gebhart/patrepeval huggingface dataset:
Multiple Serotypes and Strains ofStreptococcus Suisin Naturally Infected Swine Herds (1996)

We present a brief description of the epidemiology, clinical signs, and lesions in 21 accessions in which multiple serotypes of S. suis or multiple distinct isolates (strains) of the same capsular serotype of S. suis were identified. Isolates of the same capsular serotype that had different antibiogram profiles were considered to be distinct isolates or “strains” for the purposes of this study. Streptococcus suis isolates of the same capsular serotype and identical antibiogram profiles were considered to be identical organisms. These cases were selected to determine whether or not herds infected with multiple serotypes (or strains) of S. suis had unique features that might serve to distinguish these herds from those infected with a single serotype and strain of S. suis and to provide additional information on the development of this disease in swine. Selected cases were limited to those in which isolates were identified by capsular serotyping. Untypeable isolates of S. suis were not included in this study. Case selection criteria, data collection procedures, etc., were as previously described. 12 Of 277 accessions in which S. suis was identified, 21 accessions (7.6%) involving 37 pigs were cases in which 46 different isolates of S. suis were identified. The distribution of these isolates is shown in Tables 1 and 2. Because of the small sample size, statistical analyses were not performed. Although there was a slight increase in recovery of S. suis in the fall and winter months for all serotypes, S. suis was readily isolated throughout the year. In this study, there was a slight increase (approximately 5%) in the prevalence of serotypes 3, 7, and 8 and a decrease (approximately 10%) in the prevalence of serotype 2 from those reported previously. 12
Gaseous emboli during off-pump surgery with T-graft technique, two different mechanisms (2010)

We have concluded that carbon-dioxide emboli can also cause massive but temporary haemodynamic deterioration during off-pump surgery despite higher solubility in blood. The blower should be used only when a bull-dog clamp is applied on the graft. Also, proper de-airing and flushing of grafts is very important and avoids consequences of the trapped small emboli.
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts (2002)

http://genecensus.org/expression/translatome
An Overview of Wavelet Based Multiresolution Analyses (1994)

In this paper an overview of wavelet based multiresolution analyses is presented. First, the continuous wavelet transform in its simplest form is discussed. Then, the definition of a multiresolution analysis is given and how wavelets fit into it is shown. The authors take a closer look at orthogonal, biorthogonal and semiorthogonal wavelets. The fast wavelet transform, wavelets on an interval, multidimensional wavelets and wavelet packets are discussed. Several examples of wavelet families are introduced and compared. Finally, the essentials of two major applications are outlined: data compression and compression of linear operators.
Molecular Detection of APC, K‐ras, and p53 Mutations in the Serum of Colorectal Cancer Patients as Circulating Biomarkers (2004)

Early detection of tumor DNA in serum/plasma prior to the development of recurrence or metastases could help improve the outcome of patients with colorectal cancer (CRC) after tumor resection. Recent advances in the detection of tumor DNA in the serum/plasma has opened up numerous new areas for investigation and new possibilities for molecular diagnosis. APC and K- ras mutations are considered to be early-stage developments of CRCs, whereas p53 mutations are thought to be relatively late events in the tumorigenesis of CRCs. The aim of this study was to search for the presence of genetic mutations in the DNA extracted from the serum of CRC patients and healthy subjects. We simultaneously evaluate the significance of APC, K- ras, and p53 gene mutations in cancer tissues and their paired serum samples of 104 CRC patients by polymerase chain reaction-single strand conformation polymorphism analysis (PCR-SSCP) followed by direct sequencing. Additionally, analysis was carried out to detect the serum carcinoembryonic antigen (CEA) levels in CRC patients. Overall, we found at least one of the gene mutations in tumor tissues from 75% (78/104) of the CRC patients. Comparison of the three molecular markers showed that the detection rates in the serum were 30.4%, 34.0%, and 34.2% for APC, K- ras, and p53 genes, respectively. Of these patients, 46.2% (36/78) were identified as having positive serum results, whereas all healthy controls remained negative. The overall positive tumor DNA detection rates in the serum were 0% (0/7) for Dukes' A classification, 22.4% (11/49) for Dukes' B, 48.7% (19/39) for Dukes' C, and 66.7% (6/9) for Dukes' D. The detection rate increased as the tumor stage progressed ( p = 0.012). Concurrently, a significant difference was observed between lymph node metastases and positive serum tumor DNA detection ( p < 0.001). A significantly higher postoperative metastasis/recurrence rate in patients harboring gene mutations with serum tumor DNA than those without serum tumor DNA was also demonstrated ( p < 0.001). However, no significant correlation between the postoperative metastasis/recurrence and serum CEA levels was observed ( p = 0.247). These data suggest that the identification of circulating tumor DNA using the molecular detection of APC, K- ras, and p53 gene mutations is a potential tool for early detection of postoperative recurrence/metastases. Moreover, these genes may be potential molecular markers of poor clinical outcome in CRC patients.
Sequence variation in the 3′‐untranslated region of the dopamine transporter gene and attention‐deficit hyperactivity disorder (ADHD) (2005)

