gebhart/patrepeval huggingface dataset:
Parallel Machine Learning Algorithms In Bioinformatics And Global Optimization (2012)

This is a dissertation in three parts, in each we explore the development and analysis of a parallel statistical or machine learning algorithm and its implementation. First, we examine the Assembly Likelihood Evaluation (ALE) framework. This algorithm defines a rigorous statistical likelihood metric used to validate and score genome and metagenome assemblies. This algorithm can be used to identify specific errors within assemblies and their locations; enable comparison between assemblies allowing for optimization of the assembly process; and using re-sequencing data, detect structural variations. Second, we develop an algorithm for Expected Parallel Improvement (EPI). This optimization method allows us to optimally sample many points concurrently from an expensive to evaluate and unknown function. Instead of sampling sequentially, which can be inefficient when the available resources allow for simultaneous evaluation, EPI identifies the best set of points to sample next, allowing multiple samplings to be performed in unison. Finally, we explore Velvetrope: a parallel, bitwise algorithm for finding homologous regions within sequences. This algorithm employs a two-part filter between sequences. It first finds offsets where two sequences share a higher than expected amount of identity. It then filters areas within these offsets with higher than expected identity. The resulting positions along each sequence represent regions of statistically significant similarity.
Modelling of the human intercellular adhesion molecule‐1, the human rhinovirus major group receptor (1990)

A model has been built of the amino-terminal domain of the intercellular adhesion molecule-1 (ICAM-1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptor attachment site, the canyon, on the human rhinovirus-14 (HRV14) surface in a manner consistent with most of the mutational data for ICAM-1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449-5453, 1988).
Applications of the Polymerase Chain Reaction in Retroviral-Mediated Gene Transfer and the Analysis of Gene-Marked Human TIL Cells (1990)

The polymerase chain reaction (PCR), a widely used new technology, was applied to several aspects of retroviral-mediated gene transfer. Ten oligonucleotide primer pairs were analyzed for their ability to amplify specific regions of a retroviral vector, including the long terminal repeat (LTR), and a NeoR selectable marker gene. By using the appropriate oligonucleotide primers, cells transduced by retroviral vectors could readily be detected and analyzed for deletions in proviral sequences by PCR, without Southern blotting. In combination with a simplified RNA isolation/reverse transcription protocol, an approximate titer of vector producer cell lines could be estimated by PCR in a single day, eliminating the need for time-consuming transductions and biological selection. Quantification of data obtained from PCR dilution experiment indicates that, under appropriate conditions, amplification is linear with respect to the amount of input DNA, permitting estimations of gene dosage in unknown samples. Specific PCR procedures have been developed as part of a protocol involving the transfer of retroviral-marked human tumor infiltrating lymphocytes (TIL) to cancer patients undergoing TIL cell cancer therapy. To augment biological safety testing methods, PCR has been used to detect the presence of possible amphotropic helper virus genomes at a sensitivity of one marked cell in 10(5) unmarked cells. The further use of PCR technology in the TIL cell human gene transfer protocol is demonstrated by the ability to detect small numbers of transduced TIL cells in the presence of hundreds of thousands of untransduced TIL.
Introduction to the Proceedings of the Third International Congress of Corneal Cross-Linking (2008)

&lt;p&gt;For the past 3 years, the founders of riboflavin/ultraviolet A (UVA) cross-linking in the treatment of keratoconus, Theo Seiler, Eberhard Spoerl, and others, have hosted the International Congress of Corneal Cross-Linking during the month of December in Zurich, Switzerland. The last Congress, on December 7, 2007, was no different than the others in its diverse content and excellent presentations, except for the fact that this is the first year we have solicited a number of the best presentations to be compiled for inclusion in these Proceedings. Also, during this particular Congress, we voted as a group regarding the appropriate abbreviation to be used in reference to corneal cross-linking or collagen cross-linking. We selected “CXL” rather than CCL, CCC, C3R, etc, as the most appropriate abbreviation, and also selected “SXL” to represent scleral cross-linking.&lt;/p&gt;
Handwashing Compliance by Health Care Workers (2000)

