gebhart/patrepeval huggingface dataset:
Instruction encoding synthesis for architecture exploration using hierarchical processor models (2003)

This paper presents a novel instruction encoding generation technique for use in architecture exploration for application specific processors. The underlying exploration methodology is based on successive processor model refinement combined with simulation and profiling. Previous approaches require the tedious manual specification of binary instruction opcodes even at very early design stages due to the need to generate profiling tools. The proposed automatic technique eliminates this bottleneck in ASIP design. It is well adapted to the hierarchical processor modeling style of contemporary architecture description languages. Experimental evaluation for several real-life processor architectures confirms the practical applicability of the presented encoding techniques. Moreover, the results indicate that very compact instruction encoding schemes are generated that compete very well with hand-optimized encodings.
Sustained remissions with CD19-specific chimeric antigen receptor (CAR)-modified T cells in children with relapsed/refractory ALL. (2016)

3011 Background: Targeted immunotherapy with chimeric antigen receptor (CAR)-modified T cells can produce potent anti-tumor responses. We previously reported complete remissions (CR) and prolonged persistence in children and adults with relapsed/refractory (r/r) acute lymphoblastic leukemia (ALL) treated with CD19-specific CART cells (CTL019). We now report on outcomes and longer follow-up of 59 children with r/r ALL. Methods: T cells collected from the patient were transduced with a lentiviral vector encoding a CAR composed of anti-CD19 scFv, CD3z, and 4-1BB domains, activated/expanded ex vivo with anti-CD3/CD28 beads, and then infused at a dose of 107 to 108cells/kg with a transduction efficiency of 2.3-45%. 54/59 patients received lymphodepleting chemotherapy the week prior to cell infusion. Results: Of 59 patients aged 20mo-24y with CD19+ ALL, 44 had detectable disease prior to CTL019 cell infusion, while 15 were MRD-. 39 were treated for relapse after prior stem cell transplant (SCT). 15 patients had CNS disease within a year of infusion. At assessment 1 month after infusion, 55/59 (93%) were in CR. MRD < 0.01% by flow cytometry was achieved in 52 patients. CTL019 cells were detected in the CSF and no CNS relapses have been seen. With median follow-up 12 mo (1-43 mo), 34 patients had ongoing CR, with only 6 receiving subsequent therapy (5 SCT, 1 donor lymphocyte infusion), RFS was 76% (95% CI, 65-89%) at 6 mo and 55% at 12 mo (95% CI, 42-73%), and OS was 79% (95% CI, 69-91%) at 12 mo. 20 patients subsequently relapsed, 13 with CD19- disease. CTL019 persistence was accompanied by B cell aplasia, which continued up to last assessment (1-39 mo) in 24/34 patients with ongoing CR. Cytokine release syndrome (CRS) was seen in 88% of patients. Severe CRS requiring hemodynamic or respiratory support occurred in 27%, was associated with high disease burden, and was reversed with the anti-IL6R agent tocilizumab. We could predict development of severe CRS through regression modeling using IFNγ, sgp130, and sIL1RA measured in the first 72h (sens 86%, spec 89%, AUC 0.93). Conclusions: Single-agent CTL019 immunotherapy can induce durable responses with control of CNS disease in patients with r/r ALL. Clinical trial information: NCT01626495.
CuTE: curb tracking and estimation (2006)

The number of road accident related fatalities and damages are reduced substantially by improving road infrastructure and enacting and imposing laws. Further reduction is possible through embedding intelligence onto the vehicles for safe decision making. Road boundary information plays a major role in developing such intelligent vehicles. A prominent feature of roads in urban, semi-urban, and similar environments, is curbs on either side defining the road's boundary. In this brief, a novel methodology of tracking curbs is proposed. The problem of tracking a curb from a moving vehicle is formulated as tracking of a maneuvering target in clutter from a mobile platform using onboard sensors. A curb segment is presumed to be the maneuvering target, and is modeled as a nonlinear Markov switching process. The target's (curb's) orientation and location measurements are simultaneously obtained using a two-dimensional (2-D) scanning laser radar (LADAR) and a charge-coupled device (CCD) monocular camera, and are modeled as traditional base state observations. Camera images are also used to estimate the target's mode, which is modeled as a discrete-time point process. An effective curb tracking algorithm, known as Curb Tracking and Estimation (CuTE) using multiple modal sensor information is, thus, synthesized in an image enhanced interactive multiple model filtering framework. The use and fusion of camera vision and LADAR within this frame provide for efficient, effective, and robust tracking of curbs. Extensive experiments conducted in a campus road network demonstrate the viability, effectiveness, and robustness of the proposed method
Construction of a replication-competent murine retrovirus vector expressing the human immunodeficiency virus type 1 tat transactivator protein (1991)

