gebhart/patrepeval huggingface dataset:
The <i>mab-21</i> gene of <i>Caenorhabditis elegans</i> encodes a novel protein required for choice of alternate cell fates (1995)

The gene mab-21, which encodes a novel protein of 386 amino acids, is required for the choice of alternate cell fates by several cells in the C. elegans male tail. Three cells descended from the ray 6 precursor cell adopt fates of anterior homologs, and a fourth, lineally unrelated hypodermal cell is transformed into a neuroblast. The affected cells lie together in the lateral tail epidermis, suggesting that mab-21 acts as part of a short-range pattern-formation mechanism. Each of the changes in cell fate brought about by mab-21 mutants can be interpreted as a posterior-to-anterior homeotic transformation. mab-21 mutant males and hermaphrodites have additional pleiotropic phenotypes affecting movement, body shape and fecundity, indicating that mab-21 has functions outside the tail region of males. We show that the three known alleles of mab-21 are hypomorphs of a new gene. Mosaic analysis revealed that mab-21 acts cell autonomously to specify the properties of the sensory ray, but non-autonomously in the hypodermal versus neuroblast cell fate choice. Presence of cell signalling in the choice of the neuroblast fate was confirmed by cell ablation experiments. Mutations in mab-21 were shown previously to be genetic modifiers of the effects of HOM-C/Hox gene mutations on ray identity specification. The results presented here support the conclusion that mab-21 acts as part of a mechanism required for correct cell fate choice, possibly involving the function of HOM-C/Hox genes in several body regions.
Multiwavelength fiber ring lasing by use of a semiconductor optical amplifier (2005)

A multiwavelength fiber ring laser obtained by use of a semiconductor optical amplifier (SOA) with a simple laser cavity configuration is reported. A Fabry-Perot filter was used in the fiber laser ring cavity to achieve more than 50 simultaneous wavelength lasing oscillations with a frequency separation of 50 GHz. The resulting stable broadband multiwavelength lasing operation was attributed to broadband and flat gain of the SOA, which has a gain flatness of 0.8 dB for more than 20 nm. The laser has a total output power of -3 dBm and a signal-to-spontaneous-noise ratio of 30 dB.
A robust and reproducible animal serum-free culture method for clinical-grade bone marrow-derived mesenchymal stromal cells (2015)

Efficient xenofree expansion methods to replace fetal bovine serum (FBS)-based culture methods are strongly encouraged by the regulators and are needed to facilitate the adoption of mesenchymal stromal cell (MSC)-based therapies. In the current study we established a clinically-compliant and reproducible animal serum-free culture protocol for bone marrow-(BM-) MSCs based on an optimized platelet-derived supplement. Our study compared two different platelet-derived supplements, platelet lysate PL1 versus PL2, produced by two different methods and lysed with different amounts of freeze-thaw cycles. Our study also explored the effect of a low oxygen concentration on BM-MSCs. FBS-supplemented BM-MSC culture served as control. Growth kinetics, differentiation and immunomodulatory potential, morphology, karyotype and immunophenotype was analysed. Growth kinetics in long-term culture was also studied. Based on the initial results, we chose to further process develop the PL1-supplemented culture protocol at 20 % oxygen. The results from 11 individual BM-MSC batches expanded in the chosen condition were consistent, yielding 6.60 × 10(9) ± 4.74 × 10(9) cells from only 20 ml of bone marrow. The cells suppressed T-cell proliferation, displayed normal karyotype and typical MSC differentiation potential and phenotype. The BM-MSCs were, however, consistently HLA-DR positive when cultured in platelet lysate (7.5-66.1 %). We additionally show that culture media antibiotics and sterile filtration of the platelet lysate can be successfully omitted. We present a robust and reproducible clinically-compliant culture method for BM-MSCs based on platelet lysate, which enables high quantities of HLA-DR positive MSCs at a low passage number (p2) and suitable for clinical use.
Reply (1996)

