gebhart/patrepeval huggingface dataset:
A Genetically Engineered Spleen Necrosis Virus-Derived Retroviral Vector That Displays the HIV Type 1 Glycoprotein 120 Envelope Peptide (1999)

We reported that SNV-derived retroviral vectors, which display single-chain antibodies on the viral surface, enable cell type-specific gene delivery into various human cells. In particular, the SNV cell type-specific gene delivery vector system appears to be well suited to transduce genes into cells of the human hematopoietic system (Jiang et al., J. Virol. 72:10148-10156, 1998). Here, we report the construction of SNV vector particles that display the complete gp120 surface unit of the envelope protein of human immunodeficiency virus type 1 (HIV-1) on the viral surface. The complete gp120-coding region of a T cell-tropic HIV-1 strain (LAI/BRU) was fused to a short peptide spacer coding region [(Gly4Ser)3] linking it to the SNV TM-coding region. The corresponding protein was expressed as a single 145-kDa peptide as expected. This peptide was nontoxic and could be stably expressed in dog D17 SNV-derived packaging cells. Particles harvested from stable packaging lines infected CD4+ human hematopoietic cells with titers exceeding 10(5) CFU/ml supernatant tissue culture medium. Titers in other, CD4- cell lines expressing various coreceptors of HIV-1 were 100-fold lower than titers obtained in CD4+ cells. Specificity of infection was demonstrated by antibody inhibition assays or by preincubating cells with SDF-1alpha, the ligand, which binds to the CXCR4 coreceptor, to which this gp120 binds. Our data indicate that binding of the HIV-1 gp120 to either CD4 or CXCR4 is sufficient to enable infection of human cells with SNV vector particles. We constructed retroviral vector particles that display chimeric HIV-1-SU-SNV-TM proteins plus wild-type SNV envelope on the viral surface. Such particles allowed efficient infection of CD4-positive human T lymphocytes, and, at a lower efficiency, also cells expressing CXCR4 without CD4. These data coincide with our earlier hypothesis that the chimeric envelope is required only to bind the vector particle to a cell surface receptor of the target cell, while membrane fusion is mediated by wild-type Env, which alone is not sufficient to enable infection of human cells.
Treatment of autism spectrum children with thiamine tetrahydrofurfuryl disulfide: a pilot study. (2002)

Thiamine tetrahydrofurfuryl disulfide appears to have a beneficial clinical effect on some autistic children, since 8 of the 10 children improved clinically. We obtained evidence of an association of this increasingly occurring disease with presence of urinary SH-reactive metals, arsenic in particular.
Effects of Rice Seed Surface Sterilization with Hypochlorite on Inoculated Burkholderia vietnamiensis (2001)

When a combination of hydrogen peroxide and hypochlorite was used to surface sterilize rice seeds, a 10(2)- to 10(4)-fold decrease in CFU was observed during the first 15 h after inoculation of the rice rhizosphere organism Burkholderia vietnamiensis TVV75. This artifact could not be eliminated simply by rinsing the seeds, even thoroughly, with sterile distilled water. When growth resumed, a significant increase in the frequency of rifampin- and nalidixic acid-resistant mutants in the population was observed compared to the control without seeds. This phenomenon was a specific effect of hypochlorite; it was not observed with hydrogen peroxide alone. It was also not observed when the effect of hypochlorite was counteracted by sodium thiosulfate. We hypothesized that the hypochlorite used for disinfection reacted with the rice seed surface, forming a chlorine cover which was not removed by rinsing and generated mutagenic chloramines. We studied a set of rifampin- and nalidixic acid-resistant mutants obtained after seed surface sterilization. The corresponding rpoB and gyrA genes were amplified and sequenced to characterize the induced mutations. The mutations in five of seven nalidixic acid-resistant mutants and all of the rifampin-resistant mutants studied were found to correspond to single amino acid substitutions. Hypochlorite surface sterilization can thus be a source of artifacts when the initial bacterial colonization of a plant is studied.
Efficient Synthesis of Enantiomerically Pure β2-Amino Acids via Chiral Isoxazolidinones (2003)

