gebhart/patrepeval huggingface dataset:
Detection of aneuploidy in single cells using comparative genomic hybridization (1999)

The ability of comparative genomic hybridization (CGH) to detect aneuploidy following universal amplification of DNA from a single cell, or a small number of cells, was investigated with a view to preimplantation diagnosis following in vitro fertilization, and prenatal diagnosis using fetal erythroblasts obtained from maternal blood. The DNA obtained from lysed single cells was amplified using degenerate oligonucleotide-primed PCR (DOP-PCR). This product was labelled using nick translation and hybridized together with normal reference genomic DNA. The CGH fluorescent ratio profiles obtained could be used to determine aneuploidy with cut-off thresholds of 0.75 and 1.25. Deviation in the profiles in the heterochromatic regions was reduced by using, as a reference sample, normal genomic DNA that had also undergone DOP-PCR. Single cells known to be trisomic for chromosomes 13, 18 or 21 were analysed using this technique. The resolution of CGH with amplified DNA from a single cell is of the order of 40 Mb, sufficient for the diagnosis of trisomy 21, and possibly segmental aneuploidy of equivalent size. These results, and those of others, demonstrate that diagnosis of chromosomal aneuploidy in single cells is possible using CGH with DOP-PCR amplified DNA.
Aerobic Activity of Escherichia coli Alcohol Dehydrogenase Is Determined by a Single Amino Acid (2000)

ABSTRACT Expression of the alcohol dehydrogenase gene, adhE , in Escherichia coli is anaerobically regulated at both the transcriptional and the translational levels. To study the AdhE protein, the adhE + structural gene was cloned into expression vectors under the control of the lacZ and trp c promoters. Wild-type AdhE protein produced under aerobic conditions from these constructs was inactive. Constitutive mutants ( adhC ) that produced high levels of AdhE under both aerobic and anaerobic conditions were previously isolated. When only the adhE structural gene from one of the adhC mutants was cloned into expression vectors, highly functional AdhE protein was isolated under both aerobic and anaerobic conditions. Sequence analysis revealed that the adhE gene from the adhC mutant contained two mutations resulting in two amino acid substitutions, Ala267Thr and Glu568Lys. Thus, adhC strains contain a promoter mutation and two mutations in the structural gene. The mutant structural gene from adhC strains was designated adhE *. Fragment exchange experiments revealed that the substitution responsible for aerobic expression in the adhE * clones is Glu568Lys. Genetic selection and site-directed mutagenesis experiments showed that virtually any amino acid substitution for Glu568 produced AdhE that was active under both aerobic and anaerobic conditions. These findings suggest that adhE expression is also regulated posttranslationally and that strict regulation of alcohol dehydrogenase activity in E. coli is physiologically significant.
Status and Future Perspective of Hazardous Waste Management in Korea (1992)

In this paper, classification and generation of hazardous wastes, related laws, and the hazardous waste management system currently employed in Korea are introduced. Recently, rapid and sustaining increase of generation rate, unsatisfactory reuse and recycle, inaccurate analysis and testing, and illegal treatment and disposal have been pointed out as major problems of hazardous waste management in Korea. In order to resolve these problems, the future directions and priorities in hazardous waste management in Korea are suggested.
Cellular and molecular targets of estrogen in normal human breast tissue. (2002)

To gain insight into the in vivo role of estrogen, we isolated estrogen receptor-positive cells fromnormal human breast tissue using a recombinant adenovirus that expresses green fluorescence protein in response to estrogen. We compared the global gene expression profile of these estrogen receptor-positive cells with that of various normal and cancerous mammary epithelial cells and identified several genes not implicated previously in estrogen signaling. One of these genes, lipocalin 2, is a putative in vivo estrogen target gene and paracrine factor that mediates the growth regulatory effects of estrogen in normal breast epithelium. These results demonstrate that normal and cancerous estrogen receptor-positive cells are distinct at the molecular level and suggest that lipocalin 2 is a new therapeutic target for breast cancer prevention and treatment.
Development of a high brightness gas field ion source (1997)

