gebhart/patrepeval huggingface dataset:
The Relationship Between Apoptosis of Endplate Chondrocytes and Aging and Degeneration of the Intervertebral Disc (2001)

TUNEL-positive cells in the cartilaginous endplate increased with age, with destruction of the cartilaginous endplate after apoptosis (TUNEL-positive cell death). The application of the spondylosis model increased the incidence of apoptosis preceding the development of spondylosis. This suggests that apoptosis plays a role in the age-related changes seen in the cartilaginous endplate of the intervertebral disc and in the experimentally induced spondylosis process.
Two-handed gesture in multi-modal natural dialog (1992)

Tracking both hands in free-space with accompanying speech input can augment the user's ability to communicate with computers. This paper discusses the kinds of situations which call for two-handed input and not just the single hand, and reports a prototype in which two-handed gestures serve to input concepts, both static and dynamic, manipulate displayed items, and specify actions to be taken. Future directions include enlargement of the vocabulary of two-handed “coverbal” gestures and the modulation by gaze of gestural intent.
Robust discriminative keyword spotting for emotionally colored spontaneous speech using bidirectional LSTM networks (2009)

In this paper we propose a new technique for robust keyword spotting that uses bidirectional long short-term memory (BLSTM) recurrent neural nets to incorporate contextual information in speech decoding. Our approach overcomes the drawbacks of generative HMM modeling by applying a discriminative learning procedure that non-linearly maps speech features into an abstract vector space. By incorporating the outputs of a BLSTM network into the speech features, it is able to make use of past and future context for phoneme predictions. The robustness of the approach is evaluated on a keyword spotting task using the HUMAINE sensitive artificial listener (SAL) database, which contains accented, spontaneous, and emotionally colored speech. The test is particularly stringent because the system is not trained on the SAL database, but only on the TIMIT corpus of read speech. We show that our method prevails over a discriminative keyword spotter without BLSTM-enhanced feature functions, which in turn has been proven to outperform HMM-based techniques.
Mu-seq: Sequence-Based Mapping and Identification of Transposon Induced Mutations (2013)

Mutations tagged by transposon insertions can be readily mapped and identified in organisms with sequenced genomes. Collections of such mutants allow a systematic analysis of gene function, and can be sequence-indexed to build invaluable resources. Here we present Mu-seq (Mutant-seq), a high-throughput NextGen sequencing method for harnessing high-copy transposons. We illustrate the efficacy of Mu-seq by applying it to the Robertson's Mutator system in a large population of maize plants. A single Mu-seq library, for example, constructed from 576 different families (2304 plants), enabled 4, 723 novel, germinal, transposon insertions to be detected, identified, and mapped with single base-pair resolution. In addition to the specificity, efficiency, and reproducibility of Mu-seq, a key feature of this method is its adjustable scale that can accommodate simultaneous profiling of transposons in thousands of individuals. We also describe a Mu-seq bioinformatics framework tailored to high-throughput, genome-wide, and population-wide analysis of transposon insertions.
An Activating Mutation in the ATP Binding Site of the ABL Kinase Domain (1996)

A number of structural alterations have been shown to activate the leukemogenic potential of the ABL oncogene, but there is little understanding of the regulatory mechanisms that are subverted by such changes. We have used directed mutagenesis to examine a potential regulatory motif in cABL, which could directly influence ABL tyrosine kinase activity. A tyrosine to phenylalanine substitution within the ATP binding fold of the ABL kinase domain is sufficient to activate cABL enzymatic activity, and the mutant protein will alleviate growth factor dependence when expressed in the BA/F3 cell line. This growth promotion is dependent upon the structure of the amino terminus of the protein, and the ABL mutation will cooperate with certain BCR sequences in BCR/ABL fusion proteins to deregulate ABL kinase activity.
Dry-reagent disposable biosensor for visual genotyping of single nucleotide polymorphisms by oligonucleotide ligation reaction: application to pharmacogenetic analysis (2008)

