gebhart/patrepeval huggingface dataset:
CD40 ligand (CD154) stimulation of macrophages to produce HIV-1-suppressive β-chemokines (1998)

beta-chemokines play an important role in the development of immunologic reactions. Macrophages are major beta-chemokine-producing cells during T-cell directed, delayed-type hypersensitivity reactions in tissues, and have been reported to be important producers of beta-chemokines in the lymph nodes of HIV-1-infected individuals. However, the physiological signals responsible for inducing macrophages to produce beta-chemokines have not been established. Two soluble T cell products, interferon-gamma and granulocyte-macrophage colony stimulating factor, were added to cultured macrophages, but failed to stimulate the production of macrophage inflammatory protein-1alpha and -1beta; regulated upon activation, normal T cell expressed and secreted (RANTES); or monocyte chemoattractant protein-1. Instead, direct cell-cell contact between macrophages and cells engineered to express CD40L (also known as CD154) resulted in the production of large amounts of macrophage inflammatory protein-1alpha and -1beta, and RANTES (all ligands for CCR5), and monocyte chemoattractant protein-1 (a ligand for CCR2). Supernatants from CD40L-stimulated macrophages protected CD4(+) T cells from infection by a nonsyncytium-inducing strain of HIV-1 (which uses CCR5 as a coreceptor). These results have implications for granulomatous diseases, and conditions such as atherosclerosis and multiple sclerosis, where CD40L-bearing cells have been found in the macrophage-rich lesions where beta-chemokines are being produced. Overall, these findings define a pathway linking the specific recognition of antigen by T cells to the production of beta-chemokines by macrophages. This pathway may play a role in anti-HIV-1 immunity and the development of immunologic reactions or lesions.
The role of E. coli single‐stranded DNA binding protein in DNA metabolism (1984)

Abstract Single‐stranded DNA binding proteins have been known for some time to be crucial in many DNA metabolic reactions in both prokaryotes and eukaryotes. Despite a wealth of studies on these proteins we still do not understand their biochemical mechanism of action. Recent studies of the Escherichia coli single stranded DNA binding protein (SSB) are beginning to provide some insight into how this and similar proteins might function.
Polysialylated Neural Cell Adhesion Molecule-Positive CNS Precursors Generate Both Oligodendrocytes and Schwann Cells to Remyelinate the CNS after Transplantation (1999)

Transplantation offers a means of identifying the differentiation and myelination potential of early neural precursors, features relevant to myelin regeneration in demyelinating diseases. In the postnatal rat brain, precursor cells expressing the polysialylated (PSA) form of the neural cell adhesion molecule NCAM have been shown to generate mostly oligodendrocytes and astrocytes in vitro (Ben-Hur et al., 1998). Immunoselected PSA-NCAM+ newborn rat CNS precursors were expanded as clusters with FGF2 and grafted into a focal demyelinating lesion in adult rat spinal cord. We show that these neural precursors can completely remyelinate such CNS lesions. While PSA-NCAM+ precursor clusters contain rare P75+ putative neural crest precursors, they do not generate Schwann cells in vitro even in the presence of glial growth factor. Yet they generate oligodendrocytes, astrocytes, and Schwann cells in vivo when confronted with demyelinated axons in a glia-free area. We confirmed the transplant origin of these Schwann cells using Y chromosome in situ hybridization and immunostaining for the peripheral myelin protein P0 of tissue from female rats that had been grafted with male cell clusters. The number and distribution of Schwann cells within remyelinated tissue, and the absence of P0 mRNAs in donor cells, indicated that Schwann cells were generated by expansion and differentiation of transplanted PSA-NCAM+ neural precursors and were not derived from contaminating Schwann cells. Thus, transplantation into demyelinated CNS tissue reveals an unexpected differentiation potential of a neural precursor, resulting in remyelination of CNS axons by PNS and CNS myelin-forming cells.
Clinical trial of a farnesyltransferase inhibitor in children with Hutchinson–Gilford progeria syndrome (2012)

