gebhart/patrepeval huggingface dataset:
Reduced‐Linolenate Content Associations with Agronomic and Seed Traits of Soybean (1998)

Soybean [ Glycine max (L.) Merr.] lines with the fan1 (A5) fan1 (A5) fan2 fan2 genotype for reduced linolenate content produce an oil with improved oxidative stability. The improved oxidative stability reduces the formation of undesirable flavor compounds in the oil. The objective of this study was to determine if reduced linolenate influences agronomic or seed traits of soybean. The single‐cross populations AX11224, AX11227, and AX11240 were developed by crossing each of three high‐yielding parents with normal‐linolenate content of ≈77 g kg −1 to one of three reduced‐linolenate parents with ≈26 g kg −1 linolenate. From each of the populations, 27 F 3 ‐derived normal‐linolenate lines and 27 reduced‐linolenate lines were evaluated at three locations in Iowa during 1996. The mean seed yields of the reduced‐linolenate lines were not significantly different ( P &gt; 0.05) from the normal‐linolenate lines for AX11224 and AX11227, but the mean yield of the reduced‐linolenate lines was significantly lower than the normal‐linolenate lines for AX11240. The means of the reduced‐linolenate lines were not significantly different from the normal‐linolenate lines for maturity, lodging, plant height, and protein content in the three populations. The mean oil, stearate, and linoleate contents of reduced‐linolenate lines were significantly greater ( P &lt; 0.05) than normal‐linolenate lines in all populations. Differences between the means of the reduced‐ and normal‐linolenate lines for seed weight, palmitate content and oleate content were not consistent among the populations. The difference among crosses for the relationship of reduced linolenate with seed yield and other traits indicated that multiple reduced‐ and normal‐linolenate parents should be used in a cultivar development program.
Growth of Madin-Darby canine kidney epithelial cell (MDCK) line in hormone-supplemented, serum-free medium. (1979)

Madin-Darby canine kidney (MDCK) cells can grow in synthetic medium supplemented with five factors--insulin, transferrin, prostaglandin E1, hydrocortisone, and triiodothyronine--as a serum substitute. These five factors permit growth for 1 month in the absence of serum and a growth rate equivalent to that observed in serum-supplemented medium. Dibutyryl adenosine 3',5'-cyclic monophosphate substitutes for prostaglandin E1 in the medium. Potential applications of the serum-free medium are discussed. The medium permits a defined analysis of the mechanisms regulating hemicyst formation by hormones and permits the growth of primary kidney epithelial cell cultures in the absence of fibroblast overgrowth.
Whole genome shotgun sequencing ofBrassica oleraceaand its application to gene discovery and annotation inArabidopsis (2005)

Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering 283 Mb (0.44 x) of the estimated 650 Mb Brassica genome were searched against the Arabidopsis genome, and conserved Arabidopsis genome sequences (CAGSs) were identified. Of these 229,735 conserved regions, 167,357 fell within or intersected existing gene models, while 60,378 were located in previously unannotated regions. After removal of sequences matching known proteins, CAGSs that were close to one another were chained together as potentially comprising portions of the same functional unit. This resulted in 27,347 chains of which 15,686 were sufficiently distant from existing gene annotations to be considered a novel conserved unit. Of 192 conserved regions examined, 58 were found to be expressed in our cDNA populations. Rapid amplification of cDNA ends (RACE) was used to obtain potentially full-length transcripts from these 58 regions. The resulting sequences led to the creation of 21 gene models at 17 new Arabidopsis loci and the addition of splice variants or updates to another 19 gene structures. In addition, CAGSs overlapping already annotated genes in Arabidopsis can provide guidance for manual improvement of existing gene models. Published genome-wide expression data based on whole genome tiling arrays and massively parallel signature sequencing were overlaid on the Brassica-Arabidopsis conserved sequences, and 1399 regions of intersection were identified. Collectively our results and these data sets suggest that several thousand new Arabidopsis genes remain to be identified and annotated.
P‐glycoprotein: multidrug‐resistance and a superfamily of membrane‐associated transport proteins (1989)

