gebhart/patrepeval huggingface dataset:
Scaling limitations of silicon multichannel recording probes (1990)

This paper describes the scaling limitations of multichannel recording probes fabricated for use in neurophysiology using silicon integrated circuit technologies. Scaled silicon probe substrates 8 microns thick and 16 microns wide can be fabricated using boron etch-stop techniques. Theoretical expressions for calculating the thickness and width of silicon substrates have been derived and agree closely with experimental results. The effects of scaling probe dimensions on its strength and stiffness are described. The probe shank dimensions can be designed to vary the strength and stiffness for different applications. The scaled silicon substrates have a fracture stress of about 2 x 10(10) dyn/cm2, which is about six times that of bulk silicon, and are strong and very flexible. Scaling the feature sizes of recording electrode arrays down to 1 micron is possible with less than 1 percent electrical crosstalk between channels.
Induction of Plasma (TRAIL), TNFR-2, Fas Ligand, and Plasma Microparticles after Human Immunodeficiency Virus Type 1 (HIV-1) Transmission: Implications for HIV-1 Vaccine Design (2008)

The death of CD4(+) CCR5(+) T cells is a hallmark of human immunodeficiency virus (HIV) infection. We studied the plasma levels of cell death mediators and products--tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), Fas ligand, TNF receptor type 2 (TNFR-2), and plasma microparticles--during the earliest stages of infection following HIV type 1 (HIV-1) transmission in plasma samples from U.S. plasma donors. Significant plasma TRAIL level elevations occurred a mean of 7.2 days before the peak of plasma viral load (VL), while TNFR-2, Fas ligand, and microparticle level elevations occurred concurrently with maximum VL. Microparticles had been previously shown to mediate immunosuppressive effects on T cells and macrophages. We found that T-cell apoptotic microparticles also potently suppressed in vitro immunoglobulin G (IgG) and IgA antibody production by memory B cells. Thus, release of TRAIL during the onset of plasma viremia (i.e., the eclipse phase) in HIV-1 transmission may initiate or amplify early HIV-1-induced cell death. The window of opportunity for a HIV-1 vaccine is from the time of HIV-1 transmission until establishment of the latently infected CD4(+) T cells. Release of products of cell death and subsequent immunosuppression following HIV-1 transmission could potentially narrow the window of opportunity during which a vaccine is able to extinguish HIV-1 infection and could place severe constraints on the amount of time available for the immune system to respond to the transmitted virus.
Casein kinase 2 activity increases in the prereplicative phase of liver regeneration (1988)

Cytosolic casein kinase activity increased up to 2-fold in the first 6 h after partial hepatectomy and then decreased to control values. This increase was due mainly to casein kinase 2, which reached maximal values at 6-8 h of liver regeneration. In contrast, casein kinase 1 showed a smaller increase at 4 h and then started to decrease reaching values of about 70% of control at 16 h. The increase in total casein kinase 2 was accompanied with an activation of the enzyme, as determined by the low/high beta-casein activity ratio assay. Administration of an acute dose of glucagon to control rats also increased the activity ratio but failed to cause any rise in total casein kinase 2 activity.
Escherichia coli heat-labile toxin subunit B fusions with Streptococcus sobrinus antigens expressed by Salmonella typhimurium oral vaccine strains: importance of the linker for antigenicity and biological activities of the hybrid proteins (1993)

A set of vectors possessing the genes for aspartate semialdehyde dehydrogenase (asd) and the B subunit of the heat-labile enterotoxin of Escherichia coli (LT-B) has been developed. These vectors allow operon or gene fusions of foreign gene epitopes at the C-terminal end of LT-B. Two groups of vectors have been constructed with and without leader sequences to facilitate placing of the foreign antigen in different cell compartments. Two Streptococcus sobrinus genes coding for principal colonization factors, surface protein antigen A (SpaA), and dextranase (Dex), have been fused into the 3' end of the LT-B gene. Resulting protein fusions of approximately 120 to 130 kDa are extremely well recognized by antibodies directed against both SpaA and Dex as well as against LT-B domains and retain the enzymatic activity of dextranase and the biological activity of LT-B in that they bind to GM1 gangliosides. Maximum antigenicity was obtained with the vector possessing an intervening linker of at least six amino acids with two proline residues. Some of the fusion proteins also exhibited another property of LT-B in that they were exported into the periplasm where they oligomerized. LT-B-SpaA and LT-B-Dex hybrid proteins are expressed stably and at a high level in avirulent Salmonella typhimurium vaccine strains which are being used to investigate their immunogenicity and types of induced immune responses. The fusion vectors will also be useful for production and purification of LT-B fusion antigens to be used and evaluated in other vaccine compositions.
Characterization and Clinical Application of Human CD34 + Stem/Progenitor Cell Populations Mobilized into the Blood by Granulocyte Colony‐Stimulating Factor (2006)

