gebhart/patrepeval huggingface dataset:
Defensive applications of gene transfer technology in the face of bioterrorism: DNA-based vaccines and immune targeting (2003)

Gene transfer involves the introduction of an engineered gene into a person's cells with the expectation that the protein expressed from the gene will produce a therapeutic benefit. Strategies based on this principle have led to the approval of > 600 clinical trials and enrolment of ∼ 3500 subjects worldwide in attempts to treat diseases ranging from cancer to AIDS to cystic fibrosis. While gene therapy has met with limited success and still has many hurdles to overcome before it sees wide application, it may be useful as a defensive strategy against bioterrorism agents including infectious microbes and toxins. Although many defensive strategies are possible, immunological strategies are currently the most developed and are being actively applied to the development of strategies against several of the most virulent potential bioweapons. While most of these strategies are not yet ready for human application, DNA-based vaccines appear to be among the most promising in the fight against bioterrorism.
A Case of Sustained Remission Following an Acute Course of Ketamine in Treatment-Resistant Depression (2011)

This interesting letter by Murrough et al presented us with a dilemma. On the one hand it's an interesting case, with a good outcome. Treatment-resistant depression is a huge public health burden, and options are many but confusing. Add to the positives that intravenous ketamine is intriguing, with encouraging results and a mechanism that differs from traditional antidepressants.
Simple atom, extreme nucleus - laser trapping and probing of exotic helium isotopes. (2009)

Helium-8(8He)is the most neutron-rich matter to have been synthesized on the Earth:it consists of two protons and six neutrons,and remains stable for an average of 0.2 seconds.It is often viewed as a 4He core with four additional neutrons orbiting at a relatively large distance,forming a halo.Because of its intriguing properties,8He has the potential to reveal new aspects of the fundamental forces among the constituent nucleons.We have recently succeeded in laser trapping and cooling this exotic helium isotope,and have performed precision laser spectroscopy on individual trapped atoms.Based on the atomic frequency differences measured along the isotope chain3He-4He-6He-8He,the nuclear charge radius of 8He has now been determined for the first time.Comparing this result with the values predicted by a number of nuclear structure calculations will test our theoretical understanding of the nuclear forces in an extremely neutron-rich environment.
Integrating ARC grid middleware with Taverna workflows (2008)

http://grid.inb.uni-luebeck.de/
Current combining 60GHz CMOS power amplifiers (2009)

Two 60 GHz power amplifiers are presented in standard 90 nm CMOS using integrated power combining and matching networks. The power amplifiers incorporate 4-way/2-way power splitters and combiners into their matching networks rather than using separate structures, and achieve 1 dB output power of 12.1/10.1 dBm and saturation output power of 14.2/11.6 dBm respectively with saturation efficiency of 18.1/17.7% respectively when operated with a 1 V supply.
A high-throughput microfluidic real-time gene expression living cell array (2006)

The dynamics of gene expression are fundamental to the coordination of cellular responses. Measurement of temporal gene expression patterns is currently limited to destructive low-throughput techniques such as northern blotting, reverse transcription polymerase chain reaction (RT-PCR), and DNA microarrays. We report a scalable experimental platform that combines microfluidic addressability with quantitative live cell imaging of fluorescent protein transcriptional reporters to achieve real-time characterization of gene expression programs in living cells. Integrated microvalve arrays control row-seeding and column-stimulation of 256 nanoliter-scale bioreactors to create a high density matrix of stimulus-response experiments. We demonstrate the approach in the context of hepatic inflammation by acquiring approximately 5000 single-time-point measurements in each automated and unattended experiment. Experiments can be assembled in hours and perform the equivalent of months of conventional experiments. By enabling efficient investigation of dynamic gene expression programs, this technology has the potential to make significant impacts in basic science, drug development, and clinical medicine.
Phase I Clinical Study of Atacicept in Patients with Relapsed and Refractory B-Cell Non–Hodgkin's Lymphoma (2008)

Atacicept at doses of up to 10 mg/kg was well tolerated and showed biological activity by decreasing immunoglobulin concentrations, although tumor responses were not observed.
<title>Open-cell silicon foam for ultralightweight mirrors</title> (1999)