A replication-competent Akv murine leukemia virus-based vector encoding the human immunodeficiency virus tat cDNA under control of the simian virus 40 early promoter sequences was constructed. The simian virus 40 tat sequences were placed within the U3 region of the 3' long terminal repeat. The resulting virus, derived by transfection, replicated efficiently in mouse NIH 3T3 cells and maintained the tat cDNA insert. It has been suggested that Tat function requires the presence of a human-specific cofactor, which is absent in murine cells. However, infection of murine cells with the Akv virus encoding tat resulted in significant transactivation of a human immunodeficiency virus long terminal repeat-driven reporter gene, indicating that human cofactors are not always required for Tat function. The vector system described may be useful for introduction of foreign genes in vivo and in whole animals when virus spread is required for efficient infection and levels of gene expression.
TCR spectratyping revealed T lymphocytes associated with graft-versus-host disease after allogeneic hematopoietic stem cell transplantation (2007)

Clonal expansion of T cells after allogeneic hematopoietic stem cell transplantation (allo-HSCT) has been observed, but their characteristics remain to be fully elucidated. We report here that CD8(+) T cells were the dominant T lymphocytes seen and T-cell repertoire diversity decreased dramatically during the first 3 months after allo-HSCT. Patients with GVHD grade II - IV had significantly lower T-cell repertoire diversity compared with non-GVHD patients. TCR beta variable gene (TCRBV) subfamily 8, 5.1, 5.2, 4, and 13 were the five most frequently expanded subfamilies among these patients. Among the 49 over-expanded clones identified, clonotype "TCR3-5" and "TCR18-5" were isolated from four patients with HLA-A2 allele and skin GVHD. Their frequencies correlated well with skin symptoms (i.e. rash). Moreover, they were detected in donors but not detected in recipients before transplantation. Lastly, three common TCRBV CDR3 motifs shared by T cells related with GVHD were discovered: TGDS, GLAG, and GGG. These findings suggest that TCR spectratyping is helpful for revealing GVHD-related T cells and may have utility in early diagnosis.
Immunoglobulin isotype influences affinity and specificity (2012)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Trace bio-organic constituents of gelatins : a review (1992)

These substances can be important for distinguishing gelatins according to raw material origin and manufacturing procedure, which influence the suitability of gelatins for particular applications
A high-responsivity and broadband photoconductive terahertz detector based on a plasmonic nanocavity (2018)

We present a photoconductive terahertz detector to be used in terahertz time-domain imaging and spectroscopy systems without utilizing a short-carrier lifetime semiconductor for the photoconductive active region. A plasmonic nanocavity is used to form the photoconductive active region of the detector to limit the transport time of the majority of the photo-generated carrier to a sub-picosecond order and eliminate the need for a short-carrier lifetime semiconductor. We demonstrate that the presented detector is capable of detecting terahertz pulses over a 0.1–4.5 THz frequency band with more than a 100 dB dynamic range under a 5 mW optical pump power, exhibiting a comparable performance with the state-of-the-art photoconductive terahertz detectors based on short-carrier lifetime substrates.
Evolution, structure and function of the small heat shock proteins in plants (1996)

The a-crystallin-related, small heat shock proteins (smHSPs) are ubiquitous in nature, but are unusually abundant and diverse in higher plants as opposed to other eukaryotes. The smHSPs range in size from ~ 17 to 30 kDa and share a conserved C-terminal domain common to all eukaryotic smHSPs and to the a-crystallin proteins of the vertebrate eye lens. In higher plants six nuclear gene families encoding smHSPs have been defined. Each gene family encodes proteins found in a distinct cellular compartment, including the cytosol, chloroplast, ER, and mitochondrion. Evolutionary analysis suggests that the smHSP gene families arose by gene duplication and divergence prior to the radiation of angiosperms. In general, the smHSPs are not found in normal vegetative tissues, but accumulate to high levels in response to heat stress. Specific smHSPs are also expressed during various phases of plant development as part of the endogenous developmental programme. Thus, although the smHSPs are apparently not essential for basal cell functions as are the high molecular weight HSPs such as HSP90, HSP70 and HSP60, their functions are likely to be critical for survival and recovery from heat stress as well as for specific developmental processes. Biochemical analysis indicates that smHSPs are found in high molecular weight complexes between 200-400 kDa that are most likely composed solely of multiple smHSP subunits. Purified recombinant plant smHSPs facilitate reactivation of chemically denatured enzymes in a nucleotide-independent fashion and also prevent heat-induced aggregation or reverse inactivation of protein substrates. Based on these data, it is suggested that smHSPs act in vivo as a type of molecular chaperone to bind partially denatured proteins preventing irreversible protein inactivation and aggregation, and that smHSP chaperone activity contributes to the development of thermotolerance.
Methyl CpG-binding Protein Isoform MeCP2_e2 Is Dispensable for Rett Syndrome Phenotypes but Essential for Embryo Viability and Placenta Development (2012)

