gebhart/patrepeval huggingface dataset:
CHAOTIC MIXING OF MAGNETIC BEADS IN MICRO CELL SEPARATOR (2003)

In micro-scale biological assay systems, the mixing of bio-molecules becomes a critical issue because of their small diffusivity. Chaotic features in a novel micro-mixer designed for cell separation system based on magnetic beads (Suzuki and Ho, 2002) is investigated in detail by means of numerical simulation. The mechanism and the optimum condition to lead the motion of magnetic beads to chaos are clarified. It is found that the chaotic mixing would significantly facilitate the attachment of magnetic beads onto bio-molecules, which practically do not occur without an external perturbation. Active micro-mixers achieve rapid and efficient mixing even in the creeping flow regime, which is not accomplished with the passive micro-mixers.
Chemical modification of poly(styrene‐co‐maleic anhydride) with primary N‐alkylamines by reactive extrusion (1994)

Abstract Reactive melt‐processing of poly(styrene‐ co ‐maleic anhydride) (SMA) with primary N ‐alkylamines was carried out in one step in a twin‐screw extruder. Ring formation of the imide occurred within the residence time of the extruder, at temperatures exceeding 220°C and with an excess of primary amines. The increasing chain length of grafted amine onto the SMA backbone depressed the glass transition temperature of poly(styrene‐ co‐N ‐alkylmaleimides) remarkably. © 1994 John Wiley &amp; Sons, Inc.
Human mesenchymal stem cells reduce mortality and bacteremia in gram-negative sepsis in mice in part by enhancing the phagocytic activity of blood monocytes (2012)

The potential therapeutic value of cell-based therapy with mesenchymal stem cells (MSC) has been reported in mouse models of polymicrobial peritoneal sepsis. However, the mechanisms responsible for the beneficial effects of MSC have not been well defined. Therefore, we tested the therapeutic effect of intravenous bone marrow-derived human MSC in peritoneal sepsis induced by gram-negative bacteria. At 48 h, survival was significantly increased in mice treated with intravenous MSC compared with control mice treated with intravenous fibroblasts (3T3) or intravenous PBS. There were no significant differences in the levels of TNF-α, macrophage inflammatory protein 2, or IL-10 in the plasma. However, there was a marked reduction in the number of bacterial colony-forming units of Pseudomonas aeruginosa in the blood of MSC-treated mice compared with the 3T3 and PBS control groups. In addition, phagocytic activity was increased in blood monocytes isolated from mice treated with MSC compared with the 3T3 and PBS groups. Furthermore, levels of C5a anaphylotoxin were elevated in the blood of mice treated with MSC, a finding that was associated with upregulation of the phagocytosis receptor CD11b on monocytes. The phagocytic activity of neutrophils was not different among the groups. There was also an increase in alternately activated monocytes/macrophages (CD163- and CD206-positive) in the spleen of the MSC-treated mice compared with the two controls. Thus intravenous MSC increased survival from gram-negative peritoneal sepsis, in part by a monocyte-dependent increase in bacterial phagocytosis.
Distance Metric Learning for Large Margin Nearest Neighbor Classification (2009)

The accuracy of k-nearest neighbor (kNN) classification depends significantly on the metric used to compute distances between different examples. In this paper, we show how to learn a Mahalanobis distance metric for kNN classification from labeled examples. The Mahalanobis metric can equivalently be viewed as a global linear transformation of the input space that precedes kNN classification using Euclidean distances. In our approach, the metric is trained with the goal that the k-nearest neighbors always belong to the same class while examples from different classes are separated by a large margin. As in support vector machines (SVMs), the margin criterion leads to a convex optimization based on the hinge loss. Unlike learning in SVMs, however, our approach requires no modification or extension for problems in multiway (as opposed to binary) classification. In our framework, the Mahalanobis distance metric is obtained as the solution to a semidefinite program. On several data sets of varying size and difficulty, we find that metrics trained in this way lead to significant improvements in kNN classification. Sometimes these results can be further improved by clustering the training examples and learning an individual metric within each cluster. We show how to learn and combine these local metrics in a globally integrated manner.
Characterization of Poly-γ-Glutamate Hydrolase Encoded by a Bacteriophage Genome: Possible Role in Phage Infection of Bacillus subtilis Encapsulated with Poly-γ-Glutamate (2003)

