gebhart/patrepeval huggingface dataset:
Activation of human T cells by FcR nonbinding anti-CD3 mAb, hOKT3γ1(Ala-Ala) (2003)

Dimeric Fc receptor (FcR) nonbinding anti-CD3 antibodies have been developed to minimize toxicities associated with classical anti-CD3 monoclonal antibodies (e.g., OKT3). Studies with murine analogs of non-FcR-binding antibodies have shown reduced mitogenicity compared to OKT3. In a trial of an FcR nonbinding humanized anti-CD3 mAb hOKT3gamma1(Ala-Ala) for treatment of patients with type 1 diabetes, we found significant increases in IL-10 and IL-5 in the serum of 63% and 72% of patients, respectively, and TNF-alpha and IL-6 levels that were lower than those previously reported following OKT3 therapy. The activation signal delivered by hOKT3gamma1(Ala-Ala) was associated with calcium signaling and cytokine production by previously activated human cells in vitro. However, the production of IL-10, compared to IFN-gamma on a molar basis, was greater after culture with hOKT3gamma1(Ala-Ala) than with OKT3. Flow cytometric studies confirmed that OKT3 induced IFN-gamma and IL-10 production, but hOKT3gamma1(Ala-Ala) induced only detectable IL-10 production in CD45RO(+) cells. Moreover, in vivo, we found IL-10(+)CD4(+) T cells after drug treatment. These cells were heterogeneous but generally CD45RO(+), CTLA-4(-), and expressed CCR4. A subgroup of these cells expressed TGF-beta. Thus, the non-FcR binding anti-CD3 mAb, hOKT3gamma1(Ala-Ala) delivers an activation signal to T cells that is quantitatively and qualitatively different from OKT3. It leads to the generation of T cells that might inhibit the autoimmune response and may be involved in the beneficial effect on beta cell destruction in Type 1 diabetes.
Reversible middle cerebral artery occlusion without craniectomy in rats. (1989)

To develop a simple, relatively noninvasive small-animal model of reversible regional cerebral ischemia, we tested various methods of inducing infarction in the territory of the right middle cerebral artery (MCA) by extracranial vascular occlusion in rats. In preliminary studies, 60 rats were anesthetized with ketamine and different combinations of vessels were occluded; blood pressure and arterial blood gases were monitored. Neurologic deficit, mortality rate, gross pathology, and in some instances, electroencephalogram and histochemical staining results were evaluated in all surviving rats. The principal procedure consisted of introducing a 4-0 nylon intraluminal suture into the cervical internal carotid artery (ICA) and advancing it intracranially to block blood flow into the MCA; collateral blood flow was reduced by interrupting all branches of the external carotid artery (ECA) and all extracranial branches of the ICA. In some groups of rats, bilateral vertebral or contralateral carotid artery occlusion was also performed. India ink perfusion studies in 20 rats documented blockage of MCA blood flow in 14 rats subjected to permanent occlusion and the restoration of blood flow to the MCA territory in six rats after withdrawal of the suture from the ICA. The best method of MCA occlusion was then selected for further confirmatory studies, including histologic examination, in five additional groups of rats anesthetized with halothane. Seven of eight rats that underwent permanent occlusion of the MCA had resolving moderately severe neurologic deficits (Grade 2 of 4) and unilateral infarcts averaging 37.6 +/- 5.5% of the coronal sectional area at 72 hours after the onset of occlusion.(ABSTRACT TRUNCATED AT 250 WORDS)
Transcriptional repression by the insulator protein CTCF involves histone deacetylases (2000)

The highly conserved zinc-finger protein, CTCF, is a candidate tumor suppressor protein that binds to highly divergent DNA sequences. CTCF has been connected to multiple functions in chromatin organization and gene regulation including chromatin insulator activity and transcriptional enhancement and silencing. Here we show that CTCF harbors several autonomous repression domains. One of these domains, the zinc-finger cluster, silences transcription in all cell types tested and binds directly to the co-repressor SIN3A. Two distinct regions of SIN3A, the PAH3 domain and the extreme C-terminal region, bind independently to this zinc-finger cluster. Analysis of nuclear extract from HeLa cells revealed that CTCF is also capable of retaining functional histone deacetylase activity. Furthermore, the ability of regions of CTCF to retain deacetylase activity correlates with the ability to bind to SIN3A and to repress gene activity. We suggest that CTCF driven repression is mediated in part by the recruitment of histone deacetylase activity by SIN3A.
DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes (2015)

