gebhart/patrepeval huggingface dataset:
High-Throughput Nanoliter Sample Introduction Microfluidic Chip-Based Flow Injection Analysis System with Gravity-Driven Flows (2005)

In this work, a simple, robust, and automated microfluidic chip-based FIA system with gravity-driven flows and liquid-core waveguide (LCW) spectrometric detection was developed. The high-throughput sample introduction system was composed of a capillary sampling probe and an array of horizontally positioned microsample vials with a slot fabricated on the bottom of each vial. FI sample loading and injection were performed by linearly moving the array of vials filled alternately with 50-microL samples and carrier, allowing the probe inlet to enter the solutions in the vials through the slots sequentially and the sample and carrier solution to be introduced into the chip driven by gravity. The performance of the system was demonstrated using the complexation of o-phenanthroline with Fe(II) as a model reaction. A 20-mm-long Teflon AF 2400 capillary (50-microm i.d., 375-microm o.d.) was connected to the chip to function as a LCW detection flow cell with a cell volume of 40 nL and effective path length of 1.7 cm. Linear absorbance response was obtained in the range of 1.0-100 microM Fe(II) (r2=0.9967), and a good reproducibility of 0.6% RSD (n=18) was achieved. The sensitivity was comparable with that obtained using conventional FIA systems, which typically consume 10,000-fold more sample. The highest sampling throughput of 1000 h-1 was obtained by using injection times of 0.08 and 3.4 s for sample and carrier solution, respectively, with a sample consumption of only 0.6 nL for each cycle.
Differentiation-stage specific self-peptides bound by major histocompatibility complex class I molecules. (1993)

We have tested the hypothesis that phenotypic changes of development are accompanied by expression of differentiation-stage specific peptides bound to major histocompatibility complex (MHC) class I molecules. The U937 cell line, when cultured in the presence of phorbol myristate acetate (PMA), undergoes differentiation from monoblasts to macrophage-like cells. The high-performance liquid chromatography profile of peptides eluted from purified human histocompatibility leukocyte antigen class I molecules expressed by U937 treated with PMA differs from that obtained from control, untreated U937 cells. Chemical sequencing of eluted peptides identified a peptide derived from cytomegalovirus in both treated and untreated cells. PMA-treated, but not untreated cells, displayed an additional peptide derived from interleukin 1 beta. Hence, differentiation-induction of U937 is accompanied by the presentation of at least one differentiation-stage specific peptide. Our results indicate that, similar to viral infection, cellular development and transformation is accompanied by the de novo synthesis of proteins which are processed and presented on MHC class I molecules.
Blood gas-analyses in patients with cystic fibrosis to estimate hypoxemia during exposure to high altitudes in a hypobaric-chamber. (2000)

The results of the chamber flights indicate that chronically adapted adult lung disease patients without accompanying heart disease and a paO subset2 of > 40 mmHg during flight can anticipate a safe flight trip. These results could be confirmed by the consecutive flight trip to Spain.
New autosomal recessive lethal disorder with polycystic kidneys type Potter I, characteristic face, microcephaly, brachymelia, and congenital heart defects (1993)

We report on 3 pairs of sibs from unrelated families, who present with polycystic kidneys Potter type I claimed to be specific for the ARPKD, and with microbrachycephaly, hypertelorism with telecanthus, large posteriorly angulated fleshy ears and various congenital malformations including congenital heart defects. We suggest that they represent a previously unrecognized autosomal recessive lethal developmental disorder within the group of infantile polycystic kidney disease and Potter sequence.
Patterning nonflat substrates with a low pressure, room temperature, imprint lithography process (2001)

Step and flash imprint lithography (SFIL) is a technique that has the potential to replace photolithography for patterning resist with sub-100 nm features. SFIL is a low cost, high throughput alternative to conventional photolithography for high-resolution patterning. It is a molding process in which the topography of a template defines the patterns created on a substrate. The ultimate resolution of replication by imprint lithography is unknown but, to date, it has only been limited by the size of the structures that can be created on the template. It is entirely possible to faithfully replicate structures with minimum features of a few hundred angströms. SFIL utilizes a low-viscosity, photosensitive silylated solution that exhibits high etch contrast with respect to organic films in O2 reactive ion etching. In this article we describe the SFIL process, the development of a multilayer etch scheme that produces 6:1 aspect ratio features with 60 nm linewidths, a method for patterning high-aspect-ratio features over topography, and a metal lift-off process. A micropolarizer array consisting of orthogonal 100 nm titanium lines and spaces fabricated using this metal lift-off technique is reported.
Angiogenesis and Hematopoiesis Induced by Kaposi’s Sarcoma-Associated Herpesvirus-Encoded Interleukin-6 (1999)