Most genotyping methods for known single-nucleotide polymorphisms (SNPs) are based on hybridization with allele-specific probes, oligonucleotide ligation reaction (OLR), primer extension or invasive cleavage. OLR offers superior specificity because it involves two recognition events; namely, the hybridization of an allele-specific probe and a common probe to adjacent positions on target DNA. OLR products can be detected by microtiter well-based colorimetric, time-resolved fluorimetric or chemiluminometric assays, electrophoresis, microarrays, microspheres, and homogeneous fluorimetric or colorimetric assays. We have developed a simple, robust, and low-cost disposable biosensor in dry-reagent format, which allows visual genotyping with no need for instrumentation. The OLR mixture contains a biotinylated common probe and an allele-specific probe with a (dA)(20) segment at the 3'-end. OLR products are denatured and applied to the biosensor next to gold nanoparticles that are decorated with oligo(dT) strands. The sensor is immersed in the appropriate buffer and all components migrate by capillary action. The OLR product is captured by immobilized streptavidin at the test zone (TZ) of the sensor and hybridizes with the oligo(dT) strands of the nanoparticles. A characteristic red line is generated due to the accumulation of nanoparticles. The excess nanoparticles are captured by immobilized oligo(dA) at the control zone of the strip, giving a second red line. We have applied successfully the proposed OLR-dipstick assay to the genotyping of four SNPs in the drug-metabolizing enzyme genes CYP2D6 ((*)3 and (*)4) and CYP2C19 ((*)2 and (*)3). The results were in agreement with direct sequencing.
Chemical, mechanical, and thermal control of substrate-bound carbon nanotube growth (2006)

Carbon nanotubes (CNTs) are long molecules having exceptional properties, including several times the strength of steel piano wire at one fourth the density, at least five times the ther-mal conductivity of pure copper, and high electrical conductivity and current-carrying capac-ity. This thesis presents methods of CNT synthesis by atmospheric-pressure thermal chemical vapor deposition (CVD), where effective choice of the catalyst composition and processing con-ditions enables growth of tangled single-wall CNTs or structures of aligned multi-wall CNTs, on bare silicon, microstructured silicon, and ceramic fibers. Applying mechanical pressure during growth controls the structure of a CNT film while causing significant defects in the CNTs. This mechanochemisty approach is used to &amp;quot;grow-mold &amp;quot; CNTs into 3D-shaped microforms. A new reactor apparatus featuring a resistively-heated suspended platform enables rapid (~100 *C/s) temperature control and versatile in situ characterization, including laser measure-ment of CNT film growth kinetics, and imaging of stress-induced film cracking. By thermally pre-treating the reactant mixture before it reaches the substrate platform, aligned CNTs are
Comparison of the complete nucleotide sequences of the genomes of the neurovirulent poliovirus P3/Leon/37 and its attenuated Sabin vaccine derivative P3/Leon 12a1b. (1984)

As part of a study into the molecular basis of attenuation and reversion to neurovirulence in the Sabin poliovirus vaccines, we have determined the complete nucleotide sequence of a cloned DNA copy of the genome of P3/Leon/37, the neurovirulent progenitor of the type 3 Sabin vaccine strain, P3/Leon 12a1b. Comparison of the sequence with that which we previously obtained for the vaccine strain [Stanway, G., Cann, A. J., Hauptmann, R., Hughes, P., Clarke, L. D., Mountford, R. C., Minor, P. D., Schild, G. C. & Almond, J. W. (1983) Nucleic Acids Res. 11, 5629-5643] indicates that attenuation has been brought about by a maximum of 10 point mutations, at least 5 of which are likely to be of minor significance. Predicted amino acid sequences of all the known virus-encoded proteins show that amino acid substitutions have occurred at only three positions. Two of these are in structural proteins (i.e., Ser----Phe in VP3 and Lys----Arg in VP1), and the third, Thr----Ala, is in the nonstructural protein P2-3b. The distribution and nature of nucleotide and amino acid sequence differences suggest that a single base substitution may be responsible for the attenuated phenotype of the vaccine strain.
Renal cell carcinoma with vena caval tumor thrombus extending into the right atrium (2006)

劣等的静脉 cava (IVC ) 的发生肿瘤血栓被报导是 4%—10% 在有肾的房间癌(RCC ) 的病人。肿瘤血栓可以直延长到正确中庭。有水平Ⅲ - Ⅳ肿瘤血栓的病人的管理通常是困难的。我们在 2002 和 2004 在我们的医院里报导水平 IV 血栓的二个案例。
Transmissibility of Field Isolates of Soybean Viruses by Aphis glycines (2002)

