gebhart/patrepeval huggingface dataset:
A Comparison of Personal Name Matching: Techniques and Practical Issues (2006)

Finding and matching personal names is at the core of an increasing number of applications: from text and Web mining, search engines, to information extraction, deduplication and data linkage systems. Variations and errors in names make exact string matching problematic, and approximate matching techniques have to be applied. When compared to general text, however, personal names have different characteristics that need to be considered. In this paper, we discuss the characteristics of personal names and present potential sources of variations and errors. We then overview a comprehensive number of commonly used, as well as some recently developed name matching techniques. Experimental comparisons using four large name data sets indicate that there is no clear best matching technique
A method for measuring the cycle-to-cycle period jitter of high-frequency clock signals (2002)

This paper introduces the extended /spl Delta//spl phi/ method for measuring cycle-to-cycle period jitter in PLL outputs. The theoretical basis for this method is derived from the limited condition for the average period and analytic signal theory. Sinusoidal jitter measurements verify the relationship between cycle-to-cycle period jitter and timing jitter. To validate the method, experimental data from jitter measurements on a PowerPC/sup TM/ microprocessor is analyzed in the frequency domain. Comparisons of phase quantization errors are made between the extended /spl Delta//spl phi/ method and the conventional zero-crossing method.
A Soluble Form of Lymphocyte Activation Gene-3 (IMP321) Induces Activation of a Large Range of Human Effector Cytotoxic Cells (2007)

The principal antitumor immune response is mediated through the activation of type 1 cytotoxic (Tc1) CD8 T cells, NK cells, and monocytes/macrophages. In this study, we investigated the potency of a clinical-grade soluble form of lymphocyte activation gene-3 protein (IMP321), a physiological high-affinity MHC class II binder, at inducing in PBMCs an appropriate cytotoxic-type response in short-term ex vivo assays. We found that IMP321 binds to a minority (<10%) of MHC class II + cells in PBMCs, including all myeloid dendritic cells, and a small fraction of monocytes. Four hours after addition of IMP321 to PBMCs, these myeloid cells produce TNF-alpha and CCL4 as determined by intracellular staining. At 18 h, 1% of CD8+ T cells and 3.7% NK cells produce Tc1 cytokines such as IFN-gamma and/or TNF-alpha (mean values from 60 blood donors). Similar induction was observed in metastatic cancer patient PBMCs, but the values were lower for the NK cell subset. Early APC activation by IMP321 is needed for this Tc1-type activation because pure sorted CD8+ T cells could not be activated by IMP321. Only Ag-experienced, fully differentiated granzyme+ CD8 T cells (effector and effector memory but not naive or central memory T cells) are induced by IMP321 to full Tc1 activation. In contrast to IMP321, TLR1-9 agonists induce IL-10 and are therefore unable to induce this Tc1 IFN-gamma+ response. Thus, IMP321 has many properties that confirm its potential to be a new class of immunopotentiator in cancer patients.
New insights in the molecular biology and physiology ofStreptococcus thermophilusrevealed by comparative genomics (2005)

Streptococcus thermophilus is a major dairy starter used for the manufacture of yoghurt and cheese. The access to three genome sequences, comparative genomics and multilocus sequencing analyses suggests that this species recently emerged and is still undergoing a process of regressive evolution towards a specialised bacterium for growth in milk. Notably, S. thermophilus has maintained a well-developed nitrogen metabolism whereas its sugar catabolism has been subjected to a high level of degeneracy due to a paucity of carbon sources in milk. Furthermore, while pathogenic streptococci are recognised for a high capacity to expose proteins at their cell surface in order to achieve cell adhesion or to escape the host immune system, S. thermophilus has nearly lost this unique feature as well as many virulence-related functions. Although gene decay is obvious in S. thermophilus genome evolution, numerous small genomic islands, which were probably acquired by horizontal gene transfer, comprise important industrial phenotypic traits such as polysaccharide biosynthesis, bacteriocin production, restriction-modification systems or oxygen tolerance.
Direct immobilization of DNA probes on non-modified plastics by UV irradiation and integration in microfluidic devices for rapid bioassay (2011)