The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) adaptive immune systems use small guide RNAs, the CRISPR RNAs (crRNAs), to mark foreign genetic material, e.g. viral nucleic acids, for degradation. Archaea and bacteria encode a large variety of Cas proteins that bind crRNA molecules and build active ribonucleoprotein surveillance complexes. The evolution of CRISPR-Cas systems has resulted in a diversification of cas genes and a classification of the systems into three types and additional subtypes characterized by distinct surveillance and interfering complexes. Recent crystallographic and biochemical advances have revealed detailed insights into the assembly and DNA/RNA targeting mechanisms of the various complexes. Here, we review our knowledge on the molecular mechanism involved in the DNA and RNA interference stages of type I (Cascade: CRISPR-associated complex for antiviral defense), type II (Cas9) and type III (Csm, Cmr) CRISPR-Cas systems. We further highlight recently reported structural and mechanistic themes shared among these systems.
DNA-dependent ATPase activity associated with vaccinia virus early transcription factor. (1988)

Vaccinia virus early transcription factor (VETF) is required for efficient expression of the early class of viral genes in vitro. The factor copurified with an ATPase activity that was stimulated by DNA. In this report we show that the ATPase remains associated with the factor upon glycerol gradient sedimentation. Under these conditions VETF sedimented at a rate of 7.6 S suggesting that it may be a heterodimer of the Mr 82,000 and 77,000 polypeptides. Of the common nucleoside triphosphates, only ATP and dATP were hydrolyzed by the VETF-associated ATPase. The ATP analog gamma-thio ATP was not a substrate. The VETF-associated ATPase activity was stimulated up to 30-fold by the presence of polynucleotides. DNA was a much more effective cofactor for the ATPase than was RNA, and duplex polydeoxyribonucleotides were preferred. The enzymatic and physical properties of the VETF-associated ATPase distinguished it from all three vaccinia ATPase activities previously described, nucleoside triphosphate phosphohydrolases I and II, and capping enzyme. Except for the preference for double-stranded DNA, the substrate and cofactor requirements of the VETF-associated ATPase most closely resembled those of nucleoside triphosphate phosphohydrolase I. However, VETF-ATPase was not inhibited by polyclonal antibody to the latter enzyme. The association of an ATPase with an early gene transcription factor may explain the previously described requirement for ATP hydrolysis in transcription.
RESEARCH: Development of a mature fungal technology and production platform for industrial enzymes based on a Myceliophthora thermophila isolate, previously known as Chrysosporium lucknowense C1 (2011)

The filamentous fungus C1 was developed into an expression platform for screening and production of diverse industrial enzymes. C1 shows a lowviscosity morphology in submerged culture, enabling the use of complex growth and production media. This morphology furthermore allowed C1 to be used as a host for high-throughput robotic screening of gene libraries. A C1-genetic toolbox was developed, which enabled the generation of a large collection of dedicated C1 host strains and gene-expression strategies. The 38 Mbp genome was sequenced and found to be rich in biomass-hydrolyzing-enzyme-encoding genes. C1 production strains have been developed that produce large quantities of these enzyme mixtures (up to 100 g/L total protein). Recombinant C1 strains were constructed that produce single enzymes in a relatively pure form, facilitating enzyme purification and characterization, as well as for commercial applications. Molecular phylogenetic studies revealed that C1, previously classified as Chrysosporium lucknowense based on morphological characteristics, is actually a Myceliophthora thermophila isolate. In addition, C1 has proven to be a source of novel industrial enzymes, and the C1-technology platform developed has been applied as a tool for research on and production of industrial enzymes for various industrial applications, such as biofuels and biorefineries.
Single-Tube Nested Real-Time PCR as a New Highly Sensitive Approach to Trace Hazelnut (2012)

Hazelnut is one of the most commonly consumed tree nuts, being largely used by the food industry in a wide variety of processed foods. However, it is a source of allergens capable of inducing mild to severe allergic reactions in sensitized individuals. Hence, the development of highly sensitive methodologies for hazelnut traceability is essential. In this work, we developed a novel technique for hazelnut detection based on a single-tube nested real-time PCR system. The system presents high specificity and sensitivity, enabling a relative limit of detection of 50 mg/kg of hazelnut in wheat material and an absolute limit of detection of 0.5 pg of hazelnut DNA (1 DNA copy). Its application to processed food samples was successfully achieved, detecting trace amounts of hazelnut in chocolate down to 60 mg/kg. These results highlight the adequacy of the technique for the specific detection and semiquantitation of hazelnut as potential hidden allergens in foods.
APPLICATION OF FLOYD-WARSHALL LABELLING TECHNIQUE: IDENTIFICATION OF CONNECTED PIXEL COMPONENTS IN BINARY IMAGE (2006)

This paper presents an image analysis technique using connected components by applying SPA (shortest path algorithm) from graph theory. Software implementation of Floyd-Warshall transitive matrix labelling method is discussed. Results are also presented.
Two Level Correction Algorithms for Model Problems (2007)

