gebhart/patrepeval huggingface dataset:
Outcomes of transformed follicular lymphoma in the modern era: a report from the National LymphoCare Study (NLCS) (2015)

We assessed the incidence, prognostic features, and outcomes associated with transformation of follicular lymphoma (FL) among 2652 evaluable patients prospectively enrolled in the National LymphoCare Study. At a median follow-up of 6.8 years, 379/2652 (14.3%) patients transformed following the initial FL diagnosis, including 147 pathologically confirmed and 232 clinically suspected cases. Eastern Cancer Oncology Group performance status >1, extranodal sites >1, elevated lactate dehydrogenase, and B symptoms at diagnosis were associated with transformation risk. Relative to observation, patients initiating treatment at diagnosis had a reduced risk of transformation (hazard ratio [HR], 0.58; 95% confidence interval [CI], 0.46-0.75). The risk of transformation was similar in patients treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone compared with rituximab, cyclophosphamide, vincristine, and prednisone (adjusted HR, 0.94; 95% CI, 0.62-1.42). Maintenance rituximab was associated with reduced transformation risk (HR, 0.67; 95% CI, 0.46-0.97). Five-year survival from diagnosis was significantly worse for patients with vs without transformation (75%, 95% CI, 70-79 vs 85%, 95% CI, 83-86). The median overall survival post-transformation was 5 years. Forty-seven patients with evidence of transformation at the time of diagnosis shared similar prognostic factors and survival rates to those without transformation. Improved outcomes for transformation in the modern era are suggested by this observational study. This trial is registered at www.clinicaltrials.gov as #NCT00097565.
Tumor necrosis factor is a survival and proliferation factor for human myeloma cells. (1999)

Interleukin-6 (IL-6) is a major survival factor for malignant plasma cells. In patients with multiple myeloma (MM), cell lines whose survival and proliferation are dependent upon addition of exogenous IL-6 have been obtained. We show here that tumor necrosis factor-alpha (TNF-alpha) is also a survival factor for myeloma cell lines, although less potent than IL-6. The survival activity of TNF-alpha is not affected by anti-IL-6 or anti-gp130 monoclonal antibodies (mAbs). TNF-alpha also induces myeloma cells in the cell cycle and promotes the long-term growth of malignant plasma cell lines. As TNF-alpha is produced in patients with MM and associated with a poor prognosis, these results suggest that anti-TNF-alpha therapies could be useful in this disease.
Effects of cell density and temperature on oxygen consumption rate for different mammalian cell lines (1999)

Oxygen consumption rates were measured in a respirometer for different mammalian cell lines (BHK, murine hybridoma, and CHO), and the effects of cell density (1-20 million cells/mL) and temperature (6 to 37 degrees C) on specific oxygen consumption rate were investigated. The specific oxygen consumption was cell line dependent. For a given temperature, the murine hybridoma cells had the lowest and the CHO cells had the highest oxygen consumption rate. The specific oxygen consumption rate was not affected by the cell concentration for cell densities between 1 and 20 million cells/mL. However, artificial trends implicating the effects of cell density were obtained when traditional analysis was used and the probe response time was neglected. A detailed mathematical analysis was presented to investigate the magnitude of errors originating from neglecting the probe response time for the calculation of oxygen consumption rate. The error was significant, especially when the probe response was slow and/or the oxygen consumption was fast. Temperature influenced the specific oxygen consumption rate similarly for the cells studied, and about 10% decrease was observed in specific oxygen consumption by 1 degrees C decrease in the temperature. Between 6 and 37 degrees C, the effect of temperature on oxygen consumption rate could be described using an Arrhenius model, i.e., qO2 = qoO2. e-E/RT. The activation energy, E, in this equation was similar for different cells (between 80 and 90 kJ/mol), indicating the action of a similar mechanism for the effect of temperature on oxygen consumption.
Population Structure and Eigenanalysis (2006)