Kaposi's sarcoma-associated herpesvirus (KSHV; also known as human herpesvirus 8 [HHV-8]) is a herpesvirus linked to the development of Kaposi's sarcoma (KS), primary effusion lymphoma, and a proportion of Castleman's disease. KSHV encodes viral interleukin-6 (vIL-6), which is structurally homologous to human and murine IL-6. The biological activities of vIL-6 are largely unknown. To gain insight into the biology of vIL-6, we expressed vIL-6 in murine fibroblasts NIH3T3 cells and inoculated stable vIL-6-producing clones into athymic mice. vIL-6 was detected selectively in the blood of mice injected with vIL-6-expressing clones. Compared with controls, vIL-6-positive mice displayed increased hematopoiesis in the myeloid, erythroid, and megakaryocytic lineages; plasmacytosis in spleen and lymph nodes; hepatosplenomegaly; and polyclonal hypergammaglobulinemia. vIL-6-expressing NIH3T3 cells gave rise to tumors more rapidly than did control cells, and vIL-6-positive tumors were more vascularized than controls. Vascular endothelial growth factor (VEGF) was detected at higher levels in the culture supernatant of vIL-6-expressing cells compared with controls, and immunohistochemical staining detected VEGF in spleen, lymph nodes, and tumor tissues from mice bearing vIL-6-producing tumors but not control tumors. Thus, vIL-6 is a multifunctional cytokine that promotes hematopoiesis, plasmacytosis, and angiogenesis. Through these functions, vIL-6 may play an important role in the pathogenesis of certain KSHV-associated disorders.
Mathematical Models of the Impact of IL2 Modulation Therapies on T Cell Dynamics (2013)

Several reports in the literature have drawn a complex picture of the effect of treatments aiming to modulate IL2 activity in vivo. They seem to promote either immunity or tolerance, probably depending on the specific context, dose, and timing of their application. Such complexity might derive from the pleiotropic role of IL2 in T cell dynamics. To theoretically address the latter possibility, our group has developed several mathematical models for Helper, Regulatory, and Memory T cell population dynamics, which account for most well-known facts concerning their relationship with IL2. We have simulated the effect of several types of therapies, including the injection of: IL2; antibodies anti-IL2; IL2/anti-IL2 immune-complexes; and mutant variants of IL2. We studied the qualitative and quantitative conditions of dose and timing for these treatments which allow them to potentiate either immunity or tolerance. Our results provide reasonable explanations for the existent pre-clinical and clinical data, predict some novel treatments, and further provide interesting practical guidelines to optimize the future application of these types of treatments.
Patterns of radiological progression in early rheumatoid arthritis: results of an 8 year prospective study. (1998)

A large proportion of joints become eroded in the first 2 years of early RA. The subsequent course of radiological progression is highly variable and cannot be easily explained by any single model.
Expression of the leucocyte integrin LFA-1 (CD11a/CD18) and its ligand ICAM-1 (CD54) in lymphoid malignancies is related to lineage derivation and stage of differentiation but not to tumor grade. (1991)

The leucocyte adhesion molecule LFA-1 (CD11a/CD18) and its counter structure ICAM-1 (CD54) play a pivotal role in cell-cell interactions in the immune system and hence their expression on malignant cells might play an important role in determining the biological behavior of lymphoid malignancies. This study examined the LFA-1 (CD11a/CD18) and ICAM-1 (CD54) expression profiles of a large series of non-Hodgkin's lymphomas (NHL, n = 220) and lymphoid leukemias (LL, n = 48), which, by their differentiation-antigen phenotype represented essentially all stages of lymphoid development from stem cell to mature activated T- and B-lymphocyte. It was found that NHL and LL differentially express LFA-1 and ICAM-1 molecules according to their lineage derivation, stage of differentiation, and growth pattern. Specifically: (a) T-cell neoplasms nearly always express LFA-1 whereas B-cell tumors are often LFA-1 low/negative; (b) ICAM-1 expression is largely confined to tumors with a mature or activated T- or B-cell phenotype; (c) neoplasms with a leukemic dissemination pattern are either ICAM-1 low or negative. Importantly, neither LFA-1 nor ICAM-1 expression was related to tumor grade.
Epidemiological and immunological profile of muscle‐specific kinase myasthenia gravis in Greece (2009)

