gebhart/patrepeval huggingface dataset:
Insecticide Resistance Genes in Culex pipiens (Diptera: Culicidae) from Italy: Esterase B Locus at the Dna Level (1994)

Restriction fragment length polymorphism (RFLP) analysis at the esterase B locus was performed in samples from four populations of Italian Culex pipiens pipiens L. to identify correctly, at the molecular level, the resistance gene. The absence of the amplified B2 haplotype was confirmed, indicating that it has not increased in frequency after its detection in continental Italy around 1985. The B4 haplotype was detected in all populations at the same frequencies as a previous starch gel survey. The possibility that B4 amplification has occurred only once and has migrated across western Mediterranean region is supported by the data. A1 also was detected indirectly by the presence of its closely linked B allele. The B5 haplotype apparently was absent. No amplification at the esterase B locus was detected, except B4, indicating a low rate of occurrence of new amplification at this locus.
PAPR1 expression in testicular germ cell tumors. (2012)

e15027 Background: Testicular germ-cell tumours (TGCTs) represent a model for the cure of cancer. Nonetheless, a small proportion of patients develop disease recurrence. PARP inhibitors represent a new class of promising drugs in anticancer therapy. The aim of this study was to evaluate poly(ADP-ribose)polymerase-1 (PARP1) expression in TGCTs and to correlate expression patterns with clinico-pathological variables. Methods: In this translational study, tumor specimens from 124 patients with GCTs were identified. PARP1 expression was detected by immunohistochemistry using monoclonal antibody, scored by the multiplicative quickscore (QS) method and compared to PARP1 expression in testicular tissue of normal testis. The QS was calculated by multiplying the percentage score by the staining intensity score to yield a minimum value of 0 and a maximum value of 18. Based on the QS nuclear PARP1 expression was graded as low (0–9) or high (10–18). Results: We observed higher expression of PARP1 in testicular tumors compared to normal tissue of testis (mean QS = 10.04 vs. 3.60, p &lt; 0.0000001). Mean QS ± SD for each histological subtype was following: intratubular germ cell neoplasia (ITGCN) = 18.00 ± 0.00, embryonal carcinoma = 9.62 ± 5.64, seminoma = 9.74 ± 6.51, yolc sac tumor = 7.8 ± 7.20, teratoma = 5.87 ± 5.34, and choriocarcinoma = 4.50 ± 8.33. The PARP1 overexpression (QS &gt; 9) was most often detected in ITGCN (100% of specimen with PARP1 overexpression), seminona (52.6%), embryonal carcinoma (47.0%), yolc sac tumor (33.3%), teratoma (26.7%), and choriocarcinoma (25.0%), compared to 1.9% of normal testicular tissue specimen. There was no association between PARP1 expression and clinical variables. Conclusions: PARP1 overexpression is an early event in the development of TGCTs. We suggest that PARP1 could represent a novel treatment target in TGCTs and the assessment of PARP1 expression in tumor samples may lead to the consideration of TGCTs patients for PARP inhibitor therapy.
Automated choroid segmentation based on gradual intensity distance in HD-OCT images (2015)

The choroid is an important structure of the eye and plays a vital role in the pathology of retinal diseases. This paper presents an automated choroid segmentation method for high-definition optical coherence tomography (HD-OCT) images, including Bruch's membrane (BM) segmentation and choroidal-scleral interface (CSI) segmentation. An improved retinal nerve fiber layer (RNFL) complex removal algorithm is presented to segment BM by considering the structure characteristics of retinal layers. By analyzing the characteristics of CSI boundaries, we present a novel algorithm to generate a gradual intensity distance image. Then an improved 2-D graph search method with curve smooth constraints is used to obtain the CSI segmentation. Experimental results with 212 HD-OCT images from 110 eyes in 66 patients demonstrate that the proposed method can achieve high segmentation accuracy. The mean choroid thickness difference and overlap ratio between our proposed method and outlines drawn by experts was 6.72µm and 85.04%, respectively.
Functional three-domain single-chain T-cell receptors. (1994)

