gebhart/patrepeval huggingface dataset:
CottonGen: a genomics, genetics and breeding database for cotton research (2013)

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST.
High-level expression of secreted glycoproteins in transformed lepidopteran insect cells using a novel expression vector (1998)

An expression cassette for continuous high-level expression of secreted glycoproteins by transformed lepidopteran insect cells has been developed as an alternative to baculovirus and mammalian cell expression systems. The expression cassette utilizes the promoter of the silkmoth cytoplasmic actin gene to drive expression from foreign gene sequences, and also contains the ie-1 transactivator gene and the HR3 enhancer region of BmNPV to stimulate gene expression. Using an antibiotic-resistance selection scheme, we have cloned a Bm5 (silkmoth) cell line overexpressing the secreted glycoprotein juvenile hormone esterase (JHE-KK) at levels of 190 mg/L in batch suspension cultures. A baculovirus (AcNPV) expressing the same gene under the control of the p10 promoter of AcNPV produced only 4 mg/L active JHE in static cultures of infected Sf21 cells. A cloned Bm5 cell line overexpressing a soluble isoform of the alpha-subunit of the granulocyte-macrophage colony stimulating factor receptor (solGMRalpha) was also generated and produced five times more solGMRalpha in static cultures than a cloned BHK cell line obtained by transformation with a recombinant expression cassette utilizing the human cytomegalovirus (CMV) enhancer-promoter system. Finally, we show that recombinant protein expression levels in transformed Bm5 cells remain high in serum-free media, that expression is stable even in the absence of antibiotic selection, and that lepidopteran cells other than Bm5 may be used equally efficiently with this new expression cassette for producing recombinant proteins.
Light-Regulated Expression of a Pea Ribulose-1,5-Bisphosphate Carboxylase Small Subunit Gene in Transformed Plant Cells (1984)

A pea nuclear gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase was inserted into the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens and transferred into petunia cells by in vitro transformation. The transferred pea rbcS gene is expressed in petunia cells under the transcriptional control of its own promoter in a light-dependent fashion similar to that observed in pea leaves. In contrast, a nonphotosynthetic chimeric gene containing a nopaline synthase promoter is expressed constitutively in both light- and dark-grown tissues. In the transformed cells, transcripts from the pea rbcS gene are processed correctly and translated to yield an authentic pea small subunit polypeptide which is localized in chloroplasts.
New Palladium Carbene Catalysts for the Heck Reaction of Aryl Chlorides in Ionic Liquids (2002)

[reaction: see text] The Heck reaction of aryl chlorides was investigated in the presence of defined monocarbenepalladium(0) complexes. Activated and nonactivated aryl chlorides provide the corresponding cinnamic esters and stilbenes in (n)Bu(4)NBr as a ionic liquid in good to excellent yields.
Embedded Stress Sensors for Strained Technologies Process Control (2008)

Mechanical stress management becomes a major issue for state-of-the-art CMOS technologies. Mechanical stress induced by the process steps is often at the origin of yield losses but also opportunities for technologies performance enhancement. Usual methods for mechanical stress measurement generally require offline measurements and are not compatible with fast correction of process parameters. We propose here embedded stress piezoresistive sensors to allow fast monitoring of mechanical stress and enable real time correction of the process parameters. The test vehicle presented here is dedicated to the gate structure stress monitoring. It is especially very sensitive to the nitride contact etch stop layer stress level. It is shown, in particular, that the structure is able to monitor process-related stress change in the nitride layer. Its feasibility, sensitivity, and relevance in an advanced process control scheme are investigated.
Natural motion generation of biped locomotion robot using hierarchical trajectory generation method consisting of GA, EP layers (2002)