We report a practical and scalable synthetic route for the preparation of alpha-substituted beta-amino acids (beta(2)-amino acids). Michael addition of a chiral hydroxylamine, derived from alpha-methylbenzylamine, to an alpha-alkylacrylate followed by cyclization gives a diastereomeric mixture of alpha-substituted isoxazolidinones. These diastereomers are separable by column chromatography. Subsequent hydrogenation of the purified isoxazolidinones followed by Fmoc protection affords enantiomerically pure Fmoc-beta(2)-amino acids, which are useful for beta-peptide synthesis. This route provides access to both enantiomers of a protected beta(2)-amino acid.
Patterns of Known and Novel Small RNAs in Human Cervical Cancer (2007)

Recent studies suggest that knowledge of differential expression of microRNAs (miRNA) in cancer may have substantial diagnostic and prognostic value. Here, we use a direct sequencing method to characterize the profiles of miRNAs and other small RNA segments for six human cervical carcinoma cell lines and five normal cervical samples. Of 166 miRNAs expressed in normal cervix and cancer cell lines, we observed significant expression variation of six miRNAs between the two groups. To further show the biological relevance of our findings, we examined the expression level of two significantly varying miRNAs in a panel of 29 matched pairs of human cervical cancer and normal cervical samples. Reduced expression of miR-143 and increased expression of miR-21 were reproducibly displayed in cancer samples, suggesting the potential value of these miRNAs as tumor markers. In addition to the known miRNAs, we found a number of novel miRNAs and an additional set of small RNAs that do not meet miRNA criteria.
Interferon-α-Induced Biologic Modifications in Patients with Chronic Myelogenous Leukemia (1994)

Serum neopterin (Np), beta 2-microglobulin (beta 2-M), and 2',5'-adenylate (2',5'A) levels and intracellular 2',5'A and human Mx (Hu-Mx) protein synthesis were measured in 20-24 chronic myeloid leukemia patients before and during 1 year of IFN-alpha treatment and in a further 8-9 patients before and at the end of the first and second treatment weeks only. Univariate analysis showed that IFN-alpha increased Np and 2',5'A serum levels and intracellular concentrations of 2',5'A and Hu-Mx significantly from the end of the first week to month 12 of therapy. The biologic marker profiles were similar in cytogenetic responders and nonresponders, as well as in patients treated with IFN-alpha early (< 12 months from diagnosis) or late (after > 12 months standard chemotherapy). Further, there were no differences in the short-term (first 14 days) or long-term (during 12 month therapy) induction of the biologic markers irrespective of whether IFN-alpha 2a or IFN-alpha 2b was given. Because multivariate analysis revealed no significant interactions between cytogenetic response, time to treatment, and type of IFN-alpha used, increments in intracellular 2',5'A and Hu-Mx protein were similar at all study times for all factor combinations tested. Np levels varied significantly only during the first 14 therapy days; changes in serum 2',5'A were never statistically significant.(ABSTRACT TRUNCATED AT 250 WORDS)
A Recombinant Measles Virus Expressing Hepatitis B Virus Surface Antigen Induces Humoral Immune Responses in Genetically Modified Mice (1999)

It has been shown previously that measles virus (MV) can be successfully used to express foreign proteins (M. Singh and M. A. Billeter, J. Gen. Virol. 80:101-106, 1998). To develop an inexpensive MV-based vaccine, we generated recombinant MVs that produce structural proteins of hepatitis B virus (HBV). A recombinant virus that expressed the HBV small surface antigen (HBsAg) was analyzed in terms of its replication characteristics, its genetic stability in cell culture, and its immunogenic potential in genetically modified mice. Although this virus showed a progression of replication slightly slower than that of the parental MV, it appeared to stably maintain the added genetic information; it uniformly expressed the appropriately glycosylated HBsAg after 10 serial passages. Genetically modified mice inoculated with this recombinant MV produced humoral immune responses against both HBsAg and MV proteins.
Evidence of a Pluripotent Human Embryonic Stem Cell Line Derived from a Cloned Blastocyst (2004)

Somatic cell nuclear transfer (SCNT) technology has recently been used to generate animals with a common genetic composition. In this study, we report the derivation of a pluripotent embryonic stem (ES) cell line (SCNT-hES-1) from a cloned human blastocyst. The SCNT-hES-1 cells displayed typical ES cell morphology and cell surface markers and were capable of differentiating into embryoid bodies in vitro and of forming teratomas in vivo containing cell derivatives from all three embryonic germ layers in severe combined immunodeficient mice. After continuous proliferation for more than 70 passages, SCNT-hES-1 cells maintained normal karyotypes and were genetically identical to the somatic nuclear donor cells. Although we cannot completely exclude the possibility that the cells had a parthenogenetic origin, imprinting analyses support a SCNT origin of the derived human ES cells.
Predictable time-sharing for DryadLINQ cluster (2010)