The study of multidrug resistance (MDR) in tumor cell lines has led to the discovery of the plasma membrane P-glycoprotein (Pgp) molecule. This protein functions as an energy-dependent pump for the efflux of diverse anticancer drugs from MDR cells. It now appears that Pgp-mediated MDR tumor cells do occur in human cancers, and that they are likely to play a role in the ultimate response of patients to chemotherapy. Chemosensitizers, compounds able to reverse the MDR phenotype, have been identified and offer the exciting possibility of improving efficacy for some nonresponsive malignancies. Surprisingly, Pgp-like molecules can be found in evolutionarily distant species among both eukaryotes and prokaryotes. As a group, these proteins form a superfamily of ATP-dependent transport proteins. This finding has broad implications and provides new insights into how living organisms use this fundamental transport system to regulate the trafficking of diverse molecules across biological membranes.
Formability of ABX 3 (X = F, Cl, Br, I) halide perovskites (2008)

In this study a total of 186 complex halide systems were collected; the formabilities of ABX3 (X = F, Cl, Br and I) halide perovskites were investigated using the empirical structure map, which was constructed by Goldschmidt's tolerance factor and the octahedral factor. A model for halide perovskite formability was built up. In this model obtained, for all 186 complex halides systems, only one system (CsF-MnF2) without perovskite structure and six systems (RbF-PbF2, CsF-BeF2, KCl-FeCl2, TlI-MnI2, RbI-SnI2, TlI-PbI2) with perovskite structure were wrongly classified, so its predicting accuracy reaches 96%. It is also indicated that both the tolerance factor and the octahedral factor are a necessary but not sufficient condition for ABX3 halide perovskite formability, and a lowest limit of the octahedral factor exists for halide perovskite formation. This result is consistent with our previous report for ABO3 oxide perovskite, and may be helpful to design novel halide materials with the perovskite structure.
Treatment of rheumatoid synovitis of the knee with intraarticular injection of dysprosium 165‐ferric hydroxide macroaggregates (1986)

One hundred eight knees of 93 patients with seropositive rheumatoid arthritis and persistent synovitis of the knee were treated with an intraarticular injection of 270 mCi of dysprosium 165 bound to ferric hydroxide macroaggregate. Leakage of radioactivity from the injected joint was minimal. Mean leakage to the venous blood 3 hours after injection was 0.11% of the injected dose; this corresponds to a mean whole body dose of 0.2 rads. Mean leakage to the liver 24 hours after injection was 0.64% of the injected dose; this corresponds to a mean liver dose of 3.2 rads. In 7 additional patients examined, there was negligible or near negligible activity found in the draining inguinal lymph nodes. One-year followup was possible for 74 knees (63 patients). Sixty-one percent of the knees had good results, 23% had fair results, and 16% had poor results. There was a direct correlation between the radiographic stage and response to treatment. In knees with stage I radiographic changes, 72% showed good results; 93% showed improvement. In knees with stage II changes, 59% showed good results; 81% showed improvement. These preliminary results indicate that dysprosium 165-ferric hydroxide macroaggregate is an effective agent for radiation synovectomy. The low leakage rates observed offer a definite advantage over agents previously used.
Mapping sensory nerve communications between peripheral nerve territories (2013)

The human cutaneous sensory map has been a work in progress over the past century, depicting sensory territories supplied by both the spinal and cranial nerves. Two critical discoveries, which shaped our understanding of cutaneous innervation, were sensory dermatome overlap between contiguous spinal levels and axial lines across areas where no sensory overlap exists. These concepts define current dermatome maps. We wondered whether the overlap between contiguous sensory territories was even tighter: if neural communications were present in the peripheral nerve territories consistently connecting contiguous spinal levels? A literature search using peer-reviewed articles and established anatomy texts was performed aimed at identifying the presence of communications between sensory nerves in peripheral nerve territories and their relationship to areas of adjacent and non-adjacent spinal or cranial nerves and axial lines (lines of discontinuity) in the upper and lower limbs, trunk and perineum, and head and neck regions. Our findings demonstrate the consistent presence of sensory nerve communications between peripheral nerve territories derived from spinal nerves within areas of axial lines in the upper and lower limbs, trunk and perineum, and head and neck. We did not find examples of communications crossing axial lines in the limbs or lines of discontinuity in the face, but did find examples crossing axial lines in the trunk and perineum. Sensory nerve communications are common. They unify concepts of cutaneous innervation territories and their boundaries, and refine our understanding of the sensory map of the human skin.
ANTHOCYANINLESS2, a Homeobox Gene Affecting Anthocyanin Distribution and Root Development in Arabidopsis (1999)