Current methods for inferring population structure from genetic data do not provide formal significance tests for population differentiation. We discuss an approach to studying population structure (principal components analysis) that was first applied to genetic data by Cavalli-Sforza and colleagues. We place the method on a solid statistical footing, using results from modern statistics to develop formal significance tests. We also uncover a general ''phase change'' phenomenon about the ability to detect structure in genetic data, which emerges from the statistical theory we use, and has an important implication for the ability to discover structure in genetic data: for a fixed but large dataset size, divergence between two populations (as measured, for example, by a statistic like F ST ) below a threshold is essentially undetectable, but a little above threshold, detection will be easy. This means that we can predict the dataset size needed to detect structure.
High-throughput microarray detection of olfactory receptor gene expression in the mouse (2004)

The large number of olfactory receptor genes necessitates high throughput methods to analyze their expression patterns. We have therefore designed a high-density oligonucleotide array containing all known mouse olfactory receptor (OR) and V1R vomeronasal receptor genes. This custom array detected a large number of receptor genes, demonstrating specific expression in the olfactory sensory epithelium for approximately 800 OR genes previously designated as ORs based solely on genomic sequences. The array also enabled us to monitor the spatial and temporal distribution of gene expression for the entire OR family. Interestingly, OR genes showing spatially segregated expression patterns were also segregated on the chromosomes. This correlation between genomic location and spatial expression provides unique insights about the regulation of this large family of genes.
High characteristic temperature of near-1.3-μm InGaAs/GaAs quantum-dot lasers at room temperature (2000)

This letter reports on the high characteristic temperature of InGaAs/GaAs quantum-dot lasers at room temperature. Self-assembled quantum dots were grown using low-growth-rate molecularbeam epitaxy, and continuous-wave lasing occurred at the dot ground level of 1.26 μm at 25 °C. The characteristic temperature of the threshold currents was 120 K, and ground-level lasing was observed up to 100 °C. Comparing the lasing performances and the spontaneous emission spectra with those of 1.3 μm emission dots, we found that the large volume density, deep potential, and high quantum efficiency were key points for improving the temperature characteristics.
Sequential phosphorylation of Ser‐10 on histone H3 and ser‐139 on histone H2AX and ATM activation during premature chromosome condensation: Relationship to cell‐cycle phase and apoptosis (2006)

Because the Cal A-induced phosphorylation of histone H3 and H2AX, and of ATM, precede caspase-3 activation these modifications are pertinent to PCC and not to apoptosis-associated chromatin condensation. The sequence of histone H3 and H2AX phosphorylation and ATM activation during PCC is compatible with a role of ATM in mediating phosphorylation of H2AX but not H3. Mitosis in some cell types may proceed without ATM activation and H2AX phosphorylation.
Intracerebroventricular salmon calcitonin reduces autotomy behavior in rats after dorsal rhizotomy (1992)

We studied the effects of intracerebroventricularly (ICV) administered salmon calcitonin (sCT) on the self-mutilation behavior (autotomy) of rats after dorsal rhizotomy. sCT was given 2 micrograms/rat ICV, on alternate days) from day 15 to day 40 after surgery and autotomy was scored until day 60. Autotomy scores were significantly reduced during treatment but once the ICV sCT was stopped mean values for the treated group gradually returned to control levels. These data support the concept that autotomy is a useful model of chronic pain, sensitive to centrally acting antinociceptive agents. In addition, these findings extend the knowledge of the antinociceptive profile of sCT and are in agreement with recent clinical observations.
Stretchable, Curvilinear Electronics Based on Inorganic Materials (2010)

All commercial forms of electronic/optoelectronic technologies use planar, rigid substrates. Device possibilities that exploit bio-inspired designs or require intimate integration with the human body demand curvilinear shapes and/or elastic responses to large strain deformations. This article reviews progress in research designed to accomplish these outcomes with established, high-performance inorganic electronic materials and modest modifications to conventional, planar processing techniques. We outline the most well developed strategies and illustrate their use in demonstrator devices that exploit unique combinations of shape, mechanical properties and electronic performance. We conclude with an outlook on the challenges and opportunities for this emerging area of materials science and engineering.
IL-3 Acts Directly on Osteoclast Precursors and Irreversibly Inhibits Receptor Activator of NF-κB Ligand-Induced Osteoclast Differentiation by Diverting the Cells to Macrophage Lineage (2003)

