gebhart/patrepeval huggingface dataset:
The relationship between APL subtypes and chromosome t(15; 17)or PML-RARa fusion gene (2015)

Objective
To investigate the relationship between the subtypes of acute promyelocytic leukemia (APL) and expression of chromosome translocationt(15; 17)or fusion gene of PML-RARa.


Methods
Fifty-five APL patients were studied in the research.APL subtypes were determined according to FAB classification.Conventional karyotype analysis was performed to study chromosome translocation t(15; 17) and fluorescent in situ hybridization(FISH)was employed to detect PML-RARa fusion gene.


Results
APL patients were classified into three subtpyes: M3a, M3b and M3c.The occurrence of t(15; 17) and PML-RARa fusion gene were 82.61% (19/23)and 95.65%(22/23)in M3a, 82.35%(14/17)and 94.12%(16/17)in M3b, 80.00%(12/15)and 100.0%(15/15)in M3c respectively(χ2=0.046, P>0.05; χ2 =0.844, P>0.05). The expression of t(15; 17) and PML-RARa fusion gene were 81.82%(45/55)and 96.36%(53/55) respectively (χ2=6.476, P<0.05).


Conclusions
There are no statistic differences between the the APL subtypes and expression of chromosome translocation t(15; 17)or PML-RARa fusion gene.FISH may be a more sensitive technique than conventional karyotype analysis.


Key words: 
Leukemia, promyelocytic, acute; In situ hybridization, fluorescent; PML-RARa fusion gene
A single amino acid mutation attenuates rundown of voltage‐gated calcium channels (2006)

The activity of voltage-gated calcium channels (VGCCs) decreases with time in whole-cell and inside-out patch-clamp recordings. In this study we found that substituting a single amino acid (I1520) at the intracellular end of IIIS6 in the alpha(1) subunit of P/Q-type Ca(2+) channels with histidine or aspartate greatly attenuated channel rundown in inside-out patch-clamp recordings. The homologous mutations also slowed rundown of N- and L-type Ca(2+) channels, albeit to a lesser degree. In P/Q-type channels, the attenuation of rundown is accompanied by an increased apparent affinity for phosphatidylinositol-4,5-bisphosphate, which has been shown to be critical for maintaining Ca(2+) channel activity [L. Wu, C.S. Bauer, X.-G. Zhen, C. Xie, J. Yang, Dual regulation of voltage-gated calcium channels by PtdIns(4,5)P2. Nature 419 (2002) 947-952]. Furthermore, the histidine mutation significantly stabilized the open state, making the channels easier to open, slower to close, harder to inactivate and faster to recover from inactivation. Our finding that mutation of a single amino acid can greatly attenuate rundown provides an easy and efficient way to slow the rundown of VGCCs, facilitating functional studies that require direct access to the cytoplasmic side of the channel.
Speech recognition by machine: A review (1976)

This paper provides a review of recent developments in speech recognition research. The concept of sources of knowledge is introduced and the use of knowledge to generate and verify hypotheses is discussed. The difficulties that arise in the construction of different types of speech recognition systems are discussed and the structure and performance of several such systems is presented. Aspects of component subsystems at the acoustic, phonetic, syntactic, and semantic levels are presented. System organizations that are required for effective interaction and use of various component subsystems in the presence of error and ambiguity are discussed.
Adhesion to Dentin and Physical Properties of a Light-cured Glass-ionomer Liner/Base (1991)

The objective of this study was to determine the adhesion to dentin and the physical properties of Vitrabond Light Cure Glass Ionomer Liner/Base and to compare these values with those of a conventional material, 3M Glass Ionomer Liner (3MGI). Shear bond strengths to bovine dentin after 24 h in distilled water were determined to be 12 +/- 3 MPa for Vitrabond Liner/Base, while for 3MGI, bond strengths were 4 +/- 2 MPa. The failure mode was cohesive in dentin or the ionomer. Immediate adhesion of the light-cured material was also significantly higher than that of the conventional glass-ionomer liner. Thermal cycling experiments showed that the bond of Vitrabond Liner/Base to dentin was a stable one. Adhesion studies carried out on human dentin showed high adhesion values as well. Compressive and diametral tensile strengths for Vitrabond Liner/Base were determined immediately after light curing and also after storage in water for 24 h, one week, one month, and seven months. There was no significant difference in the values of compressive and diametral tensile strengths obtained immediately after curing and after extended storage in water at 37 degrees C.
Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9 (2018)