Hiroyoshi Kubo, Anton J. M. Peeters, Mark G. M. Aarts, Andy Pereira, Maarten Koornneef, ANTHOCYANINLESS2, a Homeobox Gene Affecting Anthocyanin Distribution and Root Development in Arabidopsis, The Plant Cell, Vol. 11, No. 7 (Jul., 1999), pp. 1217-1226
Synthesis of photoconducting ZnO nano-needles using an unbalanced magnetron sputtered ZnO/Zn/ZnO multilayer structure (2005)

The synthesis of ZnO nano-needles using unbalanced magnetron sputtering is reported. A multilayer structure comprised of ZnO(50 nm)/Zn(20 nm)/ZnO(2 µm) was grown on a stainless steel substrate without substrate heating. The growth of ZnO nano-needles was observed on the surface of the multilayer structure after post-annealing treatment at 300–400 °C. The nano-needles were distributed randomly over the entire surface and had an average diameter of 20 nm; their length varied from 2 to 5 µm. The ultra-thin Zn layer (20 nm) in the multilayer structure is attributed to act as a nucleating centre and it activates the coalescence process for the growth of ZnO nano-needles. The ZnO nano-needles showed enhanced ultraviolet photoresponse with an initial fast rise and decay. The origin of the photoconductivity is due to the bulk related process. Results show the myriad application of ZnO nano-needles in ultraviolet light detection.
ASPM-associated stem cell proliferation is involved in malignant progression of gliomas and constitutes an attractive therapeutic target (2010)

These data suggest that ASPM is involved in the malignant progression of gliomas, possibly through expansion of a cancer stem cell compartment, and is an attractive therapeutic target in glioblastoma multiforme.
Phase retrieval via spatial light modulator phase modulation in 4f optical setup: numerical inverse imaging with sparse regularization for phase and amplitude (2011)

The 4f optical setup is considered with a wave field modulation by a spatial light modulator located in the focal plane of the first lens. Phase as well as amplitude of the wave field are reconstructed from noisy multiple-intensity observations. The reconstruction is optimal due to a constrained maximum likelihood formulation of the problem. The proposed algorithm is iterative with decoupling of the inverse of the forward propagation of the wave field and the filtering of phase and amplitude. The sparse modeling of phase and amplitude enables the advanced high-accuracy filtering and sharp imaging of the complex-valued wave field. Artifacts typical for the conventional algorithms (wiggles, ringing, waves, etc.) and attributed to optical diffraction can be suppressed by the proposed algorithm.
Kinase Receptor Activation (KIRA): a rapid and accurate alternative to endpoint bioassays. (1999)

We have developed a novel strategy for a rapid bioassay that is accurate, precise, sensitive, and high capacity. It is capable of quantifying ligand bioactivity by measuring ligand-induced receptor tyrosine kinase activation in terms of receptor-phosphorylation. The assay, termed << Kinase Receptor Activation>> or KIRA, uses two separate microtiter plates, one for ligand stimulation of intact cells, and the other for receptor capture and phosphotyrosine ELISA. The assay makes use of either endogenously expressed receptors or stably transfected receptors with a polypeptide flag. KIRA assays for the ligands IGF-I and NGF were compared to their corresponding endpoint bioassays (3T3 cell proliferation for IGF-I and PC12 cell survival for NGF). The KIRA assays showed excellent correlation with the more classical endpoint bioassays. Further, they were highly reproducible, minimizing the requirement for repeat assays. The KIRA assay format has great potential as a rapid, accurate and precise bioassay, both for potency determination as well as stability-indicating analyses.
Role of Advanced Glycation End Products (AGEs) and Oxidative Stress in Diabetic Retinopathy (2008)