T-cell receptors (TCRs) are membrane anchored heterodimers structurally related to antibody molecules. Single-chain antibodies can be engineered by linking the two variable domains, which fold properly by themselves. However, proper assembly of the variable domains of a human TCR (V alpha and V beta) that recognize the HLA-DR2b/myelin basic protein-(85-99) peptide complex was critically dependent on the addition of a third domain, the constant region of the TCR beta chain (C beta), to the single-chain construct. Single-chain molecules with the three-domain design, but not those with the two-domain design, expressed in a eukaryotic cell as chimeric molecules linked either to glycosyl phosphatidylinositol or to the transmembrane/cytoplasmic domains of the CD3 zeta chain were recognized by a conformation-sensitive monoclonal antibody. The chimeric three-domain single-chain TCR linked to CD3 zeta chain signaled in response to both the specific HLA-DR/peptide and the HLA-DR/superantigen staphylococcal enterotoxin B complexes. Thus, by using this three-domain design, functional single-chain TCR molecules were expressed with high efficiency. The lipid-linked single-chain TCR was solubilized by enzymatic cleavage and purified by affinity chromatography. The apparent requirement of the constant domain for cooperative folding of the two TCR variable domains may reflect significant structural differences between TCR and antibody molecules.
Acid phosphatases of Escherichia coli: molecular cloning and analysis of agp, the structural gene for a periplasmic acid glucose phosphatase (1988)

Several unknown Escherichia coli genes for different species of acid phosphatase were cloned in vivo with the plasmid Mu dII4042. When present in a multicopy state, each gene promoted hydrolysis of p-nitrophenyl-phosphate at acidic pH. Among seven recombinant clones that encoded periplasmic acid phosphatase activities, five different genes could be distinguished by the pH optimum and substrate preference for the enzyme and by the restriction enzyme pattern. A 1.7-kilobase recombinant DNA fragment, common to two clones, was inserted into plasmid pBR322 and shown to contain a new gene, agp, which leads to the overexpression of the periplasmic acid glucose-1-phosphatase, a dimer of a 44-kilodalton polypeptide. Fusions of agp to gene phoA deprived of its own signal sequence conferred an alkaline phosphatase-positive phenotype to bacteria, showing the presence of an export signal on agp. The resulting hybrid proteins were characterized by immunoprecipitation with an antiserum directed against purified acid phosphatase or against alkaline phosphatase, showing that agp is the structural gene of the acid phosphatase. The beginning, the orientation, and the end of gene agp on the cloned DNA fragment were determined by the characteristics of such hybrid proteins.
Conditional Neuronal Nitric Oxide Synthase Overexpression Impairs Myocardial Contractility (2007)

The role of the neuronal NO synthase (nNOS or NOS1) enzyme in the control of cardiac function still remains unclear. Results from nNOS(-/-) mice or from pharmacological inhibition of nNOS are contradictory and do not pay tribute to the fact that probably spatial confinement of the nNOS enzyme is of major importance. We hypothesize that the close proximity of nNOS and certain effector molecules like L-type Ca(2+)-channels has an impact on myocardial contractility. To test this, we generated a new transgenic mouse model allowing conditional, myocardial specific nNOS overexpression. Western blot analysis of transgenic nNOS overexpression showed a 6-fold increase in nNOS protein expression compared with noninduced littermates (n=12; P<0.01). Measuring of total NOS activity by conversion of [(3)H]-l-arginine to [(3)H]-l-citrulline showed a 30% increase in nNOS overexpressing mice (n=18; P<0.05). After a 2 week induction, nNOS overexpression mice showed reduced myocardial contractility. In vivo examinations of the nNOS overexpressing mice revealed a 17+/-3% decrease of +dp/dt(max) compared with noninduced mice (P<0.05). Likewise, ejection fraction was reduced significantly (42% versus 65%; n=15; P<0.05). Interestingly, coimmunoprecipitation experiments indicated interaction of nNOS with SR Ca(2+)ATPase and additionally with L-type Ca(2+)- channels in nNOS overexpressing animals. Accordingly, in adult isolated cardiac myocytes, I(Ca,L) density was significantly decreased in the nNOS overexpressing cells. Intracellular Ca(2+)-transients and fractional shortening in cardiomyocytes were also clearly impaired in nNOS overexpressing mice versus noninduced littermates. In conclusion, conditional myocardial specific overexpression of nNOS in a transgenic animal model reduced myocardial contractility. We suggest that nNOS might suppress the function of L-type Ca(2+)-channels and in turn reduces Ca(2+)-transients which accounts for the negative inotropic effect.
Increasing the thermal stability of euphauserase (2001)