Elemental silicon is a lightweight material that shows great promise for optical applications. Specifically, open-cell silicon foam can be used as a core material for ultralightweight mirrors by bonding single-crystal silicon faceplates to the foam. Not only does silicon have a low density, but it also has a low thermal expansion coefficient and a high thermal conductivity. Further, because of its widespread use in the semiconductor industry, it is an extremely well-characterized material. The fabrication of silicon foam begins with open-cell polyurethane foam, which is available in a wide variety of cell sizes ranging from 3 to 100 pores per linear inch. After chemical conversion to a glassy carbon foam, the individual ligaments are coated with silicon by chemical vapor deposition/infiltration (CVD/CVI), and the carbon cores are removed by oxidation. The end result is an open-cell foam composed exclusively of silicon. CVD/CVI is a very versatile process because it allows the amount of silicon in the foam to be varied. As the relative density of the foam increase, so does its strength and stiffness. Consequently, the mechanical properties of the foam can be tailored to meet the needs of a given application. For example, for space-based applications where light weight is critical, lower density foams can be used. For terrestrial applications requiring high stiffness, higher density foams can be used. In all cases, the relative density of the foam is a parameter that can be optimized to meet the needs of a particular application.
Comparison of an antibody model with an X-ray structure: The variable fragment of BR96 (1996)

A model of the BR96 antibody variable regions is compared to two X-ray structures of a BR96-carbohydrate complex, independently determined after the model was built and analyzed. The comparison illustrates the opportunities and limitations of antibody modeling. Encouraging results were obtained for the prediction of single CDR loop conformations and for the outline of the BR96 antigen binding site. The comparison of CDR loop conformations in the two X-ray structures provides a realistic reference frame for the CDR loop predictions. CDR loop prediction accuracy is lower when not only conformational, but also positional criteria are taken into account.
Characterization of an NF-1/CTF Family Member as a Functional Activator of the Mouse Mammary Tumor Virus Long Terminal Repeat 5′ Enhancer (1996)

The long terminal repeat of the mouse mammary tumor virus restricts virus expression primarily to the mammary epithelium. The extreme 5' end of the long terminal repeat contains an enhancer that has been associated with tissue-specific expression of the virus. A total of six functional cis-acting elements have been identified in the enhancer. Although proteins binding to these elements have been reported, only one has been identified; this factor, mp5, is identical or closely related to the transcription factor AP-2 (Mellentin-Michelotti, J., John, S., Pennie, W. D., Williams, T., and Hager, G. L. (1994) J. Biol. Chem. 269, 31983-31990). The other factors are hitherto unidentified and poorly described. We report here the characterization of another of the six elements, previously referred to as the F3 site (Mink, S., Hartig, E., Jennewein, P., Doppler, W., and Cato, A. C. (1992) Mol. Cell Biol. 12, 4906-4918). We show that the F3 binding activity and AP-2 act synergistically to enhance mouse mammary tumor virus-directed transcription, but only in the presence of glucocorticoid hormone. The F3 element has an NF-1-like half-site, but the activity recognizing this element has binding characteristics distinct from the NF-1/CTF family as well as the rest of the CCAAT-binding proteins. We conclude that the F3 activity represents a new member of the NF-1/CTF family.
Gonadotropin-Releasing Hormone and Chorionic Gonadotropin Gene Expression in Human Placental Development (1991)

Control of human chorionic gonadotropin (hCG) synthesis during pregnancy is poorly understood, although in vitro data suggest a role for placental gonadotropin releasing hormone (GnRH) in its regulation. To study GnRH regulation during placental development, placental tissue of different gestational ages was analyzed for GnRH and beta hCG mRNA content. cRNA probes to exonic/intronic sequences of GnRH and beta hCG transcripts were constructed and used to perform solution hybridization/nuclease protection and in situ hybridization assays. The levels of GnRH mRNA were approximately 0.1-1% of that of beta hCG mRNA, in agreement with its suggested paracrine, rather than endocrine, role. While beta hCG mRNA content decreased significantly from first trimester to term (643 to 21.6 pg/microgram RNA), there was no significant change in GnRH mRNA (0.179 to 0.155 pg/microgram RNA). While beta hCG mRNA was localized almost exclusively in syncytiotrophoblasts, GnRH mRNA was present in all cell types of the placenta, including the stroma. In the course of performing sense-strand controls in the in situ hybridization, we noted that the placenta appeared to express more antisense GnRH than sense GnRH mRNA, again, in all cell types. Solution hybridization/nuclease protection analysis with exon 1 and exon 3 probes confirmed this observation, showing that there is two to three times more antisense GnRH RNA than sense GnRH mRNA. These studies suggest that GnRH gene expression and its role in regulating hCG production in human placenta is complex and does not fit a simple model for paracrine regulation of hCG.
Expression of L1 Cell Adhesion Molecule and Morphologic Features at the Invasive Front of Colorectal Cancer (2011)