Education/feedback intervention and patient awareness programs failed to improve handwashing compliance. However, introduction of easily accessible dispensers with an alcohol-based waterless handwashing antiseptic led to significantly higher handwashing rates among health care workers.
Preparation of semi‐interpenetrating polymer networks composed of silk fibroin and poly(ethylene glycol) macromer (2001)

Abstract Semi‐interpenetrating polymer networks (SIPNs) composed of silk fibroin (SF) and a poly(ethylene glycol) (PEG) diacrylate macromer were synthesized and characterized. The conformation of SF in SIPNs was changed from a random coil to a β‐sheet structure by formation of SIPNs with PEG, while the crystalline structures of SF and PEG in SIPNs was not changed. The decomposition temperature of SF in the SIPNs was inner‐shifted, an indication of SIPN formation between the SF and the PEG macromer. The tensile strength and elongation of the SIPNs were much higher than were those of SF itself or the SF/PEG blend and increased with an increase of the PEG content. The equilibrium water content of SF was remarkably increased by formation of SIPNs with PEG due to the hydrophilic property of PEG. © 2001 John Wiley &amp; Sons, Inc. J Appl Polym Sci 80: 1848–1853, 2001
Optimization of ligation reaction conditions in gene synthesis. (1988)

Several phosphorylation, annealing and ligation reaction conditions have been investigated for the enzymatic assembly of genes of interest. The use of longer oligodeoxyribonucleotides (40-60 bases long) also improved the enzymatic reaction. Furthermore, the use of longer oligonucleotides and the elimination of long stretches of G's or C's lowered the mutation rate.
Nipah Virus: A Recently Emergent Deadly Paramyxovirus (2000)

A paramyxovirus virus termed Nipah virus has been identified as the etiologic agent of an outbreak of severe encephalitis in people with close contact exposure to pigs in Malaysia and Singapore. The outbreak was first noted in late September 1998 and by mid-June 1999, more than 265 encephalitis cases, including 105 deaths, had been reported in Malaysia, and 11 cases of encephalitis or respiratory illness with one death had been reported in Singapore. Electron microscopic, serologic, and genetic studies indicate that this virus belongs to the family Paramyxoviridae and is most closely related to the recently discovered Hendra virus. We suggest that these two viruses are representative of a new genus within the family Paramyxoviridae. Like Hendra virus, Nipah virus is unusual among the paramyxoviruses in its ability to infect and cause potentially fatal disease in a number of host species, including humans.
Unique molecular markers in human endometriosis: implications for diagnosis and therapy (2001)

Endometriosis originates in the uterine lining and affects ~20% of reproductive-age women. The disease often causes chronic pelvic pain, affects ovulatory function and influences fertility. Although laparoscopic diagnosis of uterine endometriosis is quite specific, direct visualisation can be difficult or inaccurate in some circumstances, and it is not useful for diagnosing extra-abdominal disease. Laparoscopy is an invasive procedure, has significant morbidity and cannot be carried out frequently to monitor efficacy of therapy and the possibility of recurrence. Thus, a specific, non-invasive diagnostic test is required. One intriguing area of research uses the technology of radioimmunotargeting, which has previously been used for cancer detection. This technique could have potential for the specific detection and eventual treatment of endometriosis. A marker, eosinophil peroxidase (EPO), has been identified that is expressed in ~90% of endometriosis specimens, and is not expressed or only weakly expressed in normal endometrium. The US Food and Drug Administration has approved a monoclonal antibody to EPO for investigation as an immunoimaging agent in cancers that exhibit eosinophilia. EPO targeting using this antibody could be useful for detecting and/or treating endometriosis.
Closo-Dodecaborate(2-) as a Linker for Iodination of Macromolecules. Aspects on Conjugation Chemistry and Biodistribution (1999)

