gebhart/patrepeval huggingface dataset:
High-Titer Recombinant Adeno-Associated Virus Production from Replicating Amplicons and Herpes Vectors Deleted for Glycoprotein H (1999)

Production of high-titer rAAV is essential for in vivo clinical application. One limiting factor may be the failure of existing systems to replicate the packaging genome in such a way that expression of Rep and Cap proteins is coordinately amplified. DISC-HSV (disabled single-cycle virus) is a genetically modified herpes simplex virus (HSV) that by deletion of glycoprotein H (gH) is infectious only if propagated in a complementing cell line. In this study, we have used DISC-HSV as a helper for rAAV replication, and have simulated to some extent the amplication of the rep and cap genomes seen in wtAAV infection by incorporating both these and vector sequences in HSV amplicons. Facilitated production of AAV Rep and Cap proteins translates into a considerably improved recovery of rAAV, which transduces cells of the neuroretina in vivo with high efficiency. The potential for contamination with infectious herpes particles is eliminated by the use of noncomplementing (gH-) cell lines to propagate the virus, and by standard purification methods. The use of DISC-HSV and herpes-derived amplicons for production of rAAV may be a useful strategy for future in vivo studies and for clinical application.
Sustained activation and tumor targeting of NKT cells using a CD1d–anti-HER2–scFv fusion protein induce antitumor effects in mice (2008)

Invariant NKT (iNKT) cells are potent activators of DCs, NK cells, and T cells, and their antitumor activity has been well demonstrated. A single injection of the high-affinity CD1d ligand alpha-galactosylceramide (alphaGalCer) leads to short-lived iNKT cell activation followed, however, by long-term anergy, limiting its therapeutic use. In contrast, we demonstrated here that when alphaGalCer was loaded on a recombinant soluble CD1d molecule (alphaGalCer/sCD1d), repeated injections led to sustained iNKT and NK cell activation associated with IFN-gamma secretion as well as DC maturation in mice. Most importantly, when alphaGalCer/sCD1d was fused to a HER2-specific scFv antibody fragment, potent inhibition of experimental lung metastasis and established s.c. tumors was obtained when systemic treatment was started 2-7 days after the injection of HER2-expressing B16 melanoma cells. In contrast, administration of free alphaGalCer at this time had no effect. The antitumor activity of the CD1d-anti-HER2 fusion protein was associated with HER2-specific tumor localization and accumulation of iNKT, NK, and T cells at the tumor site. Targeting iNKT cells to the tumor site thus may activate a combined innate and adaptive immune response that may prove to be effective in cancer immunotherapy.
Targeted Cancer Therapies Lagging (2006)

Chicago—Scientists have long known that unlocking the mysteries of the human genome would lead to better diagnostics and therapies for a variety of diseases, but they were quick to note that the completion of its sequencing 3 years ago was just the first step toward tailoring medical care to individuals. Now, though, experts are concerned that progress is lagging and that current research strategies and designs are not up to tackling the challenges ahead. “Patients have said that we’ve heard about personalized molecular medicine for the last 5 to 10 years,” said Gordon Mills, MD, PhD, of the University of Texas M.D. Anderson Cancer Center, in Houston. “We’re going to need to move forward more quickly.” At the American Association for Cancer Research’s recent conference on Molecular Diagnostics in Cancer Therapeutic Development, Mills and others in academia, industry, and government discussed hurdles that stand in the way of adoption of this approach to care for patients with cancer.
Nopaline synthase: transcript mapping and DNA sequence. (1982)

The DNA sequence of the nopaline synthase gene (nos) from Agrobacterium tumefaciens Ti plasmid pTiT37 and adjacent regions up to the right border of the T-DNA was determined. The 5' and 3' termini of the polyadenylated nos mRNA, isolated from a T37 tobacco teratoma tumor line, were localized by S1 mapping. The final mRNA is unspliced, encoded by a region of about 1450 bp, and specifies an open reading frame of 413 amino acids. Potential transcriptional signals in the 5' flanking DNA, such as CATAAA ("TATA box") and GGTCACTAT ("CAT box"), bear close resemblance to other eukaryotic promoters. Two putative polyadenylation signals, AATAAA and AATAAT, are found about 135 and 50 bp from the 3' end, respectively. This study may provide information for the development of expression vectors for genes in plant cells; moreover, the structural gene can be used as an easy screenable marker.
A Study on the Erase and Retention Mechanisms for MONOS, MANOS, and BE-SONOS Non-Volatile Memory Devices (2007)

