gebhart/patrepeval huggingface dataset:
Bacterial Gene Inserted in an Engineered RNA Virus: Efficient Expression in Monocotyledonous Plant Cells (1986)

Brome mosaic virus (BMV) is a plant virus whose genome consists of three RNA components. A previously described viral complementary DNA expression system has been used to express both wild-type and altered genomic RNA's in barley protoplasts. Variants of BMV RNA3 were constructed in which the coat gene had been removed or replaced with sequences encoding chloramphenicol acetyltransferase (CAT). CAT sequences were also inserted near the 5' end of the intact coat gene. When inoculated on protoplasts together with transcripts of BMV RNA's 1 and 2, all of these RNA3 derivatives were replicated and produced subgenomic RNA's analogous to the normal subgenomic coat protein messenger RNA. RNA3 derivatives in which the CAT coding sequences were oriented with the same polarity as viral genes produced significant CAT activity in protoplasts. CAT expression was improved by inserting the CAT gene in frame with the upstream coat protein initiation codon, and exceeded expression in plant cells transformed with Ti plasmid-based vectors.
Cerebellar LTD facilitates but is not essential for long‐term adaptation of the vestibulo‐ocular reflex (2002)

The induction of cerebellar long-term depression (LTD) at the parallel fibre-Purkinje cell synapse is selectively blocked in L7-PKCi transgenic mice, rendering these mice unable to adaptively modify their vestibulo-ocular reflex (VOR) during visuo-vestibular training for a few hours. Despite this deficit, their eye movement performance as well as their general motor behaviour appears unaffected. This combination suggests that, in the long term, residual forms of plasticity in the vestibulo-cerebellar circuitry can compensate for the absence of cerebellar LTD. To investigate whether LTD-deficient mice exhibit motor learning in the long run, we subjected L7-PKCi transgenic mice to visuo-vestibular training paradigms that were aimed at either increasing or decreasing the VOR response in the course of eight consecutive days. During the increasing paradigm, the VOR gain of transgenic mice increased significantly, while VOR gain decreased and VOR phase-lead increased during the decreasing paradigm. The impact of these long training periods on the VOR was significantly smaller in LTD-deficient mice than in wild type littermates. Thus, while LTD may be necessary for short-term VOR adaptation, it facilitates but is not required for long-term adaptation of the VOR.
Improving the accuracy of static branch prediction using branch correlation (1994)

Recent work in history-based branch prediction uses novel hardware structures to capture branch correlation and increase branch prediction accuracy. We present a profile-based code transformation that exploits branch correlation to improve the accuracy of static branch prediction schemes. Our general method encodes branch history information in the program counter through the duplication and placement of program basic blocks. For correlation histories of eight branches, our experimental results achieve up to a 14.7% improvement in prediction accuracy over conventional profile-based prediction without any increase in the dynamic instruction count of our benchmark applications. In the majority of these applications, code duplication increases code size by less than 30%. For the few applications with code segments that exhibit exponential branching paths and no branch correlation, simple compile-time heuristics can eliminate these branches as code-transformation candidates.
Leukocyte extravasation: chemokine transport and presentation by the endothelium (2002)

At sites of inflammation and in normal immune surveillance, chemokines direct leukocyte migration across the endothelium. Many cell types that are extravascular can produce chemokines, and for these mediators to directly elicit leukocyte migration from the blood, they would need to reach the luminal surface of the endothelium. This article reviews the evidence that endothelial cells are active in transcytosing chemokines to their luminal surfaces, where they are presented to leukocytes. The endothelial binding sites that transport and present chemokines include glycosaminoglycans (GAGs) and possibly the Duffy antigen/receptor for chemokines (DARC). The binding residues on chemokines that interact with GAGs are discussed, as are the carbohydrate structures on GAGs that bind these cytokines. The expression of particular GAG structures by endothelial cells may lend selectivity to the type of chemokine presented in a given tissue, thereby contributing to selective leukocyte recruitment. At the luminal surface of the endothelium, chemokines are preferentially presented to blood leukocytes on the tips of microvillous processes. Similarly, certain adhesion molecules and chemokine receptors are also preferentially distributed on leukocyte and endothelial microvilli, and evidence suggests an important role for these structures in creating the necessary surface topography for leukocyte migration. Finally, the mechanisms of chemokine transcytosis and presentation by endothelial cells are incorporated into the current model of chemokine-driven leukocyte extravasation.
Conformation transition kinetics of Bombyx mori silk protein (2007)