During the 2001 growing season, 191 symptomatic soybean (Glycine max (L.) Merr.) plants were dug from production plots in Indiana, Wisconsin, and Kentucky. Alfalfa mosaic virus (AMV), Bean pod mottle virus (BPMV), Bean yellow mosaic virus (BYMV), Peanut stunt virus (PSV), Tobacco ringspot virus (TRSV), and Soybean mosaic virus (SMV) were identified. No mixed infections were observed. The ability of the soybean aphid (Aphis glycines Matsamura) to transmit field isolates of these viruses was tested. Using naturally infected field- or greenhouse-grown soybean plants as sources, six isolates of SMV and two isolates of AMV were transmitted using a short feeding assay. One of two isolates of TRSV was transmitted by A. glycines in one of four experiments using an extended feeding transmission assay. BPMV was not transmitted by A. glycines in assays involving 11 field isolates and over 840 aphids. One field isolate each of BYMV and PSV were tested and no transmission by A. glycines was observed.
Highly Specific and Sensitive Measurements of Human and Monkey Interleukin 21 Using Sequential Protein and Tryptic Peptide Immunoaffinity LC-MS/MS (2013)

A highly specific and sensitive immunoaffinity LC-MS/MS assay for quantification of human and cynomolgus monkey interleukin 21 (IL-21) was developed, qualified, and implemented. The workflow includes offline enrichment of IL-21 using an anti-IL-21 capture antibody, followed by isolation using magnetic beads, trypsin digestion, online enrichment of IL-21 derived tryptic peptides using antipeptide antibodies, and quantification using nanoflow LC-MS/MS. This assay was developed and qualified in human and cynomolgus monkey serum and tissues with a lower limit of quantitation of 0.78 pg/mL based on the intact cytokine. Both intra- and interbatch precision and accuracy, as well as stability and recovery, were found to be acceptable. IL-21 was not detected in serum from normal healthy volunteers or from autoimmune disease patients. However, IL-21 levels were quantified in cynomolgus monkey spleen and colon tissue and normal and inflammatory bowel disease (IBD) human colon tissue as well as hyperplasia human tonsils.
Terminal right heart failure due to complex congenital cardiac disease successfully managed by home peritoneal drainage (2003)

A man, aged 32, who had undergone surgical correction of complex congenital cardiac disease, had chronic severe right heart failure. Increasing reliance on diuretics led to deteriorating renal function, and he was rejected as a candidate for cardiac transplantation. By inserting a Tenckhoff catheter, and training him to drain his ascites at home, we achieved a dramatic improvement in both his cardiac and renal function. As far as we can ascertain, this is the first time this technique has been used for such a patient. We discuss the mechanisms of improvement, and suggest that other such patients with congenital cardiac disease might benefit from similar management.
Applications of light scatter to separation of stem cells. (1980)

A case is presented for light scatter as a potentially important discrimination parameter for electronic sorting of hemopoietic stem cells. Examples are presented of application of light scatter to sorting of primitive hemopoietic cells from bone marrow, thymus, and fetal yolk sac, using simple empirical approaches and a cell sorter equipped with a standard fixed-angle detector. Cells sorted in this way were ultrastructurally indistinguishable from stem cells observed in whole tissue sections or unfractionated suspensions and remained viable under culture conditions. Cells were further sorted into proliferative and nonproliferative stages whose morphologies were those expected for primitive and mature cells, respectively. Light scatter was a more specific marker for primitive thymocytes than binding of peanut agglutinin. Cells sorted from fetal yolk sac suspensions were ultrastructurally similar to candidate pluripotential stem cells of bone marrow. Therefore, where sorting rather than positive identification is the primary objective of flow analysis and histochemical correlations can be established after sorting, viable stem cells can be sorted from the simple hemopoietic tissues in high and verifiable purity. Sorting of pure stem cells from marrow will require an additional parameter for which an additional angle of light scatter may suffice.
Soluble cytokine receptor treatment in experimental orthodontic tooth movement in the rat (2005)

