gebhart/patrepeval huggingface dataset:
Hydrocarbon monooxygenase in Mycobacterium : recombinant expression of a member of the ammonia monooxygenase superfamily (2011)

The copper membrane monooxygenases (CuMMOs) are an important group of enzymes in environmental science and biotechnology. Areas of relevance include the development of green chemistry for sustainable exploitation of methane (CH(4)) reserves, remediation of chlorinated hydrocarbon contamination and monitoring human impact in the biogeochemical cycles of CH(4) and nitrogen. Challenges for all these applications are that many aspects of the ecology, physiology and structure-function relationships in the CuMMOs are inadequately understood. Here, we describe genetic and physiological characterization of a novel member of the CuMMO family that has an unusual physiological substrate range (C(2)-C(4) alkanes) and a distinctive bacterial host (Mycobacterium). The Mycobacterial CuMMO genes (designated hmoCAB) were amenable to heterologous expression in M. smegmatis-this is the first example of recombinant expression of a complete and highly active CuMMO enzyme. The apparent specific activity of recombinant cells containing hmoCAB ranged from 2 to 3 nmol min(-1) per mg protein on ethane, propane and butane as substrates, and the recombinants could also attack ethene, cis-dichloroethene and 1,2-dichloroethane. No detectable activity of recombinants or wild-type strains was seen with methane. The specific inhibitor allylthiourea strongly inhibited growth of wild-type cells on C(2)-C(4) alkanes, and omission of copper from the medium had a similar effect, confirming the physiological role of the CuMMO for growth on alkanes. The hydrocarbon monooxygenase provides a new model for studying this important enzyme family, and the recombinant expression system will enable biochemical and molecular biological experiments (for example, site-directed mutagenesis) that were previously not possible.
The DNA Methylome of Human Peripheral Blood Mononuclear Cells (2010)

DNA methylation plays an important role in biological processes in human health and disease. Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells. Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project. PBMC constitute an important source for clinical blood tests world-wide. We found that 68.4% of CpG sites and <0.2% of non-CpG sites were methylated, demonstrating that non-CpG cytosine methylation is minor in human PBMC. Analysis of the PBMC methylome revealed a rich epigenomic landscape for 20 distinct genomic features, including regulatory, protein-coding, non-coding, RNA-coding, and repeat sequences. Integration of our methylome data with the YH genome sequence enabled a first comprehensive assessment of allele-specific methylation (ASM) between the two haploid methylomes of any individual and allowed the identification of 599 haploid differentially methylated regions (hDMRs) covering 287 genes. Of these, 76 genes had hDMRs within 2 kb of their transcriptional start sites of which >80% displayed allele-specific expression (ASE). These data demonstrate that ASM is a recurrent phenomenon and is highly correlated with ASE in human PBMCs. Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies.
GlaxoSmithKline Adjuvant Systems in vaccines: concepts, achievements and perspectives (2007)

The need for potentiating immune responses to recombinant or subunit antigens has prompted GlaxoSmithKline (GSK) Biologicals to develop various Adjuvant Systems for the design of prophylactic and therapeutic vaccines. Adjuvant Systems are formulations of classical adjuvants mixed with immunomodulators, specifically adapted to the antigen and the target population. They can activate the appropriate innate immune system and subsequently impact on adaptive immune responses. AS04 is an Adjuvant System that has demonstrated significant achievements in several vaccines against viral diseases. AS02, another Adjuvant System, is being evaluated in various contexts, where a strong T-cell response is needed to afford protection. Likewise, AS01 has been developed for vaccines where the induction of a yet stronger T-cell-mediated immune response is required. Altogether, the promising clinical results strongly support the concept of Adjuvant Systems and allow for further development of new vaccines, best adapted to the target population and the immune mechanisms of protection.
Confinement and dynamics of laser-produced plasma expanding across a transverse magnetic field (2004)