Diabetic retinopathy is a common and potentially devastating microvascular complication in diabetes and is a leading cause of acquired blindness among the people of occupational age. However, current therapeutic options for the treatment of sight-threatening proliferative diabetic retinopathy such as photocoagulation and vitrectomy are limited by considerable side effects and far from satisfactory. Therefore, to develop novel therapeutic strategies that specifically target diabetic retinopathy is actually desired for most of the patients with diabetes. Chronic hyperglycemia is a major initiator of diabetic retinopathy. However, recent clinical study has substantiated the concept of 'hyperglycemic memory' in the pathogenesis of diabetic retinopathy. Indeed, the Diabetes Control and Complications Trial-Epidemiology of Diabetes Interventions and Complications (DCCT-EDIC) Research, has revealed that the reduction in the risk of progressive retinopathy resulting from intensive therapy in patients with type 1 diabetes persisted for at least several years after the DCCT trial, despite increasing hyperglycemia. These findings suggest a long-term beneficial influence of early metabolic control on clinical outcomes in type 1 diabetic patients. Among various biochemical pathways implicated in the pathogenesis of diabetic retinopathy, the process of formation and accumulation of advanced glycation end products (AGEs) and their mode of action are most compatible with the theory 'hyperglycemic memory'. Further, there is a growing body of evidence that AGEs-RAGE (receptor for AGEs) interaction-mediated oxidative stress generation plays an important role in diabetic retinopathy. This article summarizes the role of AGEs and oxidative stress in the development and progression of diabetic retinopathy and the therapeutic interventions that could prevent this devastating disorder. We also discuss here the pathological crosstalk between the AGEs-RAGE and the renin-angiotensin system in diabetic retinopathy and a potential clinical utility of telmisartan, an angiotensin II type 1 receptor blocker with peroxisome proliferator-activated receptor-gamma-modulating activity.
The 1997 automated highway free agent demonstration (2002)

In August 1997, the US National Automated Highway System Consortium (NAHSC) presented a proof of technical feasibility demonstration of automated driving. It took place on I-15, in San Diego, California. Members of the consortium demonstrated many different functions: vision-based road following, following magnetic nails, following a radar reflective strip, radar-based headway maintenance, ladar-based headway maintenance, evolutionary systems, close vehicle following (platooning), cooperative maneuvering, obstacle detection and avoidance, mixed automated and manual driving, mixed automated cars and buses, and semi-automated maintenance. CMU led the effort to build one of the seven demonstration scenarios, the Free Agent Demonstration (FAD). The FAD involved two fully automated cars, one partially automated car, and two fully automated city buses. The scenario demonstrates lane entry, speed and headway control, lane following, lane changing, obstacle detection, and cooperative maneuvers. This paper describes the free agent demonstration itself, the technology that made the demonstration possible, and the future work to analyze the feasibility of turning the demonstration system into a practical prototype.
Isolation and Characterization of Thermosensitive Escherichia coli Mutants Defective in Deoxyribonucleic Acid Replication (1973)

Thermosensitive deoxyribonucleic acid replication-defective mutants have been isolated by using an autoradiographic selection method. The mutants have been analyzed genetically and biochemically. Some of the mutants show thermosensitivity of in vitro deoxyribonucleic acid replication. These can be classified into three groups according to their behavior in in vitro complementation assays. This classification is congruent with that obtained by genetic mapping by using cotransduction frequencies with selected markers in P1 transduction analysis.
Confidence-based Somatic Mutation Evaluation and Prioritization (2012)