A molecular model of Antarctic krill euphauserase based on the known crystal structure of its fiddler crab analog, collagenase I, indicates that the core structure of these enzymes is almost identical. Euphauserase is a cold-active and thermally sensitive enzyme with a high affinity for Lys, Arg and large hydrophobic amino acids. Residue Phe137 in euphauserase, localized in loop D (autolysis loop), is highly exposed on the surface of the molecule. Therefore, it appeared to be an easy target for autolysis. The broadly specific euphauserase has a low affinity for negatively charged residues. In order to increase the stability of the enzyme, two mutants were created in which residue Phe137 was replaced by a Glu and an Asp residue. Both mutations resulted in increased stability of the recombinant euphauserase towards thermal inactivation.
Induction of Adipophilin-Specific Cytotoxic T Lymphocytes Using a Novel HLA-A2-Binding Peptide That Mediates Tumor Cell Lysis (2004)

Identification of tumor-associated antigens and advances in tumor immunology resulted in the development of vaccination strategies to treat patients with malignant diseases. Using a novel approach that combines DNA chip analysis of tumor samples with isolation of peptides on the surface of tumor cells, a HLA-A*0201-binding peptide derived from the adipophilin protein was identified. Adipophilin is involved in lipid storage and was thought to be expressed only in adipocytes, but it can be found in other cell types such as macrophages or tumor cells. In the present study, we analyzed the possible use of this peptide as a T-cell epitope presented by malignant cells. To accomplish this, we induced CTL responses using this HLA-A*0201-binding peptide. The in vitro-induced CTLs efficiently lysed cells pulsed with the adipophilin peptide and HLA-matched tumor cell lines in an antigen-specific and HLA-restricted manner. Finally, the induced CTLs recognized autologous dendritic cells (DCs) pulsed with the antigenic peptide or transfected with tumor RNA purified from an adipophilin-expressing tumor cell line. To further analyze the possible use of this peptide in immunotherapies of human malignancies, we induced adipophilin-specific CTLs using peripheral blood mononuclear cells and DCs from HLA-A*0201-positive patients with chronic lymphatic leukemia and plasma cell leukemia. The in vitro-generated CTLs recognized autologous chronic lymphatic leukemia cells and malignant plasma cells, whereas they spared nonmalignant resting or activated B and T lymphocytes, monocytes, or DCs. Our results demonstrate that this peptide might represent an interesting candidate for the development of cancer vaccines designed to target adipophilin-derived epitopes in a wide range of malignancies.
Fluctuations in CA 125 and CA 15 3 serum concentrations during spontaneous ovulatory cycles (1999)

The aim of this study was to investigate cycle dependent changes of serum CA 125 and CA 15-3 concentrations during spontaneous ovulatory cycles. Twenty apparently healthy women with spontaneous menstrual cycles attending our infertility clinic were included. Of these women, 18 had occluded tubes as a result of sterilization. Ovulation was confirmed by luteinizing hormone test and ultrasonography and, to exclude endometriosis, a laparoscopy was performed. Serum samples for CA 125, CA 15-3, 17 beta-oestradiol and progesterone determinations were taken every second day starting on the 2nd day of the cycle until the 7th day of the next cycle. After correction for inter-individual variation in serum concentrations, highest CA 125 concentrations were found during the menstruation. During the follicular and peri-ovulatory phase CA 125 serum concentrations were lowest. For CA 15-3, serum concentrations were not statistically different throughout the cycle. CA 125 and oestradiol concentrations were negatively correlated, CA 15-3 and oestradiol concentrations were positively correlated. Absolute serum concentrations of both CA 125 and CA 15-3 vary among females. Within the female, fluctuations of CA 125 are phase related. In the population studied most of the patients had tubal obstruction and high CA 125 serum concentrations during menstruation, which revokes the theory that the menstrual rise of CA 125 is due only to retrograde menstruation.
Multiplexed Real-Time Polymerase Chain Reaction on a Digital Microfluidic Platform (2010)