The incidence and prevalence of MuSK-MG in Greece are amongst the highest reported previously for other countries. MuSK-MG in Greece affects both sexes, but mainly females. The main epidemiological indices were calculated. The vast majority of anti-MuSK antibodies were IgG4.
Next Generation Sequencing of Serum Circulating Nucleic Acids from Patients with Invasive Ductal Breast Cancer Reveals Differences to Healthy and Nonmalignant Controls (2010)

Circulating nucleic acids (CNA) isolated from serum or plasma are increasingly recognized as biomarkers for cancers. Recently developed next generation sequencing provides high numbers of DNA sequences to detect the trace amounts of unique serum biomarkers associated with breast carcinoma. Serum CNA of 38 women with ductal carcinoma was extracted and sequenced on a 454/Roche high-throughput GS-FLX platform and compared with healthy controls and patients with other medical conditions. Repetitive elements present in CNA were detected and classified, and each repetitive element was normalized based on total sequence count or repeat count. Multivariate regression models were calculated using an information-theoretical approach and multimodel inference. A total of 423,150 and 953,545 sequences for the cancer patients and controls, respectively, were obtained. Data from 26 patients with stages II to IV tumors and from 67 apparently healthy female controls were used as the training data set. Using a bootstrap method to avoid sampling bias, a five-parameter model was developed. When this model was applied to a validation data set consisting of patients with tumor stage I (n = 10) compared with healthy and nonmalignant disease controls (n = 87; 1,261,561 sequences) a sensitivity of 70% at a specificity of 100% was obtained. At a diagnostic specificity level of 95%, a sensitivity of 90% was calculated. Identification of specific breast cancer-related CNA sequences provides the basis for the development of a serum-based routine laboratory test for breast cancer screening and monitoring.
Lymphocytic mitochondrial DNA deletions, biochemical folate status and hepatocellular carcinoma susceptibility in a case–control study (2009)

Mitochondrial (mt) DNA deletions and low folate status, proposed characteristics of carcinogenesis, in relation to human hepatocellular carcinoma (HCC) susceptibility are not clearly understood. We hypothesised that low folate status may modify frequencies of mtDNA deletions in humans, both of which could predispose individuals to HCC development. Biochemical folate status of serum and lymphocytes, and frequencies of mtDNA deletions in lymphocytes were determined in ninety HCC cases and ninety cancer-free healthy controls, individually matched by age and sex. The data revealed that HCC patients had lower levels of serum folate (P = 0.0002), lymphocytic folate (P = 0.040) and accumulated higher frequency of lymphocytic mtDNA deletions (P < 0.0001) than the controls. In the total studied subjects, frequencies of lymphocytic mtDNA deletions were associated with hepatitic B infection (P = 0.004) and HCC incidents (P = 0.001), and were correlated with serum folate (r - 0.155; P = 0.041), lymphocyte folate (r - 0.314; P = 0.0001), levels of glutamate-oxaloacetate transaminase (GOT) (r 0.206; P = 0.006), glutamate-pyruvate transaminase (GPT) (r 0.163; P = 0.037) and alpha-fetal protein concentrations (r 0.212; P = 0.005). After adjustment for age, sex, lifestyle and one-carbon metabolite factors, individuals with low blood folate ( < 11.5 nmol/l) or high mtDNA deletions (Delta threshold cycle number (Ct)>5.3) had increased risks for HCC (OR 7.7, 95 % CI 1.9, 29.9, P = 0.003; OR 5.4; 95 % CI 1.7, 16.8, P = 0.003, respectively). When combined with folate deficiency (serum folate < 14 nmol/l), the OR of HCC in individuals with high levels of lymphocytic mtDNA deletions was enhanced (OR 13.3; 95 % CI 1.45, 122; P = 0.008). Further controlling for GOT and GPT levels, however, negated those effects on HCC risk. Taken together, the data suggest that biochemical folate status and liver injuries are important modulators to lymphocytic mtDNA deletions. The mt genetic instability that results from a high rate of mtDNA deletions and/or low folate status increased the risk for HCC, which is mediated by clinical hepatic lesions.
An integrated GPU power and performance model (2010)

