gebhart/patrepeval huggingface dataset:
Combination Immunotherapy of B16 Melanoma Using Anti–Cytotoxic T Lymphocyte–Associated Antigen 4 (Ctla-4) and Granulocyte/Macrophage Colony-Stimulating Factor (Gm-Csf)-Producing Vaccines Induces Rejection of Subcutaneous and Metastatic Tumors Accompanied by Autoimmune Depigmentation (1999)

We examined the effectiveness of cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) blockade, alone or in combination with a granulocyte/macrophage colony-stimulating factor (GM-CSF)-expressing tumor cell vaccine, on rejection of the highly tumorigenic, poorly immunogenic murine melanoma B16-BL6. Recently established tumors could be eradicated in 80% (68/85) of the cases using combination treatment, whereas each treatment by itself showed little or no effect. Tumor rejection was dependent on CD8(+) and NK1.1(+) cells but occurred irrespective of the presence of CD4(+) T cells. Mice surviving a primary challenge rejected a secondary challenge with B16-BL6 or the parental B16-F0 line. The same treatment regimen was found to be therapeutically effective against outgrowth of preestablished B16-F10 lung metastases, inducing long-term survival. Of all mice surviving B16-BL6 or B16-F10 tumors after combination treatment, 56% (38/68) developed depigmentation, starting at the site of vaccination or challenge and in most cases progressing to distant locations. Depigmentation was found to occur in CD4-depleted mice, strongly suggesting that the effect was mediated by CTLs. This study shows that CTLA-4 blockade provides a powerful tool to enhance T cell activation and memory against a poorly immunogenic spontaneous murine tumor and that this may involve recruitment of autoreactive T cells.
The loading of human erythrocytes with small molecules by electroporation. (2005)

The technology for loading the cell with membrane-impermeable substances by means of electroporation consists of the following three stages: (i) the creation of pores permeable for the desired substance; (ii) the introduction of a substance into the cell cytosol; and (iii) the restoration of the membrane barrier function. In this paper, the experimental data on the loading of human erythrocytes with small molecules (molecular weight below 500 Da) is presented. The results obtained show that increasing the intensity of the electric field pulse increases the fraction of electroporated cells. The pores through which the molecules of ascorbic acid and mannitol (radius below 0.5 nm) can enter the erythrocytes appear when the field strength exceeds 2.5 kV/cm. The concentration of ascorbic acid inside the cells increases linearly. At 4 degrees C, the rate of ascorbic acid influx was constant for at least 4 hours. The original permeability of most of the cells towards ascorbic acid and mannitol was restored after about 6-7 min at 37 degrees C, and the characteristic time for complete resealing was about 20-40 min. The procedure described here can be used for loading cells with membrane-impermeable substances.
Tumor–stroma interaction in orthotopic primary pancreatic cancer xenografts during hedgehog pathway inhibition (2012)

To test the effects of hedgehog (Hh) pathway inhibition on the stroma of orthotopically grown primary pancreatic cancer xenografts, and investigate the potential to monitor these effects non-invasively using magnetic resonance imaging (MRI), mice bearing orthotopically grown primary pancreatic cancer xenografts were treated with the Hh neutralizing antibody 5E1. Pathway inhibition was determined by RT-PCR using primer sets for human and mouse Hh pathway genes, and effects on stroma assessed by automated image analysis of tissue sections stained for collagen and α-smooth muscle actin (αSMA). MRI provided quantitative biomarkers of stromal density based on magnetization transfer (MT-MRI) and dynamic contrast enhancement (DCE-MRI). Modest growth inhibition was seen in both models tested using 5E1, but was greater in OCIP19, which showed high expression of mouse Hh pathway genes and an extensive fibrous stroma. However, despite profound inhibition of both mouse and human Hh pathway genes, in neither model did we observe depletion of the stroma. Alignment of MT-MRI ratio images to histological sections showed co-registration with areas of fibrosis, although this was confounded by the presence of tumor necrosis. Due to the lack of stromal depletion by 5E1 it was not possible to determine the utility of MT-MRI for monitoring this effect. Cancer- and stromal cell-derived Hh signaling elements are expressed in orthotopic primary pancreatic cancer xenografts, and selective targeting is growth-inhibitory. In contrast to some recent reports, growth inhibition does not involve attenuation of the tumor stroma, pointing to additional effects of Hh signaling in pancreatic cancer.
FemtoFarad/TeraOhm Endpoint Detection for Microsurgery of Integrated Circuit Devices (2012)