Next generation sequencing (NGS) has enabled high throughput discovery of somatic mutations. Detection depends on experimental design, lab platforms, parameters and analysis algorithms. However, NGS-based somatic mutation detection is prone to erroneous calls, with reported validation rates near 54% and congruence between algorithms less than 50%. Here, we developed an algorithm to assign a single statistic, a false discovery rate (FDR), to each somatic mutation identified by NGS. This FDR confidence value accurately discriminates true mutations from erroneous calls. Using sequencing data generated from triplicate exome profiling of C57BL/6 mice and B16-F10 melanoma cells, we used the existing algorithms GATK, SAMtools and SomaticSNiPer to identify somatic mutations. For each identified mutation, our algorithm assigned an FDR. We selected 139 mutations for validation, including 50 somatic mutations assigned a low FDR (high confidence) and 44 mutations assigned a high FDR (low confidence). All of the high confidence somatic mutations validated (50 of 50), none of the 44 low confidence somatic mutations validated, and 15 of 45 mutations with an intermediate FDR validated. Furthermore, the assignment of a single FDR to individual mutations enables statistical comparisons of lab and computation methodologies, including ROC curves and AUC metrics. Using the HiSeq 2000, single end 50 nt reads from replicates generate the highest confidence somatic mutation call set.
Arginase-Producing Myeloid Suppressor Cells in Renal Cell Carcinoma Patients: A Mechanism of Tumor Evasion (2005)

Myeloid suppressor cells with high arginase activity are found in tumors and spleen of mice with colon and lung cancer. These cells, described as macrophages or immature dendritic cells, deplete arginine and impair T cell proliferation and cytokine production. Although arginase activity has been described in cancer patients, it is thought to originate from tumor cells metabolizing arginine to ornithine needed to sustain rapid cell proliferation. The goal of this study was to determine whether myeloid suppressor cells producing high arginase existed in renal cell carcinoma patients. Peripheral blood mononuclear cells from 123 patients with metastatic renal cell carcinoma, prior to treatment, were found to have a significantly increased arginase activity. These patients had a markedly decreased cytokine production and expressed low levels of T cell receptor CD3zeta chain. Cell separation studies showed that the increased arginase activity was limited to a specific subset of CD11b+, CD14-, CD15+ cells with a polymorphonuclear granulocyte morphology and markers, instead of macrophages or dendritic cells described in mouse models. Furthermore, these patients had low levels of arginine and high levels of ornithine in plasma. Depletion of the CD11b+, CD14- myeloid suppressor cells reestablished T cell proliferation and CD3zeta chain expression. These results showed, for the first time, the existence of suppressor myeloid cells producing arginase in human cancer patients. In addition, it supports the concept that blocking arginase may be an important step in the success of immunotherapy.
Two amyloid precursor protein transgenic mouse models with Alzheimer disease-like pathology (1997)

Mutations in the amyloid precursor protein (APP) gene cause early-onset familial Alzheimer disease (AD) by affecting the formation of the amyloid beta (A beta) peptide, the major constituent of AD plaques. We expressed human APP751 containing these mutations in the brains of transgenic mice. Two transgenic mouse lines develop pathological features reminiscent of AD. The degree of pathology depends on expression levels and specific mutations. A 2-fold overexpression of human APP with the Swedish double mutation at positions 670/671 combined with the V717I mutation causes A beta deposition in neocortex and hippocampus of 18-month-old transgenic mice. The deposits are mostly of the diffuse type; however, some congophilic plaques can be detected. In mice with 7-fold overexpression of human APP harboring the Swedish mutation alone, typical plaques appear at 6 months, which increase with age and are Congo Red-positive at first detection. These congophilic plaques are accompanied by neuritic changes and dystrophic cholinergic fibers. Furthermore, inflammatory processes indicated by a massive glial reaction are apparent. Most notably, plaques are immunoreactive for hyperphosphorylated tau, reminiscent of early tau pathology. The immunoreactivity is exclusively found in congophilic senile plaques of both lines. In the higher expressing line, elevated tau phosphorylation can be demonstrated biochemically in 6-month-old animals and increases with age. These mice resemble major features of AD pathology and suggest a central role of A beta in the pathogenesis of the disease.