gebhart/patrepeval huggingface dataset:
Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation (2018)

In dogs as well as humans, lymphoma is one of the most common hematopoietic malignancies. Furthermore, due to its characteristics, canine lymphoma is recognized as a clinically relevant in vivo model to study the corresponding human disease. Immortalized cell lines are widely used as in vitro models to evaluate novel therapeutic agents and characterize their molecular mechanisms. However, it is known that long-term cultivation leads to clonal selection, genetic instability, and loss of the initial heterogenic character, limiting the usefulness of cell lines as preclinical models. Herein, we present a systematic characterization and comparison of the transcriptomic landscape of canine primary B- and T-cell lymphomas, five lymphoid cell lines (CLBL-1, CLBL-1M, GL-1, CL-1, and OSW) and four non-neoplastic control samples. We found that lymphomas and cell lines exhibit a common "differentiation and proliferation signature". However, our analysis also showed that, independently of the cell of origin, the transcriptional signatures of lymphomas are more similar to each other than they are to those of cell lines. In particular, we observed that not all common therapeutic targets are similarly expressed between lymphomas and lymphoid cell lines, and provide evidence that different lymphoid cell-lines should be used to model distinct aspects of lymphoma dysregulation.
Assessment of yield gaps on global grazed‐only permanent pasture using climate binning (2019)

To meet rising demands for agricultural products, existing agricultural lands must either produce more or expand in area. Yield gaps (YGs)-the difference between current and potential yield of agricultural systems-indicate the ability to increase output while holding land area constant. Here, we assess YGs in global grazed-only permanent pasture lands using a climate binning approach. We create a snapshot of circa 2000 empirical yields for meat and milk production from cattle, sheep, and goats by sorting pastures into climate bins defined by total annual precipitation and growing degree-days. We then estimate YGs from intra-bin yield comparisons. We evaluate YG patterns across three FAO definitions of grazed livestock agroecosystems (arid, humid, and temperate), and groups of animal production systems that vary in animal types and animal products. For all subcategories of grazed-only permanent pasture assessed, we find potential to increase productivity several-fold over current levels. However, because productivity of grazed pasture systems is generally low, even large relative increases in yield translated to small absolute gains in global protein production. In our dataset, milk-focused production systems were found to be seven times as productive as meat-focused production systems regardless of animal type, while cattle were four times as productive as sheep and goats regardless of animal output type. Sustainable intensification of pasture is most promising for local development, where large relative increases in production can substantially increase incomes or "spare" large amounts of land for other uses. Our results motivate the need for further studies to target agroecological and economic limitations on productivity to improve YG estimates and identify sustainable pathways toward intensification.
Mapping Vegetation at Species Level with High-Resolution Multispectral and Lidar Data Over a Large Spatial Area: A Case Study with Kudzu (2020)

Mapping vegetation species is critical to facilitate related quantitative assessment, and mapping invasive plants is important to enhance monitoring and management activities. Integrating high-resolution multispectral remote-sensing (RS) images and lidar (light detection and ranging) point clouds can provide robust features for vegetation mapping. However, using multiple sources of high-resolution RS data for vegetation mapping on a large spatial scale can be both computationally and sampling intensive. Here, we designed a two-step classification workflow to potentially decrease computational cost and sampling effort and to increase classification accuracy by integrating multispectral and lidar data in order to derive spectral, textural, and structural features for mapping target vegetation species. We used this workflow to classify kudzu, an aggressive invasive vine, in the entire Knox County (1362 km2) of Tennessee (U.S.). Object-based image analysis was conducted in the workflow. The first-step classification used 320 kudzu samples and extensive, coarsely labeled samples (based on national land cover) to generate an overprediction map of kudzu using random forest (RF). For the second step, 350 samples were randomly extracted from the overpredicted kudzu and labeled manually for the final prediction using RF and support vector machine (SVM). Computationally intensive features were only used for the second-step classification. SVM had constantly better accuracy than RF, and the producer’s accuracy, user’s accuracy, and Kappa for the SVM model on kudzu were 0.94, 0.96, and 0.90, respectively. SVM predicted 1010 kudzu patches covering 1.29 km2 in Knox County. We found the sample size of kudzu used for algorithm training impacted the accuracy and number of kudzu predicted. The proposed workflow could also improve sampling efficiency and specificity. Our workflow had much higher accuracy than the traditional method conducted in this research, and could be easily implemented to map kudzu in other regions as well as map other vegetation species.
A Multilevel Screening Strategy Defines a Molecular Fingerprint of Proregenerative Olfactory Ensheathing Cells and Identifies SCARB2, a Protein That Improves Regenerative Sprouting of Injured Sensory Spinal Axons (2013)