The dopamine transporter gene (DAT1) has been reported to be associated with attention-deficit hyperactivity disorder (ADHD) in a number of studies [Cook et al. (1995): Am J Human Genet 56(4):9993-998; Gill et al. (1997): Mol Psychiatry 2(4):311-313; Waldman et al. (1998): Am J Human Genet 63(6):1767-1776; Barr et al. (2001): Biol Psychiatry 49(4):333-339; Curran et al. (2001): Mol Psychiatry 6(4):425-428; Chen et al. (2003): Mol Psychiatry 8(4):393-396]. Specifically, the 10-repeat allele of the 40-bp variable number of tandem repeats (VNTR) polymorphism located in the 3' untranslated region (UTR) of the gene has been found to be associated with ADHD. There is evidence from in vitro studies indicating that variability in the repeat number, and sequence variation in the 3'-UTR of the DAT1 gene may influence the level of the dopamine transporter protein [Fuke et al. (2001): Pharmacogenomics J 1(2):152-156; Miller and Madras (2002): Mol Psychiatry 7(1):44-55]. In this study, we investigated whether DNA variation in the DAT1 3'UTR contributed to ADHD by genotyping DNA variants around the VNTR region in a sample of 178 ADHD families. These included a MspI polymorphism (rs27072), a DraI DNA change (T/C) reported to influence DAT1 expression levels, and a BstUI polymorphism (rs3863145) in addition to the VNTR. We also screened the VNTR region by direct resequencing to determine if there was sequence variation within the repeat units that could account for the association. Our results indicate that DAT1 is associated with ADHD in our sample but not with alleles of the VNTR polymorphism. We did not find any variation in the sequence for either the 10- or 9-repeat alleles in the probands screened nor did we observe the reported DraI (T/C) variation. Our results therefore refute the possibility of the reported DraI variation or alleles of the VNTR as the functional variants contributing to the disorder.
Biogenesis and speciation of nascent apoA-I-containing particles in various cell lines (2005)

It is generally thought that the large heterogeneity of human HDL confers antiatherogenic properties; however, the mechanisms governing HDL biogenesis and speciation are complex and poorly understood. Here, we show that incubation of exogenous apolipoprotein A-I (apoA-I) with fibroblasts, CaCo-2, or CHO-overexpressing ABCA1 cells generates only alpha-nascent apolipoprotein A-I-containing particles (alpha-LpA-I) with diameters of 8-20 nm, whereas human umbilical vein endothelial cells and ABCA1 mutant (Q597R) cells were unable to form such particles. Interestingly, incubation of exogenous apoA-I with either HepG2 or macrophages generates both alpha-LpA-I and prebeta1-LpA-I. Furthermore, glyburide inhibits almost completely the formation of alpha-LpA-I but not prebeta1-LpA-I. Similarly, endogenously secreted HepG2 apoA-I was found to be associated with both prebeta1-LpA-I and alpha-LpA-I; by contrast, CaCo-2 cells secreted only alpha-LpA-I. To determine whether alpha-LpA-I generated by fibroblasts is a good substrate for LCAT, isolated alpha-LpA-I as well as reconstituted HDL [r(HDL)] was reacted with LCAT. Although both particles had similar V(max) (8.4 vs. 8.2 nmol cholesteryl ester/h/microg LCAT, respectively), the K(m) value was increased 2-fold for alpha-LpA-I compared with r(HDL) (1.2 vs. 0.7 microM apoA-I). These results demonstrate that 1) ABCA1 is required for the formation of alpha-LpA-I but not prebeta1-LpA-I; and 2) alpha-LpA-I interacts efficiently with LCAT. Thus, our study provides direct evidence for a new link between specific cell lines and the speciation of nascent HDL that occurs by both ABCA1-dependent and -independent pathways.
Volumetric Acoustic Vector Intensity Probe (2006)

