gebhart/patrepeval huggingface dataset:
ARGOS8 variants generated by CRISPR‐Cas9 improve maize grain yield under field drought stress conditions (2016)

Maize ARGOS8 is a negative regulator of ethylene responses. A previous study has shown that transgenic plants constitutively overexpressing ARGOS8 have reduced ethylene sensitivity and improved grain yield under drought stress conditions. To explore the targeted use of ARGOS8 native expression variation in drought-tolerant breeding, a diverse set of over 400 maize inbreds was examined for ARGOS8 mRNA expression, but the expression levels in all lines were less than that created in the original ARGOS8 transgenic events. We then employed a CRISPR-Cas-enabled advanced breeding technology to generate novel variants of ARGOS8. The native maize GOS2 promoter, which confers a moderate level of constitutive expression, was inserted into the 5'-untranslated region of the native ARGOS8 gene or was used to replace the native promoter of ARGOS8. Precise genomic DNA modification at the ARGOS8 locus was verified by PCR and sequencing. The ARGOS8 variants had elevated levels of ARGOS8 transcripts relative to the native allele and these transcripts were detectable in all the tissues tested, which was the expected results using the GOS2 promoter. A field study showed that compared to the WT, the ARGOS8 variants increased grain yield by five bushels per acre under flowering stress conditions and had no yield loss under well-watered conditions. These results demonstrate the utility of the CRISPR-Cas9 system in generating novel allelic variation for breeding drought-tolerant crops.
A role for CD36 in the regulation of dendritic cell function (2001)

Dendritic cells (DC) are crucial for the induction of immune responses and thus an inviting target for modulation by pathogens. We have previously shown that Plasmodium falciparum -infected erythrocytes inhibit the maturation of DCs. Intact P. falciparum -infected erythrocytes can bind directly to CD36 and indirectly to CD51. It is striking that these receptors, at least in part, also mediate the phagocytosis of apoptotic cells. Here we show that antibodies against CD36 or CD51, as well as exposure to early apoptotic cells, profoundly modulate DC maturation and function in response to inflammatory signals. Although modulated DCs still secrete tumor necrosis factor-α, they fail to activate T cells and now secrete IL-10. We therefore propose that intact P. falciparum -infected erythrocytes and apoptotic cells engage similar pathways regulating DC function. These findings may have important consequences for the treatment of malaria and may suggest strategies for modulating pathological immune responses in autoimmune diseases.
T-cell receptor-CD4 physical association in a murine T-cell hybridoma: induction by antigen receptor ligation. (1989)

By employing flow cytometric analysis and fluorescence resonance energy transfer (FRET), we examined the physical relationship between the T-cell receptor-CD3 complex (Ti-CD3) and the CD4 molecule on helper T cells. Through the use of an L3T4-negative murine T-cell hybridoma infectant expressing the human CD4 gene and having antigen specificity for HLA-DR, we show that binding of the Ti-CD3 complex with an anti-CD3 monoclonal antibody induces its redistribution proximal to cell-surface CD4. FRET efficiency was 9.4% on cells labeled with rhodaminated anti-CD3 and fluoresceinated anti-CD4. FRET was found to be temperature dependent, since similarly treated cells held at 4 degrees C displayed a FRET efficiency of less than 1%. Energy transfer was evident within 3 min after warming cells to 37 degrees C. Energy transfer was not detected between Ti-CD3 and the abundantly expressed leukocyte common antigen (CD45). Of greater significance was our observation that hybridomas infected with a truncated CD4 gene lacking the cytoplasmic domain failed to transfer energy despite the fact that CD4 was expressed on the cell surface at levels equivalent to or greater than the wild type. These studies suggest that after crosslinking of the Ti-CD3 on CD4+ T cells, a physical association occurs between the antigen receptor complex and CD4 and that the association is dependent upon the presence of the cytoplasmic domain of CD4.
Magnetoencephalography with an atomic magnetometer (2006)