In this report, we experiment a variant of the two-level ideal algorithm for parametric shape optimization that was proposed in [5]. In the linear case, the method, referred to as the Z' method, employs a permutation operator to rearrange the eigenstructure in such a way that the new high-frequency modes are associated with large eigenvalues. As a result, the classical steepest-descent iteration can be viewed as a Jacobi-type smoother, and standard multilevel stragegies be applied. An alternate method is also tested based on odd-even decoupling (L' method). For a linear model problem, both new methods are found efficient and superior to the original formulation, but the Z' method is more robust. Similar numerical results are obtained for a nonlinear model problem by considering the eigensystem of the Jacobian matrix.
Selective delivery of boron by the melanin precursor analogue p-boronophenylalanine to tumors other than melanoma. (1990)

The melanin precursor analogue p-boronophenylalanine (BPA) has been used to deliver 10B to melanoma tissue for boron neuron capture therapy. Uptake studies in tumor models other than melanoma now indicate that BPA is capable of delivering therapeutic amounts of boron to tumors other than melanoma. The KHJJ murine mammary tumor carried s.c. in BALB/c mice, the GS-9L rat glioma carried both s.c. and intracranially in F-344 rats, and the human U-87 MG glioma xenograft carried s.c. in nude mice have all shown significant accumulation of boron in tumor tissue following single p.o. (intragastric) doses of BPA. In this KHJJ mammary tumor, the L isomer of BPA was preferentially accumulated compared to the D isomer, indicative of a carrier-mediated transport process. Double-label, whole-body autoradiographic studies in a pigmented murine melanoma have shown that the boron distribution (from BPA) differs from the distribution of a tritiated melanin precursor (tyrosine). Boron accumulated only in the tumor; labeled tyrosine accumulated in tumor, liver, intestinal epithelium, bone-marrow, and secretory glands. Toxicity studies in mice and rabbits indicate that, even at very high doses, BPA p.o. caused no adverse effect in tissues, on blood chemistry, or on differential leukocyte counts. These data indicate that BPA may be generally useful as a boron delivery agent for boron neutron capture therapy of tumors.
Optical control of zebrafish behavior with halorhodopsin (2009)

Expression of halorhodopsin (NpHR), a light-driven microbial chloride pump, enables optical control of membrane potential and reversible silencing of targeted neurons. We generated transgenic zebrafish expressing enhanced NpHR under control of the Gal4/UAS system. Electrophysiological recordings showed that eNpHR stimulation effectively suppressed spiking of single neurons in vivo. Applying light through thin optic fibers positioned above the head of a semi-restrained zebrafish larva enabled us to target groups of neurons and to simultaneously test the effect of their silencing on behavior. The photostimulated volume of the zebrafish brain could be marked by subsequent photoconversion of co-expressed Kaede or Dendra. These techniques were used to localize swim command circuitry to a small hindbrain region, just rostral to the commissura infima Halleri. The kinetics of the hindbrain-generated swim command was investigated by combined and separate photo-activation of NpHR and Channelrhodopsin-2 (ChR2), a light-gated cation channel, in the same neurons. Together this "optogenetic toolkit" allows loss-of-function and gain-of-function analyses of neural circuitry at high spatial and temporal resolution in a behaving vertebrate.
Genetic Identification of a Network of Factors that Functionally Interact with the Nucleosome Remodeling ATPase ISWI (2008)

Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.
An embedded hierarchical image coder using zerotrees of wavelet coefficients (2002)

This paper describes a simple, yet remarkably effective, image compression algorithm, having the property that the bits in the bit stream are generated in order of importance. A fully embedded code represents a sequence of binary decisions that distinguish an image from the 'null' image. Using an embedded coding algorithm, an encoder can terminate the encoding at any point thereby allowing a target rate or target distortion metric to be met exactly. Also, the decoder can cease decoding at any point in the bit stream and still produce exactly the same image that would have been encoded at the bit rate corresponding to the truncated bit stream. The algorithm consistently produces compression results that are competitive with virtually all known compression algorithms on standard test images, but requires absolutely no training, no pre-stored tables or codebooks, and no prior knowledge of the image source. It is based on four key concepts: (1) wavelet transform or hierarchical subband decomposition, (2) prediction of the absence of significant information across scales by exploiting the self-similarity inherent in images (3) entropy-coded successive-approximation quantization, and (4) universal lossless data compression achieved via adaptive arithmetic coding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan (2010)

