gebhart/patrepeval huggingface dataset:
The Analysis of Milk Components and Pathogenic Bacteria Isolated from Bovine Raw Milk in Korea (2007)

Bovine mastitis can be diagnosed by abnormalities in milk components and somatic cell count (SCC), as well as by clinical signs. We examined raw milk in Korea by analyzing SCC, milk urea nitrogen (MUN), and the percentages of milk components (milk fat, protein, and lactose). The associations between SCC or MUN and other milk components were investigated, as well as the relationships between the bacterial species isolated from milk. Somatic cell counts, MUN, and the percentages of milk fat, protein, and lactose were analyzed in 30,019 raw milk samples collected from 2003 to 2006. The regression coefficients of natural logarithmic-transformed SCC (SCCt) on milk fat (-0.0149), lactose (-0.8910), and MUN (-0.0096), and those of MUN on milk fat (-0.3125), protein (-0.8012), and SCCt (-0.0671) were negative, whereas the regression coefficient of SCCt on protein was positive (0.3023). When the data were categorized by the presence or absence of bacterial infection in raw milk, SCCt was negatively associated with milk fat (-0.0172), protein (-0.2693), and lactose (-0.4108). The SCCt values were significantly affected by bacterial species. In particular, 104 milk samples infected with Staphylococcus aureus had the highest SCCt (1.67) compared with milk containing other mastitis-causing bacteria: coagulase-negative staphylococci (n = 755, 1.50), coagulase-positive staphylococci (except Staphylococcus aureus; n = 77, 1.59), Streptococcus spp. (Streptococcus dysgalactiae, n = 37; Streptococcus uberis, n = 12, 0.83), Enterococcus spp. (n = 46, 1.04), Escherichia coli (n = 705, 1.56), Pseudomonas spp. (n = 456, 1.59), and yeast (n = 189, 1.52). These results show that high SCC and MUN negatively affect milk components and that a statistical approach associating SCC, MUN, and milk components by bacterial infection can explain the patterns among them. Bacterial species present in raw milk are an important influence on SCC in Korea.
Monitoring antiproliferative responses to kinase inhibitor therapy in mice with 3'-deoxy-3'-18F-fluorothymidine PET. (2005)

These results indicate that (18)F-FLT PET provides noninvasive, quantitative, and repeatable measurements of tumor cell proliferation during treatment with ErbB kinase inhibitors and provide a rationale for the use this technology in clinical trials of kinase inhibitors.
4S-limonene synthase from the oil glands of spearmint (Mentha spicata). cDNA isolation, characterization, and bacterial expression of the catalytically active monoterpene cyclase. (1993)

The committed step in the biosynthesis of monoterpenes in mint (Mentha) species is the cyclization of geranyl pyrophosphate to the olefin (-)-4S-limonene catalyzed by limonene synthase (cyclase). Internal amino acid sequences of the purified enzyme from spearmint oil glands were utilized to design three distinct oligonucleotide probes. These probes were subsequently employed to screen a spearmint leaf cDNA library, and four clones were isolated. Three of these cDNA isolates were full-length and were functionally expressed in Escherichia coli, yielding a peptide that is immunologically recognized by polyclonal antibodies raised against the purified limonene synthase from spearmint and that is catalytically active in generating from geranyl pyrophosphate a product distribution identical to that of the native enzyme (principally limonene with small amounts of the coproducts alpha- and beta-pinene and myrcene). The longest open reading frame is 1800 nucleotides and the deduced amino acid sequence contains a putative plastidial transit peptide of approximately 90 amino acids and a mature protein of about 510 residues corresponding to the native enzyme. Several nucleotide differences in the 5'-untranslated region of all three full-length clones suggest the presence of several limonene synthase genes and/or alleles in the allotetraploid spearmint genome. Sequence comparisons with a sesquiterpene cyclase, epi-aristolochene synthase from tobacco, and a diterpene cyclase, casbene synthase from castor bean, demonstrated a significant degree of similarity between these three terpenoid cyclase types, the first three examples of this large family of catalysts to be described from higher plants.
Rapid detection of specific messenger RNAs in thyroid carcinomas by reverse transcription-PCR with degenerate primers: specific expression of oncofetal fibronectin messenger RNA in papillary carcinoma. (1997)