Colonic epithelial cells express HLA-DR in inflammatory bowel disease. The effect of drugs used in the treatment of inflammatory bowel disease and colchicine on interferon-gamma (IFN-gamma) induced DR expression has been investigated. HT-29 cells were cultured in 25 cm2 flasks. At 48 hours interferon-gamma (0, 50, or 100 U/ml) +/- drug were added. At 120 hours the cells were stained for HLA-DR and analysed by flow cytometry. 10(-2) M 5ASA reduced DR expression induced by 50 U/ml interferon-gamma from 62 (12)% of cells (mean SD) to 29 (20)% (p less than 0.005). Corresponding figures for 10(-2) M N-acetyl 5ASA were 68 (16)% to 39 (17)% (p less than 0.05); for 10(-2) M 4ASA, 61 (4)% to 57 (4)% (p = 0.6); for 10(-2) M N-acetyl 4ASA, 60 (12)% to 35 (13)% (p less than 0.05); for 10(-2) M olsalazine, 72 (9)% to 3 (1)% (p less than 0.001); for 10(-3) M olsalazine, 72 (9)% to 16 (10)% (p less than 0.001); for 10(-6) M colchicine, 62 (13)% to 5 (3)% (p less than 0.001); and for 10(-7) M colchicine, 62 (13)% to 10 (3)%. Similar results were obtained when DR was induced by 100 U/ml of interferon-gamma except with 10(-2) M 4ASA which reduced expression from 77 (4)% to 68 (3)% (p less than 0.05). Sulphapyridine, prednisolone, indomethacin and cyclosporin A had no effect. Concurrent staining with propidium iodide showed that these results were unchanged when viable cells alone were analysed. Prior incubation of cells with drug, followed by washing, had no effect on interferon-gamma induced DR expression. 5ASA, N-acetyl 5ASA, 4ASA, N-acetyl 4ASA, olsalazine and colchicine reduce interferon-gamma induced HLA-DR expression. In inflammatory bowel disease these compounds may impair antigen presentation by the colonic epithelium.
EIN FAHRZEUGSICHERUNGSSYSTEM OHNE MECHANISCHEN SCHLUESSEL (1994)

Beschrieben wird ein von Siemens entwickeltes Fahrzeugsicherungssystem, das den Zugang zum Automobil und einen Motorstart ohne zusaetzlichen mechanischen Schluessel und ohne Manipulation an elektronischen Fernsteuereinheiten erlaubt. Das System basiert auf einem elektronischen Schluessel in Form einer Kreditkarte, der ueber Funkbefehle fernabfragbar ist. Im Beitrag werden die verschiedenen Systemkomponenten beschrieben. Das System ermoeglicht die lokale Unterscheidung von bis zu fuenf Aktionsbereichen. Abhaengig von der Position des Kartentraegers werden verschiedene Bedienablaeufe freigegeben oder gesperrt. Titel in Englisch: Vehicle security system dispensing with mechanical key.
Highly Precise Measurement of HIV DNA by Droplet Digital PCR (2013)

Deoxyribonucleic acid (DNA) of the human immunodeficiency virus (HIV) provides the most sensitive measurement of residual infection in patients on effective combination antiretroviral therapy (cART). Droplet digital PCR (ddPCR) has recently been shown to provide highly accurate quantification of DNA copy number, but its application to quantification of HIV DNA, or other equally rare targets, has not been reported. This paper demonstrates and analyzes the application of ddPCR to measure the frequency of total HIV DNA (pol copies per million cells), and episomal 2-LTR (long terminal repeat) circles in cells isolated from infected patients. Analysis of over 300 clinical samples, including over 150 clinical samples assayed in triplicate by ddPCR and by real-time PCR (qPCR), demonstrates a significant increase in precision, with an average 5-fold decrease in the coefficient of variation of pol copy numbers and a >20-fold accuracy improvement for 2-LTR circles. Additional benefits of the ddPCR assay over qPCR include absolute quantification without reliance on an external standard and relative insensitivity to mismatches in primer and probe sequences. These features make digital PCR an attractive alternative for measurement of HIV DNA in clinical specimens. The improved sensitivity and precision of measurement of these rare events should facilitate measurements to characterize the latent HIV reservoir and interventions to eradicate it.
End-to-End Learning of Keypoint Detector and Descriptor for Pose Invariant 3D Matching (2018)