The authors demonstrate detection and mapping of brain magnetic fields evoked by auditory stimulation with a noncryogenic magnetometer based on spin precession of potassium atoms in spin-exchange-relaxation-free regime. Optical readout using a photodiode array allows flexibility in detector placement while using common elements for most components of the multichannel system. Absence of a cryogenic dewar eliminates magnetic Johnson noise from radiation shields and allows the use of a compact magnetic shield with a high shielding factor. The magnetometer sensitivity is currently equal to 3.5fT∕Hz1∕2 at 10Hz, similar to superconducting quantum interference device magnetoencephalography systems.
TET proteins in malignant hematopoiesis (2009)

Differentiation of hematopoietic stem cells into mature blood cells is a multistage process. During each stage, both extrinsic and intrinsic factors coordinate the expression of the genes required for the cell to adopt a particular fate. Disturbance of this accurately balanced system can lead to a variety of hematopoietic disorders. In hematopoietic malignancies, the activity of genes involved in the key processes of proliferation, apoptosis and differentiation are affected, resulting in clonal expansion of aberrant cells. Clonal disorders of erythroid, myeloid and megakaryocytic cells are combined in the group of the myeloid malignancies. Diagnosis of these malignancies is based on morphological, immunophenotypic and, with increasing importance, genetic parameters. Effective and specific treatment strategies remain subject for further development. Insight into the genes and pathways implicated in the pathogenesis of myeloid malignancies will contribute to the design of targeted therapies.
Novel Agents on the Horizon for Cancer Therapy (2009)

Although cancer remains a devastating diagnosis, several decades of preclinical progress in cancer biology and biotechnology have recently led to successful development of several biological agents that substantially improve survival and quality of life for some patients. There is now a rich pipeline of novel anticancer agents in early phase clinical trials. The specific tumor and stromal aberrancies targeted can be conceptualized as membrane-bound receptor kinases (HGF/c-Met, human epidermal growth factor receptor and insulin growth factor receptor pathways), intracellular signaling kinases (Src, PI3k/Akt/mTOR, and mitogen-activated protein kinase pathways), epigenetic abnormalities (DNA methyltransferase and histyone deacetylase), protein dynamics (heat shock protein 90, ubiquitin-proteasome system), and tumor vasculature and microenvironment (angiogenesis, HIF, endothelium, integrins). Several technologies are available to target these abnormalities. Of these, monoclonal antibodies and small-molecule inhibitors have been the more successful, and often complementary, approaches so far in clinical settings. The success of this target-based cancer drug development approach is discussed with examples of recently approved agents, such as bevacizumab, erlotinib, trastuzumab, sorafenib, and bortezomib. This review also highlights the pipeline of rationally designed drugs in clinical development that have the potential to impact clinical care in the near future.
Photoinitiated Cross-Linking of the Biodegradable Polyester Poly(propylene fumarate). Part I. Determination of Network Structure (2003)

In this work, we investigated the mechanism involved in the photoinitiated cross-linking of the polyester poly(propylene fumarate) (PPF) using the initiator bis(2,4,6-trimethylbenzoyl) phenylphosphine oxide (BAPO). It was hypothesized that BAPO has the ability to cross-link PPF into solid polymer networks, without the use of a cross-linking monomer, because two pairs of radicals, both involving a fast adding phosphinoyl radical, were formed upon UV irradiation of BAPO. Spectroscopic investigation first confirmed the addition of BAPO derived radicals to the PPF olefin. Investigations of fumarate conversion and bulk network properties were then undertaken, using the BAPO initiator and a monoacylphosphine oxide (MAPO) initiator which contains a single photolabile bond. Results show that a single BAPO phosphinoyl radical was primarily responsible for the formation of a highly cross-linked PPF network and the additional radical pair which may be formed does not dramatically alter fumarate conversion or bulk network properties. From these results, the network structure of BAPO initiated, photo-cross-linked PPF may be deduced. Finally, this study demonstrates a method for inferring cross-linked network structures by contrasting properties of bulk materials formed from similar cross-linking initiators.
The Proteomics of N-terminal Methionine Cleavage (2006)