We have investigated the emission properties of gas field ionization emitters built up from electrochemically dc-etched W〈111〉 and W〈100〉 single crystal wires. A standard thermal field method was used to confine the ion emission to a single spot at the apex of the emitter. The angular current density obtained for these kinds of tips with a small end radius (100–200 nm) is in the range of 5 μA/sr. For H2 and Ne, maximum ion current was observed in the temperature range between 18 and 21 K. We have measured the ion current density for different gases (H2, He, and Ne) as a function of extraction voltage and gas pressure. The linear dependence of the angular current density on the gas pressure shows that current densities of 10 μA/sr and above can be expected with this type of emitter.
Spectrophotometric determination of the critical micellar concentration of bile salts using bilirubin monoglucuronide as a micellar probe. Utility of derivative spectroscopy (1988)

We have developed a simple biologically non-invasive method for determining the critical micellar concentration (CMC) of bile salts using pure naturally occurring bilirubin IX alpha monoglucuronide (BMG), an important bile pigment present in virtually all mammalian biles. This methodology employs visible absorbance spectroscopy of BMG in bile salts over a range of bile salt concentrations that include the reported CMC. Using 100 microM-BMG in 0.4 M-imidazole buffer at pH 7.8, we calculated that the CMC for sodium taurochenodeoxycholate is between 2.5 and 3.0 mM based on: (1) an abrupt change in lambda max. in this concentration range, (2) a precipitous decrease in the amplitude of the absorbance shoulder at 450 nm, (3) a sudden decrease in the second derivative absorbance of BMG at 400 nm and an increase in absorbance at 470 nm, (4) a sharp change in the 4th derivative absorbance at 375 and 395 nm. In contrast, sodium taurocholate, a bile salt that reportedly does not have a CMC but continuously self-associates over a wide concentration range, exhibited none of these changes. The use of derivative spectroscopy enhances the ability to detect the CMC changes and also indicates the number of BMG species in solution and their relative energy states.
Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures (2007)

The interferon (IFN) system is an extremely powerful antiviral response that is capable of controlling most, if not all, virus infections in the absence of adaptive immunity. However, viruses can still replicate and cause disease in vivo, because they have some strategy for at least partially circumventing the IFN response. We reviewed this topic in 2000 [Goodbourn, S., Didcock, L. & Randall, R. E. (2000). J Gen Virol 81, 2341-2364] but, since then, a great deal has been discovered about the molecular mechanisms of the IFN response and how different viruses circumvent it. This information is of fundamental interest, but may also have practical application in the design and manufacture of attenuated virus vaccines and the development of novel antiviral drugs. In the first part of this review, we describe how viruses activate the IFN system, how IFNs induce transcription of their target genes and the mechanism of action of IFN-induced proteins with antiviral action. In the second part, we describe how viruses circumvent the IFN response. Here, we reflect upon possible consequences for both the virus and host of the different strategies that viruses have evolved and discuss whether certain viruses have exploited the IFN response to modulate their life cycle (e.g. to establish and maintain persistent/latent infections), whether perturbation of the IFN response by persistent infections can lead to chronic disease, and the importance of the IFN system as a species barrier to virus infections. Lastly, we briefly describe applied aspects that arise from an increase in our knowledge in this area, including vaccine design and manufacture, the development of novel antiviral drugs and the use of IFN-sensitive oncolytic viruses in the treatment of cancer.
Architecture of Supramolecular Metal Complexes for Photocatalytic CO2 Reduction:  Ruthenium−Rhenium Bi- and Tetranuclear Complexes (2005)