The dynamics and confinement of laser-created plumes expanding across a transverse magnetic field have been investigated. 1.06 microm, 8 ns pulses from a neodymium-doped yttrium aluminum garnet laser were used to create an aluminum plasma which was allowed to expand across a 0.64 T magnetic field. Fast photography, emission spectroscopy, and time of flight spectroscopy were used as diagnostic tools. Changes in plume structure and dynamics, enhanced emission and ionization, and velocity enhancement were observed in the presence of the magnetic field. Photographic studies showed that the plume is not fully stopped and diffuses across the field. The temperature of the plume was found to increase due to Joule heating and adiabatic compression. The time of flight studies showed that all of the species are slowed down significantly. A multiple peak temporal distribution was observed for neutral species.
The Structure of the Mouse Cathepsin B Gene and Its Putative Promoter (1991)

The mouse cathepsin B gene and its flanking regions were cloned and characterized. The gene contains 10 exons and 9 introns spanning about 20 kb. Although the exon-intron organization of the mouse cathepsin B gene showed some similarity to the rat cathepsin H and L genes, significant differences were found. In particular, the highly conserved sequence that contains the catalytically active cysteine in these genes is split at different sites by an intron. As with other thiol proteinases, there is no obvious correspondence between the coding exons and structural or functional units within preprocathepsin B. These results suggest that the lysosomal thiol proteinase genes are evolutionarily ancient and that intron shifting has occurred subsequent to their divergence from a common ancestral form. The 5'-flanking region and exon 1 sequences in the mouse cathepsin B gene have a high GC content of approximately 72%. The 5'-flanking region also contains several potential Sp1 binding sites, but lacks TATA and CAAT motifs. These characteristics suggest that cathepsin B is a "housekeeping" gene and its transcription may be controlled by multiple transcription factors, including Sp1.
Activation of the Alternative Complement Pathway Accompanies Disease Flares in Systemic Lupus Erythematosus During Pregnancy (1992)

While a decline in the CH50 level alone could otherwise be attributed to decreased synthesis of complement components, these data demonstrate that ongoing activation of the alternative complement pathway can accompany disease flares in pregnant women with SLE.
A role for CD9 molecules in T cell activation. (1996)

Costimulation mediated by the CD28 molecule plays an important role in optimal activation of T cells. However, CD28-deficient mice can mount effective T cell-dependent immune responses, suggesting the existence of other costimulatory systems. In a search for other costimulatory molecules on T cells, we have developed a monoclonal antibody (mAb) that can costimulate T cells in the absence of antigen-presenting cells (APC). The molecule recognized by this mAb, 9D3, was found to be expressed on almost all mature T cells and to be a protein of approximately 24 kD molecular mass. By expression cloning, this molecule was identified as CD9, 9D3 (anti-CD9) synergized with suboptimal doses of anti-CD3 mAb in inducing proliferation by virgin T cells. Costimulation was induced by independent ligation of CD3 and CD9, suggesting that colocalization of these two molecules is not required for T cell activation. The costimulation by anti-CD9 was as potent as that by anti-CD28. Moreover, anti-CD9 costimulated in a CD28-independent way because anti-CD9 equally costimulated T cells from the CD28-deficient as well as wild-type mice. Thus, these results indicate that CD9 serves as a molecule on T cells that can deliver a potent CD28-independent costimulatory signal.
Experience with personalization of Yahoo! (2000)

article Free AccessExperience with personalization of Yahoo! Authors: Udi Manber Yahoo!, Santa Clara, CA Yahoo!, Santa Clara, CAView Profile , Ash Patel Yahoo!, Santa Clara, CA Yahoo!, Santa Clara, CAView Profile , John Robison Yahoo!, Santa Clara, CA Yahoo!, Santa Clara, CAView Profile Authors Info & Claims Communications of the ACMVolume 43Issue 8Aug. 2000 pp 35–39https://doi.org/10.1145/345124.345136Published:01 August 2000Publication History 126citation4,964DownloadsMetricsTotal Citations126Total Downloads4,964Last 12 Months686Last 6 weeks257 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteView all FormatsPDF
ILA, the human 4-1BB homologue, is inducible in lymphoid and other cell lineages (1995)