This paper details the development of a digital microfluidic platform for multiplexed real-time polymerase chain reactions (PCR). Liquid samples in discrete droplet format are programmably manipulated upon an electrode array by the use of electrowetting. Rapid PCR thermocycling is performed in a closed-loop flow-through format where for each cycle the reaction droplets are cyclically transported between different temperature zones within an oil-filled cartridge. The cartridge is fabricated using low-cost printed-circuit-board technology and is intended to be a single-use disposable device. The PCR system exhibited remarkable amplification efficiency of 94.7%. To test its potential application in infectious diseases, this novel PCR system reliably detected diagnostic DNA levels of methicillin-resistant Staphylococcus aureus (MRSA), Mycoplasma pneumoniae , and Candida albicans . Amplification of genomic DNA samples was consistently repeatable across multiple PCR loops both within and between cartridges. In addition, simultaneous real-time PCR amplification of both multiple different samples and multiple different targets on a single cartridge was demonstrated. A novel method of PCR speed optimization using variable cycle times has also been proposed and proven feasible. The versatile system includes magnetic bead handling capability, which was applied to the analysis of simulated clinical samples that were prepared from whole blood using a magnetic bead capture protocol. Other salient features of this versatile digital microfluidic PCR system are also discussed, including the configurability and scalability of microfluidic operations, instrument portability, and substrate-level integration with other pre- and post-PCR processes.
Homogenization of acoustic metamaterials of Helmholtz resonators in fluid (2008)

By using a two-step homogenization approach, we derive analytical formulas of effective mass density ${\ensuremath{\rho}}_{e}$ and effective bulk modulus ${B}_{e}$ for two- and three-dimensional acoustic metamaterials of Helmholtz resonators (HRs) in fluid. A negative ${B}_{e}$ is found at certain frequencies due to the monopolar resonance, leading to a low-frequency acoustic band gap. A unified picture is presented for metamaterials of HRs and three-component metamaterials of negative ${\ensuremath{\rho}}_{e}$. Our work supports recent observations in a one-dimensional array of HRs [N. Fang et al., Nat. Mater. 5, 452 (2006)] and presents important high-dimensional extensions for exploring more fascinating phenomena.
Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing (2015)

Next generation sequencing technologies, like ultra-deep pyrosequencing (UDPS), allows detailed investigation of complex populations, like RNA viruses, but its utility is limited by errors introduced during sample preparation and sequencing. By tagging each individual cDNA molecule with barcodes, referred to as Primer IDs, before PCR and sequencing these errors could theoretically be removed. Here we evaluated the Primer ID methodology on 257,846 UDPS reads generated from a HIV-1 SG3Δenv plasmid clone and plasma samples from three HIV-infected patients. The Primer ID consisted of 11 randomized nucleotides, 4,194,304 combinations, in the primer for cDNA synthesis that introduced a unique sequence tag into each cDNA molecule. Consensus template sequences were constructed for reads with Primer IDs that were observed three or more times. Despite high numbers of input template molecules, the number of consensus template sequences was low. With 10,000 input molecules for the clone as few as 97 consensus template sequences were obtained due to highly skewed frequency of resampling. Furthermore, the number of sequenced templates was overestimated due to PCR errors in the Primer IDs. Finally, some consensus template sequences were erroneous due to hotspots for UDPS errors. The Primer ID methodology has the potential to provide highly accurate deep sequencing. However, it is important to be aware that there are remaining challenges with the methodology. In particular it is important to find ways to obtain a more even frequency of resampling of template molecules as well as to identify and remove artefactual consensus template sequences that have been generated by PCR errors in the Primer IDs.
Novel Bacterial Membrane Surface Display System Using Cell Wall-Less L-Forms of Proteus mirabilis and Escherichia coli (2002)