Methyl CpG-binding protein 2 gene (MeCP2) mutations are implicated in Rett syndrome (RTT), one of the common causes of female mental retardation. Two MeCP2 isoforms have been reported: MeCP2_e2 (splicing of all four exons) and MeCP2_e1 (alternative splicing of exons 1, 3, and 4). Their relative expression levels vary among tissues, with MeCP2_e1 being more dominant in adult brain, whereas MeCP2_e2 is expressed more abundantly in placenta, liver, and skeletal muscle. In this study, we performed specific disruption of the MeCP2_e2-defining exon 2 using the Cre-loxP system and examined the consequences of selective loss of MeCP2_e2 function in vivo. We performed behavior evaluation, gene expression analysis, using RT-PCR and real-time quantitative PCR, and histological analysis. We demonstrate that selective deletion of MeCP2_e2 does not result in RTT-associated neurological phenotypes but confers a survival disadvantage to embryos carrying a MeCP2_e2 null allele of maternal origin. In addition, we reveal a specific requirement for MeCP2_e2 function in extraembryonic tissue, where selective loss of MeCP2_e2 results in placenta defects and up-regulation of peg-1, as determined by the parental origin of the mutant allele. Taken together, our findings suggest a novel role for MeCP2 in normal placenta development and illustrate how paternal X chromosome inactivation in extraembryonic tissues confers a survival disadvantage for carriers of a mutant maternal MeCP2_e2 allele. Moreover, our findings provide an explanation for the absence of reports on MeCP2_e2-specific exon 2 mutations in RTT. MeCP2_e2 mutations in humans may result in a phenotype that evades a diagnosis of RTT.
Facile Synthesis of a Library of 9-Alkyl-8-benzyl-9H-purin-6-ylamine Derivatives (2001)

ADVERTISEMENT RETURN TO ISSUEPREVReportNEXTFacile Synthesis of a Library of 9-Alkyl-8-benzyl-9H-purin-6-ylamine DerivativesBrian Lucas, Neal Rosen, and Gabriela ChiosisView Author Information Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 271, New York, New York 10021 Cite this: J. Comb. Chem. 2001, 3, 6, 518–520Publication Date (Web):September 21, 2001Publication History Received12 April 2001Published online21 September 2001Published inissue 1 November 2001https://pubs.acs.org/doi/10.1021/cc010017thttps://doi.org/10.1021/cc010017tbrief-reportACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views486Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Alcohols,Aromatic compounds,Chemical reactions,Post-translational modification,Reaction products Get e-Alerts
High-temperature structural phase transitions in perovskite (1996)

High-temperature powder x-ray diffraction data are presented for perovskite between 293 and 1523 K. The temperature-dependence of superlattice intensities and cell parameters suggests a sequence of phase transitions from the room temperature orthorhombic (Pbnm) structure to a tetragonal (I4/mcm) polymorph at temperatures in the range 1373 - 1423 K, followed by transformation to the cubic aristotype at . The intensity of the diffuse background increases on transformation to the cubic structure and is associated with disorder (and anionic mobility) of the oxygen sub-lattice. The I4/mcm - Pbnm transition induces a large spontaneous strain, but the tetragonal spontaneous strain in the I4/mcm phase due to the - I4/mcm transition is small, below the resolution of this experiment. These results add weight to suggestions from recent computer simulations that orthorhombic may transform to a tetragonal (rather than a cubic) polymorph under the conditions of the Earth's mantle, in which case the effects on electrical conductivity would not be expected to be as great as for a transition to a cubic polymorph, although the consequences for elastic properties may be more significant.
A Single Administration of CRISPR/Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing (2018)