Finding correspondences between images or 3D scans is at the heart of many computer vision and image retrieval applications and is often enabled by matching local keypoint descriptors. Various learning approaches have been applied in the past to different stages of the matching pipeline, considering detection, description, or metric learning objectives. These objectives were typically addressed separately and most previous work has focused on image data. This paper proposes an end-to-end learning framework for keypoint detection and its representation (descriptor) for 3D depth maps or 3D scans, where the two can be jointly optimized towards task-specific objectives without a need for separate annotations. We employ a Siamese architecture augmented by a sampling layer and a novel score loss function which in turn affects the selection of region proposals. The positive and negative examples are obtained automatically by sampling corresponding region proposals based on their consistency with known 3D pose labels. Matching experiments with depth data on multiple benchmark datasets demonstrate the efficacy of the proposed approach, showing significant improvements over state-of-the-art methods.
High levels of CD45 are coordinately expressed with CD4 and CD8 on avian thymocytes (1991)

In this paper we describe the avian homolog of mammalian CD45. We show that this Ag is expressed on all leukocytes but not on erythroid cells or their immediate precursors. Immunoprecipitations demonstrated that B lineage cells from the bursa of Fabricius expressed a higher molecular mass variant (215 kDa) than did T lineage cells from the thymus (190 kDa), and crucially, these high molecular mass molecules had intrinsic phosphotyrosine phosphatase activity characteristic of mammalian CD45. We show that levels of CD45 expression as detected by mAb LT40 in the avian thymus are heterogeneous and further that mAb LT40 can deplete all phosphotyrosine phosphatase activity from thymocyte membrane preparations. Therefore total levels of CD45 are heterogeneous among avian thymocytes. Specifically, 87 to 89% of thymocytes expressed fourfold higher levels of surface CD45 (CD45hi) than the remaining 11 to 13% (CD45lo). The CD45lo population contained exclusively thymocytes with the phenotype CD3-4-8lo, characteristic of the immediate precursors to the CD3-4+8+ thymic population which are CD45hi. The shift from low to high levels of surface CD45 expression therefore occurred at the same stage as the transition from CD4-8lo to CD4+8+ and before the expression of CD3. The protein tyrosine kinase activity associated with CD4 and CD8 (p56lck) and the phosphatase activity of CD45 have been implicated elsewhere in jointly regulating peripheral T cell signal transduction and subsequent cellular responses. The coordinated expression of high levels of CD45 with both CD4 and CD8 in the avian thymus supports the possibility that these molecules may function together in regulating thymocyte growth and/or differentiation.
CD8+ T cell suppressor factors and the control of infection, replication and transcription of human immunodeficiency virus. (2001)

CD8+ T cells have been shown to produce factors which modulate HIV-1 replication in both T cells and monocytic cells. Examination of the literature reveals that this modulation may occur by the production of beta-chemokines which block viral entry. However, another CD8+ T cell-derived factor(s) targets the replication of HIV-1 at the level of transcription. CD8+ T cell factors strongly suppress replication at the level of transcription in T cells and T cell lines, the factors enhance both replication and transcription in cells of the monocyte/macrophage lineage. The enhancement of transcription and replication, which is pertussis toxin sensitive is induced by increased production of TNF-alpha by the target cells. Thus, CD8+ T cells produce factors which mediate effects on transcription and replication of HIV-1 in a cell type-dependent manner. In this review a summary of the effects of chemokines and CD8-derived factors on HIV-1 transcription and replication is presented focusing on the cellular pathways which may mediate their effects on HIV transcription and replication in different cell types. The virus-host cell interactions that participate in the persistent replication of HIV in macrophages and the suppression of these functions in T cells require definition. The identification of CD8+ T cell factors which exert these controls on HIV-1 may lead to promising new therapies for HIV infection.
Efficient estimation and uncertainty quantification in space mission dynamics (2012)

The problem of efficient and accurate orbit estimation of space trajectories is discussed. For highly sensitive low-fuel trajectories designed to exploit the complex nonlinear dynamics of the three-body problem , it is vital to have accurate state estimation during maneuvers and ability to deal with irregular observation update times. For instance, in Halo-orbit insertion and station keeping maneuvers, state estimation errors can propagate quickly. In this paper, we combine an efficient probability propagation method with a homotopy-based posterior computation method. The resulting particle filter is highly accurate even in highly nonlinear regime with intermittent observations, and yet an order of magnitude or more efficient than a generic particle filter implementation.
Fracture and large strain behavior of self-assembled triblock copolymer gels (2008)