Abstract Interactive electrical endpoint detection when thinning conductive and capacitive materials opens the door to approaching a suspect site in an IC without relying on the traditional iterative approach. Controlled approach of embedded conductors in insulators (packages) as well as controlled die thinning with submicron control will be shown, allowing safe approach to the desired feature without overshoot.
Aetiology of acute pharyngitis: the role of atypical bacteria (2004)

In order to establish the role of atypical bacteria and compare characteristics of different infectious agents in acute pharyngitis, 127 patients with acute pharyngitis (66 males; median age, 5.33 years; range, 6 months to 14 years) and 130 healthy subjects of similar sex and age were studied. Serology with paired samples and PCR on nasopharyngeal aspirates and throat cultures were used to identify bacteria and viruses. Viruses were identified in 43 patients (33.8%) and five controls (3.8%; P < 0.0001), potential bacterial pathogens in 34 patients (26.8%) and 26 controls (20%; P = 0.256) and mixed viral/bacterial pathogens in 26 patients (20.5%) and none of the controls (P < 0.0001). The main aetiological agents were adenovirus, respiratory syncytial virus (RSV), Mycoplasma pneumoniae, Streptococcus pyogenes and Chlamydia pneumoniae. M. pneumoniae was the agent found most frequently as a single pathogen. A history of recurrent pharyngitis, having older siblings and a negative outcome were significantly more common among patients with acute M. pneumoniae infection than among those with infections due to other pathogens or healthy controls. This study demonstrates that: (i) adenovirus and RSV have a prominent role in acute pharyngitis; (ii) S. pyogenes is found frequently, but it is not possible to distinguish simple carriers from patients with a true infection; (iii) M. pneumoniae appears to be able to cause acute pharyngitis per se; and (iv) C. pneumoniae seems to be mainly a co-pathogen. To avoid the risk of an incorrect therapeutic approach, simple laboratory investigations that allow rapid identification of M. pneumoniae infections are urgently needed.
Single-target molecule detection with nonbleaching multicolor optical immunolabels (2000)

We introduce and demonstrate the use of colloidal silver plasmon-resonant particles (PRPs) as optical reporters in typical biological assays. PRPs are ultrabright, nanosized optical scatterers, which scatter light elastically and can be prepared with a scattering peak at any color in the visible spectrum. PRPs are readily observed individually with a microscope configured for dark-field microscopy, with white-light illumination of typical power. Here we illustrate the use of PRPs, surface coated with standard ligands, as target-specific labels in an in situ hybridization and an immunocytology assay. We propose that PRPs can replace or complement established labels, such as those based on radioactivity, fluorescence, chemiluminescence, or enzymatic/colorimetric detection that are used routinely in biochemistry, cell biology, and medical diagnostic applications. Moreover, because PRP labels are nonbleaching and bright enough to be rapidly identified and counted, an ultrasensitive assay format based on single-target molecule detection is now practical. We also present the results of a model sandwich immunoassay for goat anti-biotin antibody, in which the number of PRP labels counted in an image constitutes the measured signal.
Comparison of the Effectiveness of Trivalent Inactivated Influenza Vaccine and Live, Attenuated Influenza Vaccine in Preventing Influenza-Like Illness Among US Military Service Members, 2006-2009 (2012)

Between 2006 and 2009, TIV and LAIV had similar effectiveness in preventing ILI and influenza/pneumonia events among healthy adults.
Phosphorylation of Eukaryotic Initiation Factor 2 by Heme-Regulated Inhibitor Kinase-Related Protein Kinases in Schizosaccharomyces pombe Is Important for Resistance to Environmental Stresses (2002)