Bacteria and bacteriophages arm themselves with various defensive and counterdefensive mechanisms to protect their own genome and degrade the other's. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated) is an adaptive bacterial defense mechanism that recognizes short stretches of invading phage genome and destroys it by nuclease attack. Unexpectedly, we discovered that the CRISPR-Cas system might also accelerate phage evolution. When <i>Escherichia coli</i> bacteria containing CRISPR-Cas9 were infected with phage T4, its cytosine hydroxymethylated and glucosylated genome was cleaved poorly by Cas9 nuclease, but the continuing CRISPR-Cas9 pressure led to rapid evolution of mutants that accumulated even by the time a single plaque was formed. The mutation frequencies are, remarkably, approximately six orders of magnitude higher than the spontaneous mutation frequency in the absence of CRISPR pressure. Our findings lead to the hypothesis that the CRISPR-Cas might be a double-edged sword, providing survival advantages to both bacteria and phages, leading to their coevolution and abundance on Earth.
In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency (2015)

ABSTRACT The CRISPR/Cas9 system provides unprecedented genome editing capabilities; however, several facets of this system are under investigation for further characterization and optimization, including the choice of guide RNA that directs Cas9 to target DNA. In particular, given that one would like to target the protein-coding region of a gene, hundreds of guides satisfy the basic constraints of the CRISPR/Cas9 Protospacer Adjacent Motif sequence (PAM); however, not all of these guides actually generate gene knockouts with equal efficiency. Leveraging a broad set of experimental measurements of guide knockout efficiency, we introduce a state-of-the art in silico modeling approach to identify guides that will lead to more effective gene knockout. We first investigated which guide and gene features are critical for prediction ( e.g. , single- and di-nucleotide identity of the gene target), which are helpful ( e.g ., thermodynamics), and which are predictive but redundant ( e.g ., microhomology). We also investigated evaluation measures for comparing predictive models in the present context, suggesting that Area Under the Receiver Operating Curve is not ideal. Finally, we explored a variety of different model classes and found that use of gradient-boosted regression trees produced the best predictive performance. Pointers to our open-source software, code, and prediction server will be available at http://research.microsoft.com/en-us/projects/azimuth .
An Investigation of Temperature Characteristics of Pulsating Heat Pipe (2005)

Pulsating heat pipe (PHP) is an interesting heat transfer device. This paper focuses on PHP heat transfer characteristics versus its operating temperature. In experiments of copper and stainless steel PHPs, results indicate that, at a same input power, both temperature differences (from the evaporator to condenser) and evaporator temperature fluctuations are relevant to operating temperature. The minimal temperature difference and fluctuation appear at an operating temperature ranging from 120 to 160°C. Experimental analysis of the evaporator temperature fluctuations show that single phase cooling in PHP causes a large temperature difference (between the evaporator and condenser) and fluctuation. Phase change proportion increases at the optimal operation condition. Static mechanical balance combining with dynamic elastic oscillation system is used to interpret PHP temperature variations versus operating temperature.
Quantitative measurement of Plasmodium‐infected erythrocytes in murine models of malaria by flow cytometry using bidimensional assessment of SYTO‐16 fluorescence (2008)

Flow cytometry is a powerful tool for measuring parasitemias in murine malaria models used to test new antimalarials. Measurement of the emission of the nonpermeable nucleic acid dye YOYO-1 (at 530 and 585 nm after excitation at 488 nm) allowed the unambiguous detection of low parasitemias (> or =0.01%) but required prolonged fixation and permeabilization of the sample. Thus, we tested whether this issue could be overcome by use of the cell-permeant dye SYTO-16 with this same bidimensional method. Blood samples from CD1 mice infected with Plasmodium yoelii, Plasmodium vinckei, or Plasmodium chabaudi or from NOD(scidbeta2m-/-) engrafted with human erythrocytes and infected with P. falciparum were stained with SYTO-16 in the presence or absence of TER-119 mAb (for engrafted mice) in 96-well plate format and acquired in Trucount tubes. Bidimensional analysis with SYTO-16 was quantitatively equivalent to YOYO-1. Moreover, by combining SYTO-16 with the use of TER-119-PE antimouse erythrocyte mAb and Trucount tubes, the measurement of the concentration of P. falciparum-infected erythrocytes over a range of five orders of magnitude was achieved. Bidimensional analysis using SYTO-16 can be used to accurately measure the concentration of Plasmodium spp.-infected erythrocytes in mice without complex sample preparation.
Intestinal Microbiota Containing Barnesiella Species Cures Vancomycin-Resistant Enterococcus faecium Colonization (2013)

