gebhart/patrepeval huggingface dataset:
Two-Wavelength Phase-Shifting Low-Coherence Digital Holography (2008)

We propose a novel interferometric method based on digital holography with low-coherence interferometry, the phase-shifting method, and the two-wavelength method. Low-coherence interferometry omits unwanted photons derived from multiple scattering. The phase-shifting method obtains the complex amplitude distribution of an object from several interference patterns. The two-wavelength method yields a surface profile without phase unwrapping from noisy interference signals. We demonstrate topographic imaging of an object in a light-scattering medium.
Multiplex Identification of Microbes (2010)

We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche.
Activation of Ito cells involves regulation of AP-1 binding proteins and induction of type I collagen gene expression (1994)

Activation of liver Ito cells is characterized by increased proliferation, fibrogenesis, loss of cellular retinoid and change of cell-shape. Here, we have described fundamental differences between freshly isolated Ito cells (FIC) and long-term cultured Ito cells (LTIC). This process of activation correlates with the absence of expression of Pro alpha 1(I) gene in FIC. LTIC expressed abundant transcripts of Pro alpha 1(I) gene. Nuclear run-off experiments showed the inability of FIC to support Pro alpha 1(I) RNA transcription while LTIC transcribed it greater than 5-fold as compared with FIC. Transforming growth factor beta (TGF beta)-treated LTIC had a preferential increase in the rate of Pro alpha 1(I) gene transcription as compared with control LTIC. A human collagen type I promoter-enhancer construct (pCOL-KT) [Thompson, Simkevich, Holness, Kang and Raghow (1991) J. Biol. Chem. 266, 2549-2556] was readily expressed in LTIC but failed to be expressed in FIC. Furthermore, TGF beta treatment of LTIC resulted in an increased expression of pCOL-KT. The deletion of an activator protein-1 (AP-1) binding site (+598 to +604) in the 360 bp enhancer region of pCOL-KT (S360) caused decreased expression of the CAT reporter gene, suggesting that this bonafide AP-1 site can, at least in part, mediate the transactivation effect of TGF beta. Using DNAase I protection, we demonstrate a single foot-print located at +590 to +625 in the S360 fragment; nuclear extracts prepared from TGF beta-treated LTIC exhibited greater activity of these AP-1 binding proteins. Gel mobility assays corroborated and extended the footprinting observation. No AP-1-binding activity was found in the nuclear extracts of FIC. Double-stranded oligonucleotides containing the consensus AP-1 motif were able to compete out the binding; consensus NF-1 motif oligonucleotides failed to do so. The preincubation of nuclear extracts from control and TGF beta-treated LTIC with antibodies against c-jun and c-fos rendered a reduced binding of AP-1 proteins to the target S360 fragment.
Specific lung mucosal and systemic immune responses after oral immunization of mice with Salmonella typhimurium aroA, Salmonella typhi Ty21a, and invasive Escherichia coli expressing recombinant pertussis toxin S1 subunit (1992)

Pertussis toxin (PT) is considered an essential protective component for incorporation into new generation vaccines against Bordetella pertussis, the causative agent of whooping cough. Traditionally, antipertussis vaccination has employed an intramuscular route. An alternative to this approach is to stimulate mucosal and systemic immune responses by oral immunization with live vaccine carrier strains of Salmonella spp. or Escherichia coli. Recombinant S1 subunit of pertussis toxin was expressed in the attenuated aroA mutant of Salmonella typhimurium, SL3261, in the human typhoid vaccine strain Salmonella typhi Ty21a, and in E. coli CAG629 containing the Shigella flexneri plasmid pWR110, which encodes bacterial invasiveness of epithelial cells. Expression of recombinant PT S1 subunit (rPT-S1) did not affect in vitro invasiveness of the tested strains, which retained the ability to adhere to and invade the embryonic human intestinal cell line HI-407. Following oral immunization of mice with the live vaccine strains expressing rPT-S1, immunoglobulin G (IgG), IgA, and IgM responses were monitored. IgG specific to PT was detected in serum samples of mice, while IgG and IgA specific to PT were detected in lung washes after oral immunization with living Salmonella spp. or E. coli (pWR110) expressing rPT-S1. Utilization of live oral vaccines expressing B. pertussis antigens, which stimulate both a systemic and lung mucosal response, may provide an attractive alternative to purified component vaccines against whooping cough.
Elliptic curve ElGamal Threshold-based Key Management Scheme against Compromise of Distributed RSUs for VANETs (2012)