The erase and retention characteristics of MONOS, MANOS and BE-SONOS devices are examined in detail in order to determine their mechanisms. The erase transient current (J) is extracted and plotted against the tunnel oxide electric field (ETUN). Our results show that the erase speed ranking is BE-SONOS > MANOS > MONOS. The difference in erase speed comes from the different erase mechanisms of these devices. The retention characteristics are also compared and discussed.
ABT-199 (venetoclax) and BCL-2 inhibitors in clinical development (2015)

With the advent of new agents targeting CD20, Bruton's tyrosine kinase, and phosphoinositol-3 kinase for chronic lymphoid leukemia (CLL), more treatment options exist than ever before. B-cell lymphoma-2 (BCL-2) plays a major role in cellular apoptosis and is a druggable target. Small molecule inhibitors of BCL-2 are in active clinical studies. ABT-199 (venetoclax, RG7601, GDC-0199) has been granted breakthrough designation by FDA for relapsed or refractory CLL with 17p deletion. In this review, we summarized the latest clinical development of ABT-199/venetoclax and other novel agents targeting the BCL-2 proteins.
The effects of substituents on the rate of saponification of biphenyl-4-carboxylates (1984)

Second-order rate constants have been measured for the saponification of methyl 2′-, 3′-, and 4′- substituted biphenyl-4-carboxylates at several temperatures in 85%(w/w) methanol–water and activation parameters have been calculated. The Hammett equation applies very well to the saponification of 3′-and 4′-substituted biphenyl-4-carboxylates with σ-constants evaluated by the FMMF method. The effect of 2′-substituents is understandable in terms of π-electron steric effects.
Hypoxia in the Gulf of Mexico (2001)

Seasonally severe and persistent hypoxia, or low dissolved oxygen concentration, occurs on the inner- to mid-Louisiana continental shelf to the west of the Mississippi River and Atchafalaya River deltas. The estimated areal extent of bottom dissolved oxygen concentration less than 2 mg L-1 during mid-summer surveys of 1993-2000 reached as high as 16,000 to 20,000 km2. The distribution for a similar mapping grid for 1985 to 1992 averaged 8000 to 9000 km2. Hypoxia occurs below the pycnocline from as early as late February through early October, but is most widespread, persistent, and severe in June, July, and August. Spatial and temporal variability in the distribution of hypoxia exists and is, at least partially, related to the amplitude and phasing of the Mississippi and Atchafalaya discharges and their nutrient flux. Mississippi River nutrient concentrations and loadings to the adjacent continental shelf have changed dramatically this century, with an acceleration of these changes since the 1950s to 1960s. An analysis of diatoms, foraminiferans, and carbon accumulation in the sedimentary record provides evidence of increased eutrophication and hypoxia in the Mississippi River delta bight coincident with changes in nitrogen loading.
The expression in Escherichia coli of recombinant human platelet factor 4, a protein with immunoregulatory activity. (1988)

In order to establish more firmly the immunoregulatory effect of platelet factor 4 (PF4) and develop a means to provide material for possible clinical use, the nucleotide sequence for PF4 was synthesized utilizing a ligation strategy of six duplexes ranging from 27 to 43 base pairs in length. The individual oligodeoxynucleotides were synthesized on an automated system. The resultant gene segment (226 base pairs), which incorporated convenient HindIII and BamHI overhangs at the 5' and 3' ends, respectively, was cloned into the pIN-III-ompA-2-expression vector in Escherichia coli, affording a fusion protein of Mr = 8900 with 7 additional amino acids at the amino terminus and 4 at the carboxyl terminus and with aspartic acid rather than asparagine in position 47. The recombinant PF4 (rPF4) was purified by heparin-agarose affinity chromatography and reverse-phase high performance liquid chromatography. It reacted with a monoclonal mouse anti-human PF4 antibody on a Western blot and in an enzyme-linked immunosorbent assay. The rPF4 protein exhibited an immunoregulatory effect like that of human PF4 in its ability to reverse concanavalin A-induced immunosuppression in BALB/c mice.
Severe inflammatory arthritis and lymphadenopathy in the absence of TNF (2001)