Some Bacillus subtilis strains, including natto (fermented soybeans) starter strains, produce a capsular polypeptide of glutamate with a gamma-linkage, called poly-gamma-glutamate (gamma-PGA). We identified and purified a monomeric 25-kDa degradation enzyme for gamma-PGA (designated gamma-PGA hydrolase, PghP) from bacteriophage PhiNIT1 in B. subtilis host cells. The monomeric PghP internally hydrolyzed gamma-PGA to oligopeptides, which were then specifically converted to tri-, tetra-, and penta-gamma-glutamates. Monoiodoacetate and EDTA both inhibited the PghP activity, but Zn(2+) or Mn(2+) ions fully restored the enzyme activity inhibited by the chelator, suggesting that a cysteine residue(s) and these metal ions participate in the catalytic mechanism of the enzyme. The corresponding pghP gene was cloned and sequenced from the phage genome. The deduced PghP sequence (208 amino acids) with a calculated M(r) of 22,939 was not significantly similar to any known enzyme. Thus, PghP is a novel gamma-glutamyl hydrolase. Whereas phage PhiNIT1 proliferated in B. subtilis cells encapsulated with gamma-PGA, phage BS5 lacking PghP did not survive well on such cells. Moreover, all nine phages that contaminated natto during fermentation produced PghP, supporting the notion that PghP is important in the infection of natto starters that produce gamma-PGA. Analogous to polysaccharide capsules, gamma-PGA appears to serve as a physical barrier to phage absorption. Phages break down the gamma-PGA barrier via PghP so that phage progenies can easily establish infection in encapsulated cells.
Prediction of total body muscle mass from simple anthropometric measurements in young Indian males. (2004)

A new prediction equation for the measurement of muscle mass was derived in young Indian men using simple anthropometric measurements such as mid-arm circumference and triceps skinfolds.
Ultrasonic Hyperthermia for Cancer Treatment . (1993)

In this paper, design of transducers, ultrasonic focusing techniques and temperature monitoring for hyperthermia are described. Efforts being made at National Physical Laboratory, New Delhi, on the development of an indigeneous ultrasonic hyperthermia and non-invasive temperature monitoring systems are discussed
Experimental testbed of reconfigurable flexgrid optical network with virtualized GMPLS control plane and autonomic controls towards SDN (2013)

This paper demonstrates a testbed of a reconfigurable optical network composed by four ROADMs equipped with flexgrid WSS modules, optical amplifiers, optical channel monitors, and supervisor boards. A controller daemon implements a node abstraction layer based in the YANG language, providing NETCONF and CLI interfaces. Additionally we demonstrate the virtualization of GMPLS control plane, while supporting automatic topology discovery and TE-Link instantiation, enabling a path towards SDN. GMPLS have been extended to collect specific DWDM measurement data allowing the implementation of adaptive/cognitive controls and policies for autonomic operation, based on global network view.
Automated screening of metabolic disorders using pattern recognition of GC-MS full scan spectra from urine organic acids (2012)

Analysis of organic acids in urine is a valuable tool in the diagnosis of the inborn errors of metaboli sm known as organic acidurias. This test is commonly ordered in newborns with symptoms such as lethargy, failure to thrive, hepatic failure, and suspected familial disorders. A drawback of published methods is the overwhelming amount of data to examine for each patient, prior to the final laboratory report. Physicians will wait as long as two weeks for these time critical results. The goal of this research was to develop an expert system to automate the process of screening for metabolic disorders of urine organic acids. The Xaminer® pattern recognition software (ThermoFinnigan, San Jose, CA) was adapted to predict and identify patterns of urine organic acid disorders. The gas chromatography-mass spectrometry (GC-MS) full scan spectra of organic acids were used to build the pattern match library and train the software to recognize methylmalonic aciduria (MMA) and associated vitamin B12 deficiency, as well as, a subset of fatty acid oxidation defects (FAOD), including medium chain acyl-CoA dehydrogenase (MCAD) deficiency. Patient data files were de-identified and reprocessed using the expert system. The expert system results were compared to the original laboratory findings. From a total of2573 samples, the original laboratory findings were 20 positives for MMA and 29 positives for F AOD. The Xaminer software identified 17 of the 20 MMA positives, plus 4 additional candidate samples that matched the search pattern criteria. The software found 26 of the 29 F AOD positives. Five additional sanlples were found to be candidates for F AOD. Software analysis time averaged less than 10 seconds per sample. This expert system can use pattern recognition of full scan GC-MS data to aid in patient screening for MMA and fatty acid oxidation disorders. The performance of Xaminer shows promise for refining or expanding the reference library to include other nletabolic disorders as well.
Parallel assessment of the impact of different hormone replacement therapies on breast density by radiologist- and computer-based analyses of mammograms (2008)