In Vehicular Ad Hoc Networks (VANETs), the vehicular scenario requires smart signaling, smart road maintenance and other services. A brand new security issue is that the semi-trusted Road Side Units (RSUs) may be compromised. In this paper, we propose an Elliptic curve ElGamal Threshold system-based key management scheme for safeguarding a VANET from RSUs being compromised and their collusion with malicious vehicles. We analyze the packet loss tolerance for security performance demonstration, followed by a discussion on the threshold. After discussion of the feasibility on privacy and processing time, overhead analysis is presented in terms of two types of application scenarios: Emergency Braking Notification (EBN) and Decentralized Floating Car Data (DFCD). Our method can promote security with low overhead in EBN and does not increase overhead in DFCD during security promotion.
Molecular regulation of cognitive functions and developmental plasticity: impact of GABAAreceptors (2007)

By controlling spike timing and sculpting neuronal rhythms, inhibitory interneurons play a key role in regulating neuronal circuits and behavior. The pronounced diversity of GABAergic (gamma-aminobutyric acid) interneurons is paralleled by an extensive diversity of GABAA receptor subtypes. The region- and domain-specific location of these receptor subtypes offers the opportunity to gain functional insights into the role of defined neuronal circuits. These developments are reviewed with regard to the regulation of sleep, anxiety, memory, sensorimotor processing and post-natal developmental plasticity.
Regression of Experimental Medulloblastoma following Transfer of HER2-Specific T Cells (2007)

Medulloblastoma is a common malignant brain tumor of childhood. Human epidermal growth factor receptor 2 (HER2) is expressed by 40% of medulloblastomas and is a risk factor for poor outcome with current aggressive multimodal therapy. In contrast to breast cancer, HER2 is expressed only at low levels in medulloblastomas, rendering monoclonal antibodies ineffective. We determined if T cells grafted with a HER2-specific chimeric antigen receptor (CAR; HER2-specific T cells) recognized and killed HER2-positive medulloblastomas. Ex vivo, stimulation of HER2-specific T cells with HER2-positive medulloblastomas resulted in T-cell proliferation and secretion of IFN-gamma and interleukin 2 (IL-2) in a HER2-dependent manner. HER2-specific T cells killed autologous HER2-positive primary medulloblastoma cells and medulloblastoma cell lines in cytotoxicity assays, whereas HER2-negative tumor cells were not killed. No functional difference was observed between HER2-specific T cells generated from medulloblastoma patients and healthy donors. In vivo, the adoptive transfer of HER2-specific T cells resulted in sustained regression of established medulloblastomas in an orthotopic, xenogenic severe combined immunodeficiency model. In contrast, delivery of nontransduced T cells did not change the tumor growth pattern. Adoptive transfer of HER2-specific T cells may represent a promising immunotherapeutic approach for medulloblastoma.
Cytophilic Immunoglobulin Responses toPlasmodium falciparumGlutamate-Rich Protein Are Correlated with Protection against Clinical Malaria in Dielmo, Senegal (2000)

The goal of this study was to analyze antibody responses to Plasmodium falciparum glutamate-rich protein (GLURP) using clinical data and plasma samples obtained from villagers of Dielmo, Senegal. This molecule was chosen because it is targeted by human antibodies which induce parasite growth inhibition in antibody-dependent cellular inhibition (ADCI) assays. The results showed a strong correlation between protection against malaria attacks and levels of immunoglobulin G2 (IgG2) and IgG3 against GLURP(94-489) (R0) and IgG3 against GLURP(705-1178) (R2) when corrected for the confounding effect of age-related exposure to malaria. Thus, GLURP may play a role in the induction of protective immunity against P. falciparum malaria.
Estimation Of Systolic And Diastolic Pressure Using The Pulse Transit Time (2010)