The purpose of this research is to generate natural motion of the biped locomotion robot like a human walking in various environments. In this paper, we report a method of natural motion generation of a biped locomotion robot. We apply the hierarchical trajectory generation method to generate the trajectory of a biped locomotion robot through energy optimization and aim to generate more natural motion by considering dynamic effect. The hierarchical trajectory generation method consists of two layers, one is the GA layer which minimizes the total energy of all actuators, and the other is the evolutionary programming (EP) layer which optimizes interpolated configuration of a biped locomotion robot. Then we formulate the trajectory generation problem, as a minimizing problem of energy and apply the hierarchical trajectory generation method. Further, we build a biped locomotion robot in trial, which has 13 joints and made of aluminium materials. Finally, we confirm that the calculated natural motion trajectory can be applied successfully to the practical biped locomotion.
Clumsiness and Disturbed Cerebellar Development: Insights From Animal Experiments (2003)

Cerebellar functioning has been implied in the fine adjustments of muscle tone, in the coordination and the feed-forward control of movements and posture, as well as in the establishment and performance of motor skills. The cerebellar cortex in mammals develops late in neuro-ontogeny and an extrapolation from experimental results indicates that in the human the proliferation of the granule cells and the development of circuitry in the cerebellar cortex starts only in the last trimester of pregnancy and lasts until beyond the first birthday. This late development makes the cerebellar development particularly vulnerable to situations like an insufficient supply of nutrients, which may follow placental dysfunction, or to side effects of pharmacological treatments like the administration of corticosteroids in the postnatal period. We studied whether such situations might also lead to motor impairments. In rats, the effects of undernutrition during the brain growth spurt were investigated as well as those of corticosteroids administered in a period that is analogous to the 7th to 8th month of pregnancy in the human. Both these interferences affect cerebellar development and our results in rats indicate that they also lead to retardations in the emergence of certain reflexes, as well as to longer lasting motor impairments during locomotion. Extrapolation of these results strongly suggests that a disturbed cerebellar development should be considered as an important etiological factor in clumsiness in human children.
Functional Domains of Axin (1999)

To understand the mechanism of how Axin acts as an inhibitory molecule in the Wnt pathway, we generated a series of mutated forms of Axin. From the binding experiments, we defined the domains of Axin that bind glycogen synthase kinase-3beta (GSK-3beta) and beta-catenin. We also examined the ability of each Axin mutant to inhibit lymphoid enhancer factor-1 (Lef-1) reporter activity in a cell line expressing high levels of beta-catenin. Axin mutants that did not bind GSK-3beta or beta-catenin were ineffective in suppressing Lef-1 reporter activity. Binding GSK-3beta and beta-catenin was not sufficient for this inhibitory effect of Axin. Axin mutants with C-terminal truncations lacked the ability to inhibit Lef-1 reporter activity, even though they bound GSK-3beta and beta-catenin. The C-terminal region was required for binding to Axin itself. Substitution of the C-terminal region with an unrelated dimerizing molecule, the retinoid X receptor restored its inhibitory effect on Lef-1-dependent transcription. The oligomerization of Axin through its C terminus is important for its function in regulation of beta-catenin-mediated response.
FDA Regulation of Stem-Cell–Based Therapies (2006)

The authors review existing regulations regarding cell and tissue products and discuss how they expect the Food and Drug Administration to apply these regulations to scientists' efforts to develop and test stem-cell–based therapies.
Congenital Adrenal Hypoplasia: Clinical Spectrum, Experience with Hormonal Diagnosis, and Report on New Point Mutations of the DAX-1 Gene (1998)