It has been postulated that TNF has a pivotal role in a cytokine cascade that results in joint inflammation and destruction in rheumatoid arthritis (RA). To evaluate this, we examined the response of TNF-deficient (Tnf(-/-)) mice in two models of RA. Collagen-induced arthritis (CIA) was induced by injection of chick type II collagen (CII) in CFA. Tnf(-/-) mice had some reduction in the clinical parameters of CIA and, on histology, significantly more normal joints. However, severe disease was evident in 54% of arthritic Tnf(-/-) joints. Tnf(-/-) mice had impaired Ig class switching, but preserved T cell proliferative responses to CII and enhanced IFN-gamma production. Interestingly, CII-immunized Tnf(-/-) mice developed lymphadenopathy and splenomegaly associated with increased memory CD4(+) T cells and activated lymph node B cells. Acute inflammatory arthritis was also reduced in Tnf(-/-) mice, although again some mice exhibited severe disease. We conclude that TNF is important but not essential for inflammatory arthritis; in each model, severe arthritis could proceed even in the complete absence of TNF. These results call into doubt the concept that TNF is obligatory for chronic autoimmune and acute inflammatory arthritis and provide a rationale for further studies into TNF-independent cytokine pathways in arthritis.
Soft x-ray emission of laser-produced plasmas using a low-debris cryogenic nitrogen target (1998)

Laser-produced nitrogen plasmas (LPPs) are intense narrow-band emitters in the “water window” spectral range which is suited for x-ray microscopy of biological samples. Frozen gases as target materials are predicted to have low debris precipitated onto laser or x-ray optics arranged inside the vacuum chamber. Gaseous nitrogen is frozen onto a metal surface at a temperature of 16 K. The solid nitrogen is illuminated with nanosecond pulsed laser radiation with intensities of 1.3×1013 W/cm2 and the emission characteristics of laser-produced nitrogen plasmas are investigated with a calibrated imaging spectrograph. The x-ray emission in the water window region is compared to the radiation of a LPP with a solid boron nitride target at the same laser parameters.
A new class of doubletalk detectors based on cross-correlation (2000)

A doubletalk detector (DTD) is used with an echo canceler to sense when far-end speech is corrupted by near-end speech. Its role is to freeze the adaptation of the model filter when near-end speech is present in order to avoid divergence of the adaptive algorithm. Several authors have proposed to use the cross-correlation coefficient vector between the input signal vector x and the scalar output y for a DTD. We show in this paper that this measure is not appropriate and propose a modified form that meets, in an optimal way, the needs for an efficient DTD. By extension, we also propose a definition of the normalized cross-correlation matrix between two vectors and show a link with the coherence function.
Towards a Forensic-Based Service Oriented Architecture Framework for Auditing of Cloud Logs (2013)

Cloud computing log digital investigations relate to the investigation of a potential crime using the digital forensic evidence from a virtual machine (VM) host operating system using the hypervisor event logs. In cloud digital log forensics, work on the forensic reconstruction of evidence on VM hosts system is required, but with the heterogeneous complexity involved with an enterprise's private cloud not to mention public cloud distributed environments, a possible Web Services-centric approach may be required for such log supported investigations. A data cloud log forensics service oriented architecture (SOA) audit framework for this type of forensic examination needs to allow for the reconstruction of transactions spanning multiple VM hosts, platforms and applications. This paper explores the requirements of a cloud log forensics SOA framework for performing effective digital investigation examinations in these abstract web services environments. This framework will be necessary in order to develop investigative and forensic auditing tools and techniques for use in cloud based log-centric SOAs.
Coordination of Immune-Stroma Crosstalk by IL-6 Family Cytokines (2019)