In this paper, algorithm estimating the blood pressure was proposed using the pulse transit time (PTT) as a more convenient method of measuring the blood pressure. After measuring ECG and pressure pulse, and photoplethysmography, the PTT was calculated from the acquired signals. Thereafter, the system to indirectly measure the systolic pressure and the diastolic pressure was composed using the statistic method. In comparison between the blood pressure indirectly measured by proposed algorithm estimating the blood pressure and real blood pressure measured by conventional sphygmomanometer, the systolic pressure indicates the mean error of ±3.24mmHg and the standard deviation of 2.53mmHg, while the diastolic pressure indicates the satisfactory result, that is, the mean error of ±1.80mmHg and the standard deviation of 1.39mmHg. These results are satisfied with the regulation of ANSI/AAMI for certification of sphygmomanometer that real measurement error value should be within the mean error of ±5mmHg and the standard deviation of 8mmHg. These results are suggest the possibility of applying to portable and long time blood pressure monitoring system hereafter.
Reactive and proactive sharing across concurrent analytical queries (2014)

Today an ever increasing amount of data is collected and analyzed by researchers, businesses, and scientists in data warehouses (DW). In addition to the data size, the number of users and applications querying data grows exponentially. The increasing concurrency is itself a challenge in query execution, but also introduces an opportunity favoring synergy between concurrent queries. Traditional execution engines of DW follows a query-centric approach, where each query is optimized and executed independently. On the other hand, workloads with increased concurrency have several queries with common parts of data and work, creating the opportunity for sharing among concurrent queries. Sharing can be reactive to the inherently existing sharing opportunities, or proactive by redesigning query operators to maximize the sharing opportunities. This demonstration showcases the impact of proactive and reactive sharing by comparing and integrating representative state-of-the-art techniques: Simultaneous Pipelining (SP), for reactive sharing, which shares intermediate results of common sub-plans, and Global Query Plans (GQP) for proactive sharing, which build and evaluate a single query plan with shared operators. We visually demonstrate, in an interactive interface, the behavior of both sharing approaches on top of a state-of-the-art storage engine using the original prototypes. We show that pull-based sharing for SP eliminates the serialization point imposed by the original push-based approach. Then, we compare, through a sensitivity analysis, the performance of SP and GQP. Finally, we show that SP can improve the performance of GQP for a query mix with common sub-plans.
Effect of therapeutic concentrations of nitric oxide on bacterial growth in vitro (1998)

We conclude that NO has a selective bacteriostatic effect on some of those bacteria most commonly cultured in tracheal specimens of premature infants and neonates. This effect appears to be dose-dependent and occurs in the upper range of dosages used with inhaled NO therapy. However, in the range of dosages applied in ongoing controlled trials of inhaled NO in neonates and premature infants (1 to 80 ppm), a bacteriostatic effect of NO is not to be expected.
Editorial Commentary: Congenital Cytomegalovirus Infection and Its Prevention (2004)

Whether likened to a changeling demon [1] or to the troll of transplantation [2], the human cytomegalovirus (HCMV) has long been known to exact a heavy toll on morbidity and mortality rates among newborn children and immunosuppressed individuals. A recent analysis by the Institute of Medicine of the National Academy of Sciences placed the development of a vaccine against HCMV in its highest category of priority: vaccines that would actually save money for society once they were applied [3]. The same conclusion was reached in a previous analysis [4]. The fact that, throughout the world, an average of -1% of all infants are infected with HCMV in utero is not widely appreciated, nor are the sequelae of deafness and mental retardation. This ignorance probably derives from the late detection of most of the sequelae, aside from the occasional classic case of cytomegalic inclusion disease and the difficulty of confirming by virological or serological analysis the relation between those sequelae and intrauterine infection. Never-
BRCA1 transcriptionally regulates genes associated with the basal-like phenotype in breast cancer (2009)