The markedly different pharmacokinetic profile of nasal estrogen seems to be associated with better breast safety. Automated computer-based analysis of digitized mammograms provides a sensitive measure of changes in breast density induced by hormones and could serve as a useful tool in future clinical trials.
Purification and properties of a new, commercial, thermostableBacillus stearothermophilusα‐amylase (1988)

A rapid purification has been developed for Bacillus stearothermophilus α‐amylase starting with the commercial enzyme product. The two‐step procedure, using hydrophobic interaction chromatography and ion exchange, results in a 6.8‐fold increase in specific activity with an 86% recovery of starting activity. The molecular weight of the enzyme was 58,000 when measured by SDS‐PAGE The enzyme preparation consisted of three isozymes with pl values of 8.1, 8.0, and 7.8–7.7. The enzyme mixture had a broad pH optimum of pH 4.0–7.0 at 40° C and a narrower optimum of pH 5.2–6.5 at 90° C. The temperature optimum was 80° C when measured by the starch‐iodine assay; hydrolysis of maltodextrin indicated a constant, maximum rate between 70° C and 100° C. Calcium was shown to increase the half life of the enzyme at 90° C approximately 10‐fold; addition of 10% maltodextrin and calcium increased the half life of the enzyme 80‐fold.
World-to-chip microfluidic interface with built-in valves for multichamber chip-based PCR assays (2005)

We report a practical world-to-chip microfluidic interfacing method with built-in valves suitable for microscale multichamber chip-based assays. One of the primary challenges associated with the successful commercialization of fully integrated microfluidic systems has been the lack of reliable world-to-chip microfluidic interconnections. After sample loading and sealing, leakage tests were conducted at 100 degrees C for 30 min and no detectable leakage flows were found during the test for 100 microchambers. To demonstrate the utility of our world-to-chip microfluidic interface, we designed a microscale PCR chip with four chambers and performed PCR assays. The PCR results yielded a 100% success rate with no contamination or leakage failures. In conclusion, we have introduced a simple and inexpensive microfluidic interfacing system for both sample loading and sealing with no dead volume, no leakage flow and biochemical compatibility.
Insertable biplanar gradient coils for magnetic resonance imaging (1991)

Insertable planar gradient coils offer the potential for significant performance increases in magnetic resonance imaging through higher gradient strength and shorter rise times. Using variational methods to minimize inductance, and thereby to optimize switching speeds, we have analyzed and constructed a biplanar y-gradient coil for insertion into a solenoidal magnet system where z is the magnet axis. We have also analyzed biplanar x-gradient and z-gradient coil designs using the same methods. These biplanar coils offer an advantage over a cylindrical coil of comparable diameter in that they achieve high gradient strengths with relatively short rise times while maintaining patient access. Although the requirement that the currents for the x gradient lie in the same plane as for the y and z gradients increases the stored energy by a factor of 3 with respect to the other two gradients, this stored energy is still smaller by a factor of 2 than that of a comparably constrained x-gradient cylindrical coil. The biplanar coil design offers improved linearity over its single planar coil alternative. The particular designs we have investigated are generally limited to small-volume imaging.
Risk Factors for Early or Delayed Stroke After Cardiac Surgery (1999)

Most strokes after cardiac surgery occurred after initial uneventful recovery from surgery. Women were at higher risk to suffer early and delayed perioperative strokes. Atrial fibrillation had no impact on postoperative stroke rate unless it was accompanied by low cardiac output syndrome.
Descriptive epidemiology of acne vulgaris in the community (1997)