ABSTRACT Norovirus GII/4 is a leading cause of acute viral gastroenteritis in humans. We examined here how the GII/4 virus evolves to generate and sustain new epidemics in humans, using 199 near-full-length GII/4 genome sequences and 11 genome segment clones from human stool specimens collected at 19 sites in Japan between May 2006 and February 2009. Phylogenetic studies demonstrated outbreaks of 7 monophyletic GII/4 subtypes, among which a single subtype, termed 2006b, had continually predominated. Phylogenetic-tree, bootscanning-plot, and informative-site analyses revealed that 4 of the 7 GII/4 subtypes were mosaics of recently prevalent GII/4 subtypes and 1 was made up of the GII/4 and GII/12 genotypes. Notably, single putative recombination breakpoints with the highest statistical significance were constantly located around the border of open reading frame 1 (ORF1) and ORF2 ( P ≤ 0.000001), suggesting outgrowth of specific recombinant viruses in the outbreaks. The GII/4 subtypes had many unique amino acids at the time of their outbreaks, especially in the N-term, 3A-like, and capsid proteins. Unique amino acids in the capsids were preferentially positioned on the outer surface loops of the protruding P2 domain and more abundant in the dominant subtypes. These findings suggest that intersubtype genome recombination at the ORF1/2 boundary region is a common mechanism that realizes independent and concurrent changes on the virion surface and in viral replication proteins for the persistence of norovirus GII/4 in human populations.
Signal Transduction Pathways Activated in Endothelial Cells Following Infection with Chlamydia pneumoniae (1999)

Chlamydia pneumoniae is an important respiratory pathogen. Recently, its presence has been demonstrated in atherosclerotic lesions. In this study, we characterized C. pneumoniae-mediated activation of endothelial cells and demonstrated an enhanced expression of endothelial adhesion molecules followed by subsequent rolling, adhesion, and transmigration of leukocytes (monocytes, granulocytes). These effects were blocked by mAbs against endothelial and/or leukocyte adhesion molecules (beta1 and beta2 integrins). Additionally, activation of different signal transduction pathways in C. pneumoniae-infected endothelial cells was shown: protein tyrosine phosphorylation, up-regulation of phosphorylated p42/p44 mitogen-activated protein kinase, and NF-kappaB activation/translocation occurred within 10-15 min. Increased mRNA and surface expression of E-selectin, ICAM-1, and VCAM-1 were noted within hours. Thus, C. pneumoniae triggers a cascade of events that could lead to endothelial activation, inflammation, and thrombosis, which in turn may result in or may promote atherosclerosis.
A method for the preparation of polylactic acid microcapsules of controlled particle size and drug loading (1988)

A solvent partition technique for the microencapsulation of hydrocortisone-polylactic acid has been developed for the preparation of microcapsules of controlled particle size distribution and drug loading. The method involves continuous injection of a drug-polymer solution with a syringe infusion pump into flowing mineral oil where microcapsules are formed as the solvent of the drug-polymer is partitioned into the mineral oil. Using preselected syringe needle size and mechanical control of the mineral oil flow rate at the needle tip, microcapsules of consistent particle sizes and desired drug loadings were prepared. Microcapsules of different internal structures were also prepared by varying the solvent system for the drug-polymer preparation. Dissolution studies showed that at the same drug loading, the rate of the percentage drug release increased with decreasing particle size, and that at similar particle size distributions, the rate increased with increasing drug loading. These results indicate that both the particle size distribution, and the drug loading must be controlled in a microencapsulation process to produce microcapsules of controlled drug release rate.
New CMOS shallow junction well FET structure (CMOS-SJET) for low power-supply voltage (1992)

A novel CMOS device structure called as CMOS shallow junction well FET (CMOS-SJET) has been proposed for high speed operation at low power-supply voltage. Since well regions underneath the channel regions of both n-channel and p-channel MOSFETs in the CMOS-SJET are fully depleted, steeper subthreshold characteristics can be achieved. Furthermore, junction capacitances are reduced by half compared with those of the conventional CMOS structure. Therefore the gate delay of 52 psec/stage at 1.5 V operation and low power-delay product of 1 fJ are verified with 0.35 mu m gate length design. The CMOS-SJET structure appears to offer high performance with low power-delay product at low voltage operation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutations in a translation initiation factor identify the target of a memory-enhancing compound (2015)

The integrated stress response (ISR) modulates messenger RNA translation to regulate the mammalian unfolded protein response (UPR), immunity, and memory formation. A chemical ISR inhibitor, ISRIB, enhances cognitive function and modulates the UPR in vivo. To explore mechanisms involved in ISRIB action, we screened cultured mammalian cells for somatic mutations that reversed its effect on the ISR. Clustered missense mutations were found at the amino-terminal portion of the delta subunit of guanine nucleotide exchange factor (GEF) eIF2B. When reintroduced by CRISPR-Cas9 gene editing of wild-type cells, these mutations reversed both ISRIB-mediated inhibition of the ISR and its stimulatory effect on eIF2B GEF activity toward its substrate, the translation initiation factor eIF2, in vitro. Thus, ISRIB targets an interaction between eIF2 and eIF2B that lies at the core of the ISR.