Boron-containing compounds like closo-dodecaborate(2-) are in theory suitable for radioactive labeling with halogens. The boron-halogen bond is stronger than carbon-halogen bond and is not likely to be recognized by deiodinating enzymes in vivo. Peptides and proteins may be conjugated with various closo-dodecaborate(2-)-containing ligands, and thereafter, the conjugate can be iodinated. Since closo-dodecaborate(2-) is more avidly iodinated than tyrosine in moderately acidic media, such conjugates may be directly labeled on the boron part with radioisotopes of iodine using the standard Chloramine-T procedure. Mercapto-undecahydro-closo-dodecaborate(2-) (BSH) was reacted with the double bond of allyldextran to form a boronated dextran compound of the molecular size of about 70 kDa. This compound, in the text denoted as Dx-BS, and cesium dodecahydro-closo-dodecaborate(2-) were labeled using iodine-125. The two compounds were administered to rats in order to study their in vivo stability. The results indicate that iodinated Dx-BS is stable for about 20 h in vivo. The degradation rate, as indicated by thyroid uptake, was found low. [125I]Iodo-closo-dodecaborate(2-), which is a possible degradation product of [125I]Dx-BS-I, was rapidly excreted in urine without significant accumulation in any organ.
In vitro translation of poliovirus RNA: utilization of internal initiation sites in reticulocyte lysate (1984)

The translation of poliovirus RNA in rabbit reticulocyte lysate was examined. Translation of poliovirus RNA in this cell-free system resulted in an electrophoretic profile of poliovirus-specific proteins distinct from that observed in vivo or after translation in poliovirus-infected HeLa cell extract. A group of proteins derived from the P3 region of the polyprotein was identified by immunoprecipitation, time course, and N-formyl-[35S]methionine labeling studies to be the product of the initiation of protein synthesis at an internal site(s) located within the 3'-proximal RNA sequences. Utilization of this internal initiation site(s) on poliovirus RNA was abolished when reticulocyte lysate was supplemented with poliovirus-infected HeLa cell extract. Authentic P1-1a was also synthesized in reticulocyte lysate, indicating that correct 5'-proximal initiation of translation occurs in that system. We conclude that the deficiency of a component(s) of the reticulocyte lysate necessary for 5'-proximal initiation of poliovirus protein synthesis resulted in the ability of ribosomes to initiate translation on internal sequences. This aberrant initiation could be corrected by factors present in the HeLa cell extract. Apparently, under certain conditions, ribosomes are capable of recognizing internal sequences as authentic initiation sites.
Immunoradiometric assay of a recombinant human alpha-2 interferon (SCH 30500) (1985)

A sensitive immunoradiometric assay for recombinant alpha-2 interferon (IFN-alpha 2; SCH 30500) was developed by using the monoclonal antibody NK2. A polystyrene bead with polyclonal sheep anti-human IFN-alpha (Hu IFN-alpha) antibody adsorbed to it formed the solid phase of the assay. The monoclonal antibody, labeled with 125I, reacted with the IFN-alpha 2 which bound to the polyclonal antibody on the bead. The assay was sensitive, capable of measuring less than 5 IU/ml, and it was precise. Coefficients of variation were less than 10%, often less than 5%. Interassay coefficients of variation for the same sample were also less than 10%. Specificity of the monoclonal antibody for IFN-alpha 2 was greater than for Hu IFN-alpha produced by leukocytes. In specificity studies it was necessary to add at least 200 IU of Hu IFN-alpha per ml to 25 IU of IFN-alpha 2 per ml before the Hu IFN-alpha affected the accuracy of the assay of IFN-alpha 2. Accuracy as determined by correlation studies with the antiviral cytopathic effect assay was very high. Results of the two assays usually agreed within 15%. This correlation was maintained in studies of IFN-alpha 2 after storage under accelerated degradation conditions, when the IFN was cleaved into smaller sequences of amino acids by cyanogen bromide and when the IFN was carboxymethylated.
Immune Consequences of Burn Injury (1993)