DNA microarrays have become one of the most powerful tools in the field of genomics and medical diagnosis. Recently, there has been increased interest in combining microfluidics with microarrays since this approach offers advantages in terms of portability, reduced analysis time, low consumption of reagents, and increased system integration. Polymers are widely used for microfluidic systems, but fabrication of microarrays on such materials often requires complicated chemical surface modifications, which hinders the integration of microarrays into microfluidic systems. In this paper, we demonstrate that simple UV irradiation can be used to directly immobilize poly(T)poly(C)-tagged DNA oligonucleotide probes on many different types of plastics without any surface modification. On average, five- and fourfold improvement in immobilization and hybridization efficiency have been achieved compared to surface-modified slides with aminated DNA probes. Moreover, the TC tag only costs 30% of the commonly used amino group modifications. Using this microarray fabrication technique, a portable cyclic olefin copolymer biochip containing eight individually addressable microfluidic channels was developed and used for rapid and parallel identification of Avian Influenza Virus by DNA hybridization. The one-step, cost-effective DNA-linking method on non-modified polymers significantly simplifies microarray fabrication procedures and permits great flexibility to plastic material selection, thus making it convenient to integrate microarrays into plastic microfluidic systems.
In Vitro Generation of Human Cytotoxic T Lymphocytes Specific for Peptides Derived From Prostate-Specific Antigen (1997)

Our studies form a rational basis for the use of PSA peptides or recombinant vectors encoding PSA in the development of anticancer vaccine immunotherapy protocols for patients with prostate cancer.
Regulation of the l-Arabinose Operon BAD in Vitro (1974)

Abstract A DNA-directed cell-free system to study the l-arabinose BAD operon has been further developed so that the rate of synthesis of enzymes coded for by the structural genes in the operon in vitro is about 5% the in vivo rate. l-Arabinose isomerase and l-ribulokinase, the products of the araA and araB genes, are synthesized at the same rate, demonstrating that the operon is coordinately expressed in vitro. The system is completely dependent upon araC protein which can be supplied either by synthesis in vitro from an araC+ DNA template or by the addition of araC protein extracted from whole cells. The properties in the in vitro system of araC protein from either source suggests that the two products are similar if not identical. Both the repressor and activator forms of the araC protein are demonstrable in vitro using the appropriate templates confirming the essential aspects of the model for gene regulation of this operon.
The impact of binaural beats on creativity (2013)

Human creativity relies on a multitude of cognitive processes, some of which are influenced by the neurotransmitter dopamine. This suggests that creativity could be enhanced by interventions that either modulate the production or transmission of dopamine directly, or affect dopamine-driven processes. In the current study we hypothesized that creativity can be influenced by means of binaural beats, an auditory illusion that is considered a form of cognitive entrainment that operates through stimulating neuronal phase locking. We aimed to investigate whether binaural beats affect creative performance at all, whether they affect divergent thinking, convergent thinking, or both, and whether possible effects may be mediated by the individual striatal dopamine level. Binaural beats were presented at alpha and gamma frequency. Participants completed a divergent and a convergent thinking task to assess two important functions of creativity, and filled out the Positive And Negative Affect Scale-mood State questionnaire (PANAS-S) and an affect grid to measure current mood. Dopamine levels in the striatum were estimated using spontaneous eye blink rates (EBRs). Results showed that binaural beats, regardless of the presented frequency, can affect divergent but not convergent thinking. Individuals with low EBRs mostly benefitted from alpha binaural beat stimulation, while individuals with high EBRs were unaffected or even impaired by both alpha and gamma binaural beats. This suggests that binaural beats, and possibly other forms of cognitive entrainment, are not suited for a one-size-fits-all approach, and that individual cognitive-control systems need to be taken into account when studying cognitive enhancement methods.
Somatic diversification of S107 from an antiphosphocholine to an anti-DNA autoantibody is due to a single base change in its heavy chain variable region. (1987)

