gebhart/patrepeval huggingface dataset:
Somatic mutations and intraclonal variations in the rearranged Vk genes of B‐non‐Hodgkin's lymphoma cell lines (1999)

Three established Burkitt's lymphoma (BL) cell lines (Daudi, Raji and DG-75) and three B-non-Hodgkin's lymphoma (B-NHL) of other types (Pfeiffer, Farage and Toledo) were analyzed with respect to the presence of somatic point mutations in their rearranged immunoglobulin Vkappa genes. Two of the Vkappa sequences of BL and two of those of the B-NHL were heavily mutated (up to 11%), when compared with their closest germline variable region counterparts ("clonal mutations"). Only one of the six cell lines contained an unmutated germline Vkappa sequence. The clonal mutations have features characteristic of the mutation machinery operating in the course of the T-dependent immune response, such as a preference of mutations in purine bases, more transitions than transversions and targeting to CDR and to known "hotspot" motifs. Sequence variations among different Vkappa PCR clones isolated from each of the cell lines ("intraclonal mutations") showed that the Vkappa of Toledo exhibited about 5-fold higher mutation frequency (MF) than the background level of Taq polymerase error (approximately 0.12% mut/bp). Similarly, the MF of Vkappa of two of the BL cell lines was 3-4-fold higher than the Taq polymerase misincorporation rate. In contrast, the mutation frequencies of the Vkappa of DG-75, Farage and Pfeiffer did not significantly exceed the level of Taq polymerase error. Our combined results show that 5 out of the 6 B-cell lines studied originated from B-cells that have already somatically mutated in vivo their rearranged Vkappa genes. Moreover, two of the Burkitt's and one of the B-NHL cell lines exhibit intraclonal variation indicating that the process of somatic hypermutation continued following the neoplastic event, either in vivo or in culture. These results are in accord with the presumed origin of the majority of the BL and some types of the B-NHL, from centrocytes or centroblasts of the germinal centers in which the process of somatic hypermutation is taking place.
Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors (2013)

<ns4:p>One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the eliciting antigen. Advances in technology on several fronts have made it possible to clone large numbers of heavy-chain light-chain pairs from individual B cells and thereby identify whole sets of clonally related antibodies. These collections could provide the information necessary to reconstruct their own history - the sequence of changes introduced into the lineage during the development of the clone - and to study affinity maturation in detail. But the success of such a program depends entirely on accurately inferring the founding ancestor and the other unobserved intermediates. Given a set of clonally related immunoglobulin V-region genes, the method described here allows one to compute the posterior distribution over their possible ancestors, thereby giving a thorough accounting of the uncertainty inherent in the reconstruction.</ns4:p> <ns4:p>I demonstrate the application of this method on heavy-chain and light-chain clones, assess the reliability of the inference, and discuss the sources of uncertainty.</ns4:p>
Interferon treatment of NZB mice: accelerated progression of autoimmune disease (1978)

The effect of long-term administration of interferon in New Zealand Black and New Zealand Black/New Zealand White F1 hybrid mice was studied. Treatment with moderate doses of interferon (10(4) units, five times weekly for 8 weeks) did not depress murine leukemia virus gp69/71 levels in serum and spleen, nor p30 levels in the spleen. Interferon given at 10(5.1) units (three times weekly for 37 weeks) caused an increased incidence of anti-erythrocyte antibodies in New Zealand Black mice. Finally, the hybrid mice given interferon at 10(6.0) units (three times weekly for 33 weeks) had increased renal immune complex deposits and increased incidences of proteinuria and anemia.
Assessment of Contractility of Purified Smooth Muscle Cells Derived from Embryonic Stem Cells (2006)