A new measurement tool capable of imaging the acoustic intensity vector throughout a large volume is discussed. This tool consists of an array of fifty microphones that form a spherical surface of radius 0.2m. A simultaneous measurement of the pressure field across all the microphones provides time-domain near-field holograms. Near-field acoustical holography is used to convert the measured pressure into a volumetric vector intensity field as a function of frequency on a grid of points ranging from the center of the spherical surface to a radius of 0.4m. The volumetric intensity is displayed on three-dimensional plots that are used to locate noise sources outside the volume. There is no restriction on the type of noise source that can be studied. The sphere is mobile and can be moved from location to location to hunt for unidentified noise sources. An experiment inside a Boeing 757 aircraft in flight successfully tested the ability of the array to locate low-noise-excited sources on the fuselage. Reference transducers located on suspected noise source locations can also be used to increase the ability of this device to separate and identify multiple noise sources at a given frequency by using the theory of partial field decomposition. The frequency range of operation is 0 to 1400Hz. This device is ideal for the study of noise sources in commercial and military transportation vehicles in air, on land and underwater.
Bovine papillomavirus vector that propagates as a plasmid in both mouse and bacterial cells. (1982)

We report the construction of a bovine papillomavirus (BPV)-derived recombinant plasmid that propagates as an extrachromosomal element in both mouse and bacterial cells. Plasmids composed of a subgenomic transforming fragment of BPV DNA, a deletion derivative of pBR322, and a 7.6-kilobase fragment of DNA from the human beta-globin gene cluster efficiently induce focus formation on mouse C127 cells. BPV-beta-globin hybrids are maintained in the transformed cells as plasmids with a copy number of about 10-30 per cell. Plasmids indistinguishable from the input DNA have been recovered by transformation of bacteria with low molecular weight DNA from transformed mouse cells. The human beta-globin gene linked to BPV DNA is transcribed from its own promoter at a high level in these cells. The expression of BPV-linked cellular genes in conjunction with the ability to shuttle DNA between bacteria and mammalian cells may provide a rapid means of analyzing and recovering genes that confer an identifiable phenotype upon mammalian cells.
Thermal Oxidation of Silicon in Dry Oxygen Growth‐Rate Enhancement in the Thin Regime: I . Experimental Results (1985)

In many studies of oxidation kinetics, it has been observed that growth in dry oxygen in the thin regime (<500Å) is faster than the classic description of growth in thicker layers by a linear‐parabolic relationship. Growth‐rate enhancement in the thin regime was studied in the 800°–1000°C range under a variety of substrate doping densities and partial pressures using in situ ellipsometry. The enhancement in oxidation rate is found to decay exponentially with thickness, and its thickness extent is approximately independent of substrate orientation, doping density, and oxygen partial pressure; its oxygen pressure and substrate doping dependence suggest that it is caused by physical mechanisms associated with the substrate. Such mechanisms are discussed in part II of this paper (11).
Synthesis of functionalised fluorescent dyes and their coupling to amines and amino acids (1997)

A series of novel functionalised benzophenoxazinones, analogues of Nile Red, is prepared and their fluorescence properties evaluated. The ring system is prepared by reaction of 5-diethylamino-2-nitrosophenol with 1,6-dihydroxynaphthalene followed by alkylation of the 2-hydroxy group with 6-bromohexanoic acid derivatives. Subsequent ester cleavage under a variety of conditions gives the acid 6. Replacement of the 9-diethylamino group with the N-ethyl-(3-sulfonylpropyl)amino group is carried out to increase water solubility and the resulting dye 14 has similar fluorescence properties. The acid 6 is coupled to a range of amino compounds.
Mussel‐Inspired Block Copolymer Lithography for Low Surface Energy Materials of Teflon, Graphene, and Gold (2011)

Mussel-inspired interfacial engineering is synergistically integrated with block copolymer (BCP) lithography for the surface nanopatterning of low surface energy substrate materials, including, Teflon, graphene, and gold. The image shows the Teflon nanowires and their excellent superhydrophobicity.
High level heterologous expression inE.coliusing mutant forms of thelacpromoter (1991)