The S107 myeloma cell line expresses the germ-line sequence of the T15 antiphosphocholine (P-Cho) antibody, which is the major antibody made by BALB/c mice in response to P-Cho, either on a variety of bacterial polysaccharides or when attached to a protein carrier. We have previously reported that a somatic mutant of the S107 cell line produces an antibody that has lost the ability to bind P-Cho and has acquired binding for double-stranded DNA. This antibody has a substitution of an alanine for a glutamic acid at residue 35 in the heavy chain variable region. We now show that this amino acid substitution is due to a single A-C transversion, which is the only nucleotide change in the heavy and light chain variable regions. Further, it appears that this change is due to somatic mutation rather than to gene conversion.
1. Diagnosis, treatment and prevention of allergic disease: the basics (2006)

Allergy is defined as an immune-mediated inflammatory response to common environmental allergens that are otherwise harmless. The diagnosis of allergy is dependent on a history of symptoms on exposure to an allergen together with the detection of allergen-specific IgE. The detection of allergen-specific IgE may be reliably performed by blood specific testing or skin prick testing. Skin prick testing is not without its attendant risks, and appropriate precautions need to be taken. A doctor should be present for safety and test interpretation. Accurate diagnosis of allergies opens up therapeutic options that are otherwise not appropriate, such as allergen immunotherapy and allergen avoidance. Allergen immunotherapy is an effective treatment for stinging insect allergy, allergic rhinitis and asthma. The most effective methods for primary prevention of allergic disease in children that can currently be recommended are breastfeeding and ceasing smoking. Emerging trends in allergen treatment include sublingual immunotherapy.
Risk Factors for Renal Dysfunction in Type 2 Diabetes (2006)

Not all patients with type 2 diabetes develop renal dysfunction. Identifying those at risk is problematic because even microalbuminuria, often used clinically as an indicator of future renal dysfunction, does not always precede worsening renal function. We sought to identify clinical risk factors at diagnosis of type 2 diabetes associated with later development of renal dysfunction. Of 5,102 U.K. Prospective Diabetes Study (UKPDS) participants, prospective analyses were undertaken in those without albuminuria (n = 4,031) or with normal plasma creatinine (n=5,032) at diagnosis. Stepwise proportional hazards multivariate regression was used to assess association of putative baseline risk factors with subsequent development of albuminuria (microalbuminuria or macroalbuminuria) or renal impairment (Cockcroft-Gault estimated creatinine clearance <60 ml/min or doubling of plasma creatinine). Over a median of 15 years of follow-up 1,544 (38%) of 4,031 patients developed albuminuria and 1,449 (29%) of 5,032 developed renal impairment. Of 4,006 patients with the requisite data for both outcomes, 1,534 (38%) developed albuminuria and 1,132 (28%) developed renal impairment. Of the latter, 575 (51%) did not have preceding albuminuria. Development of albuminuria or renal impairment was independently associated with increased baseline systolic blood pressure, urinary albumin, plasma creatinine, and Indian-Asian ethnicity. Additional independent risk factors for albuminuria were male sex, increased waist circumference, plasma triglycerides, LDL cholesterol, HbA(1c) (A1C), increased white cell count, ever having smoked, and previous retinopathy. Additional independent risk factors for renal impairment were female sex, decreased waist circumference, age, increased insulin sensitivity, and previous sensory neuropathy. Over a median of 15 years from diagnosis of type 2 diabetes, nearly 40% of UKPDS patients developed albuminuria and nearly 30% developed renal impairment. Distinct sets of risk factors are associated with the development of these two outcomes, consistent with the concept that they are not linked inexorably in type 2 diabetes.
Fabrication of iridium field emitter arrays (2000)