Hutchinson-Gilford progeria syndrome (HGPS) is an extremely rare, fatal, segmental premature aging syndrome caused by a mutation in LMNA that produces the farnesylated aberrant lamin A protein, progerin. This multisystem disorder causes failure to thrive and accelerated atherosclerosis leading to early death. Farnesyltransferase inhibitors have ameliorated disease phenotypes in preclinical studies. Twenty-five patients with HGPS received the farnesyltransferase inhibitor lonafarnib for a minimum of 2 y. Primary outcome success was predefined as a 50% increase over pretherapy in estimated annual rate of weight gain, or change from pretherapy weight loss to statistically significant on-study weight gain. Nine patients experienced a ≥50% increase, six experienced a ≥50% decrease, and 10 remained stable with respect to rate of weight gain. Secondary outcomes included decreases in arterial pulse wave velocity and carotid artery echodensity and increases in skeletal rigidity and sensorineural hearing within patient subgroups. All patients improved in one or more of these outcomes. Results from this clinical treatment trial for children with HGPS provide preliminary evidence that lonafarnib may improve vascular stiffness, bone structure, and audiological status.
Distributed Embedded Logic Analysis for Post-Silicon Validation of SOCs (2008)

Post-silicon validation is used to identify design errors in silicon. Its main limitation is real-time observability of the circuit's internal nodes. In this paper, we introduce a novel design-for-debug architecture which automatically allocates distributed trace buffers to handle debug data acquisition requests from multiple sources located in different cores. Using resource-efficient and intelligent control placed on-chip, we show how real-time observability can be improved, thus helping bridge the gap between pre-silicon verification and post-silicon validation for SOC designs.
Regulating the Regulators: The Future Prospects for Transcription-Factor-Based Agricultural Biotechnology Products (2008)

It is now more than a decade since the first commercially successful genetically engineered agricultural crops were launched ([Castle et al., 2006][1]). These first products were based in large part on simple monogenic traits, such as herbicide tolerance or insect resistance, which did not require
In vivoPhotothermal and Photoacoustic Flow Cytometry (2011)

This chapter contains sections titled: Introduction Photothermal and Photoacoustic Effects at Single-Cell Level PT Technique Integrated PTFC for In vivo Studies Integrated PAFC for In vivo Studies In vivo Lymph Flow Cytometery In vivo Mapping of Sentinel Lymph Nodes (SLNs) Concluding Remarks and Discussion Acknowledgments References
Metal/amorphous silicon multilayer radiation detectors (1989)

A multilayer structure is described for use in a number of radiation detectors. The structure consists of alternating layers of metal and amorphous silicon (a-Si). The absorption of radiation mainly occurs in the metal layers, while electron-hole pairs are generated in the a-Si layers by the emitted secondary particles from the metal layers. The fundamental applicability of this novel detector for X-ray detection was confirmed by Monte Carlo computer simulations as well as by results for an experimental five-layer Ta(0.5 mu m)/a-Si(3 mu m)/Mo(0.5 mu m) X-ray sensor fabricated on a 1.5-cm*4-cm glass plate. The authors have confirmed that the detector has rectifying characteristics, with the Mo and Ta layers forming Schottky barrier and ohmic contacts respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrophoretic Force on a Protein-Coated DNA Molecule in a Solid-State Nanopore (2009)

Using solid-state nanopores with optical tweezers, we perform force spectroscopy on DNA molecules that are coated with RecA proteins. We observe that the electrophoretic force is 2-4 times larger for RecA-DNA filaments than for uncoated DNA molecules and that this force increases at lower salt concentrations. The data demonstrate the efficacy of solid-state nanopores for locally probing the forces on DNA-bound proteins. Our results are described quantitatively by a model that treats the electrophoretic and hydrodynamic forces. The conductance steps that occur when RecA-DNA enters the nanopore change from conductance decreases at high salt to conductance increases at low salt, which allows the apparent charge of the RecA-DNA filament to be extracted. The combination of conductance measurements with local force spectroscopy increases the potential for future solid-state nanopore screening devices.
Composition of Syntroleum S-5 and Conformance to JP-5 Specification (2004)