The search for mRNAs that are specifically expressed in cancer tissues is important for gene diagnosis and therapy. However, finding such mRNAs in human cancers is usually very difficult, both because of the limited volume of RNA obtainable from the tissues and the many technical difficulties of RNA analysis. To address these problems, the present study compared mRNA from thyroid cancer tissues with those from normal and benign tissues by reverse transcription-PCR using two degenerate primers. Amplified cDNAs were separated by electrophoresis with nondenaturing acrylamide gel, then three bands that are increased in cancer tissues were selected, reamplified by PCR, and cloned into T-vector. One of the bands was determined by sequencing analysis to be oncofetal fibronectin. The expression of oncofetal fibronectin mRNA in benign and malignant tissues was examined by Northern blot and reverse transcription-PCR using specific primers of its cDNA sequence, and its increased expression was observed only in papillary and anaplastic carcinomas. Thus, the present method rapidly detected specific mRNAs in cancer tissues, and one of these, oncofetal fibronectin mRNA, is a good target for gene diagnosis of papillary carcinoma.
A quantum-inspired hybrid methodology for financial time series prediction (2010)

In this work a quantum-inspired hybrid methodology is proposed to overcome the random walk dilemma for financial time series prediction. It consists of a hybrid model composed of a Qubit Multilayer Perceptron (QuMLP) with a Quantum-Inspired Evolutionary Algorithm (QIEA), which searches for the best particular time lags able to characterize the time series phenomenon, as well as to evolve the complete QuMLP architecture and parameters. Each individual of the QIEA population is adjusted by the Complex Back-Propagation (CBP) algorithm to further improve the QuMLP parameters supplied by the QIEA. After the prediction model search procedure, it uses a behavioral statistical test and a phase fix procedure to adjust time phase distortions that appear in financial time series. An experimental analysis is conducted with the proposed methodology through four real world financial time series, and the obtained results are discussed and compared to results found with Multilayer Perceptiron (MPL) networks and the previously introduced Morphological-Rank-Linear Time-lag Added Evolutionary Forecasting (MRLTAEF) method.
Selecting the “Right” Mouse Model for Metabolic Syndrome and Type 2 Diabetes Research (2009)

This is not a "Methods" chapter in the traditional sense. Rather, it is an essay designed to help address one of the most frequently asked questions by investigators about to embark on a study requiring an animal model of diabetes - what is the "right" model for the reader's specific research application. Because genetic heterogeneity and the requirement for complex gene-environment interaction characterize the various mouse models of Type 2 diabetes as well as the human disease manifestations, the readers may come to share the author's conclusion that more than one model is required if the investigator is interested in knowing how broadly effective a given compound with putative therapeutic efficacy might be.
How to hire employees effectively (1999)

Outlines an effective procedure for recruitment. Briefly considers job analysis, methods of recruitment, methods of assessment, reference checks and job previews. Encourages employers to see this area as long term investment in their human resource portfolio.
Formation of Mutually Exclusive Rab11 Complexes with Members of the Family of Rab11-interacting Proteins Regulates Rab11 Endocytic Targeting and Function (2002)

Several Rabs, including Rab11, regulate the traffic and sorting of proteins in the endosomal pathway. Recently, six novel Rab11 family interacting proteins (FIPs) were identified. Although they share little overall sequence homology, all FIPs contain a conserved Rab11-binding domain. Here we investigate the role of FIPs as Rab11-targeting proteins and show that the Rab11-binding domain assumes an alpha-helical structure, with the conserved residues forming a hydrophobic Rab11-binding patch. This hydrophobic patch mediates the formation of mutually exclusive complexes between Rab11 and various members of FIP protein family. Furthermore, the formation of Rab11/FIP complexes regulates Rab11 localization by recruiting it to distinct endocytic compartments. Thus, we propose that Rab11/FIP complexes serve as targeting patches, regulating Rab11 localization and recruitment of additional cellular factors to different endocytic compartments.
The conserved helicase motifs of the herpes simplex virus type 1 origin-binding protein UL9 are important for function (1992)