Methionine aminopeptidase (MAP) is a ubiquitous, essential enzyme involved in protein N-terminal methionine excision. According to the generally accepted cleavage rules for MAP, this enzyme cleaves all proteins with small side chains on the residue in the second position (P1'), but many exceptions are known. The substrate specificity of Escherichia coli MAP1 was studied in vitro with a large (>120) coherent array of peptides mimicking the natural substrates and kinetically analyzed in detail. Peptides with Val or Thr at P1' were much less efficiently cleaved than those with Ala, Cys, Gly, Pro, or Ser in this position. Certain residues at P2', P3', and P4' strongly slowed the reaction, and some proteins with Val and Thr at P1' could not undergo Met cleavage. These in vitro data were fully consistent with data for 862 E. coli proteins with known N-terminal sequences in vivo. The specificity sites were found to be identical to those for the other type of MAPs, MAP2s, and a dedicated prediction tool for Met cleavage is now available. Taking into account the rules of MAP cleavage and leader peptide removal, the N termini of all proteins were predicted from the annotated genome and compared with data obtained in vivo. This analysis showed that proteins displaying N-Met cleavage are overrepresented in vivo. We conclude that protein secretion involving leader peptide cleavage is more frequent than generally thought.
Seminal ribonuclease inhibits tumor growth and reduces the metastatic potential of Lewis lung carcinoma. (1994)

The role of some RNases as antitumoral agents has been recently emphasized. We have previously demonstrated a striking inhibitory effect of bovine seminal RNase on the in vitro growth of tumor cells of metastatic origin. This has prompted us to test the effects of this protein in vivo on the induction of metastatic foci in mice lungs after i.m. injection of a highly metastatic Lewis lung carcinoma cell line. The results presented here, while confirming and expanding upon those previously reported on the antitumor effects of bovine seminal RNase in vivo on primary thyroid epithelial tumors, indicate for the first time that bovine seminal RNase can also be regarded as a potent antimetastatic agent on in vivo spontaneous metastases.
Nonlinear induction detection of electron spin resonance (2012)

We present an approach to the induction detection of electron spin resonance (ESR) signals exploiting the nonlinear properties of a superconducting resonator. Our experiments employ a yttrium barium copper oxide superconducting stripline microwave (MW) resonator integrated with a microbridge. A strong nonlinear response of the resonator is thermally activated in the microbridge when exceeding a threshold in the injected MW power. The responsivity factor characterizing the ESR-induced change in the system’s output signal is about 100 times larger when operating the resonator near the instability threshold, compared to the value obtained in the linear regime of operation. Preliminary experimental results, together with a theoretical model of this phenomenon are presented. Under appropriate conditions, nonlinear induction detection of ESR can potentially improve upon the current capabilities of conventional linear induction detection ESR.
Sequence and Characterization of the Ig Heavy Chain Constant and Partial Variable Region of the Mouse Strain 129S1 (2007)

Although the entire mouse genome has been sequenced, there remain challenges concerning the elucidation of particular complex and polymorphic genomic loci. In the murine Igh locus, different haplotypes exist in different inbred mouse strains. For example, the Igh(b) haplotype sequence of the Mouse Genome Project strain C57BL/6 differs considerably from the Igh(a) haplotype of BALB/c, which has been widely used in the analyses of Ab responses. We have sequenced and annotated the 3' half of the Igh(a) locus of 129S1/SvImJ, covering the C(H) region and approximately half of the V(H) region. This sequence comprises 128 V(H) genes, of which 49 are judged to be functional. The comparison of the Igh(a) sequence with the homologous Igh(b) region from C57BL/6 revealed two major expansions in the germline repertoire of Igh(a). In addition, we found smaller haplotype-specific differences like the duplication of five V(H) genes in the Igh(a) locus. We generated a V(H) allele table by comparing the individual V(H) genes of both haplotypes. Surprisingly, the number and position of D(H) genes in the 129S1 strain differs not only from the sequence of C57BL/6 but also from the map published for BALB/c. Taken together, the contiguous genomic sequence of the 3' part of the Igh(a) locus allows a detailed view of the recent evolution of this highly dynamic locus in the mouse.
Cloning and Functional Expression of a Human Na+and Cl−-dependent Neutral and Cationic Amino Acid Transporter B0+ (1999)