Olfactory ensheathing cells (OECs) have neuro-restorative properties in animal models for spinal cord injury, stroke, and amyotrophic lateral sclerosis. Here we used a multistep screening approach to discover genes specifically contributing to the regeneration-promoting properties of OECs. Microarray screening of the injured olfactory pathway and of cultured OECs identified 102 genes that were subsequently functionally characterized in cocultures of OECs and primary dorsal root ganglion (DRG) neurons. Selective siRNA-mediated knockdown of 16 genes in OECs (ADAMTS1, BM385941, FZD1, GFRA1, LEPRE1, NCAM1, NID2, NRP1, MSLN, RND1, S100A9, SCARB2, SERPINI1, SERPINF1, TGFB2, and VAV1) significantly reduced outgrowth of cocultured DRG neurons, indicating that endogenous expression of these genes in OECs supports neurite extension of DRG neurons. In a gain-of-function screen for 18 genes, six (CX3CL1, FZD1, LEPRE1, S100A9, SCARB2, and SERPINI1) enhanced and one (TIMP2) inhibited neurite growth. The most potent hit in both the loss- and gain-of-function screens was SCARB2, a protein that promotes cholesterol secretion. Transplants of fibroblasts that were genetically modified to overexpress SCARB2 significantly increased the number of regenerating DRG axons that grew toward the center of a spinal cord lesion in rats. We conclude that expression of SCARB2 enhances regenerative sprouting and that SCARB2 contributes to OEC-mediated neuronal repair.
ROTS: An R package for reproducibility-optimized statistical testing (2017)

Differential expression analysis is one of the most common types of analyses performed on various biological data (e.g. RNA-seq or mass spectrometry proteomics). It is the process that detects features, such as genes or proteins, showing statistically significant differences between the sample groups under comparison. A major challenge in the analysis is the choice of an appropriate test statistic, as different statistics have been shown to perform well in different datasets. To this end, the reproducibility-optimized test statistic (ROTS) adjusts a modified t-statistic according to the inherent properties of the data and provides a ranking of the features based on their statistical evidence for differential expression between two groups. ROTS has already been successfully applied in a range of different studies from transcriptomics to proteomics, showing competitive performance against other state-of-the-art methods. To promote its widespread use, we introduce here a Bioconductor R package for performing ROTS analysis conveniently on different types of omics data. To illustrate the benefits of ROTS in various applications, we present three case studies, involving proteomics and RNA-seq data from public repositories, including both bulk and single cell data. The package is freely available from Bioconductor (https://www.bioconductor.org/packages/ROTS).
An Updated Catalog of 521 Social Surveys of Residents' Reactions to Environmental Noise (1943-2000) (1991)

All social surveys of residents' reactions to environmental noise in residential areas which were described in English language publications from 1943 to 1989 are identified. A total of 318 surveys are described. The surveys are indexed by country, noise source, and data of survey. The publications and reports from each survey are listed in a bibliography. Twenty-four surveys are listed which are available for secondary analysis from a data archive.
Effect of Sonication Time and Particle Volume Fraction on Thermal Conductivity of Alumina Nanofluids (2014)