Abstract : The US Military uses JP-8/JP-5/Jet A-1 fuel. JP-8 is identical to Jet A-1 except that it contains additives required by the military. JP-8 differs from JP-8 only in that it has a slightly higher flash point. A synthetic JP-5 fuel products by Syntroleum Corporation, S-5, differers from petroleum-derived jet fuels in that it has much lower normal paraffin concentration and it does not contain any detectable S, N, or O compounds or aromatics. Despite these compositional differences, S-5 conforms to all JP-5 specification requirements for the chemical and key physical properties evaluated, except the density; S-5 density was slightly lower than the minimum density required. One other key requirement for JP-5 states that, The feed stock from which the fuel is refined shall be crude oils derived from petroleum, tar sands, oil shale, or mixtures thereof. Fuels such as S-5. synthesized from feed stocks other than those allowed, do not conform to the JP-5 specification in this regard.
The Prevention of Anastomotic Leakage After Total Gastrectomy with Local Decontamination (1997)

Decontamination with polymyxin, tobramycin, vancomycin, and amphotericin B during anastomotic wound healing is safe and effective in the prevention of esophagojejunal anastomotic leakage after total gastrectomy.
Randomized trials of adjuvant radiation therapy for rectal carcinoma (1990)

An estimated 44,000 cases of rectal carcinoma arise annually in the United States. The traditional management of this disease has been surgery alone, but advances in adjuvant therapy offer potential for improvement of local control, disease-free survival, and survival. In the last two decades, many multicenter randomized trials of adjuvant preoperative and postoperative radiation therapy for rectal carcinoma have been reported. The design and results of these trials are critically reviewed. Results from preoperative trials have been conflicting, reflecting the heterogeneity of the trial designs. Large postoperative adjuvant trials have been reported recently. The combined analysis of local recurrence data from the mature, published trials indicates that radiation therapy results in improved local control (P = 0.02), an important concern in rectal carcinoma as local recurrences present vexing and painful clinical problems often refractory to conventional management. These trials also have shown that radiation therapy can contribute to improved survival in the combined modality setting. Improvements in the clinical outcome of rectal cancer should be possible with appropriate adjuvant therapy. The success of combined modality adjuvant therapy for rectal carcinoma may serve as a model to aid in the design of therapeutic regimens for other solid tumors.
Retinoic Acid Stimulation of the Human Surfactant Protein B Promoter Is Thyroid Transcription Factor 1 Site-dependent (2000)

Surfactant B (SP-B) is a 79-amino acid peptide critical to postnatal respiratory adaptation. Expression of SP-B by respiratory epithelial cells is regulated by developmental and hormonal influences at the level of gene transcription. Previous studies supported the role of retinoic acids (RA) and their receptors (RARs) in SP-B gene transcription. In the present study, RARalpha was detected in mouse alveolar type II epithelial cells where SP-B is synthesized and processed. Deletion and site-specific mutagenesis analysis identified clustered retinoic acid-responsive element sites in the 5'-flanking enhancer region of the hSP-B gene that bound RARalpha proteins. RAR coactivators ACTR, SRC-1, and transcriptional intermediary factor 2 (TIF2) stimulated human (h) SP-B promoter activity in a dose-dependent fashion in pulmonary adenocarcinoma H441 cells. In addition, an RAR-associated protein, CREB-binding protein (CBP), potentiated the effects of RAR on hSP-B promoter activity in H441 cells. Importantly, RA stimulation of the hSP-B promoter depends on tissue-specific thyroid transcription factor (TTF-1) DNA-binding sites. TTF-1 protein synergistically stimulated the hSP-B promoter with RARalpha, CBP, and nuclear receptor coactivators in H441 cells. In addition, TTF-1 interacted directly with RARalpha and TIF2 in the mammalian two-hybrid system. These findings support a model in which RAR/retinoid X receptor, TTF-1, coactivators, and CBP form a transcription activation complex in the upstream enhancer region of the hSP-B gene.
Conclusion (1996)

This chapter discusses some important concepts that were tackled in the previous chapters. The first is a summit — specifically the Geneva Summit — which was what Churchill had longed for. It then looks at the Cold War and détente. Churchill wanted to end the Cold War, while seeking to bring about détente. The author even argues that Churchill deserves to be remembered as the forefather of détente. The final topic discussed in this chapter is Churchill's last defeat in the East-West trade.
Modifications of the Human Immunodeficiency Virus Envelope Glycoprotein Enhance Immunogenicity for Genetic Immunization (2002)