This paper addresses the scheduling problem that popular data parallel programming systems such as DryadLINQ and MapReduce are facing today. Designing a cluster system in a multi-user environment is challenging because cluster schedulers must satisfy multiple, possibly conflicting, enterprise goals and policies. Particularly for these new types of data-intensive applications, it continues to be a challenge to simultaneously achieve both high throughput and predictable end-to-end performance for jobs (e.g., predictable start/end times). The conventional approach of scheduling these types of jobs is to attempt to determine a best mapping between a task and a node before the job executes, and the scheduling system ceases to be involved for a given job once the job starts executing. Instead, as described in this paper, we define a reactive containment and control mechanism for scheduling and executing distributed tasks, schedule the jobs, and then continually monitor and adjust resources as the job executes. More specifically, a DryadLINQ task in our system is contained in virtual machine and distributed controllers regulate progress of the task at runtime. Using online, feedback-controlled VM CPU scheduling, our system provides a job a capability to speed-up or slow-down progress of concurrent sub-tasks so that the job can make predictable progress while sharing system resources with other jobs. The new capability allows an enterprise to enforce flexible scheduling policies such as fair-share and/or prioritizing jobs. Our evaluation results using five well-known DryadLINQ applications show the implemented distributed controllers achieve high throughput as well as predictable end-to-end performance.
EMMPRIN (CD147), an inducer of matrix metalloproteinase synthesis, also binds interstitial collagenase to the tumor cell surface. (2000)

Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as basigin or CD147, is a glycoprotein that is enriched on the surface of tumor cells and stimulates production of several matrix metalloproteinases by adjacent stromal cells. In this study, we have found that EMMPRIN not only stimulates the production of interstitial collagenase (MMP-1) but also forms a complex with MMP-1 at the tumor cell surface. Complex formation was demonstrated by phage display, affinity chromatography, and immunocytochemistry. Presentation of MMP-1 complexed to EMMPRIN at the tumor cell surface may be important in modifying the tumor cell pericellular matrix to promote invasion.
Clonal variation of MCF-7 breast cancer cells in vitro and in athymic nude mice. (1983)

Abstract The MCF-7 human breast cancer cell line and four derived variant sublines (R27, R3, R3–12, and R3–98), which were all estrogen receptor positive, as well as the receptor-deficient line, MDA-MB-231, were compared both in vitro and as heterotransplants into athymic nude mice. The cell lines and heterotransplanted tumors were evaluated in terms of growth, receptor status, morphology by light and electron microscopy, karyotype, and allozyme phenotype analyses. The R3 and R3–12 variant lines exhibited markedly retarded growth rates in vitro as compared with those of the MCF-7 parent line. The R3-12 line, which had the slowest growth rate in vitro as compared to those of the other cell lines, failed to produce tumors in nude mice after many attempts using various concentrations of tumor cell inocula. The MCF-7 and derived lines would not grow in oophorectomized animals without 17β-estradiol replacement, with one rare exception, while the MDA-MB-231 receptor-deficient line was able to grow in oophorectomized mice with and without 17β-estradiol replacement. Compared to the parent MCF-7 and R27 line in vivo and in vitro , the R3 line and its subclones had reduced progesterone receptor markedly. By light microscopy, all of the cell lines in vivo and in vitro could be identified as adenocarcinoma. Using electron microscopy, the MCF and variant lines showed better tissue organization and more squamous features in vivo than in vitro where glandular features were more prominent. The R27 line in vivo and in vitro showed the most cellular polarity and differentiation as compared to the MCF or R3 lines (R3, R3–12, and R3–98), while the R3 lines were the least differentiated of all the lines. The MDA-MB-231 line in vivo and in vitro had the most pronounced glandular features of all the lines and was not affected by changes in media additions of fetal calf serum, 17β-estradiol, or charcoal-treated calf serum as were the MCF-7- and MCF-7-derived lines. All the tumors in vivo and in vitro showed a human karyotype, and the MCF-7 and each of the derived lines showed both common and unique chromosome markers. The original cell line (MCF-7), the derived sublines (R27 and R3), and tumors derived in nude mice from these lines were typed for species identity using standard isozyme procedures and were found to be human. The allozyme phenotype at seven polymorphic human loci (allozyme genetic signature) demonstrated that the MCF-7 line and its derivatives were derived from the same individual and were distinct from the signatures of HeLa and a variety of other human breast cancer lines. This multifaceted study, using both in vivo and in vitro systems, may provide a model for better understanding the nature of tumor heterogeneity and its implications in therapeutic designs.
Smart Liquid SERS Substrates based on Fe3O4/Au Nanoparticles with Reversibly Tunable Enhancement Factor for Practical Quantitative Detection (2014)