Bacteria causing infections in hospitalized patients are increasingly antibiotic resistant. Classical infection control practices are only partially effective at preventing spread of antibiotic-resistant bacteria within hospitals. Because the density of intestinal colonization by the highly antibiotic-resistant bacterium vancomycin-resistant Enterococcus (VRE) can exceed 10(9) organisms per gram of feces, even optimally implemented hygiene protocols often fail. Decreasing the density of intestinal colonization, therefore, represents an important approach to limit VRE transmission. We demonstrate that reintroduction of a diverse intestinal microbiota to densely VRE-colonized mice eliminates VRE from the intestinal tract. While oxygen-tolerant members of the microbiota are ineffective at eliminating VRE, administration of obligate anaerobic commensal bacteria to mice results in a billionfold reduction in the density of intestinal VRE colonization. 16S rRNA gene sequence analysis of intestinal bacterial populations isolated from mice that cleared VRE following microbiota reconstitution revealed that recolonization with a microbiota that contains Barnesiella correlates with VRE elimination. Characterization of the fecal microbiota of patients undergoing allogeneic hematopoietic stem cell transplantation demonstrated that intestinal colonization with Barnesiella confers resistance to intestinal domination and bloodstream infection with VRE. Our studies indicate that obligate anaerobic bacteria belonging to the Barnesiella genus enable clearance of intestinal VRE colonization and may provide novel approaches to prevent the spread of highly antibiotic-resistant bacteria.
Catalytic, Asymmetric Preparation of Ketene Dimers from Acid Chlorides (2003)

[reaction: see text] The cinchona alkaloid-catalyzed dimerization of monosubstituted ketenes generated in situ from the reaction of acid chlorides and diisopropylethylamine yields ketene dimers in high yields and enantioselectivities. This reaction tolerates sterically demanding and functionally diverse substituents. Kinetic studies suggest that the rate-determining step for the reaction is the deprotonation of the acid chloride by the tertiary amine to form ketene and that the stereochemistry-forming step is addition of an ammonium enolate with ketene.
Cyclophilin binds to the region of cyclosporine involved in its immunosuppressive activity (1987)

Although several cytosolic proteins including calmodulin and cyclophilin have been shown to bind cyclosporine, the direct involvement of these proteins in the immunosuppressive activity of cyclosporine remains to be established. In the present study, a quantitative immunoassay for cyclophilin was developed which made it possible to compare its relative affinity for cyclosporine and any of its analogues. The binding of cyclophilin to cyclosporine coated on a solid phase was revealed by anti-cyclophilin rabbit antiserum followed by antiglobulin-enzyme conjugate. This reaction could be inhibited by addition of free cyclosporine or certain cyclosporine analogues. By studying the binding of cyclophilin to more than fifty cyclosporine derivatives modified singly on each of the eleven amino acid residues, it could be shown that cyclophilin binds to the residues of cyclosporine known to be critical for its immunosuppressive activity. These data identify cyclophilin as a highly discriminating stereospecific binding protein for cyclosporine.
Function of Nod‐like receptors in microbial recognition and host defense (2008)