X-linked congenital adrenal hypoplasia (AHC) is a rare developmental disorder of the human adrenal cortex and is caused by deletion or mutation of the DAX-1 gene, a recently discovered member of the nuclear hormone receptor superfamily. Hypogonadotropic hypogonadism is frequently associated with AHC. AHC occurs as part of a contiguous gene syndrome together with glycerol kinase deficiency (GKD) and Duchenne's muscular dystrophy. The present series, collected over the past 2 decades, includes 18 AHC boys from 16 families: 4 with AHC, GKD, and Duchenne's muscular dystrophy; 2 with AHC and GKD; and 12 with AHC (5 young adults with hypogonadotropic hypogonadism). Most of the boys presented with salt wasting and hyperpigmentation during the neonatal period. Plasma steroid determinations performed in the first weeks of life often showed confusing results, probably caused by steroids produced in the neonates' persisting fetocortex. Aldosterone deficiency usually preceded cortisol deficiency, which explains why the patients more often presented with salt-wasting rather than with hypoglycemic symptoms. An ACTH test was often necessary to detect cortisol deficiency in the very young infants. In some patients, serial testing was necessary to establish the correct diagnosis. In 4 boys studied during the first 3 months after birth, we found pubertal LH, FSH, and testosterone plasma levels indicating postnatal transient activation of the hypothalamic-pituitary-gonadal axis as in normal boys. Previous studies have shown that the DAX-1 gene is deleted in the AHC patients with a contiguous gene syndrome and is mutated in nondeletion patients. Most of the point mutations identified in AHC patients were frameshift mutations and stop mutations. In the 15 patients available for molecular analysis of the DAX-1 gene, there were large deletions in 6 patients and point mutations in another 7 patients. All of the point mutations identified in the present study resulted in a nonfunctional truncated DAX-1 protein. Two brothers with primary adrenal insufficiency and a medical history that strongly suggested AHC had no mutation in the DAX-1 gene. Thus, additional, as yet unknown genes must play a part in normal adrenal cortical development.
Aggressive Lymphomas (2010)

This review summarizes recent evidence concerning molecular changes in the commonest type of lymphoma, diffuse large-B-cell lymphoma. Detailed studies have revealed three subtypes, each with distinctive clinical and molecular features. The molecular dissection of these tumors is uncovering new possibilities for treatment, some of which are already in clinical trials.
Expression of the eukaryotic Trypanosoma cruzi CRA gene in Yersinia enterocolitica and induction of an immune response against CRA in mice (1992)

The 70-kb plasmid pYV of Yersinia enterocolitica directs the secretion of a set of proteins, called Yops, that are produced during infection of humans and animals. Trypanosoma cruzi, the agent of American trypanosomiasis, synthesizes a cytoplasmic protein termed CRA that is considered to be T. cruzi specific. To produce CRA in Y. enterocolitica, we constructed a hybrid yopE-CRA gene that we integrated into plasmid pYV by homologous recombination. Recombinant Y. enterocolitica produced a chimeric Yop-CRA protein that was secreted in large amounts in the surrounding medium. This protein reacted with sera directed against either CRA or YopE. To test the ability of the recombinant strain to induce an immune response against CRA, we inoculated C57BL/6J mice by gastric intubation with live recombinant bacteria. A clear antibody response directed against CRA was detected in the mouse serum. The CRA-presenting Y. enterocolitica strain also carried a bioluminescence detection marker, which allowed us to monitor colonization of the intestinal lumen of infected mice. No significant differences were observed between the infectivity of the CRA antigen-producing and -nonproducing Y. enterocolitica strains, despite the fact that one of them no longer produced YopE.
A Systematic Evaluation of the Effect of Temperature on Coagulation Enzyme Activity and Platelet Function (2004)

Our results suggest that bleeding observed at mildly reduced temperatures (33 degrees - 37 degrees C) results primarily from a platelet adhesion defect, and not reduced enzyme activity or platelet activation. However, at temperatures below 33 degrees C, both reduced platelet function and enzyme activity likely contribute to the coagulopathy.
Resolving Power of a Zone Plate* (1967)

The resolution (Rayleigh criterion for resolution) of two point sources by a zone plate is analyzed with respect to the number of zones. It is determined that for N (number of zones) less than 200 the limit of resolution is greater than that of a lens with the same aperture diameter, D, if only the zones which contribute light with a positive phase to the point of observation are used, and less than that of the lens if only the zones which contribute light with a negative phase to the point of observation are used. But, in the former case the maximum value of the side lobe (secondary maximum, first ring) is less than that of an equivalent-diameter lens whereas for the latter case the maximum value is greater. For N greater than 200 the resolution and side-lobe values approach those of a lens in both cases.
Segment-Tree Based Cost Aggregation for Stereo Matching (2013)