We study the electrochemical, spectroscopic, and photocatalytic properties of a series of Ru(II)-Re(I) binuclear complexes linked by bridging ligands 1,3-bis(4'-methyl-[2,2']bipyridinyl-4-yl)propan-2-ol (bpyC3bpy) and 4-methyl-4'-[1,10]phenanthroline-[5,6-d]imidazol-2-yl)bipyridine (mfibpy) and a tetranuclear complex in which three [Re(CO)3Cl] moieties are coordinated to the central Ru using the bpyC3bpy ligands. In the bpyC3bpy binuclear complexes, 4,4'-dimethyl-2,2'-bipyridine (dmb) and 4,4'-bis(trifluoromethyl)-2,2'-bipyridine ({CF3}2bpy), as well as 2,2'-bipyridine (bpy), were used as peripheral ligands on the Ru moiety. Greatly improved photocatalytic activities were obtained only in the cases of [Ru{bpyC3bpyRe(CO)3Cl}3]2+ (RuRe3) and the binuclear complex [(dmb)2Ru(bpyC3bpy)Re(CO)3Cl]2+ (d2Ru-Re), while photocatalytic responses were extended further into the visible region. The excited state of ruthenium in all Ru-Re complexes was efficiently quenched by 1-benzyl-1,4-dihydronicotinamide (BNAH). Following reductive quenching in the case of d2Ru-Re, generation of the one-electron-reduced (OER) species, for which the added electron resides on the Ru-bound bpy end of the bridging ligand bpyC3bpy, was confirmed by transient absorption spectroscopy. The reduced Re moiety was produced via a relatively slow intramolecular electron transfer, from the reduced Ru-bound bpy to the Re site, occurring at an exchange rate (DeltaG approximately 0). Electron transfer need not be rapid, since the rate-determining process is reduction of CO2 with the OER species of the Re site. Comparison of these results with those for other bimetallic systems gives us more general architectural pointers for constructing supramolecular photocatalysts for CO2 reduction.
Stable and Controllable Neural Texture Synthesis and Style Transfer Using Histogram Losses (2017)

Recently, methods have been proposed that perform texture synthesis and style transfer by using convolutional neural networks (e.g. Gatys et al. [2015,2016]). These methods are exciting because they can in some cases create results with state-of-the-art quality. However, in this paper, we show these methods also have limitations in texture quality, stability, requisite parameter tuning, and lack of user controls. This paper presents a multiscale synthesis pipeline based on convolutional neural networks that ameliorates these issues. We first give a mathematical explanation of the source of instabilities in many previous approaches. We then improve these instabilities by using histogram losses to synthesize textures that better statistically match the exemplar. We also show how to integrate localized style losses in our multiscale framework. These losses can improve the quality of large features, improve the separation of content and style, and offer artistic controls such as paint by numbers. We demonstrate that our approach offers improved quality, convergence in fewer iterations, and more stability over the optimization.
Regulation of nitric oxide synthase activity in human immunodeficiency virus type 1 (HIV-1)-infected monocytes: implications for HIV-associated neurological disease. (1995)

Mononuclear phagocytes (monocytes, macrophages, and dendritic cells) play major roles in human immunodeficiency virus (HIV) persistence and disease pathogenesis. Macrophage antigen presentation and effector cell functions are impaired by HIV-1 infection. Abnormalities of macrophage effector cell function in bone marrow, lung, and brain likely result as a direct consequence of cellular activation and HIV replication. To further elucidate the extent of macrophage dysfunction in HIV-1 disease, a critical activation-specific regulatory molecule, nitric oxide (NO.), which may contribute to diverse pathology, was studied. Little, if any, NO. is produced by uninfected human monocytes. In contrast, infection with HIV-1 increases NO. production to modest, but significant levels (2-5 microM). Monocyte activation (with lipopolysaccharide, tumor necrosis factor alpha, or through interactions with astroglial cells) further enhances NO. production in HIV-infected cells, whereas its levels are diminished by interleukin 4. These results suggest a possible role for NO. in HIV-associated pathology where virus-infected macrophages are found. In support of this hypothesis, RNA encoding the inducible NO synthase (iNOS) was detected in postmortem brain tissue from one pediatric AIDS patient with advanced HIV encephalitis. Corresponding iNOS mRNA was not detected in brain tissue from five AIDS patients who died with less significant brain disease. These results demonstrate that HIV-1 can influence the expression of NOS in both cultured human monocytes and brain tissue. This newly described feature of HIV-macrophage interactions suggests previously unappreciated mechanisms of tissue pathology that result from productive viral replication.
Identification and purification of a sperm surface protein with a potential role in sperm-egg membrane fusion. (1987)