Single base deletions in the lac promoter which reduced the 18bp spacing between the -35 and -10 homology regions to 17bp, increased the strength of the promoter. A single base substitution (T----G) in the -35 region to generate the consensus sequence TTG-ACA increased the strength further and no longer required a 17bp spacing. The mutated lac promoter was as powerful as a shorter form of the tac promoter which lacked two AT-rich regions upstream of the -35 region, and expressed the P69 surface antigen (pertactin) of Bordetella pertussis to 30-40% total cell protein and tetanus toxin fragment C to 16-20% total cell protein.
Operator performance and localized muscle fatigue in a simulated space vehicle control task (1979)

Fourier transforms in a special purpose computer were utilized to obtain power spectral density functions from electromyograms of the biceps brachii, triceps brachii, brachioradialis, flexor carpi ulnaris, brachialis, and pronator teres in eight subjects performing isometric tracking tasks in two directions utilizing a prototype spacecraft rotational hand controller. Analysis of these spectra in general purpose computers aided in defining muscles involved in performing the task, and yielded a derived measure potentially useful in predicting task termination. The triceps was the only muscle to show significant differences in all possible tests for simple effects in both tasks and, overall, was the most consistently involved of the six muscles. The total power monitored for triceps, biceps, and brachialis dropped to minimal levels across all subjects earlier than for other muscles. However, smaller variances existed for the biceps, brachioradialis, brachialis, and flexor carpi ulnaris muscles and could provide longer predictive times due to smaller standard deviations for a greater population range.
Incidence and prognostic significance of spontaneous and inducible antidromic tachycardia (2012)

Antidromic tachycardia induction is rare in pre-excitation syndrome and generally is associated with spontaneous or electrophysiological malignant form, but clinical outcome does not differ.
Formulating characteristics of high and low 2‐phenyl linear alkylbenzene sulfonates in liquid detergents (1988)

Abstract Detergent range linear alkylbenzene (LAB) currently is manufactured by two different processes, using either aluminum chloride or hydrogen fluoride as the alkylation catalyst. The alkylates from the two processes are not exactly the same. Furthermore, the properties of the linear alkylbenzene sulfonate (LAS) surfactants made by sulfonation of the LABs also differ. Because LAS is used in most types of detergent products, it is important to known how the properties of each type of LAS differ. This paper compares the formulating characteristics (such as viscosity, solubility and foaming) of high and low 2‐phenyl LAS in some typical household cleaning product formulations. It is concluded that the two types of LAS should not be used interchangeably without first checking carefully all the physical properties required in a product.
Amino-terminal-derived JNK Fragment Alters Expression and Activity of c-Jun, ATF2, and p53 and Increases H2O2-induced Cell Death (2000)

The stress-activated protein kinase JNK plays an important role in the stability and activities of key regulatory proteins, including c-Jun, ATF2, and p53. To better understand mechanisms underlying the regulation of JNK activities, we studied the effect of expression of the amino-terminal JNK fragment (N-JNK; amino acids 1-206) on the stability and activities of JNK substrates under nonstressed growth conditions, as well as after exposure to hydrogen peroxide. Mouse fibroblasts that express N-JNK under tetracycline-off (tet-off) inducible promoter exhibited elevated expression of c-Jun, ATF2, and p53 upon tetracycline removal. This increased coincided with elevated transcriptional activities of p53, but not of c-Jun or ATF2, as reflected in luciferase activities of p21(Waf1/Cip1)-Luc, AP1-Luc, and Jun2-Luc, respectively. Expression of N-JNK in cells that were treated with H(2)O(2) impaired transcriptional output as reflected in a delayed and lower level of c-Jun-, limited ATF2-, and reduced p53-transcriptional activities. N-JNK elicited an increase in H(2)O(2)-induced cell death, which is p53-dependent, because it was not seen in p53 null cells yet could be observed upon coexpression of p53 and N-JNK. The ability to alter the activity of ATF2, c-Jun, and p53 and the degree of stress-induced cell death by a JNK-derived fragment identifies new means to elucidate the nature of JNK regulation and to alter the cellular response to stress.
Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia (2007)