Abstract : The objective of this task was to use analytical modeling to determine thermal conductivity enhancement of nanofluid samples, with overall particle volume fraction, from 1% to 5%, at 70 W and 100 W. The highest thermal conductivity enhancement and maximum number of nanoparticle clusters were observed for different overall particle volume fractions and sonication times, at 70 W and 100 W. The second conclusion was, at both power levels, 4% volume fraction yielded nanofluids with highest thermal conductivity enhancement. For thermal conductivity enhancement from 16% to 35%, the maximum cluster size was on the order of 200 nm, while, for thermal conductivity enhancements from 135% to 173%, the maximum cluster size was restricted to 500 nm. Thermal conductivity enhancements in excess of 100% of the base fluid were achieved when the optimum overall particle volume fraction is 4%.
A model for magnetic flux leakage signal predictions (2003)

An analytical model was developed to determine the length of a surface-breaking defect along the direction of the applied field when using the magnetic flux leakage (MFL) non-destructive technique. The theoretical model fits the experimental MFL results from simulated defects. The extreme positions of the normal magnetic leakage field component were subsequently used for a quantitative evaluation of the defect length. Permeability variations were neglected by employing a flux density close to sample saturation. Four different defect geometries were experimentally investigated and the validity of the analytical model was verified. Good agreement between theoretical and experimental results suggests that this method can be used as an inverse MFL data interpretation technique.
A Thirteen Year Old Female with Primary T-Cell Rich B-Cell Lymphoma of Bone Masquerading as Chronic Recurrent Multifocal Osteomyelitis (2009)

Primary lymphoma of the bone (PLB) accounts for 2% of all non-Hodgkin's lymphomas, and until recently it had not been well characterized in literature. Most cases present in adulthood (average age 50), with localized painful lesions in the long bones, cranium, or axial skeleton.We describe a case of multifocal PLB in an adolescent female. In this case, the initial presentation, with migratory large joint polyarthralgias and bone pain, mimicked chronic recurrent multifocal osteomyelitis (CRMO). Had a biopsy not been performed the diagnosis would have been missed.
Acquired Activated Protein C Resistance in Patients with Lupus Anticoagulant and Essential Thrombocythemia (1997)

The prevalence of activated protein C (APC) resistance and the antigen levels of factor V were assessed in 37 patients with lupus anticoagulant (LA), 12 with essential thrombocythemia (ET), 17 with idiopathic thrombocytopenic purpura (ITP), and in 27 cases of thrombotic complications associated with diabetes mellitus and collagen vascular disease. Blood samples taken from 30 healthy normal subjects were also available for comparison. The mean APC ratio of patients with LA (2.9 ± 1.5), ET (2.7 ± 1.2), and secondary thrombosis (2.6 ± 0.9) were significantly lower than that of the healthy control group (3.5 ± 1.0). The APC ratio of ET patients with thrombosis (2.3 ± 0.6) was significantly lower than that measured in ET cases without thrombotic complication (3.9 ± 1.9). Patients positive for LA and with thrombotic complication (1.8 ± 1.4) presented lower APC ratios than those without thrombosis (3.3 ± 1.4). Among all patients, an APC ratio lower than 2 was found in 24 cases, of which 16 had thrombotic disease, but none of them presented the factor V:R506Q mutation. The antigen levels of factor V correlated significantly with APC ratio in all patients. The results of this investigation suggest that an acquired poor anticoagulant response to APC might explain, at least in part, the thrombophilia of patients with LA and ET and that associated with diabetes mellitus or collagen disease. Key Words: APC resistance—Lupus anticoagulant—Essential thrombocythemia.
UCN-01 in ovary cancer cells: effective as a single agent and in combination with cis-diamminedichloroplatinum(II)independent of p53 status. (1997)