Acne is a common skin condition. No universally accepted standardized classification system for acne vulgaris exists, although there is a strong need for it. Thus, the clinical definition of acne has been unclear in many studies. The reported prevalence of acne varies from 35 to over 90% of adolescents at some stage. In some studies the prevalence of comedones approaches 100% in both sexes during adolescence. The prevalence of acne varies between sexes and age groups, appearing earlier in females than in males, possibly reflecting the earlier onset of puberty. There is a greater severity of acne in males than in females in the late teens, which is compatible with androgens being a potent stimulus to sebum secretion. The prevalence of acne at a given age has been shown to be highly dependent on the degree of sexual maturity. Acne commonly shows a premenstrual increase in women. Some studies have detected seasonal variability in acne vulgaris, with the colder months associated with exacerbation and the warmer months showing improvement. Other studies have not confirmed these findings. Several studies that have investigated the psychosocial impact of acne have had conflicting results. The prevalence of severe acne has decreased over the past 20 years due to improved treatment. The general prevalence figure for acne may be confounded by treatment and this factor needs to be accounted for when collecting data.
Comparison of the glycosyl-phosphatidylinositol cleavage/attachment site between mammalian cells and parasitic protozoa (2000)

It was previously hypothesised that the requirements for glycosyl-phosphatidylinositol (GPI) anchoring in mammalian cells and parasitic protozoa are similar but not identical. We have investigated this by converting the GPI cleavage/attachment site in porcine membrane dipeptidase to that found in the trypanosomal variant surface glycoprotein 117 and expressing the resulting mutants in COS-1 cells. Changing the entire (omega), (omega)+1 and (omega)+2 triplet in membrane dipeptidase from Ser-Ala-Ala to Asp-Ser-Ser resulted in efficient GPI anchoring of the mutant proteins, as assessed by cell-surface activity assays and susceptibility to release by phosphatidylinositol-specific phospholipase C. Immunoelectrophoretic blot analysis with antibodies recognising epitopes either side of the native (omega) residue in porcine membrane dipeptidase, and expression of a mutant in which potential alternative cleavage/attachment sites were disrupted, indicated that alternative GPI cleavage/attachment sites had not been used. These results indicate that the requirements for GPI anchoring between mammalian and protozoal cells are not as different as previously suggested, and that rules for predicting the probability of a sequence acting as a GPI cleavage/attachment site need to be applied with caution.
Expression of Novel Surface Antigens on Early Hematopoietic Cellsa (1999)

The purpose of this report is to demonstrate the expression of very recently identified surface antigens on CD34+ and AC133+ bone marrow (BM) cells. Coexpression analysis of AC133 and defined antigens on CD34+ BM cells revealed that the majority of the CD164+, CD135+, CD117+, CD38low, CD33+, and CD71low cells resides in the AC133+ population. In contrast, most of the CD10+ and CD19+ B cell progenitors and a fraction of the CD71high population are AC133-, indicating that CD34+AC133+ cells are enriched in primitive and myeloid progenitor cells, whereas CD34+AC133- cells mainly consist of B cell and late erythroid progenitors. This corresponds to the highly reduced percentage of CD10+ B cells and the absence of CD71high erythroid progenitors on AC133+ selected BM cells. A portion of 0.2-0.7% of the AC133+ selected cells do not coexpress CD34. These cells are very small and define a uniform CD71-, CD117-, CD10-, CD38low, CD135+, HLA-DRhigh, CD45+ population with unknown delineation. Four color analysis on CD34+CD38- BM cells revealed that virtually all of these primitive cells express AC133. Using an improved liposome-enhanced labeling technique for the staining of weakly expressed antigens, subsets of this population could be identified which express the angiopoietin receptors TIE (67.6%) and TEK (36.8%), the vascular endothelial growth factor receptors FLT1 (7%), FLT4 (3.2%), and KDR (10.4%), or the receptor tyrosine kinases HER-2 (15.4%) and FLT3 (CD135; 77.6%). Our results suggest that the CD34+CD38- population is heterogeneous with respect to the expression of the analyzed receptor tyrosine kinases.
A Murine Renal Cell Carcinoma (1973)

Journal Article A Murine Renal Cell Carcinoma Get access G. P. Murphy, G. P. Murphy * Roswell Park Memorial Institute, New York State Department of Health, State University of New York at Buffalo, Buffalo, New York 14203 2Address reprint requests to: Dr. Gerald P. Murphy, Institute Director, Roswell Park Memorial Institute, 666 Elm Street, Buffalo, N.Y. 14203. Search for other works by this author on: Oxford Academic PubMed Google Scholar W. J. Hrushesky W. J. Hrushesky Roswell Park Memorial Institute, New York State Department of Health, State University of New York at Buffalo, Buffalo, New York 14203 Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 50, Issue 4, April 1973, Pages 1013–1025, https://doi.org/10.1093/jnci/50.4.1013 Published: 01 April 1973 Article history Received: 18 August 1972 Accepted: 29 December 1972 Published: 01 April 1973
Ciliopathies (2011)