Iridium field emitter arrays were fabricated using Spindt tip process. Ir field emitter cones show an aspect ratio of 0.95, slightly less than Mo field emitter arrays fabricated using the same microfabrication process. When compared to the Mo field emitter arrays, the current–voltage characteristics of the Ir arrays were found to scale with the work function difference between Ir and Mo. Under ultrahigh vacuum conditions, the emission current stability of the Ir arrays measured over 180 h was found to be similar or slightly better than the emission stability of Mo arrays. However, when operated in the presence of O2, Ir field emitter arrays proved to be more robust and showed improved emission current stability versus their Mo counterparts.
Impact of magnesium sulfate on serum magnesium concentrations and intracellular electrolyte concentrations among patients undergoing radio frequency catheter ablation. (2008)

iMg deficiencies exist despite normal sMg concentrations in patients undergoing RFCA. Intravenous magnesium sulfate corrects iMg deficiencies immediately postinfusion.
Studies of the membrane fusion activities of fusion peptide mutants of influenza virus hemagglutinin (1995)

Influenza virus hemagglutinin (HA) fuses membranes at endosomal pH by a process which involves extrusion of the NH2-terminal region of HA2, the fusion peptide, from its buried location in the native trimer. We have examined the amino acid sequence requirements for a functional fusion peptide by determining the fusion capacities of site-specific mutant HAs expressed by using vaccinia virus recombinants and of synthetic peptide analogs of the mutant fusion peptides. The results indicate that for efficient fusion, alanine can to some extent substitute for the NH2-terminal glycine of the wild-type fusion peptide but that serine, histidine, leucine, isoleucine, or phenylalanine cannot. In addition, mutants containing shorter fusion peptides as a result of single amino acid deletions are inactive, as is a mutant containing an alanine instead of a glycine at HA2 residue 8. Substitution of the glycine at HA2 residue 4 with an alanine increases the pH of fusion, and valine-for-glutamate substitutions at HA2 residues 11 and 15 are without effect. We confirm previous reports on the need for specific HAo cleavage to generate functional HAs, and we show that both inappropriately cleaved HA and mutant HAs, irrespective of their fusion capacities, upon incubation at low pH undergo the structural transition required for fusion.
A full transparent fiber-optic ring architecture for WDM networks (1992)

A fully transparent fiber-optic ring architecture for wavelength division multiplexed (WDM) networks is proposed. The physical topology of the proposed network is based on a single or multifiber ring. The nodes at the periphery of the network are connected onto the ring via a polarization-independent acoustically tunable optical filter (PIATOF). This device is used for injecting the transmission from each node at a predefined wavelength onto the ring and at the same time for accessing the transmission of the other nodes. Expressions are derived for the throughput of different network configurations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A SAGE (serial analysis of gene expression) view of breast tumor progression. (2001)

To identify molecular alterations involved in the initiation and progression of breast carcinomas, we analyzed the global gene expression profiles of normal mammary epithelial cells and in situ, invasive, and metastatic breast carcinomas using serial analysis of gene expression (SAGE). We identified sets of genes expressed only or most abundantly in a specific stage of breast tumorigenesis or in a certain subtype of tumors through the pair-wise comparison and by hierarchical clustering analysis of these eight SAGE libraries (two/stage). On the basis of these comparisons, we made the following observations: Normal mammary epithelial cells showed the most distinct and least variable gene expression profiles. Many of the genes highly expressed in normal mammary epithelium and lost in carcinomas encoded secreted proteins, cytokines, and chemokines, implicating abnormal paracrine and autocrine signaling in the initiation of breast tumorigenesis. Very few genes were universally up-regulated in all tumors regardless of their stage and histological grade, indicating a high degree of diversity at the molecular level that likely reflects the clinical heterogeneity characteristic of breast carcinomas. Tumors of different histology type and stage had very distinct gene expression patterns. No genes seemed to be specific for metastatic or for in situ carcinomas. We found that the most dramatic and consistent phenotypic change occurred at the normal-to-in situ carcinoma transition. This observation, combined with the fact that many of the genes involved encode secreted, cell-nonautonomous factors, implies that the normal epithelium-to-in situ carcinoma transition may be the most promising target for cancer prevention and treatment.
Review (2013)