The aims of this study were to develop a method for deriving purified populations of contractile smooth muscle cells (SMCs) from embryonic stem cells (ESCs) and to characterize their function. Transgenic ESC lines were generated that stably expressed a puromycin-resistance gene under the control of either a smooth muscle alpha-actin (SMalphaAlpha) or smooth muscle-myosin heavy chain (SM-MHC) promoter. Negative selection, either overnight or for 3 days, was then used to purify SMCs from embryoid bodies. Purified SMCs expressed multiple SMC markers by immunofluorescence, immunoblotting, quantitative reverse transcription-polymerase chain reaction, and flow cytometry and were designated APSCs (SMalphaAlpha-puromycin-selected cells) or MPSCs (SM-MHC-puromycin-selected cells), respectively. Both SMC lines displayed agonist-induced Ca(2+) transients, expressed functional Ca(2+) channels, and generated contractile force when aggregated within collagen gels and stimulated with vasoactive agonists, such as endothelin-1, or in response to depolarization with KCl. Importantly, subcutaneous injection of APSCs or MPSCs subjected to 18 hours of puromycin selection led to the formation of teratomas, presumably due to residual contamination by pluripotent stem cells. In contrast, APSCs or MPSCs subjected to prolonged puromycin selection for 3 days did not form teratomas in vivo. These studies describe for the first time a method for generating relatively pure populations of SMCs from ESCs which display appropriate excitation and contractile responses to vasoactive agonists. However, studies also indicate the potential for teratoma development in ESC-derived cell lines, even after prolonged differentiation, highlighting the critical requirement for efficient methods of separating differentiated cells from residual pluripotent precursors in future studies that use ESC derivatives, whether SMC or other cell types, in tissue engineering applications.
Theoretical study on dispersion compensation in air-core Bragg fibers (2002)

In a previous paper we developed a matrix theory that applies to any cylindrically symmetric fiber surrounded by Bragg cladding. Using this formalism, along with Finite Difference Time Domain (FDTD) simulations, we study the waveguide dispersion for the m = 1 mode in an air-core Bragg fiber and showed it is possible to achieve very large negative dispersion values (~ -20,000 ps/(nm.km)) with significantly reduced absorption loss and non-linear effects.
Cloning and expression of a novel mouse somatostatin receptor (SSTR2B) (1992)

A mouse somatostatin (SS) receptor cDNA was cloned from neuroblastoma x glioma (NG108-15) cells. The sequence is almost identical to that of the mouse SSTR2 receptor [(1992) Proc. Natl. Acad. Sci. USA 89, 251)] but lacks about 300 nucleotides between transmembrane domain VII and the C-terminus. This spliced variant of SSTR2 (designated SSTR2B) encodes a protein which is 23 residues shorter than that predicted from the SSTR2 sequence, and differs in 15 amino acids at the C-terminus. mRNA corresponding to SSTR2B occurs in mouse tissues in higher abundance than that of SSTR2. SSTR2B binds SS peptides with high affinity when expressed in mammalian cells.
Reconstitution of Diploids from Leaf Tissue of Anther‐derived Haploids in Tobacco1 (1972)

Normal diploid plants were regenerated from leaf midveins of cytologically verified, anther‐derived haploid tobacco ( Nicotiana tabacum L.) plants. Large numbers of haploids were obtained by culturing immature anthers on a chemically defined tissue culture medium. The haploids were verified cytologically soon after emergence frem the cultured anthers. They were screened under field, greenhouse, or growth chamber environments for disease resistance, chemical composition, and/or physical characteristics. Leaf midveins from selected haploid plants were trimmed of lamina and cultured on a chemicaliy defined medium. Leafy shoots emerged in about 3 weeks. Plants regenerated from midveins of young (less than fully expanded) leaves were all haploids. Those regenerated from aged leaves (those that remained on the plant 3 to 4 weeks after attaining full expansion) included some diploids and some haploids. The diploids were normal in appearance, self‐fertile and produced diploid progeny.
Direct phase projection and transcranial focusing of ultrasound for brain therapy (2012)