Stromal cells are a subject of rapidly growing immunological interest based on their ability to influence virtually all aspects of innate and adaptive immunity. Present in every bodily tissue, stromal cells complement the functions of classical immune cells by sensing pathogens and tissue damage, coordinating leukocyte recruitment and function, and promoting immune response resolution and tissue repair. These diverse roles come with a price: like classical immune cells, inappropriate stromal cell behavior can lead to various forms of pathology, including inflammatory disease, tissue fibrosis, and cancer. An important immunological function of stromal cells is to act as information relays, responding to leukocyte-derived signals and instructing leukocyte behavior in kind. In this regard, several members of the interleukin-6 (IL-6) cytokine family, including IL-6, IL-11, oncostatin M (OSM), and leukemia inhibitory factor (LIF), have gained recognition as factors that mediate crosstalk between stromal and immune cells, with diverse roles in numerous inflammatory and homeostatic processes. This review summarizes our current understanding of how IL-6 family cytokines control stromal-immune crosstalk in health and disease, and how these interactions can be leveraged for clinical benefit.
Lymphocyte Cc Chemokine Receptor 9 and Epithelial Thymus-Expressed Chemokine (Teck) Expression Distinguish the Small Intestinal Immune Compartment (2000)

The immune system has evolved specialized cellular and molecular mechanisms for targeting and regulating immune responses at epithelial surfaces. Here we show that small intestinal intraepithelial lymphocytes and lamina propria lymphocytes migrate to thymus-expressed chemokine (TECK). This attraction is mediated by CC chemokine receptor (CCR)9, a chemoattractant receptor expressed at high levels by essentially all CD4(+) and CD8(+) T lymphocytes in the small intestine. Only a small subset of lymphocytes in the colon are CCR9(+), and lymphocytes from other tissues including tonsils, lung, inflamed liver, normal or inflamed skin, inflamed synovium and synovial fluid, breast milk, and seminal fluid are universally CCR9(-). TECK expression is also restricted to the small intestine: immunohistochemistry reveals that intense anti-TECK reactivity characterizes crypt epithelium in the jejunum and ileum, but not in other epithelia of the digestive tract (including stomach and colon), skin, lung, or salivary gland. These results imply a restricted role for lymphocyte CCR9 and its ligand TECK in the small intestine, and provide the first evidence for distinctive mechanisms of lymphocyte recruitment that may permit functional specialization of immune responses in different segments of the gastrointestinal tract. Selective expression of chemokines by differentiated epithelium may represent an important mechanism for targeting and specialization of immune responses.
Ultrasound Thyroid Elastography Using Carotid Artery Pulsation (2007)

The results from this preliminary study indicate the feasibility of the pulsation-induced thyroid elastography. Ultrasound thyroid elastography using carotid artery pulsation appears to have the potential for noninvasively differentiating papillary carcinoma from benign nodular goiter. Future studies are needed to evaluate the efficacy of elastography in detecting thyroid cancer and guiding thyroid biopsies.
Catalytic conversion ofHevea brasiliensis andVirola sebifera oils to hydrocarbon fuels (1992)

Catalytic hydrocracking of Hevea brasiliensis (Seringa) and Virola sebifera (Ucuuba) oils was carried out in the presence of a NiMo/Al 2 O 3 catalyst sulfidized in situ with elemental sulfur at 360°C. The initial pressure of hydrogen was 140 bars. Conversions of nearly 100% of the vegetable oils were achieved. The compositions of the liquid fuels were studied in detail by gas chromatography/mass spectrometry. The main products were found to be alkanes, cycloalkanes, aromatics and carboxylic acids.
Strategies for Testing Long-Term Transcutaneous Amperometric Glucose Sensors (2005)

These data represent baseline sensor function against which future sensor improvements may be measured. The new devices and techniques described should be a valuable tool in the development of continuous glucose sensors.
Music Information Retrieval Using Audio Input (1997)