Protein synthesis is regulated by the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2alpha) in response to different environmental stresses. One member of the eIF2alpha kinase family, heme-regulated inhibitor kinase (HRI), is activated under heme-deficient conditions and blocks protein synthesis, principally globin, in mammalian erythroid cells. We identified two HRI-related kinases from Schizosaccharomyces pombe which have full-length homology with mammalian HRI. The two HRI-related kinases, named Hri1p and Hri2p, exhibit autokinase and kinase activity specific for Ser-51 of eIF2alpha, and both activities were inhibited in vitro by hemin, as previously described for mammalian HRI. Overexpression of Hri1p, Hri2p, or the human eIF2alpha kinase, double-stranded-RNA-dependent protein kinase (PKR), impeded growth of S. pombe due to elevated phosphorylation of eIF2alpha. Cells from strains with deletions of the hri1(+) and hri2(+) genes, individually or in combination, exhibited a reduced growth rate when exposed to heat shock or to arsenic compounds. Measurements of in vivo phosphorylation of eIF2alpha suggest that Hri1p and Hri2p differentially phosphorylate eIF2alpha in response to these stress conditions. These results demonstrate that HRI-related enzymes are not unique to vertebrates and suggest that these eIF2alpha kinases are important participants in diverse stress response pathways in some lower eukaryotes.
High-sensitivity magnetometer based on index-enhanced media (1992)

The large dispersion of a phase-coherent medium, at a point of vanishing absorption, is applied to interferometric measurements of detuning between atomic and radiation frequencies. It is shown that, under certain conditions, the interferometer quantum-limited operation is determined by vacuum-fluctuation shot noise while the noise introduced by the interaction of the probe field with the phase-coherent atoms can be made negligible. As a possible application, an optical magnetometer is analyzed whose sensitivity is shown to be potentially superior to the present state-of-the-art devices.
Two regulatory genes of the maize anthocyanin pathway are homologous: isolation of B utilizing R genomic sequences. (1989)

Genetic studies in maize have identified several regulatory genes that control the tissue-specific synthesis of the purple anthocyanin pigments during development. Two such genes, R and B, exhibit extensive allelic diversity with respect to the tissue specificity and developmental timing of anthocyanin synthesis. Previous genetic studies demonstrated that certain B alleles can substitute for R function, and in these cases only one functional allele at either locus is required for pigment synthesis in the aleurone. In addition, biochemical studies have shown that both genes act on the same biosynthetic pathway, suggesting that the genes are functionally duplicate. In this report we describe DNA hybridization experiments that demonstrate that the functionally duplicate nature of B and R is reflected in DNA sequence similarity between the two genes. We took advantage of this homology and used the R genomic sequences to clone B. Two different strategies were pursued and two genomic clones isolated, a 2.5-kilobase BgIII fragment linked to the b allele in W23 inbred stocks and a 1.0-kilobase HindIII fragment linked to the B allele in CM37 stocks. Examination of several independent transposable element insertion mutations in B and revertant derivatives demonstrated that our clones recognize the functional B gene. Genomic clones representing the entire B-Peru allele were isolated, and a detailed restriction map was prepared. Using these clones we have identified a 2.2-kilobase mRNA in husks from plants containing either B-I or B-Peru alleles, but no B mRNA was detected in plants containing a b allele. The transcript is at least 100 times more abundant in strongly pigmented B-I husks than in weakly pigmented B-Peru husk tissue. Expression of functional B alleles in husk tissue correlates with the coordinate increase in mRNA levels of two structural genes of the pathway, A1 and Bz1, consistent with the postulated role of B as a regulatory gene.
Evaluation of Bovine Embryo Biopsy Techniques according to Their Ability to Preserve Embryo Viability (2012)

The purpose of this research was to evaluate three embryo biopsy techniques used for preimplantation genetic diagnosis (PGD) in cattle and to recommend the least invasive one for current use, especially when PGD is followed by embryo cryopreservation. Three hundred bovine embryos were biopsied by either one of the needle, aspiration or microblade method, and then checked for viability by freezing/thawing and transplantation to recipient cows. The number of pregnancies obtained after the transfer of biopsied frozen/thawed embryos was assessed 30 days later using ultrasounds. The results were significantly different between the three biopsy methods: the pregnancy rate was of 57% in cows that received embryos biopsied by needle, 43% in cows that received embryos biopsied by aspiration, and 31% in cows that received embryos biopsied by microblade. Choosing an adequate biopsy method is therefore of great importance in embryos that will undergo subsequent cryopreservation, as it significantly influences their viability after thawing.
Comparative analysis of fourteen individual human cytomegalovirus proteins for helper T cell response (1995)