There is a strong correlation between the surface enhanced Raman scattering (SERS) enhancement factor (EF), the excitation wavelength, and the feature properties (composition, size, geometry, and analytes). The prediction of the EF of specific substrates, crucial to the quantitative SERS detection, is however still very difficult. The present work presents smart liquid SERS substrates consisting of suspensions of Fe3O4/Au nanoparticles, which provide high spot-to-spot uniformity, reproducibility and good reversibility. The EF of these substrates can be reversibly tuned by applying an external magnetic field. The EF magnetic tuning is within 2 orders of magnitude per substrate in the range of 10(4)-10(7). The ability to reversibly adjust the SERS EF enables to reduce EF variations caused by external effects such as substrate-to-substrate differences and long-term-storage degradation. This improves the quantitative detection of analytes and might be a significant step forward in employing SERS for practical applications.
Intramolecular G-quartet Motifs Confer Nuclease Resistance to a Potent Anti-HIV Oligonucleotide (1996)

We have identified a potentially therapeutic anti-human immunodeficiency virus (HIV)-1 oligonucleotide composed entirely of deoxyguanosines and thymidines (T30177, also known as AR177: 5'-g.tggtgggtgggtggg.t-3', where asterisk indicates phosphorothioate linkage). In acute assay systems using human T-cells, T30177 and its total phosphodiester homologue T30175 inhibited HIV-1-induced syncytium production by 50% at 0.15 and 0.3 microM, respectively. Under physiological conditions, the sequence and composition of the 17-mer favors the formation of a compact, intramolecularly folded structure dominated by two stacked guanine quartet motifs that are connected by three loops of TGs. The molecule is stabilized by the coordination of a potassium ion between the two stacked quartets. We now show that these guanine quartet-containing oligonucleotides are highly resistant to serum nucleases, with t1/2 of 5 h and >4 days for T30175 and T30177, respectively. Both oligonucleotides were internalized efficiently by cells, with intracellular concentrations reaching 5-10-fold above the extracellular levels after 24 h of incubation. In contrast, single-base mutated variants or random sequence control oligonucleotides that could not form the compactly folded structure had markedly reduced half-lives (t1/2 from approximately 3 to 7 min), low cellular uptake, and no sequence-specific anti-HIV-1 activity. These data suggest that the tertiary structure of an oligonucleotide is a key determinant of its nuclease resistance, cellular uptake kinetics, and biological efficacy.
Effect of Pituitary Hollow Fiber Units and Thyroid Supplementation on Growth in the Little Mouse (1984)

Hollow fiber units containing allogeneic pituitary cells were implanted intracranially into heterozygous (lit/+) and homozygous, mutant (lit/lit) C57BL/6J “little” weanling mice. Over the 48 days of the experiment, heterozygous mice with pituitary cell implants had a lower percentage weight gain than control mice. Homozygous, mutant mice with cell implants, however, made significant weight gains over mutant controls. Long bone lengths were lower, and organ and carcass weights were higher, in heterozygous mice receiving pituitary cell implants than in control mice, but corresponding measurements in mutant mice with and without implants were not significantly different. Supplementation of the diet with thyroid powder increased the percentage weight gain during the latter half of the 48-day period in both genotypes with and without implanted cells. Thyroid-supplemented mutant mice with pituitary cell implants had significantly higher organ and carcass weights than other mutant groups. The little mouse may serve as a model for pituitary studies and for the treatment of isolated growth hormone deficiency type 1 in man.
Fibronectin attenuates increased endothelial monolayer permeability after RGD peptide, anti-alpha 5 beta 1, or TNF-alpha exposure (1995)