This paper describes a system designed to retrieve melodies from a database on the basis of a few notes sung into a microphone. The system first accepts acoustic input from the user, transcribes it into common music notation, then searches a database of 9400 folk tunes for those containing the sung pattern, or patterns similar to the sung pattern; retrieval is ranked according to the closeness of the match. The paper presents an analysis of the performance of the system using different search criteria involving melodic contour, musical intervals and rhythm; tests were carried out using both exact and approximate string matching. Approximate matching used a dynamic programming algorithm designed for comparing musical sequences. Current work focuses on developing a faster algorithm.
Optic nerve sheath fenestration with a novel wavelength produced by the free electron laser (FEL) (2000)

The FEL at low energy performs an optic nerve sheath fenestration in a small space with ease. Both FEL and knife incisions cause a similar rapid glial response near the fenestration site that remains 1 month later.
Measurement of Human and Murine Stem Cell Factor (c‐kit Ligand) (1992)

Stem cell factor (SCF) is an early-acting, hematopoietic growth factor that binds to the receptor encoded by the proto-oncogene c-kit. It is a potent growth factor for primitive bone marrow cells as well as thymocytes. This unit describes three protocols for detecting human and murine SCF. In the first, human or rodent SCF is measured by its ability to stimulate proliferation of the human megakaryoblastic leukemia cell line, UT-7. Because rat and mouse SCF bind well to human c-kit, human and rodent SCF can both be measured using the first basic protocol. In an Alternate Protocol, rodent SCF is assayed by its ability to stimulate proliferation of the clonal murine mast cell line, MC/9. Human SCF is not very active on rodent cells and thus cannot be measured using this protocol. Both of the cell proliferation assays lack specificity because they are capable of detecting other cytokines in addition to SCF. The third protocol is a radioreceptor assay using the human erythroleukemia cell line, OCIM1; it specifically measures murine or human SCF and not other cytokines. Support protocols describe maintenance of UT-7 and MC/9 cells and preparation of plasma membranes from OCIM1 cells.
Pathogenesis of HIV infection: total CD4+ T-cell pool, immune activation, and inflammation. (2010)

Recent studies have yielded important findings on the pathogenesis of HIV infection. HIV infection leads to immune dysfunction through CD4+ T-cell depletion (immunodeficiency) and immune activation (immunosuppression). In vivo imaging studies of nonhuman primates indicate that the total body pool of CD4+ T cells may provide more accurate quantitation of immune depletion in HIV infection than the peripheral blood CD4+ count. Immune activation appears to be driven by both a homeostatic response to CD4+ cell depletion and an inflammatory response to HIV infection. The evidence is mounting that ongoing inflammation and coagulation account for the increased risk of serious nonopportunistic events in patients with HIV infection. Studies in long-term nonprogressors indicate that the HIV-specific immune responses in these patients are distinguished by clonal expansions of antigen-specific CD8+ T cells. Additional study of the precise mechanisms that allow immunologic control of infection in these patients may contribute to development of vaccines and immune-based therapies. This article summarizes a presentation made by H. Clifford Lane, MD, at the International AIDS Society-USA continuing medical education program held in May 2009 in Chicago. The original presentation is available as a Webcast at www.iasusa.org.
High- and low-affinity receptors for murine interleukin 6. distinct distribution on b and t cells (1989)

The distribution of the murine receptor for interleukin (IL) 6 was examined on a variety of cells. Binding sites for IL 6 were found on many cell lines including fibroblasts and bone marrow-derived macrophages. The highest density of binding sites was found on B cell hybridomas and plasmacytomas, irrespective of their IL 6 dependence for growth. Scatchard analysis carried out with these cells identified about 1000 high-affinity sites (Kd = 25 pM) and 10,000 low-affinity sites (Kd = 2.5 nM). The binding was specific for IL 6 and led to the internalization of the ligand. Receptors for IL 6 were also present on other B cell lines, but binding on normal resting or activated B cells was below the limit of detection (less than 3 molecules/cell). In contrast, receptors were found on mature thymocytes and on peripheral T cells. However, unlike plasmacytomas and hybridomas, T cells expressed only high-affinity binding sites. The difference in the relative numbers of high- and low-affinity receptors on different cells suggests that IL 6 interacts with several proteins, the expression of which varies from one cell type to another.