The rate dependence of fracture has been studied in a series of physically associating triblock copolymer gels that have a well-defined molecular structure. Compressive experiments were performed to develop a strain energy function that accurately captures the strain hardening behavior of these materials. This same strain energy function was utilized in a finite element model of the crack tip stresses, which become highly anisotropic at stress values below the failure strength of the gels. The rate dependence of the energy release rate, G, is independent of the gel concentration when G is normalized by the small strain Young's modulus, E. The gels exhibit a transition from rough, slow crack propagation to smooth, fast crack propagation for a well-defined value of the characteristic length, G/E.
<i>BCR-ABL</i> translocation as a favorable prognostic factor in elderly patients with acute lymphoblastic leukemia in the era of potent tyrosine kinase inhibitors (2017)

BCR-ABL translocation as a favorable prognostic factor in elderly patients with acute lymphoblastic leukemia in the era of potent tyrosine kinase inhibitors
Achievable Rate Region of Multiple Access with Linearly Precoded Parallel Block-Fading MIMO Channels (2005)

The goal is to derive achievable rate region of multiple access MIMO channel with finite number of flat-fading parallel observations when novel user-wise independent linear precoding (pre-equalizing) is performed as the second level encoding procedure for each user separately. No channel state information is assumed to be known at transmitters and each user wants to communicate at the maximum but constant rate during the frame consisted of finite number of parallel channels with block-fading channel realizations. Employing the linear transmit energy preserving precoding we aim at better performance in the terms of outage capacity which is essential for application services relying on sustainable transmission even through the channel with instantaneous very poor channel conditions
Tree-Ring Carbon Isotopic Constraints on Carbon-Water Exchanges between Atmosphere and Biosphere in Drought Regions in Northwestern China (2000)

The comparison between the carbon isotope and the index of ring width of a pine disc from the Tuomuer Peak region in Xinjiang shows that the effects of climate changes on the tree-ring growth and carbon iso-topic fractionation varies with time. The reason is probably relative to the characters of climate changes and adaptability of the tree-ring growth to climate changes. The relationships between the atmospheric CO2 level and the revised δ13Cair by the tree-ring carbon isotope indicate that the carbon cycle is not in a steady state, but under a stage-change condition in this area. It also can be concluded that the ratio of CO2 from the terrestrial eco-system has increased, and the flux of CO2 exchange between the atmosphere and the biosphere was gradually increasing over the past century. In addition, the results also confirm the validity and superiority of the carbon isotope to the research of the water-use efficiency.
Conditioned media from mouse osteosarcoma cells promote MC3T3‐E1 cell proliferation using JAKs and PI3‐K/Akt signal crosstalk (2008)

The maintenance of bone mass requires a strict balance between bone formation by osteoblasts and bone resorption by osteoclasts. In tumoral bone environment, tumor cells frequently disturb this balance by interaction with bone cells to create a favorable site for tumor growth, and promote pathological bone changes. Thus, elucidation of the mechanisms underlying interaction between tumor cells and bone cells might eventually lead to a more rational strategy for therapeutic intervention for bone tumors and better understanding of bone biology. In the present study, the effects of mouse osteosarcoma cells on mouse preosteoblastic cells were determined by assessment of cell viability, osteoblastic differentiation and signal transduction pathways. MOS-J/POS-1 conditioned media (CM) significantly induced MC3T3-E1 cell proliferation in a dose-dependent manner and reduced both alkaline phosphatase activity and mineralized nodule formation. Piceatannol, AG490, LY294002 and rapamycin significantly abrogated this up-regulated cell proliferation; however, UO126 and STAT3 inhibitor peptide did not affect this up-regulated cell proliferation. MOS-J/POS-1 CM activated ERK 1/2, STAT3 and Akt signal transduction pathways; however, pro-proliferating signal induced by MOS-J/POS-1 CM was transmitted via Akt not ERK 1/2 and STAT3 pathways. Furthermore, Western blot analyses clearly revealed novel signal crosstalk between JAKs and PI3-K/Akt in osteoblastic cells. The specific factor(s) involved in MOS-J/POS-1 CM-induced MC3T3-E1 cell proliferation that use JAKs/PI3-K/Akt/mTOR pathway remain(s) to be determined. Determination of the specific factor(s) responsible for JAKs and PI3-K/Akt signal crosstalk that results in up-regulated preosteoblast proliferation will offer new insight into the pathology of osteosarcoma as well as other bone-related diseases.
Structural control via semi-active and hybrid control (1997)