Pro-inflammatory cytokines, such as interleukin-1 (IL-1) and tumour necrosis factor-alpha (TNF-alpha), are believed to play a role in the biological processes involved in the course of orthodontic tooth movement and especially in root resorption. The inhibition of cytokine activity, e.g. by soluble receptors, could be beneficial in reducing this unwanted side-effect. The aim of this study was to investigate the role of cytokines IL-1 and TNF-alpha in the course of experimentally induced tooth movement. The upper left first molar was moved orthodontically in 80 male Wistar rats using a coil spring with a force of 0.5 N. Starting at day -1, three groups of 20 animals each received daily intraperitoneal injections (ip) of 2 ml of 1 mug/ml soluble receptors (a) to IL-1(sIL-RII), (b) to TNF-alpha (sTNF-alpha-RI) and (c) a combination of (a) and (b). Twenty animals served as the control. After 3, 6, 9 and 12 days, the animals were killed in groups of five. The amount of tooth movement was registered and the maxillae were prepared for histological and histomorphometric analysis. Osteoclasts and odontoclasts were identified using tartrate-resistant acid phosphatase (TRAP) histochemistry. The amount of tooth movement was reduced in all receptor-treated groups by approximately 50 per cent. At the same time, the number of TRAP-positive cells on the desmodontal bone surface and on the surface of the roots was reduced. Thus, systemic application of soluble receptors to IL-1 and TNF-alpha following experimental induction of tooth movement in the rat reduced the number of osteoclasts as well as odontoclasts.
Botulinum Toxin A for Hyperkinetic Facial Lines: Results of a Double-Blind, Placebo-Controlled Study (1994)

Previous work on patients with muscular dystonia has shown that small intramuscular doses of botulinum toxin A eliminated hyperkinetic facial lines for approximately 6 months. The purpose of this study was to determine the efficacy of botulinum toxin A injections in eliminating facial wrinkles in aesthetic surgery patients who do not have muscular dystonia. Eleven healthy subjects were studied in a double-blind fashion. On both sides of the face, 0.2 cc of either normal saline or botulinum toxin A was injected into the forehead or into the periorbital wrinkles (crow's feet). Documentation of results was made by photographs taken of the patients during repose and during facial animation before and after injection. Assessment of facial wrinkles was done from a grading system in which the patient and the facial plastic surgeon were asked to judge the severity of the wrinkles on a scale from 0 to 3, with 0 reflecting no facial wrinkles and 3 reflecting severe facial wrinkling. Nine of 11 subjects injected with botulinum toxin A noted a significant improvement in the severity of their facial wrinkles in comparison with the side of the face injected with saline, with a rating improvement of 2 points. Two of 11 subjects noted a moderate improvement, with a rating improvement of 1 point. No patient injected with saline reported an improvement in the severity of the facial wrinkles on the control side. There were no serious complications. Botulinum toxin A is an efficacious method of nonsurgically eliminating facial wrinkles and may play a role in the cosmetic enhancement of the aging face.
Inhibition of angiogenesis by antiestrogens. (1993)

In this study, we have determined the ability of the partial estrogen antagonists, clomiphene, tamoxifen, and nafoxidine, and the pure estrogen antagonists, ICI 164,384 and ICI 182,780, to inhibit angiogenesis in the chick egg chorioallantoic membrane. All of the partial estrogen antagonists and the pure estrogen antagonist, ICI 182,780, showed significant angiostatic activity in a dose-related manner. The addition of up to 5-fold of 17 beta-estradiol to the disks containing clomiphene, tamoxifen, or ICI 182,780 did not alter the angiostatic activity of these antiestrogens. These novel findings show that the antiestrogens are effective inhibitors of angiogenesis. The finding that angiostatic activity is not altered in the presence of excess estrogens suggests that this activity is exerted via mechanisms other than their inhibition of estrogen action. This angiostatic activity may contribute to the therapeutic effect of antiestrogens in estrogen receptor-negative tumors.
Cyclic nucleotide phosphodiesterase isozymes expressed in mouse skeletal muscle (2002)

To understand changes in cyclic nucleotide metabolism in muscle disease states, the expression of phosphodiesterase (PDE) isozymes in normal mouse leg muscle was examined. Four subcellular fractions were generated by differential centrifugation at 10,000 x g and 100,000 x g. cAMP PDE activity was found predominately in the soluble fractions, while cGMP PDE activity was more evenly distributed amongst soluble and particulate fractions. Pharmacological inhibitors demonstrate that PDE4 represents the major cAMP hydrolyzing activity and PDE2 represents the major cGMP hydrolyzing activity in mouse leg muscle. PDE1 is expressed at low levels, while PDE3 and PDE5 are intermediate. Between 20 and 40% of total PDE activity remained in the presence of inhibitors for PDE1-PDE5, indicating that other PDE families contribute to the total PDE pool. Reverse-transcription PCR with family-specific primers showed expression of mRNA for PDE7-PDE9, supporting this conclusion. Total PDE activity was found to be elevated in tissue extracts from a mouse model of Duchenne's muscular dystrophy.
IL-17 Regulates Adipogenesis, Glucose Homeostasis, and Obesity (2010)