A phase I study was performed to determine the safety and tolerability of injecting autologous CD34(+) cells into five patients with liver insufficiency. The study was based on the hypothesis that the CD34(+) cell population in granulocyte colony-stimulating factor (G-CSF)-mobilized blood contains a subpopulation of cells with the potential for regenerating damaged tissue. We separated a candidate CD34(+) stem cell population from the majority of the CD34(+) cells (99%) by adherence to tissue culture plastic. The adherent and nonadherent CD34(+) cells were distinct in morphology, immunophenotype, and gene expression profile. Reverse transcription-polymerase chain reaction-based gene expression analysis indicated that the adherent CD34(+) cells had the potential to express determinants consistent with liver, pancreas, heart, muscle, and nerve cell differentiation as well as hematopoiesis. Overall, the characteristics of the adherent CD34(+) cells identify them as a separate putative stem/progenitor cell population. In culture, they produced a population of cells exhibiting diverse morphologies and expressing genes corresponding to multiple tissue types. Encouraged by this evidence that the CD34(+) cell population contains cells with the potential to form hepatocyte-like cells, we gave G-CSF to five patients with liver insufficiency to mobilize their stem cells for collection by leukapheresis. Between 1 x 10(6) and 2 x 10(8) CD34(+) cells were injected into the portal vein (three patients) or hepatic artery (two patients). No complications or specific side effects related to the procedure were observed. Three of the five patients showed improvement in serum bilirubin and four of five in serum albumin. These observations warrant further clinical trials.
A Facile Synthesis of Some Benzothiopyrano[4,3-b]pyrroles† (1997)

A simple synthesis of some benzothiopyrano[4,3-b]pyrroles from benzothiopyran-4-ones is described which has been used to prepare the novel heterocyclic system 4H-naphtho[1′,2′:5,6]thiopyrano[4,3-b ]pyrrole.
Eurofix: GNSS Augmented Loran-C & Loran-C Augmented GNSS (1995)

Sole DGNSS concepts loose some availability and
continuity-of-service performance due to the risk of
failmes of the added system components. Eurofix is a
hybridization of DGNSS and calibrated Loran-C
which offer soft degradation capabilities which in turn
improve availability and continuity of service. The
DGNSS data are broadcast by additionally time
modulating the Loran-C pulses. The high Loran-C
cross-rate interference is counteracted by efficient
modulation and coding techniques. The paper
describes the soft degradation concept of Eurofix and
discusses two different types of coding schemes. Real-
life measurements show that cross-rate is the dominant
source of interference. Demonstrations of Eurofix,
carried out by DOT and Megapulse, show that tinal
accuracies of better than 10 meters can be obtained
throughout the continental US.
Immunotoxins show rapid entry of diphtheria toxin but not ricin via the T3 antigen. (1986)