This paper presents a novel tree-based cost aggregation method for dense stereo matching. Instead of employing the minimum spanning tree (MST) and its variants, a new tree structure, "Segment-Tree", is proposed for non-local matching cost aggregation. Conceptually, the segment-tree is constructed in a three-step process: first, the pixels are grouped into a set of segments with the reference color or intensity image, second, a tree graph is created for each segment, and in the final step, these independent segment graphs are linked to form the segment-tree structure. In practice, this tree can be efficiently built in time nearly linear to the number of the image pixels. Compared to MST where the graph connectivity is determined with local edge weights, our method introduces some 'non-local' decision rules: the pixels in one perceptually consistent segment are more likely to share similar disparities, and therefore their connectivity within the segment should be first enforced in the tree construction process. The matching costs are then aggregated over the tree within two passes. Performance evaluation on 19 Middlebury data sets shows that the proposed method is comparable to previous state-of-the-art aggregation methods in disparity accuracy and processing speed. Furthermore, the tree structure can be refined with the estimated disparities, which leads to consistent scene segmentation and significantly better aggregation results.
Specificity of a sandwich enzyme-linked immunosorbent assay for detecting Aspergillus galactomannan (1997)

The specificity of a sandwich enzyme-linked immunosorbent assay (ELISA) for detecting Aspergillus galactomannan was tested with exoantigens of 29 fungi cultured from clinical specimens. Cross-reactivity was observed with Penicillium chrysogenum, Penicillium digitatum, and Paecilomyces variotii. Furthermore, 40 serum samples obtained from bacteremic patients with hematologic malignancies were retrospectively tested by sandwich ELISA. False-positive reactions with the serum were reproducible but did not correspond with the results of culture of specific microorganisms. Moreover, the microorganisms cultured from the blood showed no reactivity by the sandwich ELISA.
Dendritic antigen‐presenting cells from the peripheral blood of renal‐cell‐carcinoma patients (1995)

Dendritic cells are considered to be the initiators of immune responses, including those directed against tumors. Clinical research on dendritic cells was long hampered by the limited availability of these cells. The recent identification of cytokine combinations that mobilize dendritic cells with potent antigen-presenting cell function from peripheral blood represented a major progress. We show in this study that substantial numbers of dendritic cells can be obtained from the peripheral blood of patients with renal-cell carcinoma. The procedure requires a relatively small blood sample (40 ml) and avoids both priming of the patient with granulocyte-colony stimulating factor and leukapheresis. Approximately 2 to 8 million cells with the characteristics of dendritic cells could be obtained: phase-contrast microscopy revealed the typical cytoplasmic processes or veils; phenotypic analysis confirmed expression of dendritic-cell-associated molecules, including MHC class II, CD1a, CD4, ICAM-1 (CD54), LFA-3 (CD58), B7-1 (CD80) and B7-2 (CD86), and absence of T-cell, B-cell and monocyte markers; in addition, these cells rapidly attached to and migrated on collagen-type-1-coated surfaces. Interestingly, attachment was accompanied by acquisition of the CD14 antigen; functionally, cultured dendritic cells proved to be very potent co-stimulators of the phytohemagglutinin-induced proliferation of autologous tumor-infiltrating lymphocytes. The reproducible growth of functional dendritic cells from cancer patients is encouraging for the design of immunotherapy protocols.
p80 ROKα binding protein is a novel splice variant of CRMP‐1 which associates with CRMP‐2 and modulates RhoA‐induced neuronal morphology (2002)