Time-resolved FTIR analysis was used to monitor the conformation transition induced by treating regenerated Bombyx mori silk fibroin films and solutions with different concentrations of ethanol. The resulting curves showing the kinetics of the transition for both films and fibroin solutions were influenced by the ethanol concentration. In addition, for silk fibroin solutions the protein concentration also had an effect on the kinetics. At low ethanol concentrations (for example, less than 40% v/v in the case of film), films and fibroin solutions showed a phase in which beta-sheets slowly formed at a rate dependent on the ethanol concentration. Reducing the concentration of the fibroin in solutions also slowed the formation of beta-sheets. These observations suggest that this phase represents a nucleation step. Such a nucleation phase was not seen in the conformation transition at ethanol concentrations > 40% in films or > 50% in silk fibroin solutions. Our results indicate that the ethanol-induced conformation transition of silk fibroin in films and solutions is a three-phase process. The first phase is the initiation of beta-sheet structure (nucleation), the second is a fast phase of beta-sheet growth while the third phase represents a slow perfection of previously formed beta-sheet structure. The nucleation step can be very fast or relatively slow, depending on factors that influence protein chain mobility and intermolecular hydrogen bond formation. The findings give support to the previous evidence that natural silk spinning in silkworms is nucleation-dependent, and that silkworms (like spiders) use concentrated silk protein solutions, and careful control of the pH value and metallic ion content of the processing environment to speed up the nucleation step to produce a rapid conformation transition to convert the water soluble spinning dope to a tough solid silk fiber.
The String-to-String Correction Problem (1974)

The string-to-string correction problem is to determine the distance between two strings as measured by the minimum cost sequence of “edit operations” needed to change the one string into the other. The edit operations investigated allow changing one symbol of a string into another single symbol, deleting one symbol from a string, or inserting a single symbol into a string. An algorithm is presented which solves this problem in time proportional to the product of the lengths of the two strings. Possible applications are to the problems of automatic spelling correction and determining the longest subsequence of characters common to two strings.
Parametric Acoustic Array (1963)

This paper presents the theory of highly directional receivers and transmitters that may be “constructed” with the nonlinearity of the equations of fluid motion.
Biodistribution, radiation dosimetry and scouting of 90Y-ibritumomab tiuxetan therapy in patients with relapsed B-cell non-Hodgkin’s lymphoma using 89Zr-ibritumomab tiuxetan and PET (2012)

Biodistribution of (89)Zr-ibritumomab tiuxetan is not influenced by simultaneous therapy with (90)Y-ibritumomab tiuxetan, and (89)Zr-ibritumomab tiuxetan scout scans can thus be used to predict biodistribution and dose-limiting organ during therapy. Absorbed doses to spleen were lower than those previously estimated using (111)In-ibritumomab tiuxetan. The dose-limiting organ in patients undergoing stem cell transplantation is the liver.
Review Hepatitis B Virus Resistance to Lamivudine and its Clinical Implications (2002)

Lamivudine is the first orally available drug approved for treatment of chronic hepatitis B, but hepatitis B virus (HBV) resistance to lamivudine appears to be a sine qua non in the therapy of HBV. The mutations at the FLLA and YMDD motif in the domains B and C of HBV polymerase contribute to this resistance. These mutations are found at codon (or AA) rtL180M and rtM204V/I in the reverse transcriptase (RT) domain of the HBV polymerase for all genotypes according to a new standardized RT domain numbering system. The resistant HBV may be less replication-competent in vitro and in vivo, and it is rarely associated with markedly increased HBV replication or liver injury. Therefore, certain physicians favour continuing lamivudine therapy even after emergence of HBV resistance with the expectation of maintaining lower-than baseline HBV DNA, alanine amino-transferase, and histological improvement, and avoiding reversion to wild-type HBV until additional antiviral strategies are developed. Ultimately, once several antiviral agents are approved, combination strategy is likely to be incorporated in antiviral treatment for chronic HBV to suppress, prevent or minimize the emergence of resistant virus.
Addressing the autofluorescence issue in deep tissue imaging by two-photon microscopy: the significance of far-red emitting dyes (2017)