We compared immunotoxins made with ricin and diphtheria toxin (DT) and with two monoclonal antibodies against different T cell-specific antigens, CD5 (T101) and CD3 (UCHT1). Only one reagent, UCHT1 linked to DT (UCHT1-DT), had exceptional properties. UCHT1-DT killed human peripheral T cells and T leukemia cells (Jurkat) at 2 to 10 pM, a concentration 10- to 100-fold lower than UCHT1-ricin and 10 to 500 times lower than native DT. The toxicity was blocked 50- to 100-fold by excess UCHT1 antibody. Human multipotent stem cells were not killed at up to 2000 pM UCHT1-DT. UCHT1-DT shows greater selectivity between T cells and stem cells than UCHT1-ricin, and may better prevent graft-vs-host disease in allogeneic bone marrow transplantation. The kinetics of UCHT1-DT were extremely rapid. UCHT1-DT inhibited Jurkat cell protein synthesis faster than DT and had a different ratio of lag time to inactivation rate. UCHT1-DT killed 90% of Jurkat cells within 2 hr at concentrations nontoxic to human stem cells. In contrast, UCHT1-ricin required more than 18 hr to kill one log of Jurkat cells. Another monoclonal antibody, T101, against the 65 kD CD5 antigen on Jurkat cells was linked to DT and ricin, and was compared with the UCHT1 immunotoxins. UCHT1-DT was 100 times more potent and five to 10 times faster than T101-DT and T101-ricin. Standardization to other antibodies with regard to the number of molecules bound per cell shows that UCHT1-DT is 10 to 100 times faster than previously reported immunotoxins. The role of the T3 antigen in transporting DT to the cytosol is discussed.
Fabrication of 3D Microstructures with Single uv Lithography Step (2002)

Abstract − This paper presents a novel microfabri-cation technology of 3D microstructures with inclined/rotated UV lithography using negative photoresist, SU-8. In some cases, reflected UV as well as incident UV is used to form microstructures. Various 3D microstructures are simply fabricated such as embedded channels, bridges, V-grooves, truncated cones, and so on.
TCR Mimic Monoclonal Antibody Targets a Specific Peptide/HLA Class I Complex and Significantly Impedes Tumor Growth In Vivo Using Breast Cancer Models (2010)

Our laboratory has developed a process for generating mAbs with selectivity to unique peptides in the context of MHC molecules. Recently, we reported that RL4B, an mAb that we have called a TCR mimic (TCRm) because it recognizes peptide in the context of MHC, has cytotoxic activity in vitro and prevented growth of tumor cells in a prophylactic setting. When presented in the context of HLA-A2, RL4B TCRm recognizes the peptide GVLPALPQV derived from human chorionic gonadotropin (hCG)-beta. In this study, we show that RL4B TCRm has strong binding affinity for the GVLPALPQV peptide/HLA-A2 epitope and fine binding specificity for cells that express endogenous hCGbeta Ag and HLA-A2. In addition, suppression of tumor growth with RL4B TCRm was observed in orthotopic models for breast cancer. Using two aggressive human tumor cell lines, MDA-MB-231 and MCF-7, we provide evidence that RL4B TCRm significantly retards tumor growth, supporting a possible role for TCRm agents in therapeutic settings. Moreover, tumors in mice responded to RL4B TCRm therapy in a dose-dependent manner, eliminating tumors at the highest dose. RL4B TCRm strongly detects the hCGbeta peptide/HLA-A2 epitope in human primary breast tumor tissue, but does not react or reacts weakly with normal breast tissue from the same patient. These results further illustrate the selective nature of TCRm Abs and the clinical relevance of the GVLPALPQV peptide/HLA-A2 epitope expression in tumor cells, because they provide the first evidence that Abs that mimic the TCR can be used to markedly reduce and suppress tumor growth.
Multivariate analysis and reverse engineering of signal transduction pathways (2009)

This thesis presents mathematical and computational approaches to studying signal transduction pathways. The biology.of cellular signalling is introduced, highlighting the importance of signalling pathways in regulating the processes of cell division and proliferation. A brief history of mathematical approaches to such systems is presented. Two multivariate analysis methods, principal component analysis and clustering, are introduced and applied to both gene expression and simulated protein concentration data. Several recent reverse engineering methods that have been used to study genetic networks are introduced. Finally, a reverse engineering method intended to elucidate the structure of genetic networks is adapted to the study of signal transduction systems.
Transforming growth factor‐beta and fibroblast growth factor act synergistically to inhibit collagen II synthesis through a mechanism involving regulatory DNA sequences (1989)