Using antibody against the Rho binding domain of ROKalpha, two neuronal phosphoproteins of 62 and 80 kDa were co-immunoprecipitated from brain extracts. Peptide analysis revealed their identity as collapsin response mediator proteins (CRMPs); p62 was CRMP-2 whereas p80 was a novel splice form of CRMP-1 with an extended N-terminus. p80 CRMP-1 was able to complex with CRMP-2, suggesting that p80 CRMP-1 and CRMP-2 form oligomers. CRMP-2 was the major substrate of ROK. p80 CRMP-1 interacted with the kinase domain of ROKalpha, resulting in inhibition of the catalytic activity towards other substrates. Over-expression of p80 CRMP-1 and CRMP-2 together counteracted the effects of RhoA on neurite retraction, an effect enhanced by mutation of the ROK phosphorylation site in CRMP-2. p80 CRMP-1 and CRMP-2 may be modulators of RhoA-dependent signaling, through interaction with and regulation of ROKalpha.
Enzymatic Conversion of Biomass for Fuels Production (1994)

Ideally, the scope of this introductory chapter would encompass all of the major issues that face bioconversion technology for fuel production in the United States, both technical and social. This is, obviously, a far more ambitious scope than can actually be covered in the space allotted here. For many of the social and political issues presented here, I make no claims of expertise. My perspective is presented strictly as that -- my own perspective on issues facing bioconversion technology development. I will be satisfied if I am able to provide a flavor for some of the bigger issues and to give the technical audience of this book an appreciation for the broad range of opportunities and challenges that face the research community in this area.
A new technique to generate a sparse matrix using the method of moments for electromagnetic scattering problems (1998)

In this work, we present a simple numerical technique, viz. the generalized sparse matrix reduction (GSMR) technique, to generate a sparse matrix while applying the well-known method of moments (MoM) to electromagnetic scattering problems. The crucial step in the numerical procedure to generate the sparse matrix involves choosing a set of current distributions defined over the entire structure. Since the present technique generates a sparse matrix, this amounts to considerable savings in terms of computer storage/CPU requirements. Finally, we present some representative numerical examples to demonstrate the validity of this new method. © 1998 John Wiley & Sons, Inc. Microwave Opt Technol Lett 19: 271–274, 1998.
Revised technique of heterotopic heart transplantation in rabbits. (1991)

The technique of heterotopically transplanting a rabbit heart into the abdominal position of a recipient rabbit is discussed. Myocardial preservation, vascular anatomy of the recipient, and general anesthetic considerations are described, as are techniques to avoid anesthetic death, hemorrhage, and paraplegia. Application of these techniques to experimental models of accelerated coronary atherosclerosis and reperfusion injury are suggested.
COSTS MANAGEMENT OF A PROJECT OF THE EDUCATION DISTANCE: ACASE STUDY (2008)

The current Brazilian superior education panorama
					possesses a restrained demand while the individual cost is one of
					the highest in the world. It is necessary to create another
					processes and methods of work that make possible to increase the
					education systems productivity. One of the alternatives is referred
					to the distance education. Ahead of this context, the Brazilian
					government created the Program Open University of Brazil, which
					offers the pilot project of the graduation course in Administration
					in the distance modality. The UFSC is one of the superior education
					institutions that participate of the program. This way, the
					research has as general objective to analyze the cost of offering
					this project in the UFSC. The research can be classified as
					applied, case study, qualitative and descriptive. The total cost of
					offering the course is R$ 3.455.827,80 and the cost of each student
					of the 650 is of R$ R$ 5.316,66. However, considering the evasion
					index, the cost for student suffers an addition from 82,6%.
Effect of alkylated and intercalated DNA on the generation of superoxide anion by riboflavin (1988)

Superoxide anion (O2.-) was photogenerated upon illumination of riboflavin in fluorescent light. The rate of O2.- formation was stimulated by double stranded DNA but not by denatured DNA or RNA. Depurinated DNA, which was predominantly depleted in guanine residues, did not exhibit the stimulatory effect, indicating an interaction of riboflavin, or active oxygen species derived from it, with guanine bases. Also, the stimulation of O2.- photogeneration was not observed with ethidium bromide but was seen with proflavin-intercalated DNA. Since ethidium bromide intercalates preferentially between purines and pyrimidines, and proflavin prefers dA-dT rich sites, these results were interpreted to suggest that the interaction of riboflavin with DNA is mainly with GC or CG base pairs.