Osteoclasts, the multinucleated cells that resorb bone, differentiate from hemopoietic precursors of the monocyte/macrophage lineage in the presence of M-CSF and receptor activator of NF-kappaB ligand (RANKL). In this study we investigated the role of IL-3 in osteoclast differentiation. We show here that IL-3, a cytokine secreted by activated T lymphocytes, inhibits RANKL-induced osteoclast differentiation by a direct action on early osteoclast precursors. Anti-IL-3 Ab neutralized the inhibitory effect of IL-3 on osteoclast differentiation. In addition, IL-3 inhibits TNF-alpha-induced osteoclast differentiation in bone marrow-derived macrophages. However, IL-3 has no inhibitory effect on mature osteoclasts. In osteoclast precursors, IL-3 prevents RANKL-induced nuclear translocation of NF-kappaB by inhibiting the phosphorylation and degradation of IkappaB. RT-PCR analysis revealed that IL-3 down-regulated c-Fos transcription. Interestingly, the osteoclast precursors in the presence of IL-3 showed strong expression of macrophage markers such as Mac-1, MOMA-2, and F4/80. Furthermore, the inhibitory effect of IL-3 on osteoclast differentiation was irreversible, and the osteoclast precursors preincubated in IL-3 were resistant to RANKL action. Thus, our results reveal for the first time that IL-3 acts directly on early osteoclast precursors and irreversibly blocks RANKL-induced osteoclast differentiation by diverting the cells to macrophage lineage.
Functional reconstitution of wild-type and mutant Tetrahymena telomerase. (1994)

Telomerase is a ribonucleoprotein that catalyzes telomere elongation in vitro and in vivo. The 159-nucleotide RNA component of Tetrahymena telomerase contains the sequence 5'-CAACCCCAA-3' ("template region"), which serves as a template for the addition of the sequence d(TTGGGG)n to Tetrahymena telomeres. To dissect the Tetrahymena telomerase enzyme mechanism, we developed a functional in vitro reconstitution assay. After removal of the essential telomerase RNA by micrococcal nuclease digestion of partially purified telomerase, the addition of in vitro-transcribed telomerase RNA reconstituted telomerase activity. The reconstituted activity was processive and showed the same primer specificities as native telomerase. Mutants in the RNA template region were tested in reconstitution assays to determine the role of the residues in this region in primer recognition and elongation. Two template mutants, encoding the sequences 5'-UAACCCCAA-3' and 5'-UAACCCUAA-3', specified the incorporation of dATP into the sequence d(TTAGGG). Telomerase reconstituted with a template mutant encoding the sequence 5'-CAACCCUAA-3' did not specify dATP incorporation and elongation by this mutant was not terminated by the addition of ddATP. In addition, a template mutant encoding the sequence 5'-CGGCCCCAA-3' specified the incorporation of ddCTP but not ddTTP while a mutant encoding the sequence 5'-CAACCCCGG-3' specified the incorporation of ddTTP but not ddCTP. These data suggest that only the most 5' six residues of the template region dictate the addition of telomeric repeats.
The Absence of the DNA-Dependent Protein Kinase Catalytic Subunit in Mice Results in Anaphase Bridges and in Increased Telomeric Fusions with Normal Telomere Length and G-Strand Overhang (2001)