Sperm-egg plasma membrane fusion during fertilization was studied using guinea pig gametes and mAbs to sperm surface antigens. The mAb, PH-30, strongly inhibited sperm-egg fusion in a concentration-dependent fashion. When zona-free eggs were inseminated with acrosome-reacted sperm preincubated in saturating (140 micrograms/ml) PH-30 mAb, the percent of eggs showing fusion was reduced 75%. The average number of sperm fused per egg was also reduced by 75%. In contrast a control mAb, PH-1, preincubated with sperm at 400 micrograms/ml, caused no inhibition. The PH-30 and PH-1 mAbs apparently recognize the same antigen but bind to two different determinants. Both mAbs immunoprecipitated the same two 125I-labeled polypeptides with Mr 60,000 (60 kD) and Mr 44,000 (44 kD). Boiling a detergent extract of sperm severely reduced the binding of PH-30 but had essentially no effect on the binding of PH-1, indicating that the two mAbs recognize different epitopes. Immunoelectron microscopy revealed that PH-30 mAb binding was restricted to the sperm posterior head surface and was absent from the equatorial region. The PH-30 and PH-1 mAbs did not bind to sperm from the testis, the caput, or the corpus epididymis. PH-30 mAb binding was first detectable on sperm from the proximal cauda epididymis, i.e., sperm at the developmental stage where fertilization competence appears. After purification by mAb affinity chromatography, the PH-30 protein retained antigenic activity, binding both the PH-30 and PH-1 mAbs. The purified protein showed two polypeptide bands of 60 and 44 kD on reducing SDS PAGE. The two polypeptides migrated further (to approximately 49 kD and approximately 33 kD) on nonreducing SDS PAGE, showing that they do not contain interchain disulfide bonds, but probably have intrachain disulfides. 44 kD appears not to be a proteolytic fragment of 60 kD because V8 protease digestion patterns did not reveal related peptide patterns from the 44- and 60-kD bands. In the absence of detergent, the purified protein precipitates, suggesting that either 60 or 44 kD could be an integral membrane polypeptide.
Metal–Organic Framework Nodes as Nearly Ideal Supports for Molecular Catalysts: NU-1000- and UiO-66-Supported Iridium Complexes (2015)

Metal-organic frameworks with Zr6 nodes, UiO-66 and NU-1000, were investigated as supports for Ir(CO)2 and Ir(C2H4)2 complexes. A single bonding site for the iridium is identified on the nodes of NU-1000, whereas two sites are identified on UiO-66, although at low iridium loadings only one site is occupied. Density functional theory calculations provide structural results that are in good agreement with infrared and X-ray absorption fine-structure spectra. The reactivity of node-supported Ir(CO)2 with C2H4 and the catalytic activity and selectivity of the species initially present as Ir(C2H4)2 for ethylene hydrogenation and dimerization were investigated both experimentally and computationally and shown to be strongly influenced by the node.
Superconductivity at 52.5 K in the Lanthanum-Barium-Copper-Oxide System (1987)

A superconducting transition with an onset temperature of 52.5 K has been observed under hydrostatic pressure in compounds with nominal compositions given by (La(0.9)Ba(0.1))(2) CuO4-Y. Possible causes for the high-temperature superconductivity are discussed.
Developmental Expression of Rat Transforming Growth Factor-α mRNA (1985)

Expression of the gene encoding transforming growth factor-alpha (TGF alpha) was examined in developing rat embryos by using a cloned TGF alpha cDNA as a hybridization probe. Northern blot analysis of RNA isolated from whole fetuses revealed that TGF alpha mRNA was present at relatively high levels in 8- through 10-day-old embryos and then declined to the low or undetectable level, which is characteristic of adult tissues before birth. The level of TGF alpha mRNA present during early gestation was similar to that present in retrovirus-transformed cells in culture, suggesting that TGF alpha expression is not highly localized in the embryo. These observations are consistent with the hypothesis that TGF alpha plays a role in development, possibly as a fetal growth factor.
Expression and localization of scatter factor/hepatocyte growth factor inhuman astrocytomas (2001)