GPU architectures are increasingly important in the multi-core era due to their high number of parallel processors. Performance optimization for multi-core processors has been a challenge for programmers. Furthermore, optimizing for power consumption is even more difficult. Unfortunately, as a result of the high number of processors, the power consumption of many-core processors such as GPUs has increased significantly.
Acousto- and electro-osmotic microfluidic controllers (1998)

Acoustic and electroosmotic uni-directional pumping mechanisms for single and multichannel valve-less fluidic pumps and controllers are compared. Geometry, scaling, efficiency and heating, fluid restrictions, and wall materials for the mechanisms are analyzed.
Geometric Theory of Diblock Copolymer Phases (2003)

We analyze the energetics of spherelike micellar phases in diblock copolymers in terms of well-studied, geometric quantities for their lattices. We argue that the A15 lattice with Pm3;n symmetry should be favored as the blocks become more symmetric and corroborate this through a self-consistent field theory. Because phases with columnar or bicontinuous topologies intervene, the A15 phase, though metastable, is not an equilibrium phase of symmetric diblocks. We investigate the phase diagram of branched diblocks and find that the A15 phase is stable.
Role of glycoprotein Ibα in phagocytosis of platelets by macrophages (2006)

It is concluded that binding of an antibody against AA 1-35 on GPIbalpha reflects changes in GPIbalpha that make PLTs targets for phagocytosis by macrophages.
The TAMU security package: an ongoing response to internet intruders in an academic environment (1993)

Texas A&amp;amp;M University (TAMU) UNIX computers came under coordinated attack in August 1992 from an organized group of internet crackers. This package of security tools represents the results of over seven months of development and testing of the software currently being used to protect the estimated 12,000 networked devices at TAMU (of which roughly 5,000 are IP devices). This package includes three related sets of tools: &amp;quot;drawbridge,&amp;quot; a powerful bridging filter package; &amp;quot;tiger,&amp;quot; a set of easy to use yet thorough machine checking programs; and &amp;quot;netlog,&amp;quot; a set of intrusion detection network monitoring programs. 2. Introduction A Brief History of the Incidents On Tuesday, 25 August 1992, the Texas A&amp;amp;M University Supercomputer Center (TAMUSC) was notified by the Ohio Supercomputer Center that a specific Texas A&amp;amp;M University (TAMU) machine was being used to attack one of their computers over the internet. The local machine turned out to be a Sun workstation in a faculty member&amp;apos;s office. Un...
Vessel Traffic System for the Port of Melbourne (1988)

The Vessel Traffic System (VTS) is a radar based automated ship monitoring system used to assist port authorities in their activities. Its main functions include:-- - Detection of vessels, navigation aids, and other fixed or moving objects. - Correlation and identification of objects by radar, VHF radio or visual means, and of related information. - Storage of track data, ship statistics and movements. - Prediction of future ship positions from track processing, and arrivals and departures from movement registers. - Communication of display information to remote sites, remote sensor information to the Vts centre, and database information from other systems. - Presentation and maintenance of the Port status. - Control of radar tracking resources. - Recording of radar video, vessel tracks, and operator actions.
INVESTIGATION OF THE EFFECT OF CHITIN NANO WHISKERS ON THE STRUCTURAL AND PHYSICAL PROPERTIES OF HIGH IMPACT POLYPROPYLENE/CHITIN COMPOSITES (2014)