Endothelial permeability can be altered by tumor necrosis factor-alpha (TNF-alpha), a cytokine released in association with inflammation-induced tissue injury. In the subendothelial matrix, fibronectin (Fn) influences endothelial cell adhesion by the interaction of integrins with RGD and non-RGD attachment sites in Fn. We compared the effect of TNF-alpha, RGD-containing peptides (GRGDSP), or antibody to alpha 5 beta 1-integrins on the protein permeability of bovine lung endothelial monolayers as assessed by transendothelial 125I-labeled albumin clearance. We also examined the influence of purified human plasma fibronectin (hFn) on this permeability response. TNF-alpha, RGD peptides, and antibodies to alpha 5 beta 1-integrins elicited a dose- and time-dependent increase in protein permeability as well as a reorganization and/or disruption of the endogenous Fn matrix. A control RGE peptide (GRGESP) as well as immunoglobulin G purified from nonimmune rabbit serum did not increase endothelial protein permeability or disrupt the endogenous fibrillar Fn pattern in the matrix. Likewise, a LDV peptide derived from the alternatively spliced type III connecting segment (IIICS) within bovine Fn (bFn) was unable to increase permeability of the bovine endothelial monolayer. Co-incubation of purified soluble hFn (300 or 600 micrograms/ml) with either TNF-alpha, the RGD peptide, or the antibody to alpha 5 beta 1-integrins prevented the increase in endothelial permeability. This protective effect was also observed when the purified hFn (600 micrograms/ml) was added after the TNF-alpha-induced increase in endothelial permeability had taken place. Immunofluorescent analysis confirmed the incorporation of the hFn into the subendothelial matrix and its co-localization with the endogenous bFn. The similar alteration of the subendothelial matrix after exposure to RGD peptides, anti-alpha 5 beta 1-antibodies, or TNF-alpha, coupled with the ability for hFn to attenuate the permeability increase typically elicited by all three agents, suggests that disruption of cell-matrix interactions may be the mechanism by which TNF-alpha alters endothelial permeability.
A Combination of Immune Checkpoint Inhibition with Metronomic Chemotherapy as a Way of Targeting Therapy-Resistant Cancer Cells (2017)

Therapeutic resistance remains a major obstacle in treating many cancers, particularly in advanced stages. It is likely that cytotoxic lymphocytes (CTLs) have the potential to eliminate therapy-resistant cancer cells. However, their effectiveness may be limited either by the immunosuppressive tumor microenvironment, or by immune cell death induced by cytotoxic treatments. High-frequency low-dose (also known as metronomic) chemotherapy can help improve the activity of CTLs by providing sufficient stimulation for cytotoxic immune cells without excessive depletion. Additionally, therapy-induced removal of tumor cells that compete for shared nutrients may also facilitate tumor infiltration by CTLs, further improving prognosis. Metronomic chemotherapy can also decrease the number of immunosuppressive cells in the tumor microenvironment, including regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs). Immune checkpoint inhibition can further augment anti-tumor immune responses by maintaining T cells in an activated state. Combining immune checkpoint inhibition with metronomic administration of chemotherapeutic drugs may create a synergistic effect that augments anti-tumor immune responses and clears metabolic competition. This would allow immune-mediated elimination of therapy-resistant cancer cells, an effect that may be unattainable by using either therapeutic modality alone.
Transfusion-related Acute Lung Injury in the Critically Ill (2007)

Both patient and transfusion risk factors determine the probability of ALI after transfusion. Transfusion factors represent attractive targets for the prevention of ALI.
Effect of Interfacial Liquid Structuring on the Coherence Length in Nanolubrication (2002)

The degree of interfacial structuring of n-hexadecane and octamethylcyclotetrasiloxane (OMCTS) was measured within a nanometer boundary regime to silicon surfaces. Boundary-layer effects on lubricating sliding (in terms of a thermodynamic stress activation parameter) and the layer thickness were determined by scanning force microscopy. A 2.0+/-0.3 nm thick, entropically cooled layer was found for n-hexadecane. Measurements on spherically shaped OMCTS molecules exhibited only an interfacial "monolayer," and identified the molecular shape of n-hexadecane responsible for augmented interfacial structuring. Interfacial liquid structuring was found to reduce friction.