging has not yet advanced from academic research to routine histopathology due to long acquisition times for the microscopic hyperspectral images and/or cost and availability of the necessary equipment. Here we show that the combination of a fast-tuning quantum cascade laser with a microbolometer array detector allows for a rapid image acquisition and bares the potential for substantial cost reduction. A 3.1 x 2.8 mm2 unstained thin section of mouse jejunum has been imaged in the 9.2 to 9.7 μm wavelength range (spectral resolution ~1 cm(-1)) within 5 min with diffraction limited spatial resolution. The comparison of this hyperspectral imaging approach with standard Fourier transform infrared imaging or mapping of the identical sample shows a reduction in acquisition time per wavenumber interval and image area by more than one or three orders of magnitude, respectively.
Pulmonary hamartoma (2011)

Pulmonary hamartomas are the most common benign tumor in the lungs. They present as solitary, round, well-circumscribed soft tissue opacities in the lung parenchyma on CT imaging [1–3]. Areas of fat (60%) or calcification (26%) can be seen within the nodule [1]. When areas of fat are identified in a nodule on CT imaging, the diagnosis of hamartoma can typically be made (Figures 22.1–22.3).
ADD1/SREBP-1c Is Required in the Activation of Hepatic Lipogenic Gene Expression by Glucose (1999)

The transcription of genes encoding proteins involved in the hepatic synthesis of lipids from glucose is strongly stimulated by carbohydrate feeding. It is now well established that in the liver, glucose is the main activator of the expression of this group of genes, with insulin having only a permissive role. While ADD1/SREBP-1 has been implicated in lipogenic gene expression through temporal association with food intake and ectopic gain-of-function experiments, no genetic evidence for a requirement for this factor in glucose-mediated gene expression has been established. We show here that the transcription of ADD1/SREBP-1c in primary cultures of hepatocytes is controlled positively by insulin and negatively by glucagon and cyclic AMP, establishing a link between this transcription factor and carbohydrate availability. Using adenovirus-mediated transfection of a powerful dominant negative form of ADD1/SREBP-1c in rat hepatocytes, we demonstrate that this factor is absolutely necessary for the stimulation by glucose of L-pyruvate kinase, fatty acid synthase, S14, and acetyl coenzyme A carboxylase gene expression. These results demonstrate that ADD1/SREBP-1c plays a crucial role in mediating the expression of lipogenic genes induced by glucose and insulin.
361. Attempts to find new spasmolytics. Part VIII. The synthesis of 6 : 7-diethoxy-3-alkyl- and 6 : 7-diethoxy-3-phenyl-isoquinolines (1949)

G. Fodor, J. Kiss and M. Szekerke, J. Chem. Soc., 1949, 1681 DOI: 10.1039/JR9490001681
HERP, a New Primary Target of Notch Regulated by Ligand Binding (2001)

Notch signaling dictates cell fate and critically influences cell proliferation, differentiation, and apoptosis in metazoans. Ligand binding initiates the signal through regulated intramembrane proteolysis of a transmembrane Notch receptor which releases the signal-transducing Notch intracellular domain (NICD). The HES/E(spl) gene family is a primary target of Notch and thus far the only known Notch effector. A newly isolated HERP family, a HES-related basic helix-loop-helix protein family, has been proposed as a potential target of Notch, based on its induction following NICD overexpression. However, NICD is physiologically maintained at an extremely low level that typically escapes detection, and therefore, nonregulated overexpression of NICD-as in transient transfection-has the potential of generating cellular responses of little physiological relevance. Indeed, a constitutively active NICD indiscriminately up-regulates expression of both HERP1 and HERP2 mRNAs. However, physiological Notch stimulation through ligand binding results in the selective induction of HERP2 but not HERP1 mRNA and causes only marginal up-regulation of HES1 mRNA. Importantly, HERP2 is an immediate target gene of Notch signaling since HERP2 mRNA expression is induced even in the absence of de novo protein synthesis. HERP2 mRNA induction is accompanied by specific expression of HERP2 protein in the nucleus. Furthermore, using RBP-Jk-deficient cells, we show that an RBP-Jk protein, a transcription factor that directly activates HES/E(spl) transcription, also is essential for HERP2 mRNA expression and that expression of exogenous RBP-Jk is sufficient to rescue HERP2 mRNA expression. These data establish that HERP2 is a novel primary target gene of Notch that, together with HES, may effect diverse biological activities of Notch.
Optimal estimation for global ground‐level fine particulate matter concentrations (2013)