Scatter factor/hepatocyte growth factor (SF/HGF) is a pleiotropic cytokine that has been implicated in glioma invasion and angiogenesis. The SF/HGF receptor, MET, has been found to be expressed in neoplastic astrocytes as well as in endothelial cells of the tumor vasculature. Both SF/HGF and MET expression have also been described to correlate with the malignancy grade of human gliomas. However, most glioblastoma cell lines lack SF/HGF expression, raising the question of the cellular origin of SF/HGF in vivo. Using in situ hybridization, we analyzed glioblastomas, anaplastic astrocytomas, diffuse astrocytomas, pilocytic astrocytomas, and normal brain for the expression of SF/HGF mRNA. We detected strong SF/HGF expression by the majority of the tumor cells and by vascular endothelial cells in all glioblastoma specimens analyzed. Combined use of in situ hybridization with fluorescence immunohistochemistry confirmed the astrocytic origin of the SF/HGF-expressiong cells. In contrast, CD68-immunoreactive microglia/macrophages, as well as vascular smooth muscle cells reactive to alpha-smooth muscle actin, lacked SF/HGF expression. In anaplastic, diffuse, and pilocytic astrocytomas, SF/HGF expression was confined to a subset of tumor cells, and signals were less intense than in glioblastomas. In addition, we detected SF/HGF mRNA in cortical neurons. SF/HGF expression was not up regulated around necroses or at tumor margins. MET immunoreactivity was observed in GFAP-expressing astrocytic tumor cells and endothelial cells as well as in a subset of microglia/macrophages. We conclude that in vivo, both autocrine and paracrine stimulation of tumor cells and endothelium through the SF/HGF-MET system are likely to contribute to tumor invasion and angiogenesis. Lack of SF/HGF expression by most cultured glioblastoma cells is not representative of the in vivo situation and most likely represents a culture artifact.
2‐Aminobenzimidazole Derivatives Strongly Inhibit and Disperse Pseudomonas aeruginosa Biofilms (2012)

Bacterial biofilms are exceptionally difficult to clear using traditional antibiotics and constitute a significant health threat. 2-Aminobenzimidazole derivatives (see scheme) are capable of strongly inhibiting the growth of and dispersing Pseudomonas aeruginosa biofilms. These molecules were found to modulate quorum sensing in reporter strains, and represent some of strongest P. aeruginosa biofilm inhibitors known. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Choice of dressing has a major impact on blistering and healing outcomes in orthopaedic patients (2005)

Dressings that employ a clear film and have a high moisture vapour transmission rate have been shown to reduce both the rate of blistering and wound discharge. The additional expense inherent in using such dressings may, in reality, prove cost-effective because of the reduced need for dressings changes and the subsequent earlier discharge of these patients from hospital with an uncomplicated wound.
The present and the future in the diagnosis and management of celiac disease (2014)

Celiac disease is an autoimmune enteropathy caused by gluten in genetically predisposed individuals. In celiac disease, adaptive and innate immune activation results in intestinal damage and a wide range of clinical manifestations. In the past, celiac disease was thought to result in signs and symptoms solely related to the gastrointestinal tract. Now, more than half of the adult population presents with extra-intestinal manifestations that can also be expected to improve on a gluten-free diet. For this reason, it is recommended that physicians have a low threshold of suspicion for celiac disease. Current knowledge of the immune pathogenesis of this autoimmune disease has served as a catalyst for the development of novel diagnostic tools and therapeutics. Over the years, highly sensitive and specific serological assays, in addition to genetic markers, have been found to target specific steps in the cascade pathway of celiac disease. Also the advent of the gluten challenge has enabled experts to design diagnostic algorithms and monitor clinical responses in clinical trials. The gluten challenge has provided substantial benefit in the advance of novel therapeutics as an adjuvant treatment to the gluten free diet. Generally, a strict gluten-free diet is highly burdensome to patients and can be limited in its efficacy. Alternative therapies-including gluten modification, modulation of intestinal permeability and immune response-could be central to the future treatment of celiac disease.
Interfacial reaction between chemically vapor-deposited HfO2 thin films and a HF-cleaned Si substrate during film growth and postannealing (2002)

Interfacial reactions between HfO2 thin films and a Si substrate during thin-film growth and postannealing under a N2 atmosphere were investigated by high-resolution transmission electron microscopy, Auger electron spectroscopy, and electrical measurements of metal–insulator–semiconductor capacitors. HfO2 thin films were deposited on HF-cleaned Si wafers by a chemical-vapor-deposition technique at a wafer temperature of 200 °C using a carbon-free precursor [Hf(NO3)4]. The film thicknesses ranged from 1.5 to 5.6 nm. During the initial stage of film growth, the Si surface oxidized to form a Si-rich hafnium silicate film. With increasing deposition time, Hf-rich hafnium silicate films grew. Postannealing resulted in a double-layered film structure with upper and interfacial layers having dielectric constants of approximately 9.3 and 5.6, respectively. The results were compared with the results from HfO2 films grown on SiO2-passivated Si wafers.