Our goal was to determine the cytotoxicity of 7-OH-hydroxystaurosporine (UCN-01) as a single agent and in combination with cis-diamminedichloroplatinum(II) (CDDP) in a panel of ovarian carcinoma cells. We sought to examine the role of p53 gene function and alterations in cell cycle progression or other mechanisms of action of UCN-01 including perturbation of the apoptosis pathway mediated by NF-kappaB and Bcl-2/Bax. Cytotoxicity was determined from dose-response curves established by the Alamar blue vital dye indicator assay. Restoration of wild-type p53 in a p53 null cell line, SKOV 3, was achieved by transfection of a p53 expression vector. Cell cycle distribution was measured by fluorescence-activated cell sorting analysis of ethidium bromide-stained nuclei. Apoptosis was measured by quantitative fluorescence microscopy. NF-kappaB DNA binding activity was measured by electrophoretic mobility shift assay. Bcl-2 and Bax levels were determined by Western immunoblotting. UCN-01 was effective as a cytotoxic agent alone and in combination with CDDP in all cell lines studied, regardless of p53 status. The degree of sensitization to CDDP conferred by UCN-01, however, was found to correlate with p53 gene status. p53 wild-type cells seem to be more sensitive to the cytotoxic effects of the combination of UCN-01 + CDDP than the p53 mutant cells. This was confirmed in cells in which p53 wild-type function was restored by transfection of p53 cDNA, but these cells are also significantly more sensitive to CDDP alone. The effects of UCN-01 on cell cycle progression also appear to be p53 dependent but may not be the primary mechanism of action. The rate of apoptosis is increased 4-fold in UCN-01 + CDDP-treated cells compared to either agent alone. UCN-01 does not effect NF-kappaB DNA binding activity or Bcl-2 and Bax levels. UCN-01 enhances CDDP cytotoxicity and apoptosis in ovary cancer cells. This occurs regardless of p53 status, but wild-type p53 seems to increase the degree of sensitization.
Modified Dachengqi Tang improves decreased gastrointestinal motility in postoperative esophageal cancer patients (2015)

Modified DCQT effectively improved decreased gastrointestinal motility in postoperative esophageal cancer patients by increasing MTL and reducing VIP.
Extracorporeal shock wave therapy does not improve hypertensive nephropathy (2016)

Low-energy extracorporeal shock wave therapy (SWT) has been shown to improve myocardial dysfunction, hind limb ischemia, erectile function, and to facilitate cell therapy and healing process. These therapeutic effects were mainly due to promoting angiogenesis. Since chronic kidney diseases are characterized by renal fibrosis and capillaries rarefaction, they may benefit from a proangiogenic treatment. The objective of our study was to determine whether SWT could ameliorate renal repair and favor angiogenesis in L-NAME-induced hypertensive nephropathy in rats. SWT was started when proteinuria exceeded 1 g/mmol of creatinine and 1 week after L-NAME removal. SWT consisted of implying 0.09 mJ/mm(2) (400 shots), 3 times per week. After 4 weeks of SWT, blood pressure, renal function and urinary protein excretion did not differ between treated (LN + SWT) and untreated rats (LN). Histological lesions including glomerulosclerosis and arteriolosclerosis scores, tubular dilatation and interstitial fibrosis were similar in both groups. In addition, peritubular capillaries and eNOS, VEGF, VEGF-R, SDF-1 gene expressions did not increase in SWT-treated compared to untreated animals. No procedural complications or adverse effects were observed in control (C + SWT) and hypertensive rats (LN + SWT). These results suggest that extracorporeal kidney shock wave therapy does not induce angiogenesis and does not improve renal function and structure, at least in the model of hypertensive nephropathy although the treatment is well tolerated.
Facile strategy for the synthesis of non-covalently bonded and para-toluene sulfonic acid-functionalized fibrous polyaniline@graphene–PVC nanocomposite for the removal of Congo red (2015)

Possible interactions between CR and <italic>p</italic>TSA–Pani@GN–PVC fiber.
Die Chondrocalcinose (Pseudogicht) des Kniegelenkmeniskus* (1979)

Among 1060 histologically examined meniscus cartilages from patients aged 11--74 years 20 (2%) had chondrocalcinosis. Age at onset of symptoms was 28--67 years, duration of symptoms until surgical removal of the meniscus six weeks to 20 years. All patients had pain, 12 had pain-independent limitations of knee movement. Effusions of the knee were present in ten. Independent of the radiological findings, in the majority of patients the symptoms were markedly improved or completely absent one-two years after meniscus removal. All meniscus specimens revealed severe changes both macroscopically and histologically. The clinical diagnosis confirmed by demonstrating calcium pyrophosphate crystals in haemalauneosin stained sections, examined by polarisation microscopy. The X-ray films demonstrated arthrosis in at least 50% of cases. There appeared to be a close mutual relationship between chondrocalcinosis and arthrosis of the knee-joint.
On Study of Fluorescence Spectrum in Surfactant System (2004)