The major pathway in mammalian cells for repairing DNA double-strand breaks (DSB) is via nonhomologous end joining. Five components function in this pathway, of which three (Ku70, Ku80, and the DNA-dependent protein kinase catalytic subunit [DNA-PKcs]) constitute a complex termed DNA-dependent protein kinase (DNA-PK). Mammalian Ku proteins bind to DSB and recruit DNA-PKcs to the break. Interestingly, besides their role in DSB repair, Ku proteins bind to chromosome ends, or telomeres, protecting them from end-to-end fusions. Here we show that DNA-PKcs(-/-) cells display an increased frequency of spontaneous telomeric fusions and anaphase bridges. However, DNA-PKcs deficiency does not result in significant changes in telomere length or in deregulation of the G-strand overhang at the telomeres. Although less severe, this phenotype is reminiscent of the one recently described for Ku86-defective cells. Here we show that, besides DNA repair, a role for DNA-PKcs is to protect telomeres, which in turn are essential for chromosomal stability.
Electrospun scaffold tailored for tissue‐specific extracellular matrix (2006)

The natural extracellular matrix (ECM) is a complex structure that is built to meet the specific requirements of the tissue and organ. Primarily consisting of nanometer diameter fibrils, ECM may contain other vital substances such as proteoglycans, glycosaminoglycan and various minerals. Current research in tissue engineering involves trying to replicate the ECM such that it provides the environment for tissue regeneration. Electrospinning is a versatile process that results in nanofibers by applying a high voltage to electrically charge a liquid. A variety of polymers and other substances have been incorporated into the artificial nanofibrous scaffold. Surface modification and cross-linking of the nanofibers are some ways to improve the biocompatibility and stability of the scaffold. Electrospun scaffolds with oriented nanofibers and other assemblies can be constructed by modifying the electrospinning setup. Using electrospinning, researchers are able to specifically tailor the electrospun scaffold to meet the requirements of the tissue that they seek to regenerate. In vitro and in vivo experiments demonstrate that electrospun scaffolds hold great potential for tissue engineering applications.
A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells (2008)

Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 degrees C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37 mW m(-2) with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray and clone library analysis with small subunit ribosomal RNA (16S rRNA) and ribosomal RNA gene (16S rDNA). The results illustrated the dominance (80% of clone library sequences) of the Firmicutes in electricity production. Similarly, rRNA sequences from Firmicutes accounted for 50% of those taxa that increased in relative abundance from current-producing MFCs, implying their functional role in current production. We complemented these analyses by isolating the first organisms from a thermophilic MFC. One of the isolates, a Firmicutes Thermincola sp. strain JR, not only produced more current than known organisms (0.42 mA) in an H-cell system but also represented the first demonstration of direct anode reduction by a member of this phylum. Our research illustrates the importance of using a variety of molecular and culture-based methods to reliably characterize bacterial communities. Consequently, we revealed a previously unidentified functional role for Gram-positive bacteria in MFC current generation.
Activin A promotes multiple myeloma-induced osteolysis and is a promising target for myeloma bone disease (2010)

Understanding the pathogenesis of cancer-related bone disease is crucial to the discovery of new therapies. Here we identify activin A, a TGF-β family member, as a therapeutically amenable target exploited by multiple myeloma (MM) to alter its microenvironmental niche favoring osteolysis. Increased bone marrow plasma activin A levels were found in MM patients with osteolytic disease. MM cell engagement of marrow stromal cells enhanced activin A secretion via adhesion-mediated JNK activation. Activin A, in turn, inhibited osteoblast differentiation via SMAD2-dependent distal-less homeobox–5 down-regulation. Targeting activin A by a soluble decoy receptor reversed osteoblast inhibition, ameliorated MM bone disease, and inhibited tumor growth in an in vivo humanized MM model, setting the stage for testing in human clinical trials.
Universal Quantum Gate Set Approaching Fault-Tolerant Thresholds with Superconducting Qubits (2012)