SUMMARY The potential of selected proteins of human cytomegalovirus (HCMV) to induce a helper T (Th) cell immune response was investigated in healthy HCMV-seropositive donors. Recombinant derived glycoproteins B (gpUL55), H (gpUL75), integral membrane protein (pUL100), the US6-US11 glycoprotein family (pUS6-US11), the matrix proteins pp65 (ppUL83), pp28 (ppUL99) and the immediate early proteins IE1 (pUL123), IE2 (pUL122) and UL69 (pUL69) were used as stimulating antigens in a lymphocyte proliferation assay. The antigen-specific proliferative response was measured in HCMV-specific T cell lines (phenotype CD4+ CD8-) generated from five donors by stimulation of peripheral blood mononuclear cells with purified HCMV or HCMV-infected fibroblasts. A proliferative T cell response was induced by pp65, gB, gH, IE1, IE2 and UL69, with a dominant response to pp65 in all donors. Three T cell lines responded to gB and gH, respectively. For IE1, IE2 and UL69 a T cell stimulation could be demonstrated in single cell lines generated with lysate of HCMV-infected fibroblasts.
Expression of a stable articular cartilage phenotype without evidence of hypertrophy by adult human articular chondrocytes in vitro (1998)

Chondrocytes that were isolated from adult human articular cartilage changed phenotype during monolayer tissue culture, as characterized by a fibroblastic morphology and cellular proliferation. Increased proliferation was accompanied by downregulation of the cartilage-specific extracellular matrix proteoglycan, aggrecan, by cessation of type-II collagen expression, and by upregulation of type-I collagen and versican. This phenomenon observed in monolayer was reversible after the transfer of cells to a suspension culture system. The transfer of chondrocytes to suspension culture in alginate beads resulted in the rapid upregulation of aggrecan and type-II collagen and the downregulation of expression of versican and type-I collagen. Type-X collagen and osteopontin, markers of chondrocyte hypertrophy and commitment to endochondral ossification, were not expressed by adult articular chondrocytes cultured in alginate, even after 5 months. In contrast, type-X collagen was expressed within 2 weeks in a population of cells derived from a fetal growth plate. The inability of adult articular chondrocytes to express markers of chondrocyte hypertrophy has underscored the fundamental distinction between the differentiation pathways that lead to articular cartilage or to bone. Adult articular chondrocytes expressed only hyaline articular cartilage markers without evidence of hypertrophy.
Enhanced optical coherence tomography imaging by multiple scan averaging (2005)

Averaging of multiple OCT B-scans enhances the quality of retinal imaging sufficiently to reveal new details of retinal pathophysiology. Using the technique on OCT3 scans enables visualisation of details comparable with the results obtained using ultra high resolution OCT.
An extensive phenotypic characterization of the hTNFα transgenic mice (2007)

These results highlight the potential usefulness of this transgenic model as a resource for studying the progressive effects of constitutively expressed low levels of circulating TNFalpha, a condition mimicking that observed in a number of human pathological conditions.
Time-tailored laser pulses: a new approach for laser micromachining and microfabrication processing (2003)

We describe novel designs for production of laser pulses from the nanosecond to the femtosecond regime which allow optimization to specific material processing requirements. These lasers are based on use of multimode Yb:fiber amplifiers (MM YDFA) to provide microJoule-level output in a single-mode beam. First, we present laser designs based on MM YDFA that produce 10 kHz - 5 MHz pulses of picosecond and femtosecond duration. Next, by seeding a MM YDFA with pre-shaped nanosecond laser diode seed pulses, we have created a laser that provides temporally nearly-rectangular output pulses. The duration is adjustable between 4 and 20 ns, with sharp rise times of <1.5 ns, and repetition rate of up to 20 kHz. Output pulse energy of >15 microJoules is maintained over the full tuning range. With this "tailorable" pulse design, control of laser energy deposition in confined laser interaction zones (“dosage”) can be user-optimized in real-time from the controller. For example, in biomedical microelectronics and other applications where the creation of micron-size features (in width and in depth) is required the user can adjust dosage in response to meas-ured structural changes over the material. Results of Si wafer and other material micromachining using this unique tem-porally-tailored pulsed laser are presented.
Novel antitumor antibiotics, saptomycins. I. Taxonomy of the producing organism, fermentation, HPLC analysis and biological activities. (1993)