The purpose of the immune system is to protect cells from invasion by microorganisms. The body has three equally important interactive immune defense systems, all of which are profoundly disrupted with major burn injury. The immune response to burn injury is immediate, prolonged, and severe. The end result in individuals surviving burn shock is immunosuppression, with increased susceptibility to potentially fatal systemic burn wound or pulmonary sepsis. Nursing actions to support the humoral and cell-mediated immune system of the burned patient include providing nutritional support to maintain serum protein levels at optimal levels; measures to decrease edema and promote angiogenesis in areas of partial-thickness injury; meticulous treatment of the wound to prevent infection and promote healing; monitoring of antibiotic use; conservative use of invasive techniques, including intubation and vascular access devices; maintenance of fluid and electrolyte balance and body temperature; and energy conservation measures.
A novel type of RET rearrangement (PTC8) in childhood papillary thyroid carcinomas and characterization of the involved gene (RFG8). (2000)

As part of ongoing studies on the RET rearrangement frequency in children with papillary thyroid carcinoma (PTC) after their exposure to radioactive iodine after the Chernobyl reactor accident, new methods for the detection of novel types of RET rearrangements are being developed. In this study, an improved reverse transcription-PCR strategy is used successfully to identify a new type of RET rearrangement. This rearrangement is designated PTC8 and the involved RET-fused gene (RFG) as RFG8. The identification of two reciprocal transcripts coding for the RFG8/RET and RET/RFG8 fusions suggests that the PTC8 rearrangement results from a balanced chromosomal translocation. With a view to clarify its role in tumor induction, we compared the fusion products with those of previously described RET rearrangements. We therefore sequenced and characterized the RFG8 cDNA, which showed no significant similarity to any functional protein described as yet. RFG8 is located on chromosome 18q21-22 and is expressed ubiquitously. Bioinformatic analysis predicts with a high probability that the corresponding rfg8 protein is located in the cytoplasm and is involved putatively in intracellular transport processes. Furthermore, we identified coiled-coil structures upstream of the breakpoint with one of the coiled-coils showing dimerization capability. Thus the rfg8/ret fusion protein exhibits structures for oncogenic activation that are similar to those observed in previously described RET fusions.
Superhydrophobicity of a material made from multiwalled carbon nanotubes (2006)

Superhydrophobic carbon nanotubes (CNTs) were prepared by low-pressure CF4 glow plasma to provide roughness and fluorination in CNTs. The water droplet falling freely on the superhydrophobic CNT powders bounced dynamically. The superhydrophobicity resulted from the combined effects of the chemical modification and surface roughness. Using the contact angles obtained from the capillary rise method based on the Washburn equation, the total surface free energy of CNT powder treated by CF4 plasma for 20min was calculated to be drastically decreased from 27.04to4.06×10−7mJ∕m2.
Mixture Behavior and Microwave Dielectric Properties in the Low-fired TiO2–CuO System (2000)

The mixture behavior and microwave dielectric properties of TiO 2 doped with CuO sintered at around 900°C for 2 h were investigated using X-ray powder diffraction and a network analyzer. Low-fired TiO 2 with 2% CuO had a quality factor of 14000, relative dielectric constant ( ε r ) of 98, and a temperature coefficient of resonant frequency (τ f ) of 374 ppm/°C. The microwave dielectric properties of low-fired, CuO doped TiO 2 could be interpreted by observing the dielectric properties of CuO: high loss tangent (tan δ), low dielectric constant, and a negative temperature coefficient of resonant frequency. The microwave dielectric properties of low-fired, CuO doped TiO 2 showed a dependence on the mixture formation of TiO 2 and CuO. More importantly, the ε r of low-fired TiO 2 with CuO could be predicted by the logarithmic mixing model. Therefore, the variation of the microwave dielectric properties was attributed to the mixture behavior of TiO 2 and CuO.
MultiContrast Delayed Enhancement (MCODE) improves detection of subendocardial myocardial infarction by late gadolinium enhancement cardiovascular magnetic resonance: a clinical validation study (2012)

While both PSIR LGE and MCODE were good in identifying MI, MCODE demonstrated more subendocardial MI's than LGE and identified a larger number of infarcted sectors. The simultaneous acquisition of T1 and T2-weighted images improved differentiation of blood pool from enhanced subendocardial MI.
Object Tracking using Color Correlogram (2006)