Ultrasound can be used to noninvasively treat the human brain with hyperthermia by focusing through the skull. To obtain an accurate focus, especially at high frequencies (>500 kHz), the phase of the transmitted wave must be modified to correct the aberrations introduced by the patient's individual skull morphology. Currently, three-dimensional finite-difference time-domain simulations are used to model a point source at the target. The outward-propagating wave crosses the measured representation of the human skull and is recorded at the therapy array transducer locations. The signal is then time reversed and experimentally transmitted back to its origin. These simulations are resource intensive and add a significant delay to treatment planning. Ray propagation is computationally efficient because it neglects diffraction and only describes two propagation parameters: the wave's direction and the phase. We propose a minimal method that is based only on the phase. The phase information is projected from the external skull surface to the array locations. This replaces computationally expensive finite-difference computations with an almost instantaneous direct phase projection calculation. For the five human skull samples considered, the phase distribution outside of the skull is shown to vary by less than λ/20 as it propagates over a 5 cm distance and the validity of phase projection is established over these propagation distances. The phase aberration introduced by the skull is characterized and is shown to have a good correspondence with skull morphology. The shape of this aberration is shown to have little variation with propagation distance. The focusing quality with the proposed phase-projection algorithm is shown to be indistinguishable from the gold-standard full finite-difference simulation. In conclusion, a spherical wave that is aberrated by the skull has a phase propagation that can be accurately described as radial, even after it has been distorted. By combining finite-difference simulations with a phase-projection algorithm, the time required for treatment planning is significantly reduced. The correlation length of the phase is used to validate the algorithm and it can also be used to provide guiding parameters for clinical array transducer design in terms of transducer spacing and phase error.
Effects of embryo culture on global pattern of gene expression in preimplantation mouse embryos (2004)

Culture of preimplantation embryos affects gene expression. The magnitude of the effect on the global pattern of gene expression, however, is not known. We compared global patterns of gene expression in blastocysts cultured from the one-cell stage in either Whitten's medium or KSOM + amino acids (KSOM/AA) with that of blastocysts that developed in vivo, using the Affymetrix MOE430A chip. The analysis revealed that expression of 114 genes was affected after culture in Whitten's medium, whereas only 29 genes were mis-expressed after culture in KSOM/AA. Expression Analysis Systematic Explorer was used to identify biological and molecular processes that are perturbed after culture and indicated that genes involved in protein synthesis, cell proliferation and transporter function were down-regulated after culture in Whitten's medium. A common set of genes involved in transporter function was also down-regulated after culture in KSOM/AA. These results provide insights as to why embryos develop better in KSOM/AA than in Whitten's medium, and highlight the power of microarray analysis to assess global patterns of gene expression.
An Electrodeless Discharge at 60 Hz (1974)

Inductive glow discharges have been generated in argon at pressures between 0.6 and 3.0 Torr in an 80-mm wide toroidal tube that was threaded by a magnet core system of 400 cm2 cross section. The fields required to maintain the discharges were produced by exciting the core at 60 Hz. Starting was accomplished either by a capacitor discharge through auxiliary electrodes or in an electrodeless manner by exciting the core at 9600 Hz. Plasma currents at 1 Torr exceeded 100 A andc were slightly trailing the voltage. Mean electron densities at this condition were estimated to be 5 × 1013/cm3. Power dissipation in the discharge was between 0.5 and 1.9 kW at an average conversion efficiency of 60%.
Human Vital Signs Detection Methods and Potential Using Radars: A Review (2020)

Continuous monitoring of vital signs, such as respiration and heartbeat, plays a crucial role in early detection and even prediction of conditions that may affect the wellbeing of the patient. Sensing vital signs can be categorized into: contact-based techniques and contactless based techniques. Conventional clinical methods of detecting these vital signs require the use of contact sensors, which may not be practical for long duration monitoring and less convenient for repeatable measurements. On the other hand, wireless vital signs detection using radars has the distinct advantage of not requiring the attachment of electrodes to the subject's body and hence not constraining the movement of the person and eliminating the possibility of skin irritation. In addition, it removes the need for wires and limitation of access to patients, especially for children and the elderly. This paper presents a thorough review on the traditional methods of monitoring cardio-pulmonary rates as well as the potential of replacing these systems with radar-based techniques. The paper also highlights the challenges that radar-based vital signs monitoring methods need to overcome to gain acceptance in the healthcare field. A proof-of-concept of a radar-based vital sign detection system is presented together with promising measurement results.
ENC-1: A Novel MammalianKelch-Related Gene Specifically Expressed in the Nervous System Encodes an Actin-Binding Protein (1997)