The UL9 gene of herpes simplex virus encodes a protein that specifically recognizes sequences within the viral origins of replication and exhibits helicase and DNA-dependent ATPase activities. The specific DNA binding domain of the UL9 protein was localized to the carboxy-terminal one-third of the molecule (H. M. Weir, J. M. Calder, and N. D. Stow, Nucleic Acids Res. 17:1409-1425, 1989). The N-terminal two-thirds of the UL9 gene contains six sequence motifs found in all members of a superfamily of DNA and RNA helicases, suggesting that this region may be important for helicase activity of UL9. In this report, we examined the functional significance of these six motifs for the UL9 protein through the introduction of site-specific mutations resulting in single amino acid substitutions of the most highly conserved residues within each motif. An in vivo complementation test was used to study the effect of each mutation on the function of the UL9 protein in viral DNA replication. In this assay, a mutant UL9 protein expressed from a transfected plasmid is used to complement a replication-deficient null mutant in the UL9 gene for the amplification of herpes simplex virus origin-containing plasmids. Mutations in five of the six conserved motifs inactivated the function of the UL9 protein in viral DNA replication, providing direct evidence for the importance of these conserved motifs. Insertion mutants resulting in the introduction of two alanines at 100-residue intervals in regions outside the conserved motifs were also constructed. Three of the insertion mutations were tolerated, whereas the other five abolished UL9 function. These data indicate that other regions of the protein, in addition to the helicase motifs, are important for function in vivo. Several mutations result in instability of the mutant products, presumably because of conformational changes in the protein. Taken together, these results suggest that UL9 is very sensitive to mutations with respect to both structure and function, perhaps reflecting its multifunctional character.
ROBUST RECONSTRUCTION OF BUILDING MODELS FROM THREE-DIMENSIONAL LINE SEGMENTS (2003)

This paper proposes a robust method for reconstructing building models from three-dimensional (3D) line segments using a semi-automatic approach. The method, which is called split-merge-shape can treat both complete line segments as well as incomplete line segments due to image occlusions. The proposed method is comprised of five major parts: (1) the creation of the region of interest and pre-processing; (2) splitting the model by using the 3D line segments to construct a combination of roof primitives; (3) merging connected roof primitives to complete the boundary of each building; (4) shaping each building rooftop by connected coplanar analysis and coplanar fitting; and (5) quality assurance. The experimental results indicated that the proposed method can soundly rebuild the topology from the 3D line segments and reconstruct building models with up to a 98 percent success rate, even when processing connected or complex buildings.
Single-agent arsenic trioxide in the treatment of newly diagnosed acute promyelocytic leukemia: durable remissions with minimal toxicity (2005)

Arsenic trioxide, as a single agent, has proven efficacy in inducing molecular remission in patients with acute promyelocytic leukemia (APL). There is limited long-term outcome data with single-agent As2O3 in the management of newly diagnosed cases of APL. Between January 1998 to December 2004, 72 newly diagnosed cases of APL were treated with a regimen of single-agent As2O3 at our center. Complete hematologic remission was achieved in 86.1%. At a median follow-up of 25 months (range: 8-92 months), the 3-year Kaplan-Meier estimate of EFS, DFS, and OS was 74.87% +/- 5.6%, 87.21% +/- 4.93%, and 86.11% +/- 4.08%, respectively. Patients presenting with a white blood cell (WBC) count lower than 5 x 10(9)/L and a platelet count higher than 20 x 10(9)/L at diagnosis (n = 22 [30.6%]) have an excellent prognosis with this regimen (EFS, OS, and DFS of 100%). The toxicity profile, in the majority, was mild and reversible. After remission induction, this regimen was administered on an outpatient basis. Single-agent As2O3, as used in this series, in the management of newly diagnosed cases of APL, is associated with responses comparable with conventional chemotherapy regimens. Additionally, this regimen has minimal toxicity and can be administered on an outpatient basis after remission induction.
Purification and Properties of Maleylacetone cis-trans Isomerase from Vibrio 01 (1973)