Transforming growth factor-beta (TGF-beta) and fibroblast growth factor (FGF) are two growth factors that will modulate chondrocyte growth and matrix synthesis. Here we report that these two growth factors act in a synergistic fashion to suppress the synthesis of type II collagen by embryonic chicken sternal chondrocytes. Treatment of chondrocytes with 20 ng/ml TGF-beta or 100 ng/ml FGF (acidic or basic) results in a 60-70% suppression of expression of the pro alpha 1 chain of type II collagen. By comparison, when chondrocytes are exposed to a combination of 1 ng/ml TGF-beta and 10 ng/ml FGF, a complete suppression of type II collagen synthesis was observed. Epidermal growth factor (EGF), platelet-derived growth factor (PDGF), or insulin-like growth factor-1 (IGF-1) produce no suppression of synthesis either individually or in combination with TGF-beta. The decreased expression of the protein results from a decrease in the steady-state level of the mRNA transcript coding for type II procollagen, as indicated by a northern analysis. Finally, chondrocytes transfected with a plasmid carrying the CAT gene driven by the collagen II promoter/enhancer sequence displayed high levels of CAT activity when cultured in control media, but treatment of the cells with a combination of the two growth factors resulted in a dramatic reduction of CAT activity, indicating diminished promoter activity. These results suggest that both TGF-beta and FGF can down-regulate transcription of the collagen II gene through regulatory DNA sequences in the promoter and/or enhancer region. In addition, the finding of synergy suggests that these two growth factors may act through different pathways.
Dengue virus-specific human T cell clones. Serotype crossreactive proliferation, interferon gamma production, and cytotoxic activity. (1989)

The severe complications of dengue virus infections, hemorrhagic manifestation and shock, are much more commonly observed during secondary infections caused by a different serotype of dengue virus than that which caused the primary infections. It has been speculated, therefore, that dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) are caused by serotype crossreactive immunopathological mechanisms. We analyzed clones of dengue serotype crossreactive T lymphocytes derived from the PBMC of a donor who had been infected with dengue 3 virus. These PBMC responded best to dengue 3 antigen, but also responded to dengue 1, 2, and 4 antigens, in bulk culture proliferation assays. 12 dengue antigen-specific clones were established using a limiting dilution technique. All of the clones had CD3+ CD4+ CD8 phenotypes. Eight clones responded to dengue 1, 2, 3, and 4 antigens and are crossreactive, while four other clones responded predominantly to dengue 3 antigen. These results indicate that the serotype crossreactive dengue-specific T lymphocyte proliferation observed in bulk cultures reflects the crossreactive responses detected at the clonal level. Serotype crossreactive clones produced high titers of IFN-gamma after stimulation with dengue 3 antigens, and also produced IFN-gamma to lower levels after stimulation with dengue 1, 2, and 4 antigens. The crossreactive clones lysed autologous lymphoblastoid cell line (LCL) pulsed with dengue antigens, and the crossreactivity of CTL lysis by T cell clones was consistent with the crossreactivity observed in proliferation assays. Epidemiological studies have shown that secondary infections with dengue 2 virus cause DHF/DSS at a higher rate than the other serotypes. We hypothesized that the lysis of dengue virus-infected cells by CTL may lead to DHF/DSS; therefore, the clones were examined for cytotoxic activity against dengue 2 virus-infected LCL. All but one of the serotype crossreactive clones lysed dengue 2 virus-infected autologous LCL, and they did not lyse uninfected autologous LCL. The lysis of dengue antigen-pulsed or virus-infected LCL by the crossreactive CTL clones that we have examined is restricted by HLA DP or DQ antigens. These results indicate that primary dengue virus infections induce predominantly crossreactive memory CD4+ T lymphocytes. These crossreactive T lymphocytes proliferate and produce IFN-gamma after stimulation with a virus strain of another serotype, and demonstrate crossreactive cyotoxic activity against autologous cells infected with heterologous dengue viruses.(ABSTRACT TRUNCATED AT 400 WORDS)
A Genomic Island, Termed High-Pathogenicity Island, Is Present in Certain Non-O157 Shiga Toxin-Producing Escherichia coli Clonal Lineages (1999)