We recently identified a gene that is induced by lymphocyte activation (ILA). The sequence of the full-length 1.4-kb cDNA characterized ILA as a new member of the nerve growth factor/tumor necrosis factor (NGF/TNF) receptor family and the human homologue of the murine T-cell-specific receptor 4-1BB. The present study demonstrates ILA mRNA isoforms at 4.4, 4.0, and 1.8 kb in poly-A+ RNA from activated, but not from resting human peripheral blood T lymphocytes. A reverse transcriptase-polymerase chain reaction (RT-PCR) assay was used to study tissue distribution and regulation of ILA expression. The gene was induced in T lymphocytes by phytohemagglutinin (PHA), phorbol myristate acetate (PMA), and antibody to CD3, in B lymphocytes by PMA and antibodies to cell surface Ig, and in blood monocytes by interleukin-1 beta (IL-1 beta), lipopolysaccharide (LPS), and PMA. In T lymphocytes, ILA mRNA was detectable 1.5 hours after stimulation, reached maximal levels at 8 hours, and declined to background levels by 48 hours. Induction of ILA mRNA required protein synthesis and was primarily due to increased transcription. Actinomycin D reduced ILA mRNA levels in activated lymphocytes 50% within 30 minutes, demonstrating a relatively short half-life of this mRNA. Analysis of nonlymphoid cells showed that ILA mRNA was not detectable in resting cells. However, in contrast to the lymphoid-specific expression of the murine 4-1BB gene, ILA was detected in nonlymphoid cells, including epithelial and hepatoma cells after stimulation with IL-1 beta. ILA was not detectable in several brain derived cell lines. The ILA cDNA encodes a 30-kD protein as demonstrated by in vitro translation, and this protein is immunoprecipitated by antisera that were raised against ILA peptides or a glutathione-S-transferase fusion protein. Flow cytometry showed expression of ILA protein on a subset of activated T or B lymphocytes. In conclusion, activation-dependent expression of ILA is found not only in T lymphocytes, but also in B lymphocytes, monocytes, and diverse nonlymphoid cell types.
A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes (2015)

Several lines of evidence suggest a role for the gut microbiome in type 1 diabetes. Treating diabetes-prone rodents with probiotics or antibiotics prevents the development of the disorder. Diabetes-prone rodents also have a distinctly different gut microbiome compared with healthy rodents. Recent studies in children with a high genetic risk for type 1 diabetes demonstrate significant differences in the gut microbiome between children who develop autoimmunity for the disease and those who remain healthy. However, the differences in microbiome composition between autoimmune and healthy children are not consistent across all studies because of the strong environmental influences on microbiome composition, particularly diet and geography. Controlling confounding factors of microbiome composition uncovers bacterial associations with disease. For example, in a human cohort from a single Finnish city where geography is confined, a strong association between one dominant bacterial species, Bacteroides dorei, and type 1 diabetes was discovered (Davis-Richardson et al. Front Microbiol 2014;5:678). Beyond this, recent DNA methylation analyses suggest that a thorough epigenetic analysis of the gut microbiome may be warranted. These studies suggest a testable model whereby a diet high in fat and gluten and low in resistant starch may be the primary driver of gut dysbiosis. This dysbiosis may cause a lack of butyrate production by gut bacteria, which, in turn, leads to the development of a permeable gut followed by autoimmunity. The bacterial community responsible for these changes in butyrate production may vary around the world, but bacteria of the genus Bacteroides are thought to play a key role.
Clinical and genetic predictors of weight gain in patients diagnosed with breast cancer (2013)

Post-diagnosis weight gain in breast cancer patients has been associated with increased cancer recurrence and mortality. Our study was designed to identify risk factors for this weight gain and create a predictive model to identify a high-risk population for targeted interventions. Chart review was conducted on 459 breast cancer patients from Northwestern Robert H. Lurie Cancer Centre to obtain weights and body mass indices (BMIs) over an 18-month period from diagnosis. We also recorded tumour characteristics, demographics, clinical factors, and treatment regimens. Blood samples were genotyped for 14 single-nucleotide polymorphisms (SNPs) in fat mass and obesity-associated protein (FTO) and adiponectin pathway genes (ADIPOQ and ADIPOR1). In all, 56% of patients had >0.5 kg m–2 increase in BMI from diagnosis to 18 months, with average BMI and weight gain of 1.9 kg m–2 and 5.1 kg, respectively. Our best predictive model was a primarily SNP-based model incorporating all 14 FTO and adiponectin pathway SNPs studied, their epistatic interactions, and age and BMI at diagnosis, with area under receiver operating characteristic curve of 0.85 for 18-month weight gain. We created a powerful risk prediction model that can identify breast cancer patients at high risk for weight gain.
Activity of recombinant mitogillin and mitogillin immunoconjugates. (1992)