Nucleotide oligomerization domain (NOD)-like receptors (NLRs) are a specialized group of intracellular proteins that play a critical role in the regulation of the host innate immune response. NLRs act as scaffolding proteins that assemble signaling platforms that trigger nuclear factor-kappaB and mitogen-activated protein kinase signaling pathways and control the activation of inflammatory caspases. Importantly, mutations in several members of the NLR family have been linked to a variety of inflammatory diseases consistent with these molecules playing an important role in host-pathogen interactions and the inflammatory response. In this review, we focus on the role of Nod1 and Nod2 in host defense and in particular discuss recent finding regarding the role of Nlrc4, Nlpr1, and Nlrp3 inflammasomes in caspase-1 activation and subsequent release of proinflammatory cytokines such as interleukin-1 beta.
SENTIMENT CLASSIFICATION of MOVIE REVIEWS USING CONTEXTUAL VALENCE SHIFTERS (2006)

We present two methods for determining the sentiment expressed by a movie review. The semantic orientation of a review can be positive, negative, or neutral. We examine the effect of valence shifters on classifying the reviews. We examine three types of valence shifters: negations, intensifiers, and diminishers. Negations are used to reverse the semantic polarity of a particular term, while intensifiers and diminishers are used to increase and decrease, respectively, the degree to which a term is positive or negative. The first method classifies reviews based on the number of positive and negative terms they contain. We use the General Inquirer to identify positive and negative terms, as well as negation terms, intensifiers, and diminishers. We also use positive and negative terms from other sources, including a dictionary of synonym differences and a very large Web corpus. To compute corpus‐based semantic orientation values of terms, we use their association scores with a small group of positive and negative terms. We show that extending the term‐counting method with contextual valence shifters improves the accuracy of the classification. The second method uses a Machine Learning algorithm, Support Vector Machines. We start with unigram features and then add bigrams that consist of a valence shifter and another word. The accuracy of classification is very high, and the valence shifter bigrams slightly improve it. The features that contribute to the high accuracy are the words in the lists of positive and negative terms. Previous work focused on either the term‐counting method or the Machine Learning method. We show that combining the two methods achieves better results than either method alone.
Caspase-independent Cell Killing by Fas-associated Protein with Death Domain (1998)

The binding of Fas ligand to Fas recruits caspase 8 to Fas via an adaptor, FADD/MORT1, and activates a caspase cascade leading to apoptosis. Here, we describe a human Jurkat-derived cell line (JB-6) that is deficient in caspase 8. This cell line was resistant to the apoptosis triggered by Fas engagement. However, the multimerization of Fas-associated protein with death domain, through the use of a dimerizing system, killed the JB-6 cells. This killing process was not accompanied by the activation of caspases or DNA fragmentation. The dying cells showed neither condensation nor fragmentation of cells and nuclei, but the cells and nuclei swelled in a manner similar to that seen in necrosis. These results suggested that Fas-associated protein with death domain can kill the cells via two pathways, one mediated by caspases and another that does not involve them.
Cell-mediated immune response and stability of intraocular transgene expression after adenovirus-mediated delivery. (1997)

A T-cell-mediated immune response appears to play a role in the loss of adenovirus-mediated lacZ expression after intravitreal but not after subretinal injection. This result implies that the subretinal space is an immune-privileged site and a favorable site for gene transfer.
Human satellites 2 and 3. (1994)

The most abundant human satellites are alphoid sequences and simple sequence satellites (satellite 2 and 3). Alphoid sequences are now regarded as the DNA component of the centromere and have therefore attracted most attention, leaving satellite 2 and 3 in outer darkness. The classical satellite definition stems from the characterisation of the most abundant repeat family of density gradient fractions. This definition has been reviewed in the light of recent publications. Satellite 2 and 3 sequences and organisation are clearly distinct. Satellite 3 shows a strict periodicity of 5 bp, and satellite 2 is built from two related units of 23 and 26 bp. The distinctive behaviour of satellite-2-containing regions in genetic alterations of cytosine methylation suggests that these two tandemly repeated families participate in distinct heterochromatin organisations, and that variations in satellite sequences at many separate position in the genome may be caused by alterations of heterochromatin-associated proteins. Restriction enzyme analysis indicates that satellite 2 and 3 arrays contain regularly spaced sequence alterations creating a restriction site. This homogeneity contrasts with the scattering of numerous variant sequences all over the length of the higher-order unit, and suggests that two distinct molecular processes are the cause of local variant scattering and higher-order regular homogeneity. Higher-order homogeneity reflects paradoxically a local alterations of homogeneity. Since fixation of mutations by unequal crossovers is very efficient only in small arrays, sequence replacement by biased gene conversion must explain homogeneity in the larger arrays.
BISA: Built-in self-authentication for preventing hardware Trojan insertion (2013)