A combination of standard active control and low power (often called 'semi-active') devices for control of buildings under seismic excitation is presented. Performance, stability, actuator saturation, and design considerations are among the topics discussed.
Infrared radiometric stress instrumentation application range study (1968)

Infrared radiometric stress instrumentation system for estimating detectable stress measurements
Identification of a haem-utilization protein (Hup) in Haemophilus influenzae (2004)

Haemophilus influenzae has an absolute growth requirement for a porphyrin source. This growth requirement can be satisfied in vitro by haem, haemoglobin or the haemoglobin-haptoglobin, haem-haemopexin and haem-albumin complexes. A family of proteins, termed the Hgp proteins, which are essential for utilization of the haemoglobin-haptoglobin complex, has previously been identified. A strain lacking the Hgp proteins also has a residual ability to utilize haemoglobin, indicating that additional moieties contribute to haemoglobin utilization. Using a haemoglobin affinity method an approximately 105 kDa protein was isolated. Mutation of the identified gene in an Hgp null background reduced the ability of the mutant strain to utilize haemoglobin in vitro. The mutation also resulted in a reduced ability to utilize haem, haem-haemopexin, haem-albumin and haemoglobin-haptoglobin, thus identifying a general haem-utilization protein (Hup) in Haemophilus influenzae.
Analysis of oxysterols by electrospray tandem mass spectrometry (2006)

Oxysterols are oxygenated derivatives of cholesterol. They are intermediates in cholesterol excretion pathways and may also be regarded as transport forms of cholesterol. The introduction of additional hydroxyl groups to the cholesterol skeleton facilitates the flux of oxysterols across the blood brain barrier, and oxysterols have been implicated in mediating a number of cholesterol-induced metabolic effects. Oxysterols are difficult to analyze by atmospheric pressure ionization mass spectrometry on account of the absence of basic or acidic functional groups in their structures. In this communication, we report a method for the derivatization and analysis of oxysterols by electrospray mass spectrometry. Oxysterols with a 3beta-hydroxy-Delta5 structure were converted by cholesterol oxidase to 3-oxo-Delta4 steroids and then derivatized with the Girard P reagent to give Girard P hydrazones, which were subsequently analyzed by tandem mass spectrometry. The improvement in sensitivity for the analysis of 25-hydroxycholesterol upon oxidation and derivatization was over 1000.
Deconvolution methods for mitigation of transverse blurring in optical coherence tomography (2005)

Imaging resolution in optical coherence tomography (OCT) is a key determinant for acquiring clinically useful optical biopsies of tissues. In contrast to light or confocal microscopy, the axial and transverse resolutions in OCT are independent and each can be analyzed individually. A method for mitigating transverse blurring and the apparent loss of transverse resolution in OCT by means of Gaussian beam deconvolution is presented. Such a method provides better representation of a specimen by using known physical parameters of a lens. To implement this method, deconvolution algorithms based on a focal-dependent kernel are investigated. First, the direct inverse problem is investigated using two types of regularization, truncated singular value decomposition, and Tikhonov. Second, an iterative expectation maximization algorithm, the Richardson-Lucy algorithm, with a beam-width-dependent iteration scheme is developed. A dynamically iterative Richardson-Lucy algorithm can reduce transverse blurring by providing an improvement in the transverse point-spread-function for sparse scattering samples in regions up to two times larger than the confocal region of the lens. These deblurring improvements inside and outside of the confocal region, which are validated experimentally, are possible without introducing new optical imaging hardware or acquiring multiple images of the same specimen. Implementation of this method in sparse scattering specimens, such as engineered tissues, has the potential to improve cellular detection and categorization.