In this study, we have investigated the effect of specific mutations in human immunodeficiency virus type 1 (HIV-1) envelope (Env) on antibody production in an effort to improve humoral immune responses to this glycoprotein by DNA vaccination. Mice were injected with plasmid expression vectors encoding HIV Env with modifications in regions that might affect this response. Elimination of conserved glycosylation sites did not substantially enhance humoral or cytotoxic-T-lymphocyte (CTL) immunity. In contrast, a modified gp140 with different COOH-terminal mutations intended to mimic a fusion intermediate and stabilize trimer formation enhanced humoral immunity without reducing the efficacy of the CTL response. This mutant, with deletions in the cleavage site, fusogenic domain, and spacing of heptad repeats 1 and 2, retained native antigenic conformational determinants as defined by binding to known monoclonal antibodies or CD4, oligomer formation, and virus neutralization in vitro. Importantly, this modified Env, gp140 Delta CFI, stimulated the antibody response to native gp160 while it retained its ability to induce a CTL response, a desirable feature for an AIDS vaccine.
ECOS: An SOCP solver for embedded systems (2013)

In this paper, we describe the embedded conic solver (ECOS), an interior-point solver for second-order cone programming (SOCP) designed specifically for embedded applications. ECOS is written in low footprint, single-threaded, library-free ANSI-C and so runs on most embedded platforms. The main interior-point algorithm is a standard primal-dual Mehrotra predictor-corrector method with Nesterov-Todd scaling and self-dual embedding, with search directions found via a symmetric indefinite KKT system, chosen to allow stable factorization with a fixed pivoting order. The indefinite system is solved using Davis' SparseLDL package, which we modify by adding dynamic regularization and iterative refinement for stability and reliability, as is done in the CVXGEN code generation system, allowing us to avoid all numerical pivoting; the elimination ordering is found entirely symbolically. This keeps the solver simple, only 750 lines of code, with virtually no variation in run time. For small problems, ECOS is faster than most existing SOCP solvers; it is still competitive for medium-sized problems up to tens of thousands of variables.
Minireview: Fetal-Maternal Hormonal Signaling in Pregnancy and Labor (2009)

Mechanisms underlying the initiation of parturition remain unclear. Throughout most of pregnancy, uterine quiescence is maintained by elevated progesterone acting through progesterone receptor (PR). Although in most mammals, parturition is associated with a marked decline in maternal progesterone, in humans, circulating progesterone and uterine PR remain elevated throughout pregnancy, suggesting a critical role for functional PR inactivation in the initiation of labor. Both term and preterm labor in humans and rodents are associated with an inflammatory response. In preterm labor, intraamniotic infection likely provides the stimulus for increased amniotic fluid interleukins and migration of inflammatory cells into the uterus and cervix. However, at term, the stimulus for this inflammatory response is unknown. Increasing evidence suggests that the developing fetus may produce physical and hormonal signals that stimulate macrophage migration to the uterus, with release of cytokines and activation of inflammatory transcription factors, such as nuclear factor kappaB (NF-kappaB) and activator protein 1 (AP-1), which also is activated by myometrial stretch. We postulate that the increased inflammatory response and NF-kappaB activation promote uterine contractility via 1) direct activation of contractile genes (e.g. COX-2, oxytocin receptor, and connexin 43) and 2) impairment of the capacity of PR to mediate uterine quiescence. PR function near term may be compromised by direct interaction with NF-kappaB, altered expression of PR coregulators, increased metabolism of progesterone within the cervix and myometrium, and increased expression of inhibitory PR isoforms. Alternatively, we propose that uterine quiescence during pregnancy is regulated, in part, by PR antagonism of the inflammatory response.
Aspirin to prevent growth of vegetations and cerebral emboli in infective endocarditis (1992)

The incidence of stroke on cranial computed tomography (CT) and change in echocardiographic vegetation area was prospectively compared in a preliminary observational study involving nine patients with infective endocarditis randomized to either low-dose aspirin (75 mg d-1, Group I, n = 4) or no aspirin (Group II, n = 5). Two symptomatic cerebral infarcts and one myocardial infarct occurred in the controls, compared to no events in patients on aspirin during a total observation period of 343 d (range 28-49 d). The mean vegetation area decreased in the aspirin group (mean change = -0.24 cm2), compared to an increase in controls (mean change = +0.35 cm2). The platelet half-life (normal range 5-6 d), which was measured using Indium-111 radiolabelling, tended to be lower in Group II (4.6 +/- 0.2 vs. 3.9 +/- 0.5 d). No side-effects or complications attributable to aspirin were observed. A possible role for adjunctive aspirin therapy in the prevention of embolic complications in infective endocarditis is suggested, and warrants further study.
Pyrimidine Derivatives and Related Compounds. XII. : The Vilsmeier Reaction of Barbituric Acid Derivatives and Uracil Derivatives (1971)