The fluorescence imaging of tissue is essential for studying biological events beyond the cellular level. Two-photon microscopy based on the nonlinear light absorption of fluorescent dyes is a viable tool for the high resolution imaging of tissue. A key limitation for deep tissue imaging is the autofluorescence from intrinsic biomolecules. Here, we report a systematic study that discloses relative autofluorescence interference, which is dependent on the type of tissue and the excitation and emission wavelengths in two-photon imaging. Among the brain, kidney, liver, lung, and spleen mouse tissues examined, the kidney tissue exhibited prominent autofluorescence followed by the liver and others. Notably, regardless of the tissue type, prominent autofluorescence is observed not only from the green emission channel but also from the yellow emission channel where common two-photon absorbing dyes also emit, whereas there is minimal autofluorescence from the red channel. The autofluorescence is slightly influenced by the excitation wavelength. Toward minimal autofluorescence, we developed a new class of two-photon absorbing dyes that are far-red emitting, water-soluble, and very bright inside cells as well as in tissue. A comparative assessment of the imaging depth, which is dependent on the three selected dyes that emit in the blue-green, yellow, and far-red regions, shows the importance of far-red emitting dyes for deep tissue imaging.
The C5a Receptor Impairs IL-12–Dependent Clearance of Porphyromonas gingivalis and Is Required for Induction of Periodontal Bone Loss (2010)

The C5a anaphylatoxin receptor (C5aR; CD88) is activated as part of the complement cascade and exerts important inflammatory, antimicrobial, and regulatory functions, at least in part, via crosstalk with TLRs. However, the periodontal pathogen Porphyromonas gingivalis can control C5aR activation by generating C5a through its own C5 convertase-like enzymatic activity. In this paper, we show that P. gingivalis uses this mechanism to proactively and selectively inhibit TLR2-induced IL-12p70, whereas the same pathogen-instigated C5aR-TLR2 crosstalk upregulates other inflammatory and bone-resorptive cytokines (IL-1β, IL-6, and TNF-α). In vivo, the ability of P. gingivalis to manipulate TLR2 activation via the C5a-C5aR axis allowed it to escape IL-12p70-dependent immune clearance and to cause inflammatory bone loss in a murine model of experimental periodontitis. In the latter regard, C5aR-deficient or TLR2-deficient mice were both resistant to periodontal bone loss, in stark contrast with wild-type control mice, which is consistent with the interdependent interactions of C5aR and TLR2 in P. gingivalis immune evasion and induction of bone-resorptive cytokines. In conclusion, P. gingivalis targets C5aR to promote its adaptive fitness and cause periodontal disease. Given the current availability of safe and effective C5aR antagonists, pharmacological blockade of C5aR could act therapeutically in human periodontitis and reduce associated systemic risks.
Discovery of Dinaciclib (SCH 727965): A Potent and Selective Inhibitor of Cyclin-Dependent Kinases (2010)

Inhibition of cyclin-dependent kinases (CDKs) has emerged as an attractive strategy for the development of novel oncology therapeutics. Herein is described the utilization of an in vivo screening approach with integrated efficacy and tolerability parameters to identify candidate CDK inhibitors with a suitable balance of activity and tolerability. This approach has resulted in the identification of SCH 727965, a potent and selective CDK inhibitor that is currently undergoing clinical evaluation.
Exon skipping during splicing of dystrophin mRNA precursor due to an intraexon deletion in the dystrophin gene of Duchenne muscular dystrophy kobe. (1991)