The development of clinically viable delivery methods presents one of the greatest challenges in the therapeutic application of CRISPR/Cas9 mediated genome editing. Here, we report the development of a lipid nanoparticle (LNP)-mediated delivery system that, with a single administration, enabled significant editing of the mouse transthyretin (Ttr) gene in the liver, with a >97% reduction in serum protein levels that persisted for at least 12 months. These results were achieved with an LNP delivery system that was biodegradable and well tolerated. The LNP delivery system was combined with a sgRNA having a chemical modification pattern that was important for high levels of in vivo activity. The formulation was similarly effective in a rat model. Our work demonstrates that this LNP system can deliver CRISPR/Cas9 components to achieve clinically relevant levels of in vivo genome editing with a concomitant reduction of TTR serum protein, highlighting the potential of this system as an effective genome editing platform.
Benzodiazepines with psychotropic activity. 7. Synthesis and biological action of 4-amino-1,5-benzodiazepines (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBenzodiazepines with psychotropic activity. 7. Synthesis and biological action of 4-amino-1,5-benzodiazepinesAdolf Bauer, Peter Danneberg, Karl Heinz Weber, and Klaus MinckCite this: J. Med. Chem. 1973, 16, 9, 1011–1014Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/jm00267a011https://doi.org/10.1021/jm00267a011research-articleACS PublicationsRequest reuse permissionsArticle Views153Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
On the recognition and cleavage mechanism of Escherichia coli endodeoxyribonuclease V, a possible DNA repair enzyme. (1982)

Escherichia coli endodeoxyribonuclease V acts at many sites of damage in duplex DNA, including apurinic/apyrimidinic sites, lesions induced by ultraviolet light which are not pyrimidine dimers, adducts of 7-bromomethylbenz[a]anthracene, and, as demonstrated earlier (Gates, F. T., and Linn, S. (1977a) J. Biol. Chem. 252. 1647-1653), it degrades uracil-containing duplex DNA most efficiently. The cleavage rate increases with increasing substitution of uracil for thymine in T5 DNA, with a replacement of one-eight of thymine generating the apparent maximum cleavage rate. However, the apparent reaction limit with DNA containing 3.8% of thymine replaced by uracil corresponds to cleavage at only 6% of the dUMP residues. Evidently, the enzyme recognizes some peculiarities of abnormal DNA structure, but not simply distortions, since some lesions, including pyrimidine dimers, are not substrates. Endonuclease V generates double strand breaks in a constant ratio to single strand nicks, regardless of the substrate. It degrades DNA processively, completing the digestion of one substrate molecule before proceeding to the next. The enzyme also appears to act cooperatively. Cleavage at methylbenz[a]anthracene adducts is usually or always 5' to the lesion. Endonuclease V seems well suited to act as a DNA repair enzyme, surveying the genome for structural distortions generated by lesions for which specific repair systems might not exist.
Rotation of polarimetric matrices and its effects on classification accuracy of man-made structures by synthetic aperture radar (2011)

This paper presents the effects of rotation of polarimetric matrices on man-made structure classification by polarimetric synthetic aperture radar (POLSAR). Both coherence and covariance matrices are used for classification. Some important modification is also applied to the previously suggested rotation algorithm. The advantage of this modification is to guarantee that the cross-polarized component is surely minimized. As a result, we were able to distinguish man-made structures from other areas more effectively than the related methods.
Boron Diffusion with Boric Acid for High Efficiency Silicon Solar Cells (2010)

A boron diffusion process using boric acid as a low cost, nontoxic spin-on source is introduced. Using dilute solutions of boric acid, sheet resistances ranging from 20 to were achieved, along with saturation current densities as low as . These results indicate that boric acid is a suitable source for forming both emitters and back surface fields for high efficiency n- and p-type solar cells. The degradation of the minority carrier bulk lifetime, which is a common efficiency-limiting characteristic of low cost boron sources, was also minimized through the use of a high purity boric acid source. The ability to achieve low sheet resistances, high bulk lifetimes and low saturation current densities with boric acid were exploited to achieve a 19.7% efficient screen printed solar cell exhibiting a bulk lifetime .
Kinetic-dependent Killing of Oral Pathogens with Nitric Oxide (2015)

Nitric oxide (NO)-releasing silica nanoparticles were synthesized via the co-condensation of tetramethyl orthosilicate with aminosilanes and subsequent conversion of secondary amines to N-diazeniumdiolate NO donors. A series of ~150 nm NO-releasing particles with different NO totals and release kinetics (i.e., half-lives) were achieved by altering both the identity and mol% composition of the aminosilane precursors. Independent of identical 2 h NO-release totals, enhanced antibacterial action was observed against the periodontopathogens Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis with extended NO-release kinetics at pH 7.4. Negligible bactericidal effect was observed against cariogenic Streptococcus mutans at pH 7.4, even when using NO-releasing silica particles with greater NO-release totals. However, antibacterial activity was observed against S. mutans at lower pH (6.4). This result was attributed to more rapid proton-initiated decomposition of the N-diazeniumdiolate NO donors and greater NO-release payloads. The data suggest a differential sensitivity to NO between cariogenic and periodontopathogenic bacteria with implications for the future development of NO-releasing oral care therapeutics.