We use quantum process tomography to characterize a full universal set of all-microwave gates on two superconducting single-frequency single-junction transmon qubits. All extracted gate fidelities, including those for Clifford group generators, single-qubit π/4 and π/8 rotations, and a two-qubit controlled-not, exceed 95% (98%), without (with) subtracting state preparation and measurement errors. Furthermore, we introduce a process map representation in the Pauli basis which is visually efficient and informative. This high-fidelity gate set serves as a critical building block towards scalable architectures of superconducting qubits for error correction schemes and pushes up on the known limits of quantum gate characterization.
Adenosine deaminase affects ligand‐induced signalling by interacting with cell surface adenosine receptors (1996)

Adenosine deaminase (ADA) is not only a cytosolic enzyme but can be found as an ecto-enzyme. At the plasma membrane, an adenosine deaminase binding protein (CD26, also known as dipeptidylpeptidase IV) has been identified but the functional role of this ADA/CD26 complex is unclear. Here by confocal microscopy, affinity chromatography and coprecipitation experiments we show that A1 adenosine receptor (A1R) is a second ecto-ADA binding protein. Binding of ADA to A1R increased its affinity for the ligand thus suggesting that ADA was needed for an effective coupling between A1R and heterotrimeric G proteins. This was confirmed by the fact that ASA, independently of its catalytic behaviour, enhanced the ligand-induced second messenger production via A1R. These findings demonstrate that, apart from the cleavage of adenosine, a further role of ecto-adenosine deaminase on the cell surface is to facilitate the signal transduction via A1R.
In vivo fiber tractography using DT-MRI data (2000)

Fiber tract trajectories in coherently organized brain white matter pathways were computed from in vivo diffusion tensor magnetic resonance imaging (DT-MRI) data. First, a continuous diffusion tensor field is constructed from this discrete, noisy, measured DT-MRI data. Then a Frenet equation, describing the evolution of a fiber tract, was solved. This approach was validated using synthesized, noisy DT-MRI data. Corpus callosum and pyramidal tract trajectories were constructed and found to be consistent with known anatomy. The method's reliability, however, degrades where the distribution of fiber tract directions is nonuniform. Moreover, background noise in diffusion-weighted MRIs can cause a computed trajectory to hop from tract to tract. Still, this method can provide quantitative information with which to visualize and study connectivity and continuity of neural pathways in the central and peripheral nervous systems in vivo, and holds promise for elucidating architectural features in other fibrous tissues and ordered media.
Comparative Performance of Two Mite-Resistant Stocks of Honey Bees (Hymenoptera: Apidae) in Alabama Beekeeping Operations (2008)

Journal Article Comparative Performance of Two Mite-Resistant Stocks of Honey Bees (Hymenoptera: Apidae) in Alabama Beekeeping Operations Get access Kenneth Ward, Kenneth Ward 1 Department of Natural Resources and Environmental Sciences, P.O. Box 1208, Alabama A&M University, Normal, AL 35762 1Corresponding author, e-mail: kenneth.ward@aamu.edu Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert Danka, Robert Danka Department of Natural Resources and Environmental Sciences, P.O. Box 1208, Alabama A&M University, Normal, AL 35762 Search for other works by this author on: Oxford Academic PubMed Google Scholar Rufina Ward Rufina Ward Department of Natural Resources and Environmental Sciences, P.O. Box 1208, Alabama A&M University, Normal, AL 35762 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 101, Issue 3, 1 June 2008, Pages 654–659, https://doi.org/10.1093/jee/101.3.654 Published: 01 June 2008 Article history Received: 25 October 2007 Accepted: 03 January 2008 Published: 01 June 2008
Schizonepeta tenuifolia: Chemistry, Pharmacology, and Clinical Applications (2002)

This article presents an up-to-date review of the plant Schizonepeta tenuifolia (Jingjie), of family Labiatae, with respect to its traditional uses, chemical constituents, various pharmacological activities, and clinical effects. Nonetheless, its mechanism of actions, adverse effects, drug interactions, and contraindications remain unclear. With the global growth on the use of herbal products, Jingjie has been commonly marketed for the treatment of common cold and fever in Chinese proprietary medicines. Hence, further studies will be warranted to show its efficacy and safety.