The Vilsmeier reaction was examined in order to synthesize 5-formylbarbituric acid and 5-formyluracil derivatives. The Vilsmeier reaction of barbituric acid derivatives (I to VI) in excess phosphoryl chloride afforded 6-chloro-5-formylbarbituric acid derivatives (VII to XII), while the same reaction in benzene gave 5-dimethylaminomethylenebarbituric acid derivatives (XIV to XVII) as intermediates whose hydrolysis with alkali afforded 5-formylbarbituric acids (XVIII and XIX). The Vilsmeier reaction of 1, 3-disubstituted uracil derivatives (XV to XVIII) produced 1, 3-disubstituted 5-formyluracil deivatives (XXIX to XXXII).
In Cellulo Examination of a Beta-Alpha Hybrid Construct of Beta-Hexosaminidase A Subunits, Reported to Interact with the GM2 Activator Protein and Hydrolyze GM2 Ganglioside (2013)

The hydrolysis in lysosomes of GM2 ganglioside to GM3 ganglioside requires the correct synthesis, intracellular assembly and transport of three separate gene products; i.e., the alpha and beta subunits of heterodimeric beta-hexosaminidase A, E.C. # 3.2.1.52 (encoded by the HEXA and HEXB genes, respectively), and the GM2-activator protein (GM2AP, encoded by the GM2A gene). Mutations in any one of these genes can result in one of three neurodegenerative diseases collectively known as GM2 gangliosidosis (HEXA, Tay-Sachs disease, MIM # 272800; HEXB, Sandhoff disease, MIM # 268800; and GM2A, AB-variant form, MIM # 272750). Elements of both of the hexosaminidase A subunits are needed to productively interact with the GM2 ganglioside-GM2AP complex in the lysosome. Some of these elements have been predicted from the crystal structures of hexosaminidase and the activator. Recently a hybrid of the two subunits has been constructed and reported to be capable of forming homodimers that can perform this reaction in vivo, which could greatly simplify vector-mediated gene transfer approaches for Tay-Sachs or Sandhoff diseases. A cDNA encoding a hybrid hexosaminidase subunit capable of dimerizing and hydrolyzing GM2 ganglioside could be incorporated into a single vector, whereas packaging both subunits of hexosaminidase A into vectors, such as adeno-associated virus, would be impractical due to size constraints. In this report we examine the previously published hybrid construct (H1) and a new more extensive hybrid (H2), with our documented in cellulo (live cell- based) assay utilizing a fluorescent GM2 ganglioside derivative. Unfortunately when Tay-Sachs cells were transfected with either the H1 or H2 hybrid construct and then were fed the GM2 derivative, no significant increase in its turnover was detected. In vitro assays with the isolated H1 or H2 homodimers confirmed that neither was capable of human GM2AP-dependent hydrolysis of GM2 ganglioside.
Association of Zinc and Antioxidant Nutrients With Age-Related Maculopathy (1996)

The data are weakly supportive of a protective effect of zinc on the development of some forms of early ARM. Prospective studies are needed to further evaluate the potential influence of these and other nutritional factors on different types and stages of age-related macular degeneration.
Transient Global Amnesia-An Unusual Case Report (2005)

Transient global amnesia (TGA) is characterized by the sudden onset of transient memory loss, including antegrade amnesia and retrograde amnesia. The attack usually occurs in persons around age 50, and only lasting for several hours to 24 hours. The definite cause to this syndrome is not well known, although transient global amnesia has been documented in associated with transient ischemic attacks, migraine, epilepsy or drugs in some studies. We report a typical case of transient global amnesia, in reviewing the discharge medical charts over the previous 6 years in our medical center (＞1200 beds). Of the 163,512 discharged records, there are none of TGA. Several indirect evidences for regional brain hypo-perfusion were found in this case, we believe that disrupted regional brain perfusion was the main cause for this case.