Shiga toxin-producing Escherichia coli (STEC) strains cause a wide spectrum of diseases in humans. In this study, we tested 206 STEC strains isolated from patients for potential virulence genes including stx, eae, and enterohemorrhagic E. coli hly. In addition, all strains were examined for the presence of another genetic element, the high-pathogenicity island (HPI). The HPI was first described in pathogenic Yersinia species and encodes the pesticin receptor FyuA and the siderophore yersiniabactin. The HPI was found in the genome of distinct clonal lineages of STEC, including all 31 eae-positive O26:H11/H(-) strains and 7 of 12 eae-negative O128:H2/H(-) strains. In total, the HPI was found in 56 (27.2%) of 206 STEC strains. However, it was absent from the genome of all 37 O157:H7/H(-), 14 O111:H(-), 13 O103:H2, and 13 O145:H(-) STEC isolates, all of which were positive for eae. Polypeptides encoded by the fyuA gene located on the HPI could be detected by using immunoblot analysis in most of the HPI-positive STEC strains, suggesting the presence of a functional yersiniabactin system. The HPI in STEC was located next to the tRNA gene asnT. In contrast to the HPI of other pathogenic enterobacteria, the HPI of O26 STEC strains shows a deletion at its left junction, leading to a truncated integrase gene int. We conclude from this study that the Yersinia HPI is disseminated among certain clonal subgroups of STEC strains. The hypothesis that the HPI in STEC contributes to the fitness of the strains in certain ecological niches rather than to their pathogenic potential is discussed.
Improved estimation of anomalous diffusion exponents in single-particle tracking experiments (2013)

The mean square displacement is a central tool in the analysis of single-particle tracking experiments, shedding light on various biophysical phenomena. Frequently, parameters are extracted by performing time averages on single-particle trajectories followed by ensemble averaging. This procedure, however, suffers from two systematic errors when applied to particles that perform anomalous diffusion. The first is significant at short-time lags and is induced by measurement errors. The second arises from the natural heterogeneity in biophysical systems. We show how to estimate and correct these two errors and improve the estimation of the anomalous parameters for the whole particle distribution. As a consequence, we manage to characterize ensembles of heterogeneous particles even for rather short and noisy measurements where regular time-averaged mean square displacement analysis fails. We apply this method to both simulations and in vivo measurements of telomere diffusion in 3T3 mouse embryonic fibroblast cells. The motion of telomeres is found to be subdiffusive with an average exponent constant in time. Individual telomere exponents are normally distributed around the average exponent. The proposed methodology has the potential to improve experimental accuracy while maintaining lower experimental costs and complexity.
Proneural Transcription Factor Atoh1 Drives Highly Efficient Differentiation of Human Pluripotent Stem Cells Into Dopaminergic Neurons (2014)

Human pluripotent stem cells (PSCs) are a promising cell resource for various applications in regenerative medicine. Highly efficient approaches that differentiate human PSCs into functional lineage-specific neurons are critical for modeling neurological disorders and testing potential therapies. Proneural transcription factors are crucial drivers of neuron development and hold promise for driving highly efficient neuronal conversion in PSCs. Here, we study the functions of proneural transcription factor Atoh1 in the neuronal differentiation of PSCs. We show that Atoh1 is induced during the neuronal conversion of PSCs and that ectopic Atoh1 expression is sufficient to drive PSCs into neurons with high efficiency. Atoh1 induction, in combination with cell extrinsic factors, differentiates PSCs into functional dopaminergic (DA) neurons with >80% purity. Atoh1-induced DA neurons recapitulate key biochemical and electrophysiological features of midbrain DA neurons, the degeneration of which is responsible for clinical symptoms in Parkinson's disease (PD). Atoh1-induced DA neurons provide a reliable disease model for studying PD pathogenesis, such as neurotoxin-induced neurodegeneration in PD. Overall, our results determine the role of Atoh1 in regulating neuronal differentiation and neuron subtype specification of human PSCs. Our Atoh1-mediated differentiation approach will enable large-scale applications of PD patient-derived midbrain DA neurons in mechanistic studies and drug screening for both familial and sporadic PD.
The Yeasts. A Taxonomic Study (1972)

Pt. 1. Classification of yeasts -- pt. 2. Importance of yeasts -- pt. 3. Phenotypic, ultrastructural, biochemical and molecular properties used for yeast classification -- pt. 4a. Classification of the Ascomycetous Taxa -- pt. 4. Descriptions of Teleomorphic Ascomycetous Genera and species -- pt. 4c. Descriptions of Anamorphic Ascomycetous Genera and species -- pt. 5a. Classification of the Basidiomycetous Taxa -- pt. 5b. Descriptions of Teleomorphic Basidiomycetous Genera and species -- pt. 5c. Descriptions of Anamorphic Basidiomycetous Genera and species -- pt. 6. Prototheca, a yeast-like alga.