A Na(+)-dependent neutral and cationic amino acid transport system (B(0+)) plays an important role in many cells and tissues; however, the molecular basis for this transport system is still unknown. To identify new transporters, the expressed sequence tag database was queried, and cDNA fragments with sequence similarity to the Na(+)/Cl(-)-dependent neurotransmitter transporter family were identified. Based on these sequences, rapid amplification of cDNA ends of human mammary gland cDNA was used to obtain a cDNA of 4.5 kilobases (kb). The open reading frame encodes a 642-amino acid protein named amino acid transporter B(0+). Human ATB(0+) (hATB(0+)) is a novel member of the Na(+)/Cl(-)-dependent neurotransmitter transporter family with the highest sequence similarity to the glycine and proline transporters. Northern blot analysis identified transcripts of approximately 4.5 kb and approximately 2 kb in the lung. Another tissue survey suggests expression in the trachea, salivary gland, mammary gland, stomach, and pituitary gland. Electrophysiology and radiolabeled amino acid uptake measurements were used to functionally characterize the transporter expressed in Xenopus oocytes. hATB(0+) was found to transport both neutral and cationic amino acids, with the highest affinity for hydrophobic amino acids and the lowest affinity for proline. Amino acid transport was Na(+) and Cl(-)-dependent and was attenuated in the presence of 2-aminobicyclo-[2.2.1]-heptane-2-carboxylic acid, a system B(0+) inhibitor. These characteristics are consistent with system B(0+) amino acid transport. Thus, hATB(0+) is the first cloned B(0+) amino acid transporter.
Planar waveguide optical spectrum analyzer using a UV-induced grating (1998)

An optical spectrum analyzer is demonstrated using a UV-induced, chirped grating on a planar waveguide and a linear detector array. The grating provides both the dispersion with respect to wavelength and the imaging function. The spectral response has a full-width at half-maximum of 0.15 nm and a bandwidth of 7.8 nm. A chirp of -1.75 nm/cm and a 12-cm focal length were used. The design parameters are discussed in terms of the chirp, focal length and resolution. The wavelength dependence of the optimal chirp limits the resolution for small focal lengths. For longer focal lengths, the spotsize is diffraction limited and high resolution can be achieved with minimal fabrication complexity.
Runx proteins are involved in regulation of CD122, Ly49 family and IFN-γ expression during NK cell differentiation (2007)

Runx family proteins play indispensable roles in the development of various hematopoietic lineage cells. However, their function in NK cells is still uncertain. We found that NK cells and CD8 T cells dominantly express Runx3 protein, whereas NKT cells and CD4 T cells express Runx1. Reverse transcription-PCR analysis revealed that Runx3 expression is initiated at the NK precursor stage and is maintained along the course of NK cell differentiation. In order to examine their role in the earlier stage of NK cell development, we introduced Runx dominant-negative (Runx dn) form into Lin(-)c-kit(+)Sca-1(+) hematopoietic stem cells, which were applied to NK cell-inducing culture. Post-cultured cells showed a decreased expression of IL-2/IL-15 common receptor beta subunit (CD122), consistent with another finding that Runx binds to promoter region of CD122 gene. To examine the Runx function in the later developmental stage, we used transgenic mouse, in which Runx dn form is expressed in immature and mature NK cells. This mouse showed decreased expressions of NK maturation markers, such as Ly49 family, Mac-1 and CD43, whereas IFN-gamma production was greatly enhanced. These findings suggest that Runx proteins, especially Runx3, play multiple roles in NK cell differentiation.
Genetic Recombination in Streptomyces fradiae by Protoplast Fusion and Cell Regeneration (1978)

Conditions for highly efficient genetic recombination in Streptomyces by protoplast fusion are described. Protoplasts of S. fradiae and S. griseofuscus were formed by a modification of the glycine-lysozyme-lytic enzyme method (Okanishi, Suzuki & Umezawa, 1974). Regeneration of cells from protoplasts was monitored throughout the growth cycle and was most efficient when cells of either S. fradiae or S. griseofuscus were taken from the transition phase between the exponential and stationary growth phases. Fusion of protoplasts carrying different auxotrophic or chromosomal drug-resistance markers was achieved by treatment with polyethylene glycol, and high frequencies of stable genetic recombinants were obtained.
Bioactivity of freeze-dried platelet-rich plasma in an adsorbed form on a biodegradable polymer material (2012)