A synthetic gene for the Aspergillus protein toxin mitogillin has been synthesized and expressed in Escherichia coli. The recombinant mitogillin is a potent inhibitor of protein synthesis in vitro with an IC50 of 9.7 pM. Immunoconjugates of recombinant mitogillin derivatized with S-acetylmercaptosuccinic anhydride and 5-methyl-2-iminothiolane modified H65 antibody kill T cell lines and peripheral blood mononuclear cells expressing the human CD5 surface antigen. Native mitogillin contains 4 cysteine residues which form two disulfide pairs (Fernandez-Luna, J. L., Lopez-Otin, C., Soriano, F., and Mendez, E. (1985) Biochemistry 24, 861-867). Three derivatives of mitogillin have been assembled which substitute alanine residues for cysteine residues 5, 147, or 5 and 147. Each of these molecules retains the ability to inhibit protein synthesis in vitro with at most a 2-fold reduction in activity. The derivative mitogillinC147A can be conjugated to 5-methyl-2-iminothiolane- modified H65 antibody directly without pretreatment with S-acetylmercaptosuccinic anhydride, and the immunoconjugate is active against HSB2 cells. Genetic manipulation of toxin genes to expose an accessible cysteine residue into a recombinant product can thus be used to generate immunotoxins without initial derivatization by nonspecific cross-linking reagents.
V(D)J Recombination: Molecular Biology and Regulation (1992)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Individual versus standard dose of rFSH in a mild stimulation protocol for intrauterine insemination: a randomized study (2009)

ClinicalTrials.gov Identifier NCT00374634.
Early heart failure in the SMNΔ7 model of spinal muscular atrophy and correction by postnatal scAAV9-SMN delivery (2010)

Proximal spinal muscular atrophy (SMA) is a debilitating neurological disease marked by isolated lower motor neuron death and subsequent atrophy of skeletal muscle. Historically, SMA pathology was thought to be limited to lower motor neurons and the skeletal muscles they control, yet there are several reports describing the coincidence of cardiovascular abnormalities in SMA patients. As new therapies for SMA emerge, it is necessary to determine whether these non-neuromuscular systems need to be targeted. Therefore, we have characterized left ventricular (LV) function of SMA mice (SMN2+/+; SMNΔ7+/+; Smn-/-) and compared it with that of their unaffected littermates at 7 and 14 days of age. Anatomical and physiological measurements made by electrocardiogram and echocardiography show that affected mouse pups have a dramatic decrease in cardiac function. At 14 days of age, SMA mice have bradycardia and develop a marked dilated cardiomyopathy with a concomitant decrease in contractility. Signs of decreased cardiac function are also apparent as early as 7 days of age in SMA animals. Delivery of a survival motor neuron-1 transgene using a self-complementary adeno-associated virus serotype 9 abolished the symptom of bradycardia and significantly decreased the severity of the heart defect. We conclude that severe SMA animals have compromised cardiac function resulting at least partially from early bradycardia, which is likely attributable to aberrant autonomic signaling. Further cardiographic studies of human SMA patients are needed to clarify the clinical relevance of these findings from this SMA mouse.
Probabilistic Warning Times for Earthquake Ground Shaking in the San Francisco Bay Area (2006)

Current earthquake mitigation in the United States focuses on long-term characterization of the likely levels of ground shaking and the frequency of occurrence (Frankel et al. , 1996). These estimates are the basis for building codes, which aim to prevent collapse during earthquakes. In other countries, including Mexico, Japan, Taiwan, and Turkey, earthquake warning systems (EWS) are used in addition to building codes to further reduce the impact of earthquakes (Espinosa Aranda et al. , 1995; Wu et al. , 1998; Wu and Teng, 2002; Erdik et al. , 2003; Odaka et al. , 2003; Boese et al. , 2004; Kamigaichi, 2004; Nakamura, 2004; Horiuchi et al. , 2005; Wu and Kanamori, 2005). Short-term mitigation actions are taken to reduce both financial losses and casualties.