To obtain the correlation between morphologic features in the invasive fronts of colorectal cancer (CRC) and L1 cell adhesion molecule (L1CAM) expression, 275 CRCs were assessed with L1CAM immunostaining and 29 CRCs were examined for L1CAM messenger RNA (mRNA) expression. Based on immunostaining, the positive rate of L1CAM expression increased according to the grade of tumor budding (P = .0002) and solid cancer nests (SCNs; P = .0046). L1CAM mRNA levels at the invasive front of the tumor were higher than those at the center of the tumor (median, 3.7-fold). The gap of L1CAM mRNA level between the invasive front and the central area was 7.3-fold in tumors having SCN lesions, whereas it was 1.9-fold in tumors having non-SCN lesions (P = .0004). L1CAM expression was correlated with nodal involvement in protein and mRNA levels (P = .0007 and P = .036, respectively). Tumor regulation of L1CAM expression is associated with morphologic features at the invasive front in CRC.
TRAF5, a novel tumor necrosis factor receptor-associated factor family protein, mediates CD40 signaling. (1996)

Signals emanating from CD40 play crucial roles in B-cell function. To identify molecules that transduce CD40 signalings, we have used the yeast two-hybrid system to done cDNAs encoding proteins that bind the cytoplasmic tail of CD40. A cDNA encoding a putative signal transducer protein, designated TRAF5, has been molecularly cloned. TRAF5 has a tumor necrosis factor receptor-associated factor (TRAF) domain in its carboxyl terminus and is most homologous to TRAF3, also known as CRAF1, CD40bp, or LAP-1, a previously identified CD40-associated factor. The amino terminus has a RING finger domain, a cluster of zinc fingers and a coiled-coil domain, which are also present in other members of the TRAF family protein except for TRAF1. In vitro binding assays revealed that TRAF5 associates with the cytoplasmic tail of CD40, but not with the cytoplasmic tail of tumor receptor factor receptor type 2, which associates with TRAF2. Based on analysis of the association between TRAF5 and various CD40 mutants, residues 230-269 of CD40 are required for the association with TRAF5. In contrast to TRAF3, overexpression of TRAF5 activates transcription factor nuclear factor kappa B. Furthermore, amino-terminally truncated forms of TRAF5 suppress the CD40-mediated induction of CD23 expression, as is the case with TRAF3. These results suggest that TRAF5 and TRAF3 could be involved in both common and distinct signaling pathways emanating from CD40.
Molecular cloning and expression of cDNAs encoding human alpha-mannosidase II and a previously unrecognized alpha-mannosidase IIx isozyme. (1995)

Golgi alpha-mannosidase II (alpha-MII) is an enzyme involved in the processing of N-linked glycans. Using a previously isolated murine cDNA clone as a probe, we have isolated cDNA clones encompassing the human alpha-MII cDNA open reading frame and initiated isolation of human genomic clones. During the isolation of genomic clones, genes related to that encoding alpha-MII were isolated. One such gene was found to encode an isozyme, designated alpha-MIIx. A 5-kb cDNA clone encoding alpha-MIIx was then isolated from a human melanoma cDNA library. However, comparison between alpha-MIIx and alpha-MII cDNAs suggested that the cloned cDNA encodes a truncated polypeptide with 796 amino acid residues, while alpha-MII consists of 1144 amino acid residues. To reevaluate the sequence of alpha-MIIx cDNA, polymerase chain reaction (PCR) was performed with lymphocyte mRNAs. Comparison of the sequence of PCR products with the alpha-MIIx genomic sequence revealed that alternative splicing of the alpha-MIIx transcript can result in an additional transcript encoding a 1139-amino acid polypeptide. Northern analysis showed transcription of alpha-MIIx in various tissues, suggesting that the alpha-MIIx gene is a housekeeping gene. COS cells transfected with alpha-MIIx cDNA containing the full-length open reading frame showed an increase of alpha-mannosidase activity. The alpha-MIIx gene was mapped to human chromosome 15q25, whereas the alpha-MII gene was mapped to 5q21-22.
Conserved modularity and potential for alternate splicing in mouse and human Slit genes (2002)