Owing to the necessity for the immediate preparation from patients' blood, autologous platelet-rich plasma (PRP) limits its clinical applicability. To address this concern and respond to emergency care and other unpredictable uses, we have developed a freeze-dried PRP in an adsorbed form on a biodegradable polymer material (Polyglactin 910). On the polymer filaments of PRP mesh, which was prepared by coating the polymer mesh with human fresh PRP and subsequent freeze-drying, platelets were incorporated, and related growth factors were preserved at high levels. This new PRP mesh preparation significantly and reproducibly stimulated the proliferation of human periodontal ligament cells in vitro and neovascularization in a chorioallantoic membrane assay. A full-thickness skin defect model in a diabetic mouse demonstrated the PRP mesh, although prepared from human blood, substantially facilitated angiogenesis, granulation tissue formation, and re-epithelialization without inducing severe inflammation in vivo. These data demonstrate that our new PRP mesh preparation functions as a bioactive material to facilitate tissue repair/regeneration. Therefore, we suggest that this bioactive material, composed of allogeneic PRP, could be clinically used as a promising alternative in emergency care or at times when autologous PRP is not prepared immediately before application.
Merlin Phosphorylation by p21-activated Kinase 2 and Effects of Phosphorylation on Merlin Localization (2002)

The Nf2 tumor suppressor gene product merlin is related to the membrane-cytoskeleton linker proteins of the band 4.1 superfamily, including ezrin, radixin, and moesin (ERMs). Merlin is regulated by phosphorylation in a Rac/cdc42-dependent fashion. We report that the phosphorylation of merlin at serine 518 is induced by the p21-activated kinase PAK2. This is demonstrated by biochemical fractionation, use of active and dominant-negative mutants of PAK2, and immunodepletion. By using wild-type and mutated forms of merlin and phospho-directed antibodies, we show that phosphorylation of merlin at serine 518 leads to dramatic protein relocalization.
Lagrange relaxation based method for the QoS routing problem (2002)

In this paper a practically efficient QoS routing method is presented, which provides a solution to the delay constrained least cost routing problem. The algorithm uses the concept of aggregated costs and provides an efficient method to find the optimal multiplier based on Lagrange relaxation. This method is proven to be polynomial and it is also efficient in practice. The benefit of this method is that it also gives a lower bound on the theoretical optimal solution along with the result. The difference between the lower bound and the cost of the found path is very small proving the good quality of the result. Moreover, by further relaxing the optimality of paths, an easy way is provided to control the trade-off between the running time of the algorithm and the quality of the found paths. We present a comprehensive numerical evaluation of the algorithm, by comparing it to a wide range of QoS routing algorithms proposed in the literature. It is shown that the performance of the proposed polynomial time algorithm is close to the optimal solution computed by an exponential algorithm.
Re-evaluation of the classical Mycoplasma lipophilum cluster (Weisburg et al. 1989) and description of two new clusters in the hominis group based on 16S rDNA sequences. (2001)

The Mycoplasma lipophilum cluster (Weisburg et al. 1989) in the hominis group of the mollicutes is re-evaluated in this work to update the phylogenetic framework for classification of species within the genus Mycoplasma. Therefore, sequences of the 16S rRNA gene were determined from previously described species, and 11 were found to be closely related to the M. lipophilum cluster. A selection of members of the other hitherto defined clusters of the hominis group was included for phylogenetic analysis, revealing that the classical M. lipophilum cluster could be re-organized into two clusters, namely the M. lipophilum cluster and the Mycoplasma bovis cluster. The former was found to contain two species, while the latter contained 20 species. The two clusters were closely related, sharing an ancestral branch with the Mycoplasma synoviae cluster. Furthermore, the M. bovis cluster could be divided into subclusters. Interestingly, two species, Mycoplasma equigenitalium and Mycoplasma elephantis, formed a distinct and early branch of the M. lipophilum, M. bovis and M. synoviae clusters. This entity was termed the M. equigenitalium cluster. The clusters and subclusters could be verified by using neighbour-joining and maximum-likelihood analyses on a variety of data sets, bootstrap calculations, secondary structure analysis and signature nucleotides. Therefore, the new 16S rDNA data presented in this work were used to re-evaluate the M. lipophilum cluster, leading to the definition of two additional clusters. At present, the mollicutes belonging to the hominis group can be classified into ten evolutionary lineages.