We describe a novel membrane surface display system that allows the anchoring of foreign proteins in the cytoplasmic membrane (CM) of stable, cell wall-less L-form cells of Escherichia coli and Proteus mirabilis. The reporter protein, staphylokinase (Sak), was fused to transmembrane domains of integral membrane proteins from E. coli (lactose permease LacY, preprotein translocase SecY) and P. mirabilis (curved cell morphology protein CcmA). Both L-form strains overexpressed fusion proteins in amounts of 1 to 100 microg ml(-1), with higher expression for those with homologous anchor motifs. Various experimental approaches, e.g., cell fractionation, Percoll gradient purification, and solubilization of the CM, demonstrated that the fusion proteins are tightly bound to the CM and do not form aggregates. Trypsin digestion, as well as electron microscopy of immunogold-labeled replicas, confirmed that the protein was localized on the outside surface. The displayed Sak showed functional activity, indicating correct folding. This membrane surface display system features endotoxin-poor organisms and can provide a novel platform for numerous applications.
Characterization of Reconstructed Skin Models (2002)

The aim of the present study was to evaluate tissue architecture and lipid composition of commercially available reconstructed human skin models; EpiDerm, SkinEthic and Episkin in comparison to in-house reconstructed epidermis on a de-epidermized dermis (RE-DED) model and native tissue. For this purpose, the tissue architecture was examined using light microscopy, electron microscopy and immunohistochemistry; epidermal lipid composition was analyzed by HPTLC. Histological examination showed a completely stratified epithelium in all skin models closely resembling normal human epidermis. Low intra-batch variation in tissue architecture was observed in all skin models, but moderate to considerable inter-batch variation was noticed. In the stratum corneum extracellular space, lipid lamellae consisting of multiple alternating electron-dense and electron-lucent bands were present. Lipid analyses revealed the presence of all major epidermal lipid classes. Compared with native epidermis and RE-DED in EpiDerm, SkinEthic and Episkin models, the content of polar ceramides 5 and 6 was lower, ceramide 7 was absent, and the content of free fatty acids was very low. Evaluation of the expression and localization of a number of differentiation-specific protein markers revealed that all skin models showed an aberrant expression of keratin 6, skin-derived antileukoproteinase, small-proline-rich proteins, involucrin and transglutaminase. Although variation within batches was low, in particular keratin 6, involucrin and skin-derived antileukoproteinase expression demonstrated some inter-batch variation. In conclusion, all skin models provide a promising means for studying the effects of topically applied chemicals, although the observed deviations in tissue homeostasis and barrier properties need to be diminished. All skin models tested reproduced many of the characteristics of normal human epidermis and therefore provide a morphologically relevant in vitro means to assess skin irritation and perform other skin-related studies.
Factors to Consider When Applying Oxidizing Biocides in the Field (2002)

Abstract Legionella pneumophila, the organism responsible for Legionnaires’ disease, is an ongoing health concern in recreational, industrial, and potable water systems. For example, Legionnaires’ disease outbreaks continue to be associated with hot tubs and spas, cooling towers, and potable hot water systems. Oxidizing biocides based on chlorine, bromine, and other chemistries are recognized as effective microbiological control agents. Many organizations within the last several years have issued standards that recommend the use of oxidizing biocides for minimizing the risk associated with such outbreaks. Although oxidizing biocides can be effective when applied properly, use of them alone cannot be construed as a guaranty of successful microbiological control. Indeed, many factors can adversely impact the performance of oxidizing biocides - the type of make-up water, system impurities, ancillary corrosion and deposit control agents, system metallurgy, system design, operational parameters, sunlight exposure, maintenance practices, etc. Some of these factors are within the control of the water treatment professional; others are not. One thing clear is that biocides must be stored and applied properly in order to achieve the optimum effect. The purpose of this paper is to discuss factors which influence the proper handling and application of oxidizing biocides in building water systems. Some of the factors discussed will include handling characteristics, reactions with common system impurities, compatibility with phosphonates, compatibility with biodispersants, long-term storage stability, and UV stability.
Image indexing using color correlograms (2002)

We define a new image feature called the color correlogram and use it for image indexing and comparison. This feature distills the spatial correlation of colors, and is both effective and inexpensive for content-based image retrieval. The correlogram robustly tolerates large changes in appearance and shape caused by changes in viewing positions, camera zooms, etc. Experimental evidence suggests that this new feature outperforms not only the traditional color histogram method but also the recently proposed histogram refinement methods for image indexing/retrieval.