Recurrent genomic alterations, mainly losses and gains of specific chromosomes and/or regions, in chronic lymphocytic leukemia (CLL) are recognized as important independent predictors of prognosis and disease progression. The current standard clinical practice for identifying these alterations is chromosome analysis and in situ hybridization with probes targeting 4-5 chromosome regions. We sought to apply array comparative genomic hybridization (array-CGH) technology for the simultaneous detection of genomic imbalances of all loci implicated in CLL. DNA from enriched B-cells from CLL patients were analyzed by array-CGH on a customized CLL BAC array. Copy number changes were detected in 87% of samples with a sensitivity of 100% in samples with clonal abnormalities present in at least 23% of the cells. Furthermore, in nine cases genomic alterations were observed that were undetectable by standard cytogenetic and/or FISH analyses. One of these patients had a 13q14 deletion that was missed by the clinical CLL FISH panel probe set. Our results suggest that a subset of potentially significant genomic alterations in CLL is being missed by the current available techniques. Furthermore, this pilot study clearly shows the robustness, high sensitivity, and high specificity for the targeted CLL microarray analysis as well as the potential for use in routine screening in CLL.
Identity of HML‐1 Antigen on Intestinal Intraepithelial T Cells and of B‐ly7 Antigen on Hairy Cell Leukaemia (1990)

Immunoprecipitation of radioiodinated hairy cell leukaemia (HCL) cell lysates with monoclonal antibody (MoAb) HML-1, originally reported to recognize intraepithelial T cells, and with MoAb B-ly7, originally reported to react with HCL, led to identical biochemical characteristics. In SDS-PAGE under reducing conditions, a major band of 143 kDa, a broad band ranging from 112 to 122 kDa, and two additional faint bands of 175 and 100 kDa could be determined. Deglycosylation of N-linked sugar moieties by treatment of immunoprecipitates with endoglycosidases indicated that the two main protein cores of the antigen are predominantly if not exclusively glycosylated by complex and hybrid types of oligosaccharide chains. Competitive binding inhibition demonstrated that both MoAb are directed against different epitopes. Immunohistochemically, the staining patterns obtained with both MoAb in normal tissues, in T- and B-cell lymphomas, and in HCL were identical except for a single case of HCL which was HML-1-/B-ly-7+. We conclude that MoAb HML-1 and B-ly7 recognize the same antigen.
Melanoma prevention strategy based on using tetrapeptide α‐MSH analogs that protect human melanocytes from UV‐induced DNA damage and cytotoxicity (2006)

Melanoma is the deadliest form of skin cancer, with no cure for advanced disease. We propose a strategy for melanoma prevention based on using analogs of alpha-melanocyte stimulating hormone (alpha-MSH) that function as melanocortin 1 receptor (MC1R) agonists. Treatment of human melanocytes with alpha-MSH results in stimulation of eumelanin synthesis, reduction of apoptosis that is attributable to reduced hydrogen peroxide generation and enhanced repair of DNA photoproducts. These effects should contribute to genomic stability of human melanocytes, thus preventing their malignant transformation to melanoma. Based on these findings, we synthesized and tested the effects of 3 tetrapeptide alpha-MSH analogs, Ac-His-D-Phe-Arg-Trp-NH2, n-Pentadecanoyl- and 4-Phenylbutyryl-His-D-Phe-Arg-Trp-NH2, on cultured human melanocytes. The latter two analogs were more potent than the former, or alpha-MSH, in stimulating the activity of tyrosinase, thus melanogenesis, reducing apoptosis and release of hydrogen peroxide and enhancing repair of DNA photoproducts in melanocytes exposed to UV radiation (UVR). The above analogs are MC1R agonists, as their effects were abrogated by an analog of agouti signaling protein, the physiological MC1R antagonist, and were absent in melanocytes expressing loss-of-function MC1R. Analogs, such as 4-Phenylbutyryl-His-D-Phe-Arg-Trp-NH2 with prolonged and reversible effects, can potentially be developed into topical agents to prevent skin photocarcinogenesis, particularly melanoma.
Assessment of the Low-Cost Cavidi ExaVir Load Assay for Monitoring HIV Viral Load in Pediatric and Adult Patients (2009)

The HIV RT assay was comparable to the HIV RNA assay with sensitivity approaching that of HIV RNA. Smaller volumes than the recommended 1 mL can be used, improving utility of this assay for pediatric monitoring.