We have identified and characterized a novel murine gene, Ectoderm-Neural Cortex-1 (ENC-1), that is an early and highly specific marker of neural induction in vertebrates. ENC-1, which encodes a kelch family related protein, is expressed during early gastrulation in the prospective neuroectodermal region of the epiblast and later in development throughout the nervous system (NS). ENC-1 expression is highly dynamic and, after neurulation, preferentially defines prospective cortical areas. The only apparent expression of ENC-1 outside the NS is restricted to the rostral-most somitomere of the presomitic mesoderm, at the times corresponding to the epithelialization that precedes somite formation. Cellular expression of epitope-tagged ENC-1 shows extensive co-localization of ENC-1 with the actin cytoskeleton, and immunoprecipitation studies demonstrate a physical association between ENC-1 and actin. ENC-1 functions as an actin-binding protein that may be important in the organization of the actin cytoskeleton during neural fate specification and development of the NS.
Transport Between the Cell Nucleus and the Cytoplasm (1999)

The compartmentation of eukaryotic cells requires all nuclear proteins to be imported from the cytoplasm, whereas, for example, transfer RNAs, messenger RNAs, and ribosomes are made in the nucleus and need to be exported to the cytoplasm. Nuclear import and export proceed through nuclear pore complexes and can occur along a great number of distinct pathways, many of which are mediated by importin beta-related nuclear transport receptors. These receptors shuttle between nucleus and cytoplasm, and they bind transport substrates either directly or via adapter molecules. They all cooperate with the RanGTPase system to regulate the interactions with their cargoes. Another focus of our review is nuclear export of messenger RNA, which apparently largely relies on export mediators distinct from importin beta-related factors. We discuss mechanistic aspects and the energetics of transport receptor function and describe a number of pathways in detail.
The detection and management of unruptured intracranial aneurysms (2000)

The incidence of subarachnoid haemorrhage (SAH) is 6-8 per 100 000 person years, peaking in the sixth decade. SAH, mostly due to rupture of an intracranial aneurysm, accounts for a quarter of cerebrovascular deaths. Aneurysms increase in frequency with age beyond the third decade, are 1.6 times more common in women and are associated with a number of genetic conditions. Prospective autopsy and angiographic studies indicate that between 3.6 and 6% of the population harbour an intracranial aneurysm. Studies have found an increased rate of SAH in first degree relatives of SAH patients (relative risk 3.7-6.6). In affected families, the most frequent relationship between sufferers is sibling to sibling. The rupture rate of asymptomatic aneurysms was thought to be 1-2% per annum, but the recent International Study of Unruptured Intracranial Aneurysms found that the rupture rate of small aneurysms was only 0.05% per annum in patients with no prior SAH, and 0.5% per annum for large (>10 mm diameter) aneurysms and for all aneurysms in patients with previous SAH. Non-invasive tests such as magnetic resonance angiography (MRA), computed tomographic angiography (CTA) and transcranial Doppler (TCD) have been advocated as alternatives to intra-arterial digital subtraction angiography to screen for aneurysms. Although all are promising techniques, the quality of data testing their accuracy is limited. Overall reported sensitivity for CTA and MRA (TCD is poorer) was 76-98% and specificity was 85-100%, but many subjects had an aneurysm or recent SAH, which could overestimate accuracy. CTA and MRA are much poorer methods for the detection of aneurysms <5 mm diameter, which account for up to one-third of unruptured aneurysms. Elective surgical clipping of asymptomatic aneurysms has a morbidity of 10.9% and mortality of 3. 8%. Treatment of aneurysms by Guglielmi coils, for which there is less long-term follow-up available, has a 4% morbidity and 1% mortality, but only achieves complete aneurysm occlusion in 52-78% of cases. There has been interest in screening for aneurysms, but the indication for, and cost effectiveness of screening are unclear because aneurysm prevalence varies, rupture rate is low, non-invasive imaging tests are not yet accurate enough to exclude small aneurysms and the morbidity and mortality for elective surgical treatment of unruptured aneurysms is high. There may be a limited role for investigation of high risk subgroups. Ideally, screening in such subgroups should be tested in a randomized trial. The avoidance of risk factors for aneurysms such as smoking, hypertension and hypercholesterolaemia should be part of the management of at-risk subjects.
DBCAT: Database of CpG Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells (2011)