Expression profiling of BRCA1-deficient tumours has identified a pattern of gene expression similar to basal-like breast tumours. In this study, we examine whether a BRCA1-dependent transcriptional mechanism may underpin the link between BRCA1 and basal-like phenotype. In methods section, the mRNA and protein were harvested from a number of BRCA1 mutant and wild-type breast cancer cell lines and from matched isogenic controls. Microarray-based expression profiling was used to identify potential BRCA1-regulated transcripts. These gene targets were then validated (by in silico analysis of tumour samples) by real-time PCR and Western blot analysis. Chromatin immunoprecipitation (ChIP) assays were used to confirm recruitment of BRCA1 to specific promoters. In results, we demonstrate that functional BRCA1 represses the expression of cytokeratins 5(KRT5) and 17(KRT17) and p-Cadherin (CDH3) in HCC1937 and T47D breast cancer cell lines at both mRNA and protein level. ChIP assays demonstrate that BRCA1 is recruited to the promoters of KRT5, KRT17 and CDH3, and re-ChIP assays confirm that BRCA1 is recruited independently to form c-Myc and Sp1 complexes on the CDH3 promoter. We show that siRNA-mediated inhibition of endogenous c-Myc (and not Sp1) results in a marked increase in CDH3 expression analogous to that observed following the inhibition of endogenous BRCA1. The data provided suggest a model whereby BRCA1 and c-Myc form a repressor complex on the promoters of specific basal genes and represent a potential mechanism to explain the observed overexpression of key basal markers in BRCA1-deficient tumours.
Antiproliferative Effect of a Lectin- and Anti-Thy-1.2 Antibody-Targeted HPMA Copolymer-Bound Doxorubicin on Primary and Metastatic Human Colorectal Carcinoma and on Human Colorectal Carcinoma Transfected with the Mouse Thy-1.2 Gene (2000)

The aim of this study was to compare the potential of two plant lectins [peanut agglutinin (PNA) and wheat germ agglutinin (WGA)], monoclonal antibody (anti-Thy-1.2), its F(ab')(2) fragments, and galactosamine as targeting moieties bound to the polymer drug carrier to deliver a xenobiotic, doxorubicin, to selected cancer cell lines. We have used primary (SW 480, HT 29) and metastatic (SW 620) human colorectal cancer cell lines and a transfectant, genetically engineered SW 620 cell line with mouse gene Thy-1.2 (SW 620/T) to test the possibility of marking human cancer with xenogeneic mouse gene and use it for effective site-specific targeting. The targeting moieties and doxorubicin were conjugated to a water-soluble copolymer based on N-(2-hydroxypropyl)methacrylamide (HPMA) acting as a carrier responsible for controlled intracellular release of the targeted drug. FACS analysis showed a strong binding of WGA-FITC to all tested cell lines. Binding of PNA-FITC was considerably weaker. The in vitro antiproliferative effect of lectin-targeted HPMA carrier-bound doxorubicin evaluated as [(3)H]TdR incorporation reflected both the intensity of the binding and the different sensitivity of the tested cancer cells lines to doxorubicin. The antiproliferative effect of conjugates targeted with WGA was comparable to that with the conjugates targeted with the anti-Thy-1.2 monoclonal antibody or their F(ab')(2) fragments. The magnitude of the cytotoxic effect of HPMA-doxorubicin targeted with PNA was lower in all tested cell lines. While the conjugates with WGA were more cytotoxic, the conjugates with PNA were more specific as their binding is limited to cancer cells and to the sites of inflammation. Noncytotoxic conjugates with a very low concentration of doxorubicin and targeted with PNA, anti-Thy-1.2, or their F(ab')(2) fragments exerted in some lines (SW 480, SW 620) low mitogenic activity. The Thy-1.2 gene-transfected SW 620 metastatic colorectal cancer cell line was sensitive to the antiproliferative effect of Thy-1.2-targeted doxorubicin as was shown for the Thy-1. 2(+) EL4 cell line and for Thy-1.2(+) concanavalin A-stimulated mouse T lymphocytes. These results represent the first indication of the suitability of transfection of human cancer cells with selected targeting genes for site-specific therapy of malignancies.
Molecular Cocrystals of Carboxylic Acids. XXXIII The Crystal Structure of the 1 : 1 Adduct of Indole-2-carboxylic Acid with 5-Nitroquinoline (1998)