This paper summarized the development of fluorescence spectrum in surfactant system in recent years and increasing dissolving and increasing sensitivity mechanism of surfactant to fluorescence matter. The prospects for the development direction on surfactant application was discussed in fluorescence spectrum.
Tunneling atνT=1in quantum Hall bilayers (2013)

Interlayer tunneling measurements in the strongly correlated bilayer quantized Hall phase at ${\ensuremath{\nu}}_{T}=1$ are reported. The maximum, or critical, current for tunneling at ${\ensuremath{\nu}}_{T}=1$ is shown to be a well-defined global property of the coherent phase, insensitive to extrinsic circuit effects and the precise configuration used to measure it, but also exhibiting a surprising scaling behavior with temperature. Comparisons between the experimentally observed tunneling characteristics and a recent theory are favorable at high temperatures, but not at low temperatures where the tunneling closely resembles the dc Josephson effect. The zero-bias tunneling resistance becomes extremely small at low temperatures, vastly less than that observed at zero magnetic field, but nonetheless remains finite. The temperature dependence of this tunneling resistance is similar to that of the ordinary in-plane resistivity of the quantum Hall phase.
Evaluating logarithms in GF(2n) (1984)

We present a method for determining logarithms in GF(2n). Its asymptotic running time is O( exp (cn1/3log2/3n)) for a small constant c, while, by comparison, Adleman's scheme runs in time O( exp (c'n1/2log1/2n)). The ideas give a dramatic improvement even for moderate-sized fields such as GF(2127), and make (barely) possible computations in fields of size around 2400. The method is not applicable to GF(q) for a large prime q.
Synovial cysts of the lumbar spine: surgery-related results and outcome (2003)

The findings in this series suggest that synovial cysts can occur at multiple lumbar sites within a short period of time and could be predisposed to developing in certain individuals, predominantly in women older than 40 years of age. Postoperative follow up is recommended and MR imaging mandatory in cases of recurrent sciatica.
Synthesis of Sulfide Solid Electrolytes through the Liquid Phase: Optimization of the Preparation Conditions (2020)

All-solid-state lithium batteries using inorganic sulfide solid electrolytes have good safety properties and high rate capabilities as expected for a next-generation battery. Presently, conventional preparation methods such as mechanical milling and/or solid-phase synthesis need a long time to provide a small amount of the product, and they have difficult in supplying a sufficient amount to meet the demand. Hence, liquid-phase synthesis methods have been developed for large-scale synthesis. However, the ionic conductivity of sulfide solid electrolytes prepared via liquid-phase synthesis is typically lower than that prepared via solid-phase synthesis. In this study, we have controlled three factors: (1) shaking time, (2) annealing temperature, and (3) annealing time. The factors influencing lithium ionic conductivity of Li<sub>3</sub>PS<sub>4</sub> prepared via liquid-phase synthesis were quantitatively evaluated using high-energy X-ray diffraction (XRD) measurement coupled with pair distribution function (PDF) analysis. It was revealed from PDF analysis that the amount of Li<sub>2</sub>S that cannot be detected by Raman spectroscopy or XRD decreased the ionic conductivity. Furthermore, it was revealed that the ionic conductivity of Li<sub>3</sub>PS<sub>4</sub> is dominated by other parameters, such as remaining solvent in the sample and high crystallinity of the sample.
Using Digital Technology to See Angles from Different Angles. Part 2: Openings and Turns. (2015)

Ever wondered how to use technology to teach angles? This article follows on from an earlier article published last year, providing a range of ideas for integrating technology and concrete materials with the teaching of angle concepts. The authors also provide a comprehensive list of free online games and learning objects that can be used to teach angles in an engaging way.