Biopolymers are known for their beneficial properties such as having antimicrobial abilities, being renewable, biocompatible and biodegradable 1 . This made biopolymers, such as chitin, very popular in recent studies for applications in the latest medical, industrial and environmental developments. Composites that contain the acid hydrolyzed derivatives of chitin, chitin nanowhiskers (chnw), are also becoming of increasing importance in these types of applications. Chnw have a much higher surface area, smaller dimensions and are more crystalline than chitin 3 . In this study chnw was incorporated into high impact polypropylene (HiPP) in order to investigate the effects that this filler have on the mechanical and structural properties of the polymer matrix. The poor interaction between chnw and HiPP made it necessary to investigate the use of compatibilisers 2 . The effect of two types of compatibilisers, poly-graft maleic anhydride (PPgMA) and poly (ethylene-vinyl alcohol) (EVOH), were investigated for the use of making improved and compatible HiPP composites. Injection molding was mainly used to incorporate chnw into the HiPP matrix. Electrospinning and melt pressing of electrospun fiber mats containing chnw and EVOH was an additional method of incorporation that was investigated. The fiber mats were sandwiched between two HiPP films to create a composite. Tensile testing was done on the films and injection molded bars to analyze the mechanical properties of the composites. SEM, TEM, ATR-FTIR and DSC and TGA were used to investigate the structural and thermal properties respectively. It was found that after incorporation of chnw along with each of the compatibilisers, improvement in some mechanical properties of the polymer matrix can be seen, however the influence that each type of compatibliser has, varies depending on the wt% of the compatibliser and the chnw with regard to the polymer matrix.
Myb expression is higher in malignant human colonic carcinoma and premalignant adenomatous polyps than in normal mucosa. (1992)

Expression of the protooncogene c-Myb protein was assessed in normal mucosa and in tumor samples resected from six patients. We found that the tumor samples always expressed higher levels of full length Myb protein than the normal tissue. This contrasts with the situation in c-myb-associated hemopoietic malignancies of the mouse and chicken, in which Myb proteins are generally amino or carboxyl truncated. Tissues from five patients with colonic adenomatous polyps were also examined and found to express levels of Myb that were, in general, intermediate between those found in normal tissues and tumors. Of particular interest is that the more dysplastic polyps displayed higher Myb levels. In one patient with carcinoma and multiple colonic polyps, some polyps had intermediate levels of Myb, whereas one polyp with carcinoma in situ expressed tumor-like levels of Myb. To directly test the hypothesis that Myb expression may be important in determining the rate of colonic cell proliferation, we examined three colonic carcinoma cell lines and one polyp cell line. We found that the cell lines with the most rapid doubling times exhibited the highest Myb levels. In addition, we show that antisense myb oligonucleotides retard the proliferation of one of these colonic cell lines which expresses the highest level of Myb.
Regulation of iron uptake in Saccharomyces cerevisiae. The ferrireductase and Fe(II) transporter are regulated independently. (1992)

Iron is required for the growth of Saccharomyces cerevisiae. High concentrations of iron, however, are toxic, forcing this yeast to tightly regulate its concentration of intracellular free iron. We demonstrate that S. cerevisiae accumulates iron through the combined action of a plasma membrane ferrireductase and an Fe(II) transporter. This transporter is highly selective for Fe(II). Several other transition metals did not inhibit iron uptake when these metals were present at a concentration 100-fold higher than the Km (0.15 microM) for iron transport. Pt(II) inhibited ferrireductase activity but not the ability of cells to transport iron that was chemically reduced to Fe(II). Incubation of cells in a synthetic iron-limited media resulted in the induction of both ferrireductase and Fe(II) transporter activities. In complex media, Fe(II) transport activity was regulated in response to media iron concentration, while the activity of the ferrireductase was not. When stationary phase cells were inoculated into fresh media, ferrireductase activity increased independent of the iron content of the media; in contrast, transporter activity varied inversely with iron levels. These results demonstrate that the ferrireductase and Fe(II) transporter are separately regulated and that iron accumulation may be limited by changes in either activity.
Improved flow cytometry of cellular DNA and RNA by on‐line reagent addition (1987)

Acridine orange (AO) staining enables flow cytometric measurement of cellular DNA and RNA. With the conventional procedure, red and green fluorescence intensities alter considerably in time, affecting the reliability and reproducibility of the results. A standardized simple technique of AO staining is described that keeps the time between addition of detergent and AO and the subsequent measurement constant. Measurements by means of this on-line method appear to be much more reproducible in comparison to those obtained using the conventional procedure.