The vertebrate Slit gene family currently consists of three members; Slit1, Slit2 and Slit3. Each gene encodes a protein containing multiple epidermal growth factor and leucine rich repeat motifs, which are likely to have importance in cell-cell interactions. In this study, we sought to fully define and characterise the vertebrate Slit gene family. Using long distance PCR coupled with in silico mapping, we determined the genomic structure of all three Slit genes in mouse and man. Analysis of EST and genomic databases revealed no evidence of further Slit family members in either organism. All three Slit genes were encoded by 36 (Slit3) or 37 (Slit1 and Slit2) exons covering at least 143 kb or 183 kb of mouse or human genomic DNA respectively. Two additional potential leucine-rich repeat encoding exons were identified within intron 12 of Slit2. These could be inserted in frame, suggesting that alternate splicing may occur in Slit2. A search for STS sequences within human Slit3 anchored this gene to D5S2075 at the 5' end (exon 4) and SGC32449 within the 3' UTR, suggesting that Slit3 may cover greater than 693 kb. The genomic structure of all Slit genes demonstrated considerable modularity in the placement of exon-intron boundaries such that individual leucine-rich repeat motifs were encoded by individual 72 bp exons. This further implies the potential generation of multiple Slit protein isoforms varying in their number of repeat units. cDNA library screening and EST database searching verified that such alternate splicing does occur.
Chemoimmunotherapy of Tumors: Cyclophosphamide Synergizes with Exosome Based Vaccines (2006)

Dendritic cell-derived exosomes (DEX) are nanomeric vesicles harboring MHC/peptide complexes capable of promoting primary T cell responses and tumor rejection in the presence of adjuvants. In this study, we show that, in the absence of adjuvants, DEX mediate potent Ag-dependent antitumor effects against preestablished tumors in mice pretreated with immunopotentiating dosing of cyclophosphamide. Cyclophosphamide could 1) abolish the suppressive function of CD4+CD25+Foxp3+ regulatory T cells, 2) markedly enhance the magnitude of secondary but not primary CTL responses induced by DEX vaccines, 3) synergize with DEX in therapy but not prophylaxis tumor models. Therefore, therapeutic vaccines such as DEX aimed at boosting tumor-primed effector T cells could benefit procedures that minimize the effects of CD4+CD25+ regulatory T cells.
"Designer Yeast": an Enantioselective Oxidizing Reagent for Organic Synthesis (1999)

The new bioengineered oxidizing yeast is an efficient, enantioselective reagent for Baeyer-Villiger reactions of a variety of cyclic ketones. The successfully tested reactions are discussed and tabulated and the protocols for small scale oxidations are described.
Estimation of ECG parameters using photoplethysmography (2013)

Regular ECG check up is a good practice for cardiac patients as well as elderly people. In this paper we propose a low cost methodology to coarsely estimate the range of some important parameters of ECG using Photoplethysmography (PPG). PPG is easy to measure (even with a smart phone) and strongly related to human cardio-vascular system. The proposed methodology extracts a set of time domain features from PPG signal. A statistical analysis is performed to select the most relevant set of PPG features for the ECG parameters. Training model for the ECG parameters are created based on those selected features. Both artificial neural network and support vector machine based supervised learning approach is used for performance comparison. Experimental results, performed on benchmark dataset shows that good accuracy in the estimation of ECG parameters can be achieved in our proposed methodology. Results also show that the overall performance improves in using feature selection technique rather than using all the PPG features for classification.
Studies on fluoroalkylation and fluoroalkoxylation. Part 33. Direct trifluoromethylation of aryl halides with fluorosulphonyldifluoromethyl iodide in the presence of copper: an electron transfer induced process (1989)

Aryl halides are readily trifluoromethylated with fluorosulphonyldifluoromethyl iodide (1) in the presence of copper in DMF in high yield. A single electron transfer (s.e.t.) scavenger, p-dinitrobenzene, and free radical inhibitor, hydroquinone, partly suppress the reaction. Addition of 2,3-dimethylbut-2-ene to the reaction mixture gives a free radical addition-elimination product and difluorocarbene derivatives besides the trifluoromethyl displaced compound. A copper SET-induced mechanism is proposed.
Transverse Redistribution of Phospholipids during Human Platelet Activation: Evidence for a Vectorial Outflux Specific to Aminophospholipids (1995)