Recent molecular studies have shown that in a patient with Duchenne muscular dystrophy (DMD) Kobe, the size of exon 19 of the dystrophin gene was reduced to 36 bp due to the deletion of 52 bp out of 88 bp of the exon. The consensus se- quences at the 5' and 3' splice sites of exon 19 were unaltered (Matsuo, M., et al. 1990. Biochem. Biophys. Res. Commun. 170:963-967). To further elucidate the molecular nature of the defect, we examined the primary structure of cytoplasmic dys- trophin mRNA of the DMD Kobe patient across the junctions of exons 18, 19, and 20 by gel electrophoresis and sequencing of polymerase chain reaction-amplified cDNA. The mRNA cod- ing for dystrophin was reverse transcribed using random primers, and the cDNA was then enzymatically amplified in vitro. The targeted fragment was smaller than expected from the genomic DNA analysis. By sequencing of the amplified product, we found that exon 18 was joined directly to exon 20, so that exon 19 was completely absent, suggesting that this exon was skipped during processing of the dystrophin mRNA precursor. All other bases in the amplified product were unal- tered. Therefore, the data strongly suggest that the internal exon deletion generates an abnormally spliced mRNA in which the sequence of exon 18 is joined to the sequence of exon 20. We propose that the deletion is responsible for abnormal pro- cessing of the DMD Kobe allele. This finding has important implications regarding the determinants of a functional splice site. (
Prodrug Approaches to the Improved Delivery of Peptide Drugs (1999)

Undesirable pharmaceutical and biopharmaceutical properties, which include low water solubility, poor stability, and low permeability through biological membrane barriers, often hinder the clinical development of biologically active peptides. Finding solutions to these problems is a contemporary issue in developing clinically the vast number of biologically active peptides as drugs. In recent years, significant progress has been made in developing prodrug approaches for the improvement of the water solubility, stability, and membrane permeability of peptides. For improving water solubility, the focus has been on the bioreversible introduction of ionizable functional groups to peptides, which helps to increase the polarity and thus water solubility of the peptide drugs. For improving stability, efforts have focused on stabilizing peptides against exopeptidase-mediated hydrolysis by bioreversibly masking the terminal carboxyl and/or amino groups. For improving permeability through biological barriers, recent efforts have focused on both improving the lipophilicity of a peptide in order to facilitate its passive permeation through biological membranes and conjugation of a peptide to a carrier which allows for the active transport of the peptide-carrier conjugate. Many of the prodrug systems developed recently have the potential to be used clinically for the delivery of peptide drugs to the desired site of action.
Long-Term Outcome of Patients with Relapsed and Refractory Germ Cell Tumors Treated with High-Dose Chemotherapy and Autologous Bone Marrow Rescue (1992)

Treatment with high-dose carboplatin and etoposide in conjunction with autologous bone marrow rescue in patients with relapsed or refractory germ cell tumors is a potentially curative therapeutic option, even for heavily pretreated or cisplatin-refractory patients. Some degree of disease resistance to cisplatin can be overcome with dose escalation of platinum compounds. Patients with multiple recurrences of relapsed or refractory primary mediastinal germ cell tumors were not helped by this approach.
Characterization of a novel maize retrotransposon family sprite that shows high levels of variability among maize inbred lines (2009)

A novel LTR retrotransposon, SPRITE, was discovered inserted within an intron of the Mo17 allele of Zmet2. This retrotransposon does not affect the expression or function of the Mo17 Zmet2. There are 19 SPRITE elements in the B73 genome including nine with canonical LTRs and 10 with alternate LTR sequences. The individual SPRITE insertions are highly polymorphic in a sample of eight inbred lines. There is evidence for transcription of certain SPRITE elements following exposure with the DNA methylation or histone deacetylases inhibitors 5-aza-2-deoxycytidine or trichostatin A or after long-term tissue culture. The effects of these treatments cause differences in the specific elements that are activated.
Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures (2011)

We have recently identified seven mutations in commonly used stocks of the sequenced Escherichia coli strain MG1655 which do not appear in the reference sequence. The mutations are likely to cause loss of function of the glpR and crl genes, which may have serious implications for physiological experiments using the affected strains.
Activation of EGFP expression by Cre-mediated excision in a new ROSA26 reporter mouse strain (2001)

Reporter mouse strains are important tools for monitoring Cre recombinase-mediated excision in vivo. In practice, excision may be incomplete in a given population due to threshold level or variegated expression of Cre. Hence, it is desirable in many experimental contexts to isolate cells that have undergone excision to assess the consequences of gene ablation. To generate alternative reporter mice, an enhanced green fluorescent protein (EGFP) gene was targeted to the retroviral-trapped ROSA26 locus. Upon Cre-mediated excision of "Stop" sequences, EGFP was expressed ubiquitously during embryogenesis and in adult tissues (including T cells, B cells, and myeloid cells). Using this new reporter strain, separation of excised from nonexcised cells in vitro was achieved in thymocytes in a noninvasive manner based on activated EGFP expression. This new EGFP reporter strain should facilitate a variety of conditional gene-targeting experiments, including the functional studies of hematopoietic cells in lineage-specific knockout mice.
SRAM design on 65-nm CMOS technology with dynamic sleep transistor for leakage reduction (2005)