Inflammatory mediators have the potential to impact a surprising range of diseases, including obesity and its associated metabolic syndrome. In this paper, we show that the proinflammatory cytokine IL-17 inhibits adipogenesis, moderates adipose tissue (AT) accumulation, and regulates glucose metabolism in mice. IL-17 deficiency enhances diet-induced obesity in mice and accelerates AT accumulation even in mice fed a low-fat diet. In addition to potential systemic effects, IL-17 is expressed locally in AT by leukocytes, predominantly by γδ T cells. IL-17 suppresses adipocyte differentiation from mouse-derived 3T3-L1 preadipocytes in vitro, and inhibits expression of genes encoding proadipogenic transcription factors, adipokines, and molecules involved in lipid and glucose metabolism. IL-17 also acts on differentiated adipocytes, impairing glucose uptake, and young IL-17-deficient mice show enhanced glucose tolerance and insulin sensitivity. Our findings implicate IL-17 as a negative regulator of adipogenesis and glucose metabolism in mice, and show that it delays the development of obesity.
High CD40 membrane expression in AIDS‐related lymphoma B cell lines is associated with the CD45RA, CD45RO, CD95 phenotype and high levels of its soluble form in culture supernatants (1997)

CD40 is a membrane glycoprotein expressed on normal and neoplastic B lymphocytes. Stimulation through CD40 regulates important cellular functions, but the effects depend on its membrane density. While extensive studies have characterized CD40 in non-Hodgkin lymphomas of immunocompetent individuals, little is known on the characteristics of this molecule in lymphomas arising in immunocompromised hosts. The aim of this study was to characterize the pattern of CD40 expression in an in vitro model constituted by AIDS small non-cleaved lymphoma (SNCCL) cell lines. The analysis of CD45 isoforms, a group of molecules alternatively spliced during B cell differentiation, has been chosen to correlate this process to the number of CD40 molecules per cell in these cell lines. Since Apo 1/Fas expression is upregulated on B lymphocytes after CD40 ligation and this expression is functionally relevant, we wanted to know whether a different CD40 pattern in AIDS-SNCCL cell lines could influence CD95 expression. We have shown that 3 of these cell lines (PA 682, Es III, and HBL-2) have high membrane CD40 expression (> 100,000 molecules/cell); they release large amounts of soluble CD40 (sCD40) in culture supernatants (> 500 pg/ml), are CD45RA/RO double labelled, and express the Apo 1/Fas (CD95) antigen. On the contrary, low CD40 membrane antigen cell lines (BRGIgA, HBL-2, NC 71, AS 283A, and LAM C3+, < 50,000 molecules/cell) release low amounts of sCD40 (< 300 pg/ml), are CD45RA+ but CD45RO−, and do not express CD95. EBV has no role in CD40 and CD45 isoform behaviour, because EBV superinfection of the EBV negative, low membrane CD40 HBL-2 cell line does not modify CD40 membrane expression, sCD40 production, or CD45 isoform and CD95 expression. Our data suggest that membrane CD40 in AIDS-SNCCL cell lines might be a key element in the regulation of their pathophysiology by influencing the expression of CD45 isoforms and of CD95, and by the release of its soluble form. Cytometry 30:33–38, 1997. © 1997 Wiley-Liss, Inc.
Wnt Signaling in Normal and Malignant Hematopoiesis (2013)

One of the most remarkable characteristics of stem cells is their ability to perpetuate themselves through self-renewal while concomitantly generating differentiated cells. In the hematopoietic system, stem cells balance these mechanisms to maintain steady-state hematopoiesis for the lifetime of the organism, and to effectively regenerate the system following injury. Defects in the proper control of self-renewal and differentiation can be potentially devastating and contribute to the development of malignancies. In this review, we trace the emerging role of Wnt signaling as a critical regulator of distinct aspects of self-renewal and differentiation, its contribution to the maintenance of homeostasis and regeneration, and how the pathway can be hijacked to promote leukemia development. A better understanding of these processes could pave the way to enhancing recovery after injury and to developing better therapeutic approaches for hematologic malignancies.