A ciliopathy is a disease in which a hairlike cellular organelle called the cilium is dysfunctional. Most proteins altered in these single-gene disorders function at the level of the cilium–centrosome complex. This review considers the role of the cilium in disease.
Imaging DNA molecules on mica surface by atomic force microscopy in air and in liquid (2005)

DNA molecules immobilized on mica surface by various methods have been observed by atomic force microscopy both in air and in liquid. Divalent cations and 3-aminopropyltriethoxysilane (APTES) modified mica surface have been used to immobilize the DNA molecules. Optimal DNA and divalent cations concentration for AFM imaging are presented. Among the different methods of modifying mica surface with APTES, the water solution modifying method appears to get the best results. When using high DNA concentration for AFM imaging, DNA networks can be formed. A simple method to extend long DNA molecules is demonstrated. The optimal imaging conditions and AFM operating techniques are discussed. Different DNA immobilizing methods have been compared and evaluated.
Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing (2013)

There has been a growing interest in using next-generation sequencing (NGS) to profile extracellular small RNAs from the blood and cerebrospinal fluid (CSF) of patients with neurological diseases, CNS tumors, or traumatic brain injury for biomarker discovery. Small sample volumes and samples with low RNA abundance create challenges for downstream small RNA sequencing assays. Plasma, serum, and CSF contain low amounts of total RNA, of which small RNAs make up a fraction. The purpose of this study was to maximize RNA isolation from RNA-limited samples and apply these methods to profile the miRNA in human CSF by small RNA deep sequencing. We systematically tested RNA isolation efficiency using ten commercially available kits and compared their performance on human plasma samples. We used RiboGreen to quantify total RNA yield and custom TaqMan assays to determine the efficiency of small RNA isolation for each of the kits. We significantly increased the recovery of small RNA by repeating the aqueous extraction during the phenol-chloroform purification in the top performing kits. We subsequently used the methods with the highest small RNA yield to purify RNA from CSF and serum samples from the same individual. We then prepared small RNA sequencing libraries using Illumina's TruSeq sample preparation kit and sequenced the samples on the HiSeq 2000. Not surprisingly, we found that the miRNA expression profile of CSF is substantially different from that of serum. To our knowledge, this is the first time that the small RNA fraction from CSF has been profiled using next-generation sequencing.
Soft-x-ray projection lithography: printing of 02-μm features using a 20:1 reduction (1990)

We demonstrate nearly diffraction-limited printing of 0.2-microm features, using soft x rays of approximately 36-nm wavelength. An open-stencil transmission mask with minimum features of 4 microm was imaged by a twentyfold-reduction Schwarzschild-type objective onto silicon wafers coated with various e-beam resists. Implications for soft-x-ray projection lithography are discussed.
Structure‐activity study of a laminin α1 chain active peptide segment Ile‐Lys‐Val‐Ala‐Val (IKVAV) (1995)

The IKVAV sequence, one of the most potent active sites of laminin-1, has been shown to promote cell adhesion, neurite outgrowth, and tumor growth. Here we have determined the structural requirements of the IKVAV sequence for cell attachment and neurite outgrowth using various 12-mer synthetic peptide analogs. All-L- and all-D-IKVAV peptides showed cell attachment and neurite outgrowth activities. In contrast, all-L- and all-D-reverse-sequence peptides were not active. Some of the analogs, in which the lysine and isoleucine residues of the IKVAV peptide were substituted with different amino acids, promoted cell attachment, but none of the analog peptides showed neurite outgrowth activity comparable to that of the IKVAV peptide. These results suggest that the lysine and isoleucine residues are critical for the biological functions of the IKVAV peptide.
An Eye-tracking Study of User Interactions with Query Auto Completion (2014)

Query Auto Completion (QAC) suggests possible queries to web search users from the moment they start entering a query. This popular feature of web search engines is thought to reduce physical and cognitive effort when formulating a query.