The molecular adducts of indole-3-acetic acid (iaa) and indole-2-carboxylic acid (ica) with 5-nitroquinoline (nq), [(iaa)(nq)2] (1) and [(ica)(nq)] (2), have been prepared and characterized by X-ray diffraction and spectroscopic methods. Both examples involve charge transfer as well as a network of hydrogen-bonding interactions. Thin films of compound (2), and other similar adduct complexes of ica, can be prepared by thermal evaporation techniques and in this form exhibit a weak second-order non-linear optical signal. However, these films display poor optical quality and, without improvement, are not suitable for any potential non-linear optical applications.
Quantitative assessment of antimalarial activity in vitro by a semiautomated microdilution technique (1979)

A rapid, semiautomated microdilution method was developed for measuring the activity of potential antimalarial drugs against cultured intraerythrocytic asexual forms of the human malaria parasite Plasmodium falciparum. Microtitration plates were used to prepare serial dilutions of the compounds to be tested. Parasites, obtained from continuous stock cultures, were subcultured in these plates for 42 h. Inhibition of uptake of a radiolabeled nucleic acid precursor by the parasites served as the indicator of antimalarial activity. Results of repeated measurements of activity with chloroquine, quinine, and the investigational new drug mefloquine demonstrated that the method is sensitive and precise. Several additional antimalarial drugs and compounds of interest were tested in vitro, and the results were consistent with available in vivo data. The use of P. falciparum isolates with known susceptibility to antimalarial drugs also permitted evaluation of the cross-resistance potential of each compound tested. The applications and expectations of this new test system within a drug development program are discussed.
Comparison of light intensity on the brain surface due to laser exposure during optical topography and solar irradiation (2007)

Optical topography (OT), which is based on the near-infrared spectroscopy, is a powerful tool for observing brain activity noninvasively. To estimate the effect of laser exposure on the brain, photon-distribution profiles in bald heads of adults and neonates during the OT were calculated using the photon-diffusion equation. These calculations showed that although the absolute values of the intensity depend on details of the head model, the relative values of OT exposure to sunlight exposure were less sensitive to the model details. As an example, the light intensities on the brain surface during OT obtained by using a commercially available system were about 2% for adults and 3% for neonates of those values obtained under midday sunlight on a sunny day in midsummer. These values were obtained under the reasonable assumptions with a large safety factor.
CALCIUM BLOCKADE REDUCES RENAL APOPTOSIS DURING ISCHEMIA REPERFUSION (1997)

Apoptosis is well described in invertebrates and recently documented in mammals. The prevalence and pathophysiology of mammalian apoptosis is unknown and may have clinical ramifications. The aim of this study is to investigate the apoptotic response during kidney ischemia-reperfusion (I/R) injury. Kidney I/R was initiated in anesthetized rats by occlusion of the renal pedicle for 45 min with or without pretreatment with .2 mg/kg verapamil: control animals received sham exposure. Flow was re-established after ischemia and the animals were allowed to recover for 24 h. Bilateral kidneys were harvested for DNA electrophoresis, Western analysis for p53, Northern analysis for c-myc expression, and light and electron microscopic analysis. Kidney I/R caused characteristic DNA laddering in the clamped kidney, and less extensive laddering was seen in the contralateral kidney. Light and electron microscopic analysis confirmed apoptotic morphology in the reperfused tissues. Verapamil pretreatment completely abolished DNA laddering and attenuated the microscopic evidence of apoptosis. p53 levels were increased by I/R in the ischemic kidney and moderately increased in the contralateral organ. c-myc mRNA levels were increased by the I/R insult. Kidney I/R injury may induce global apoptosis, which seems to be associated with an alteration in calcium homeostasis. The increase in p53 and c-myc mRNA levels seen with I/R may facilitate apoptosis. Calcium modulation seems to reduce apoptosis during I/R and may have therapeutic implications.