DBCAT (database of CpG islands and analytical tools, http://dbcat.cgm.ntu.edu.tw/ ), developed to characterize comprehensive DNA methylation profiles in human cancers, is a web-based application and methylation database containing several convenient tools for investigating epigenetic regulation in human diseases. To our knowledge, DBCAT is the first online methylation analytical tool, and is composed of three parts: a CpG island finder, a genome query browser, and a tool for analyzing methylation microarray data. The analytical tools can quickly identify genes with methylated regions from microarray data, compare the methylation status changes between different arrays, and provide functional analysis in addition to colocalizing transcription factor binding sites.
On Using Very Large Target Vocabulary for Neural Machine Translation (2015)

Sébastien Jean, Kyunghyun Cho, Roland Memisevic, Yoshua Bengio. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.
Importance of immunoglobulin isotype in human antibody-dependent, cell-mediated cytotoxicity directed by murine monoclonal antibodies. (1985)

Using the fluorescence activated cell sorter to select rare IgG2a- and IgG2b-producing variants, we developed switch variant families of hybridomas from IgG1-producing hybridomas, ME1 and MA2.1. The IgG2a and IgG2b antibodies produced by such switch variants have the same binding activities for HLA as the IgG1 antibodies produced by the parent hybridomas. Using these antibodies, we directly compared the IgG1, IgG2a, and IgG2b murine Ig isotypes for their capacities to direct human peripheral blood lymphocytes (PBL) in antibody-dependent cell-mediated cytotoxicity (ADCC) against a B lymphoblastoid cell line. We demonstrate that, for antibodies of identical binding affinity and specificity, the murine IgG2a isotype is the most effective in directing ADCC by human effector cells. The murine IgG2b directs intermediate levels of ADCC activity while IgG1 is inactive. We identified the effector cells in human PBL that mediate IgG2a or IgG2b ADCC as nonadherent killer (K) cells. These cells express the C3bi receptor and have cytolytic activity which is specifically blocked by a monoclonal antibody (anti-Leu-11a) that binds the Fc receptor (FcR) of such cells. Finally, FcR-bearing K cells bind to target cell-bound, rather than free, IgG2a or IgG2b molecules.
Quantitative high-resolution measurement of cerebrovascular physiology with slip-ring CT. (1996)

Functional CT and constructed functional maps provide an optimal, high-resolution tool with which to visualize cerebrovascular parameters and their changes.
On calculating the capacity of an infinite-input finite (infinite)-output channel (1988)

A version of the Arimoto-Blahut algorithm for continuous channels involves evaluating integrals over an entire input space and thus is not tractable. Two generalized discrete versions of the Arimoto-Blahut algorithm are presented for this purpose. Instead of calculating integrals, both algorithms require only the computation of a sequence of finite sums. This significantly reduces numerical computational complexity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improved dye-sensitized solar cells with a ZnO-nanoflower photoanode (2007)

In this letter, the authors report a dye-sensitized solar cell (DSSC) using a ZnO-nanoflower film photoanode, which was grown by a hydrothermal method at 95°C. The dye used was cis-bis(isothiocyanato)bis(2,2′-bipyridyl-4,4′-dicarboxylato)-ruthenium(II) bis-tetrabutylam-monium (N-719). At AM1.5G irradiation with 100mW∕cm2 light intensity, the DSSC based on ZnO-nanoflower film showed an energy conversion efficiency of 1.9%, which is much higher compared to that (1.0%) of the control device constructed using a photoanode of upstanding ZnO-nanorod array fabricated by hydrothermal method as well. The better performance of ZnO-nanoflower DSSC was due to a better dye loading and light harvesting of the ZnO-nanoflower film. The results demonstrate potential application of ZnO-nanoflower array for efficient dye-sensitized solar cells.