Abstract An enzyme from Vibrio 01 catalyzing cis-trans isomerization of maleylacetone has been identified and purified. The enzyme has a molecular weight of about 35,000 and appears to be a single unit. Its density is low compared to other proteins. Glutathione is specifically required as a coenzyme. Treatment of the enzyme with sodium borohydride in the presence of substrate and GSH leads to increased activity while in the absence of substrate, treatment with sodium borohydride leads to inhibition. Formation of a Schiff base intermediate between substrate and enzyme appears to be unlikely. N-Ethylmaleimide leads to inactivation of enzyme and suggests the importance of one or more thiol groups near the active site. Other inhibitors and potential inhibitors have been tested. The enzyme also isomerized maleylacetoacetate at a slightly faster rate.
Studies on p-Hydroxybenzoate Hydroxylase from Pseudomonas putida (1969)

Enzymatic hydroxylation mechanism of p- hydroxybenzoate hydroxylase from Pseudomonas putidas, describing product separation and purification
In vitro 3D Full‐Thickness Skin‐Equivalent Tissue Model Using Silk and Collagen Biomaterials (2012)

Current approaches to skin equivalents often only include the epidermis and dermis. Here, a full-thickness skin equivalent is described including epidermis, dermis, and hypodermis, that could serve as an in vitro model for studying skin biology or as a platform for consumer product testing. The construct is easy to handle and is maintained for >14 d while expressing physiological morphologies of the epidermis and dermis, seen by keratin 10, collagens I and IV expression. The skin equivalent produces glycerol and leptin, markers of adipose metabolism. This work serves as a foundation for understanding a few necessary factors needed to develop a stable, functional model of full-thickness skin.
Alternative Splicing of Chicken Fibronectin in Embryos and in Normal and Transformed Cells (1987)

To study the alternative splicing of fibronectin during embryogenesis and oncogenic transformation, we isolated cDNA clones of chicken fibronectin. The partial amino acid sequence deduced from sequencing of these clones showed that, overall, chicken fibronectin is approximately 80% identical with mammalian fibronectins. However, two of the three known regions of alternative splicing differed from this average. The V region was significantly more divergent, and RNA from embryonic chicken liver showed a pattern of V exon splicing which was distinct from that seen in human or rat fibronectins. In contrast, the EIIIB segment was very highly conserved (96%). As in mammals, this segment and another (EIIIA) were alternatively spliced in a cell-type-specific fashion. EIIIA+ and EIIIB+ species were almost absent in liver but predominated in total embryo RNA at all times from 2.5 to 11 days postfertilization. We also examined the possible contributions of fibronectin splicing and integrin receptor expression to the loss of fibronectin on oncogenic transformation. We detected little change in fibronectin splicing, other than a slight increase in representation of EIIIB+ species in fibroblasts after transformation by Rous sarcoma virus. It was also established that the overall reduction in fibronectin mRNA level observed after transformation was not accompanied by a decrease in integrin mRNA levels, indicating that fibronectin and integrin receptors are not coordinately regulated at the transcriptional level.
Splenic Atrophy in Experimental Stroke Is Accompanied by Increased Regulatory T Cells and Circulating Macrophages (2006)

Induction of stroke not only produces local ischemia and brain damage, but also has profound effects on peripheral immune responses. In the current study, we evaluated effects on spleen and blood cells 4 days after stroke induction. Surprisingly, there was a less inflammatory cytokine profile in the middle cerebral artery occlusion-affected right brain hemisphere at 96 h compared with earlier time points. Moreover, our results demonstrate that stroke leads to splenic atrophy characterized by a reduction in organ size, a drastic loss of splenocyte numbers, and induction of annexin V+ and TUNEL+ cells within the spleen that are in the late stages of apoptosis. The consequence of this process was to reduce T cell proliferation responses and secretion of inflammatory cytokines, resulting in a state of profound immunosuppression. These changes produced a drastic reduction in B cell numbers in spleen and blood, and a novel increase in CD4+FoxP3+ regulatory T cells. Moreover, we detected a striking increase in the percentage of nonapoptotic CD11b+ VLA-4-negative macrophages/monocytes in blood. Immunosuppression in response to brain injury may account for the reduction of inflammatory factors in the stroke-affected brain, but also potentially could curtail protective immune responses in the periphery. These findings provide new evidence to support the contention that damage to the brain caused by cerebral ischemia provides a powerful negative signal to the peripheral immune system that ultimately induces a drastic state of immunosuppression caused by cell death as well as an increased presence of CD4+FoxP3+ regulatory T cells.
Retirement intentions of older nurses in the Northern Territory (2009)