The redistribution kinetics of phospholipids during human platelet activation by calcium ionophore were investigated to determine the specificity of the observed phospholipid outflux [Bassé et al. (1993) Biochemistry 32, 2337]. (1) Two double-labeling experiments were performed with a combination of equal amounts of spin- and fluorescently-labeled phosphatidylserine and phosphatidylcholine. During A23187-induced activation, 50% of the internal phosphatidylserine analogs were rapidly (t1/2 < 1 min) reexposed on the platelet surface while no reciprocal influx of the external phosphatidylcholine analogs was observed. (2) Treatment with chlorpromazine allowed the internalization of 20% of external spin-labeled sphingomyelin or spin-labeled phosphatidylcholine, without either inducing platelet activation or interfering with aminophospholipid translocase activity or with A23187-induced activation (dense granule secretion and vesicle shedding). During A23187-induced activation, none of the previously internalized choline head phospholipids were exposed externally, while spin-labeled phosphatidylserine outward movements were similar irrespective of whether platelets were pretreated or not pretreated with chlorpromazine. Our results demonstrated that during strong platelet activation (1) the PL excess in the internal leaflet, due to the probe addition, is not responsible for their outflux; (2) the rapid aminophospholipid outflux is definitely a vectorial outflux not counterbalanced by a rapid reciprocal influx of choline head phospholipids (i.e., not scrambling); and (3) the vectorial outflux is specific for aminophospholipids since previously internalized sphingomyelin and phosphatidylcholine did not move outward. This suggests that the specific vectorial outflux of aminophospholipids could be catalyzed by a "reverse aminophospholipid translocase" activity.
Development and Testing of Freeze-Dried Plasma for the Treatment of Trauma-Associated Coagulopathy (2008)

Plasma can be lyophilized and freeze-dried to create a logistically superior product without compromising its hemostatic properties. This product may be suitable for use in austere environments, such as a battlefield, for the treatment of trauma-associated coagulopathy.
Controlling the Diameter of Carbon Nanotubes in Chemical Vapor Deposition Method by Carbon Feeding (2006)

It was found that the diameter distribution of single-walled carbon nanotubes (SWNTs) grown by the chemical vapor deposition (CVD) method could be controlled by the carbon feeding rate at the growth stage. A unified hypothesis on the relationship between nanoparticle size, growth condition, growth temperature, and diameter of the resulting nanotubes was developed and used to explain the relationship. It was shown that the diameters of SWNTs can be controlled even when highly polydisperse nanoparticles were used as catalyst. Such control enabled us to synthesize uniform small-diameter SWNTs at low carbon feeding rates. Additionally, understanding of the important role of the carbon feeding rate can be used to explain the cause of low growth efficiency in most CVD processes. It would also help us to design methods to improve the growth efficiency of CVD growth of nanotubes.
TGF‐β signaling: A tale of two responses (2007)

Transforming growth factor-beta (TGF-beta) regulates a wide variety of cellular processes including cell growth, apoptosis, differentiation, migration, and extracellular matrix production among others. The canonical signaling pathway induced by the TGF-beta receptor complex involves the phosphorylation of Smad proteins which upon activation accumulate in the nucleus and regulate transcription. Interestingly, the cellular response to TGF-beta can be extremely variable depending on the cell type and stimulation context. TGF-beta causes epithelial cells to undergo growth arrest and apoptosis, responses which are critical to suppressing carcinogenesis, whereas it can also induce epithelial-mesenchymal transition and mediate fibroblast activation, responses implicated in promoting carcinogenesis and fibrotic diseases. However, TGF-beta induces all these responses via the same receptor complex and Smad proteins. To address this apparent paradox, during the last few years a number of additional signaling pathways have been identified which potentially regulate the different cellular responses to TGF-beta. The identification of these signaling pathways has shed light onto the mechanisms whereby Smad and non-Smad pathways collaborate to induce a particular cellular phenotype. In this article, we review TGF-beta signaling in epithelial cells and fibroblasts with a focus on understanding the mechanisms of TGF-beta versatility.