Color histogram based representations have been widely used for blob tracking. In this paper, a new color histogram based approach for object representation is proposed. By using a simplified version of color correlogram as object feature, spatial information is incorporated into object representation, which allows variations of rotation to be detected throughout the tracking therefore rotational objects can be more accurately tracked. The gradient decent method mean shift algorithm is adopted as the central computational module and further extended to a 3D domain to find the mostprobable target position and orientation simultaneously. The capability of the tracker to tolerate appearance changes like orientation changes, small scale changes, partial occlusions and background scene changes is demonstrated using real image sequences.
Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus resembling plant ‘potex-like’ viruses (2001)

This study reports the first sequence of a flexuous rod-shaped mycovirus and also the first molecular characterization of a virus that infects the plant-pathogenic fungus BOTRYTIS: cinerea. The mycovirus BOTRYTIS: virus F (BVF) contains an ssRNA genome of 6827 nucleotides and a poly(A) tract at or very near the 3' terminus. Computer analysis of the genomic cDNA sequence of BVF revealed two potential open reading frames (ORFs) encoding proteins of 212 kDa (ORF1) and 32 kDa (ORF2). ORF1 showed significant sequence identity to the RNA-dependent RNA polymerase (RdRp)-containing proteins of plant 'tymo-' and 'potex-like' viruses. However, the ORF1 protein contained an opal putative readthrough codon between the helicase and RdRp regions, a feature not seen in this position in 'tymo-' and 'potex-like' replicases sequenced to date. ORF2 shared amino acid similarity with coat proteins of plant 'potex-like' viruses. Three untranslated regions were present in the genome, comprising a region of 63 nucleotides preceding the initiation codon of ORF1, a 93 nucleotide stretch between ORFs 1 and 2 and a 3'-terminal region of 70 nucleotides preceding the poly(A) tract. The nucleotide sequence of a putative defective RNA (D-RNA) of 829 nucleotides was also determined. The D-RNA contained one potential ORF comprising the N-terminal region of the replicase fused in-frame to the C-terminal region of the coat protein. It is proposed that the mycovirus BVF belongs to a new, as yet unassigned genus in the plant 'potex-like' virus group.
High-Fidelity Raman Imaging Spectrometry: A Rapid Method Using an Acousto-Optic Tunable Filter (1992)

In this communication, we describe a technique for obtaining high-fidelity Raman images and Raman spectra. The instrumentation provides the ability to rapidly collect large-format images with the number of image pixels limited only by the number of detector elements in the silicon charge-coupled device (CCD). Wavelength selection is achieved with an acousto-optic tunable filter (AOTF), which maintains image fidelity while providing spectral selectivity. Under computer control the AOTF is capable of µs tuning speeds within the operating range of the filter (400–1900 nm). The AOTF is integrated with the CCD and holographic Raman filters to comprise an entirely solid-state Raman imager containing no moving parts. In operation, the AOTF is placed in front of the CCD and tuned over the desired spectral interval. The two-dimensional CCD detector is employed as a true imaging camera, providing a full multichannel advantage over competitive Raman imaging techniques. Images and spectra are presented of a mixture of dipalmitoylphosphatidylcholine (DPPC) and L-asparagine, which serves as a model system for the study of both lipid/peptide and lipid/protein interactions in intact biological materials. The Raman images are collected in only several seconds and indicate the efficacy of this rapid technique for discriminating between multiple components in complex matrices. Additionally, high-quality Raman spectra of the spatially resolved microscopic regions are easily obtained.
The influence of emotions displayed and personal selling on customer behaviour intention (2011)

The impact of employee performance on customer behavioural intentions and consumption behaviour is important to service marketers. In many service settings, service organizations require emotional display and personal selling to stay competitive in todays market. Based on a review of service literature, this study investigates the effect of emotions displayed and personal selling on customer purchase amount and re-patronage intention in convenience-goods retail service settings. This work applies mystery shopper methods to data collected from a Taiwan bakery chain. Analysis of the results from 519 responded questionnaires in this study reveal that positive emotions displayed by contact personnel are unrelated to consumption expenditure, but do affect re-patronage intention. Further, the results show that personal selling negatively influences consumption amount. This study suggests that service managers consider enhancing their emotional display perspective in human resource practices, and focus on performing personal selling as a consumer need, in different service industries.