Abstract ‘l’eleganza In Esilio: Tra Moda E Costume, Il Tempo Di Djagilev’/‘elegance In Exile: Between Fashion And Costume In The Time Of Diaghilev’, Museo Di Palazzo Mocenigo, Venice, 17 September 2011–6 January 2012
Human Embryoid Bodies Containing Nano‐ and Microparticulate Delivery Vehicles (2008)

Differentiation of human embryonic stem cells is affected by the incorporation of growth-factor-releasing particles in embryoid bodies. Incorporation of these particles has a minimal effect on cell viability and proliferation but a large impact on differentiation. The figure shows the distribution of TRITC-labeled microparticles in embryoid bodies, as evaluated by confocal microscopy. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200702404_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Recombinase Polymerase Amplification for Diagnostic Applications (2016)

RPA is becoming a molecular tool of choice for the rapid, specific, and cost-effective identification of pathogens. Owing to minimal sample-preparation requirements, low operation temperature (25-42 °C), and commercial availability of freeze-dried reagents, this method has been applied outside laboratory settings, in remote areas, and interestingly, onboard automated sample-to-answer microfluidic devices. RPA is undoubtedly a promising isothermal molecular technique for clinical microbiology laboratories and emergence response in clinical settings.
Antibacterial activity of positive and negative polarity low‐voltage pulsed current (LVPC) on six typical Gram‐positive and Gram‐negative bacterial pathogens of chronic wounds (2007)

The positive effect of electrical stimulation (ES) on wound healing has been shown in vitro and in vivo. On the basis of increased blood flow, protein denaturation, and stimulation of cellular defense, an antibacterial effect of ES is to be expected. Although the antibacterial effect of ES already has been demonstrated in vitro, little attention has been paid to the direct antibacterial effect of changing polarity of the applied current. The aim of this study was to investigate the antibacterial effect of positive and negative monophasic low-voltage pulsed current on typical Gram-positive and Gram-negative pathogens of chronic wounds. Using the Dermapulse-System, three Gram-negative (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and three Gram-positive (Staphylococcus aureus, Staphylococcus epidermidis, Escherichia faecium) organisms were tested against positive and negative polarity low voltage pulsed current. All tested organisms were significantly reduced by ES. The reduction differed significantly between positive polarity and control and negative polarity and control, with the highest log10 reduction factor (RF) achieved with positive polarity. Using positive polarity, the maximum RF was measured for E. coli (median log10 RF 0.83; 25th percentile 0.59, 75th percentile 0.98) and the lowest for S. epidermidis (median log10 RF 0.20; 25th percentile 0.17, 75th percentile 0.24). Yet, there was no significant difference with positive ES against Gram-positive or Gram-negative organisms.
Prevention of the Salt Wind Damage on Tea Plants (1989)

In order to protect tea plants from salt wind damage, the effects of washing method and intercropping system were tested.The results obtained were as follows.1) The damage was at about the same level either with or without the "GREENER" (an evaporation controller, included a wax) when sea water was sprayed. The Greener was sprayed nine days before the typhoon, and the sea water was deliberately sprayed right after the typhoon.2) The damage could not be prevented by spraying 10, 000l/ha of water on the tea plants 4 hours after they received the spray of sea water. When the washing water was sprayed 30 minutes after the application of sea water, the damage was about 61-71% of the unwashed leaves.3) Sweet sorghums were intercropped in the tea field. When the typhoon came, their heights was 128-142cros. The death rate of tea plants was 59-82% before the first row of sorghum fences, but was reduced to 2-9% behind the second row.4) From the results of these experiments, we found that windbreak method (with a grasses more resistant to lodging such as sorghum) was more effective than the washing method.For young tea plants, intercropping should be an effective mean to prevent damage from the salt wind.
Role of the complement system in NK cell-mediated antitumor T-cell responses (2014)

The role of the complement system in oncogenesis and tumor progression remains poorly understood. We have recently demonstrated that the induction of a tumor-specific CD8<sup>+</sup> T-cell response is improved upon transient inhibition of the complement system, which is coupled to an increased availability of natural killer cells. The complement system may therefore turn out to constitute a promising target for the development of novel anticancer therapeutics.