A 70-Mb SRAM is designed and fabricated on a 65-nm CMOS technology. It features a 0.57-/spl mu/m/sup 2/ 6T SRAM cell with large noise margin down to 0.7 V for low-voltage operation. The fully synchronized subarray contains an integrated leakage reduction scheme with dynamically controlled sleep transistor. SRAM virtual ground in standby is controlled by programmable bias transistors to achieve good voltage control with fine granularity under process skew. It also has a built-in programmable defect "screen" circuit for high volume manufacturing. The measurements showed that the SRAM leakage can be reduced by 3-5/spl times/ while maintaining the integrity of stored data.
Cloning and expression of cDNA encoding human lysosomal acid lipase/cholesteryl ester hydrolase. Similarities to gastric and lingual lipases. (1991)

Molecular cloning of a full-length cDNA for human lysosomal acid lipase/cholesteryl ester hydrolase (EC 3.1.1.13) reveals that it is structurally related to previously described enteric acid lipases, but lacks significant homology with any characterized neutral lipases. The lysosomal enzyme catalyzes the deacylation of triacylglyceryl and cholesteryl ester core lipids of endocytosed low density lipoproteins; this activity is deficient in patients with Wolman disease and cholesteryl ester storage disease. Its amino acid sequence, as deduced from the 2.6-kilobase cDNA nucleotide sequence, is 58 and 57% identical to those of human gastric lipase and rat lingual lipase, respectively, both of which are involved in the preduodenal breakdown of ingested triglycerides. Notable differences in the primary structure of the lysosomal lipase that may account for discrete catalytic and transport properties include the presence of 3 new cysteine residues, in addition to the 3 that are conserved in this lipase gene family, and of two additional potential N-linked glycosylation sites. Transfection of the cDNA into Cos-1 cells resulted in the expression of acid lipase activity with the substrate range of the native enzyme at a level that was greater than 40 times the endogenous activity.
Estrogen modulation of JE/monocyte chemoattractant protein-1 mRNA expression in murine macrophages. (1995)

The chemotactic cytokine, monocyte chemoattractant protein-1 (MCP-1), and its murine homologue, JE, have been detected in atherosclerotic lesions but not in normal arteries, implicating that these proinflammatory cytokines may be involved in the pathogenesis of atherosclerosis. Epidemiologic studies reveal that postmenopausal women receiving estrogen replacement for treatment of osteoporosis have a greatly reduced risk of developing cardiovascular disease. Because JE/MCP-1 and estrogen play regulatory roles in the development of atherosclerotic lesions, we chose to examine the effect of estrogen treatment on JE/MCP-1 mRNA expression in macrophages. 17 beta-estradiol (E2) inhibited LPS-stimulated JE/MCP-1 mRNA expression in ANA-1 and J774A.1 murine macrophage cell lines and in thioglycolate-elicited murine peritoneal macrophages. Inhibition of JE/MCP-1 mRNA ranged from 50 to 90%, with a maximal effect occurring at a concentration of 300 pg/ml E2. Conversely, E2 had little effect on LPS-stimulated TNF-alpha mRNA production. Treatment of LPS-stimulated macrophages with moxestrol, an estrogen agonist, resulted in a similar inhibition, and the addition of the estrogen antagonist, tamoxifen, reversed E2 inhibition of JE/MCP-1 mRNA expression. Progesterone failed to inhibit LPS-induced JE/MCP-1 mRNA expression. Immunohistochemical analysis revealed the presence of estrogen receptors in ANA-1 cells, indicating that E2 inhibition of LPS-induced JE/MCP-1 mRNA expression in murine macrophages may be mediated through the estrogen receptor. Thus, another mechanism whereby estrogen exerts antiatherogenic effects may be through prevention of macrophage accumulation in the atherosclerotic lesion.
Electron beam (EB)-assisted materials fabrication (1995)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1995.