Streptomyces sp. HP530 was found to produce novel antitumor antibiotics, saptomycins, closely related to the pluramycin-group and was further found to mutate frequently. The natural mutant produced several new saptomycins as determined by HPLC analyses. We isolated saptomycins A, B, C1, C2 and F from the parent strain and saptomycins D, E, G and H from the mutant. The saptomycins showed antimicrobial activities and potent antitumor activities against human or murine tumor cell lines in vitro and against Meth A fibrosarcoma in vivo. In particular, saptomycin D was most effective component in vivo of all saptomycins.
Glucocorticoid and thyroid hormones transcriptionally regulate growth hormone gene expression. (1982)

In order to define the molecular mechanisms by which glucocorticoids and thyroid hormone act to regulate growth hormone gene expression, the sites at which they exert their effects on growth hormone biosynthesis were examined in vivo and in a pituitary cell line. Glucocorticoids were shown to rapidly increase accumulation of growth hormone mRNA and nuclear RNA precursors. Glucocorticoids and thyroid hormone were shown to rapidly and independently increase growth hormone gene transcription. These events are shown to occur physiologically in animals and further establish the importance of growth hormone gene expression as a model for steroid regulation.
Interaction of Catechol and Gallic Acid with Titanium Dioxide in Aqueous Suspensions. 1. Equilibrium Studies (2005)

The adsorption isotherms of catechol (1,2-dihydroxybenzene) and gallic acid (3,4,5-trihydroxybenzoic acid) onto titanium dioxide (Degussa P-25) were measured at various pH values and room temperature using attenuated total reflection Fourier transform infrared (FTIR-ATR) data, processed by singular value decomposition. The affinity is largely pH independent, although the deprotonatation of the carboxylic group in gallic acid might produce a slight increase in the affinity. Catechol was shown to form two complexes, with Langmuir stability constants log K of 4.66 (strong mode) and 3.65 (weak mode). Both complexes have the same spectral signature, and mononuclear and binuclear chelate structures are proposed for them. Gallic acid chemisorbs by complexation through two -OH groups and forms one complex only, log K = 4.70. The third -OH and the pendant carboxylate do not influence much the stability of the surface complex. Comparison with literature data demonstrates that the affinity of 4-chlorocatechol is also similar, whereas 2,3-dihidroxynaphthalene and 4-nitrocatechol form more stable complexes, probably because of the solvation contribution to the overall Gibbs adsorption energy. All quoted constants refer to the surface complexation equilibria written as follows: ([triple bond]Ti-OH)2 + H2L = ([triple bond]Ti)2-L + 2H2O, i.e., as electroneutral processes. The FTIR-ATR spectra of the surface complexes are also discussed.
Document understanding system using stochastic context-free grammars (2005)

We present a document understanding system in which the arrangement of lines of text and block separators within a document are modeled by stochastic context free grammars. A grammar corresponds to a document genre; our system may be adapted to a new genre simply by replacing the input grammar. The system incorporates an optical character recognition system that outputs characters, their positions and font sizes. These features are combined to form a document representation of lines of text and separators. Lines of text are labeled as tokens using regular expression matching. The maximum likelihood parse of this stream of tokens and separators yields a functional labeling of the document lines. We describe business card and business letter applications.
Disorders of Bone and Mineral Metabolism (1992)

Normal mineral metabolism bone structure and biology mineral metabolism during the human life cycle introduction to clinical mineral disorders disorders of serum mineral levels disorders of stone formation disorders of bone.
Selectively Damped Least Squares for Inverse Kinematics (2005)

We introduce two methods for the inverse kinematics of multibodies with multiple end effectors. The first method clamps the distance of the target positions. Experiments show this is effective in reducing oscillation when target positions are unreachable. The second method is an extension of damped least squares called selectively damped least squares (SDLS), which adjusts the damping factor separately for each singular vector of the Jacobian singular value decomposition based on the difficulty of reaching the target positions. SDLS has advantages in converging in fewer iterations and in not requiring ad-hoc damping constants. Source code is available online.