Earthquake warning systems rapidly detect the initiation of earthquakes and warn of the forthcoming ground shaking. For a specific city, such as San Francisco, the warning time could be tens of seconds for some earthquakes but essentially zero seconds for others. Even in situations when San Francisco has zero seconds warning, however, neighboring cities such as Oakland would likely have a few seconds and San Jose would have ∼15 seconds warning. Thus, for any earthquake scenario in a densely populated region, such as the San Francisco Bay area (SFBA), an EWS could provide warning to at least some of the affected population in a damaging earthquake.

Here I present estimates of the warning times that would be available for locations across the SFBA if an EWS were implemented in northern California. These warning times are calculated for identified likely earthquake scenarios in northern California. For each scenario an estimate of the probability of occurrence has been made (WGCEP, 2003), allowing calculation of probabilistic warning times. The …
MEASUREMENT AND APPLICATION OF ZETA-POTENTIAL (1992)

The electrokinetic or zeta-potential is an important parameter of the electrical double layer and represents a characteristic of electrical properties of solid/liquid and liquid/gaseous interfaces. In the paper electrokinetic phenomena in this contact are described as well as measuring methods. Changes of the values of zeta-poten-tial depending on some properties of solid/liquid interface are being considered.
Fractionated radioimmunotherapy with 90 Y‐clivatuzumab tetraxetan and low‐dose gemcitabine is active in advanced pancreatic cancer (2012)

Fractionated radioimmunotherapy with (90) Y-hPAM4 and low-dose gemcitabine demonstrated promising therapeutic activity and manageable myelosuppression in patients with advanced pancreatic ductal carcinoma.
Photoinduced Ethylene Polymerization on the CrVI/SiO2 Phillips Catalyst (2018)

Herein we report on two photoinduced reactions occurring at the surface of the CrVI/SiO2 Phillips catalyst. The first is the photoreduction of CrVI/SiO2 in CO at room temperature, that leads to the reduction of a fraction of the CrVI sites to CrIV(═O) intermediates and then to CrII. With respect to the thermal reduction of CrVI/SiO2 in CO, the relative amount of highly uncoordinated CrII sites is larger, suggesting that the relaxation of the CrII sites at the silica surface strongly depends on the temperature at which they are formed. The second is the photoinduced ethylene polymerization on CrVI/SiO2 at room temperature that is reported here for the first time. We demonstrate that UV–vis light has the potential to trigger the reduction of chromates by ethylene and the successive ethylene polymerization. Diffuse reflectance (DR) UV–vis and FT-IR spectroscopies allowed us to identify the nature of the Cr sites involved in the polymerization (i.e., 6-fold coordinated CrII) and of the oxidized byproducts remaining in their coordination sphere, which are methylformate and ethylene oxide. While the former was previously observed during the thermally induced ethylene polymerization on CrVI/SiO2, the latter was never observed.
Electro‐optical Performance of a Vertically‐Aligned LCD Mode Using Electrically Controlled Self‐Compensation (1998)

Abstract Very recently, a novel homeotropic nematic LCD with excellent grayscale performance has been introduced. This rub‐free mode adopts the homeotropic alignment in the off‐state and switching is controlled by an in‐plane field. It has electrically‐induced dual domain‐like director configuration. In this work, we simulate the electro‐optical behavior of this device to optimize its performance. We investigate the dependence of electro‐optical performance on cell thickness and electrode gap distance. The angular dependence is also studied, which shows the effect of self‐compensation. We find from modeling that the director configuration above the electrodes is well behaved and masking of the electrodes is unnecessary. In fact, this homeotropic mode has better performance if the electrodes are unmasked.
A study of placental bed spiral arteries and trophoblast invasion in normal and severe pre‐eclamptic pregnancies (1994)

Endovascular trophoblast did not show an all or none invasive phenomenon in normal and pre-eclamptic pregnancies. More decidual than myometrial arteries were invaded in both groups of patients, and there was a gradient in the percentage of decidual and myometrial arteries invaded from normal pregnancy to pre-eclampsia. Morphological features in one spiral artery may not necessarily be representative of all of those in a placental bed.