Hardware Trojans have become a significant threat to government agencies and enterprises that require security and trustworthiness in systems with critical applications. Detecting hardware Trojans is very challenging because of the diversity of Trojans and unpredictable process variations during fabrication. In this paper, we propose a novel technique, called built-in self-authentication (BISA), that can fill unused spaces in a circuit layout by functional filler cells instead of non-functional filler cells. All functional filler cells will be tested by BISA itself and a digital signature would be generated. Any modification on BISA will result in a different signature. Thus, BISA can be used to prevent Trojan insertion or make Trojan insertion extremely difficult. BISA can be applied to any single-module or bottom-up hierarchical design, and we evaluate it on different circuits to demonstrate the effective of this technique.
532‐nanometer green laser beam treatment of superficial varicosities of the lower extremities (1988)

Green laser light at 532 nm was utilized in an attempt to thrombose and blanch superficial varicosities of the lower extremity in 14 patients. Selective vascular damage with sparing of overlying skin was the theoretical rationale for use of green light. Seven of the 14 patients achieved satisfactory results (total or near-total obliteration of vessels without scarring) after a 6-month period of observation.
Effect of bivalent interaction upon apparent antibody affinity: experimental confirmation of theory using fluorescence photobleaching and implications for antibody binding assays. (1992)

The affinity of a monoclonal antibody for its tumor-associated antigen is one of several parameters governing in vivo monoclonal antibody distribution. However, there is a lack of apparent correlation between the affinity of a bivalent monoclonal antibody measured using equilibrium binding experiments and its in vivo delivery. Furthermore, differences in the reported affinity for identical antibody/antigen pairs are quite common in the literature. In this paper, both of these discrepancies are addressed in terms of variation in avidity due to bivalent interaction. The enhancement of avidity afforded by bivalent attachment is addressed theoretically by extending the model of Crothers and Metzger (Immunochemistry, 9: 341-357, 1972). Theoretical assessment of Lineweaver-Burk, Scatchard, Steward-Petty, Langmuir, fluorescence recovery after photobleaching, and Sips models demonstrates quantitatively that the measured affinity using equilibrium binding experiments may vary over four orders of magnitude with similar variation in experimental cellular antigen density. Further, the measured affinity is a function of the experimental protocol. Predictions of avidity enhancement were confirmed experimentally using fluorescence recovery after photobleaching. These experiments measured the equilibrium binding constant and concentration of binding sites for an immunoglobulin G monoclonal antibody and its F(ab) fragment directed against the rabbit VX2 carcinoma cell line. Bivalent binding data agree quantitatively with those predicted by the bivalent model with no adjustable parameters. It is concluded that bivalent equilibrium binding constants are useful only in antibody screening, where experimental conditions are identical for all series. They must be used with caution in predicting in vivo antibody distribution, and it is recommended that the intrinsic, monovalent affinity be measured in tandem with any bivalent antibody study as a standard reference.
Molecular Basis of Deficient IL-2 Production in T Cells from Patients with Systemic Lupus Erythematosus (2001)

Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease characterized by diverse cellular and biochemical aberrations, including decreased production of IL-2. Here we show that nuclear extracts from unstimulated SLE T cells, unlike extracts from normal T cells, express increased amounts of phosphorylated cAMP-responsive element modulator (p-CREM) that binds the -180 site of the IL-2 promoter. Nuclear extracts from stimulated normal T cells display increased binding of phosphorylated cAMP-responsive element binding protein (p-CREB) to the -180 site of the IL-2 promoter, whereas nuclear extracts from stimulated SLE T cells display primarily p-CREM and decreased p-CREB binding. In SLE T cells, p-CREM bound to the transcriptional coactivators, CREB binding protein and p300. Increased expression of p-CREM correlated with decreased production of IL-2. The transcription of a reporter gene driven by the -180 site was enhanced in normal T cells, but was suppressed in SLE T cells. These experiments demonstrate that transcriptional repression is responsible for the decreased production of IL-2 by SLE T cells.