\n \t\t\tRESEARCH AIMTo examine the retirement intentions of older nurses in the Northern Territory and develop strategies for post-retirementcontribution to the profession.\n
Pulsatile Cardiac Tissue Grafts Using a Novel Three-Dimensional Cell Sheet Manipulation Technique Functionally Integrates With the Host Heart, In Vivo (2006)

We devised a method of fabricating easily transplantable scaffoldless 3D heart tissue, made with a novel cell-sheet (CS) technology from cultured cardiomyocytes using a fibrin polymer coated dish. In the present study, we tested in vivo electrical communication which is essential for improving heart function between the host heart and the grafted CS. The epicardial surface of the ventricle of an anesthetized open-chest nude rat was ablated by applying a heated metal. Bilayered CS was obtained from neonatal rat primary culture. CS was transplanted onto the injured myocardial surface (sMI) (sMI+sheet group). The rats were allowed to recover for 1 to 4 weeks, to stabilize the grafts. Action potentials (APs) from the excised perfused heart were monitored by the fluorescence signal of di-4ANEPPS with a high speed charge-coupled device camera. The APs were observed under epicardial pacing of the host heart or the CS grafts. The pacing threshold of the current output was measured in the sMI+sheet group and in the nongrafted sMI group at the center of the sMI and in the normal zone (Nz). Bidirectional AP propagation between the sMI and Nz was observed in the sMI+sheet group (n=14), but was blocked at the marginal area of the sMI in the sMI group (n=9). The ratio of the pacing threshold (sMI/Nz) was significantly lower in the sMI+sheet than in the sMI group (3.0+/-0.7, 19.0+/-6.1 respectively P<0.05). There were neither spontaneous nor pacing-induced arrhythmias in these two groups. Bidirectional smooth AP propagation between the host heart and the grafted CS was observed. This finding suggested functional integration of this CS graft with the host heart without serious arrhythmia.
Pathology and Pathogenesis of FatalBordetella pertussisInfection in Infants (2008)

Pertussis should be suspected in any infant death associated with marked leukocytosis, bronchopneumonia, or refractory pulmonary hypertension, particularly in children aged <or=4 months. The pathologic findings identified in the respiratory tracts of these children, in addition to recognized physiologic responses of the infant lung to hypoxia, suggest that B. pertussis pneumonia triggers a cascade of events that includes acute pulmonary vasoconstriction and pertussis toxin-mediated increases in circulating leukocyte mass. These responses ultimately compromise pulmonary blood flow, exacerbate hypoxemia, and create a vicious cycle of refractory pulmonary hypertension.
Neural network architecture for robot hand control (1989)

A robot hand control system called GeSAM, which is under development at the University of Southern California, is described. The goal of the GeSAM architecture is to provide a generic robot hand controller that is based on a model of human prehensile function. It focuses on the relationship between geometric object primitives and the ways a hand can perform prehensile behaviors. It is shown how the relationship between object primitives and a useful set of grasp modes can be learned by an adaptive neural network. By adding training points as necessary, system performance can be improved, avoiding the tedious job of computing every relationship individually.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Photochemical Kinetics of Corneal Cross-Linking with Riboflavin (2012)

Using a chemical kinetics modeling approach, the authors developed a simple model that is in agreement with their experimental results on oxygen consumption in the cornea during corneal cross-linking with Rf. It is suggested that the main photochemical kinetics mechanism is the direct interaction between Rf triplets and reactive groups of corneal proteins, which leads to the cross-linking of the proteins mainly through radical reactions.