We develop an optimal estimation (OE) algorithm based on top‐of‐atmosphere reflectances observed by the MODIS satellite instrument to retrieve near‐surface fine particulate matter (PM 2.5 ). The GEOS‐Chem chemical transport model is used to provide prior information for the Aerosol Optical Depth (AOD) retrieval and to relate total column AOD to PM 2.5 . We adjust the shape of the GEOS‐Chem relative vertical extinction profiles by comparison with lidar retrievals from the CALIOP satellite instrument. Surface reflectance relationships used in the OE algorithm are indexed by land type. Error quantities needed for this OE algorithm are inferred by comparison with AOD observations taken by a worldwide network of sun photometers (AERONET) and extended globally based upon aerosol speciation and cross correlation for simulated values, and upon land type for observational values. Significant agreement in PM 2.5 is found over North America for 2005 (slope = 0.89; r = 0.82; 1‐ σ error = 1 µg/m 3 + 27%), with improved coverage and correlation relative to previous work for the same region and time period, although certain subregions, such as the San Joaquin Valley of California are better represented by previous estimates. Independently derived error estimates of the OE PM 2.5 values at in situ locations over North America (of ±(2.5 µg/m 3 + 31%) and Europe of ±(3.5 µg/m 3 + 30%) are corroborated by comparison with in situ observations, although globally (error estimates of ±(3.0 µg/m 3 + 35%), may be underestimated. Global population‐weighted PM 2.5 at 50% relative humidity is estimated as 27.8 µg/m 3 at 0.1° × 0.1° resolution.
A phase I study of an anti-CD22-deglycosylated ricin A chain immunotoxin in the treatment of B-cell lymphomas resistant to conventional therapy (1993)

Abstract Twenty-six patients, whose B-cell lymphoma had relapsed after conventional therapies, were treated in a phase I dose escalation study with an immunotoxin consisting of a mouse CD22 monoclonal antibody (RFB4:IgG1K) coupled to chemically deglycosylated ricin A chain (dgA). Two to 12 doses of the immunotoxin were infused intravenously at 48- hour intervals. The peak serum concentration and half-life (T1/2) did not correlate directly with the dose and averaged 3.8 micrograms/mL and 7.8 hours, respectively. The main dose-limiting toxicity was caused by the vascular leak syndrome (VLS) consisting of weight gain, edema, serum albumin decrease, and critically by pulmonary edema. Myalgia occurred frequently and was only dose limiting in one patient who developed rhabdomyolysis. The presence of lymphoma cells in the blood (&gt; or = 10(10)/L) and clinically detectable splenomegaly were associated with reduced toxicity and a shorter T1/2. Nine of 24 evaluable patients (37.5%) made antibody to either mouse Ig or dgA. There were five partial responses (PR) and one complete response (CR) lasting 30 to 78 days. High peak concentrations of immunotoxin in the serum, a long T1/2, and large areas under the curve (AUC) correlated with both clinical response and toxicity. None of three patients with CD5+ lymphomas (including two CLL patients) had more than mild toxicity or responded to the immunotoxin.
Highly Efficient Multicistronic Lentiviral Vectors with Peptide 2A Sequences (2009)

Gene discovery and gene therapy call for advanced technologies to reliably assess gene expression; efficient coupling of gene expression to the expression of reporter genes is critical. Various noninvasive molecular imaging modalities have emerged to track biological processes in animal models. Here, we evaluate various strategies to link transgene expression with that of an (imaging) reporter gene. Using lentiviral vectors containing internal ribosomal entry sites (IRES), 2A-like peptides, or a bidirectional promoter, we compared their ability to ensure efficient coexpression of multiple reporter genes. Although the encephalomyocarditis virus (EMCV) IRES yielded functional bicistronic vectors, the expression level of the reporter downstream of IRES was consistently lower than that of the upstream transgene. Interestingly, peptide 2A constructs performed best in vitro and in vivo, providing effective noninvasive follow-up of transgene expression and having reporter gene expression levels in line with that of the single reporter constructs. The intrinsic "cleavage" property of the peptide 2A sequences allows each protein to be produced at proportional levels, opening ample possibilities for functional genomics and future gene therapeutic applications. Last, using various peptide 2A sequences, we engineered the triple reporter LV-3R (i.e., eGFP, fLuc, HSV1-sr39tk), enabling efficient multimodality readouts in vivo.