gebhart/patrepeval huggingface dataset:
Characterization of MR-1, a Novel Myofibrillogenesis Regulator in Human Muscle (2004)

The actin-myosin contractile apparatus consists of several thick filament and thin filament proteins. Specific regulatory mechanisms are involved in this highly ordered process. In this paper, we reported the identification and characterization of a novel myofibrillogenesis regulator, MR-1. The MR-1 gene was cloned from human skeletal muscle cDNA library by using a strategy that involves EST data base searching, PCR and RACE. The MR-1 gene is located on human chromosome 2q35 and encodes a 142 aa protein. Northern blot revealed that the mRNA level of MR-1 was highest in the skeletal muscle and certain level of MR-1 expression was also observed in heart, liver and kidney. Immunohistochemical assay confirmed that the MR-1 protein existed in human myocardial myofibrils. It was found by yeast two-hybrid screening and confirmed by in vitro binding assay that MR-1 could interact with sarcomeric proteins, such as myosin regulatory light chain, myomesin 1 and beta-enolase. These studies suggested that MR-1 might play a regulatory role in the muscle cell and it was worth investigating further.
Reduction of collagen type I in the ciliary muscle of inflamed monkey eyes. (1999)

These results indicate that the density of collagen type I in the extracellular matrix (ECM) of monkey ciliary muscle is reduced during anterior segment inflammation and support the view that reduction of ciliary muscle ECM may contribute to increased uveoscleral outflow facility during anterior segment inflammation.
Selecting DNA fragments for mutation detection by temperature gradient gel electrophoresis: Application to the p53 gene cDNA (1993)

Temperature gradient gel electrophoresis (TGGE) and related methods are widely employed to detect mutations in DNA fragments. DNA melting map calculations and GC clamps have been used to enhance the detection of mutations. While generally successful, these methods have not always revealed base changes within a DNA fragment. Previous work suggested that mutations are detected if they are in a DNA's first melting domain, and the melting domain is well separated from final strand dissociation. Two criteria from the DNA melting theory were established to determine when both of these conditions are met. The criteria involve calculating the derivative melting curve as well as the melting map of a DNA sequence. The approach was applied to the cDNA sequence of the human p53 gene. Mutations in the p53 gene are common in human cancers and are generally located in four 'hot spot' regions. Calculations indicated that three DNA fragments are needed to detect base substitutions in the four hot-spot regions. Predicted melting behavior was experimentally tested with eight single base substitutions distributed among the four hot-spot regions. All mutations tested behaved as predicted and were detected by vertical TGGE. Heteroduplex DNAs formed by melting and reannealing various ratios of wild type and mutant DNA fragments were also examined. Results indicated that point mutations can be detected by ethidium bromide staining from samples containing 10% mutant and 90% wild-type sequences.
A simplified method for extraction of high quality genomic DNA from Jatropha curcas for genetic diversity and molecular marker studies (2009)

A simple and efficient protocol for the extraction of high quality genomic DNA from different tissues, including callus generated from leaves of Jatropha curcas has been developed. The important steps in this protocol include (a) use of 3.5 M NaCl in extraction buffer; (b) 2.0 M NaCl (final concentration) during precipitation; (c) Tris saturated phenol in place of phenol:chloroform:isoamyl alcohol at purification phase; (d) 80% ethanol for DNA precipitation, and (e) performing all the steps at RT. The DNA thus extracted from the leaves had 1.81±0.063, OD at A 260/280 and the yield was 120 to 140 µg/g of material. The extracted DNA was found suitable for restriction digestion, ligation and PCR amplification. It was also used for DNA fingerprinting techniques, RAPD and AFLP, for development of molecular markers and studies on genetic diversity.
Discovery of a β-Hairpin Octapeptide, c[Pro-Arg-Phe-Phe-Dap-Ala-Phe-DPro], Mimetic of Agouti-Related Protein(87–132) [AGRP(87–132)] with Equipotent Mouse Melanocortin-4 Receptor (mMC4R) Antagonist Pharmacology (2015)

Agouti-related protein (AGRP) is a potent orexigenic peptide that antagonizes the melanocortin-3 and -4 receptors (MC3R and MC4R). While the C-terminal domain of AGRP, AGRP(87-132), is equipotent to the full-length peptide, further truncation decreases potency at the MC3R and MC4R. Herein, we report AGRP-derived peptides designed to mimic the active β-hairpin secondary structure that contains the hypothesized Arg-Phe-Phe pharmacophore. The most potent scaffold, c[Pro-Arg-Phe-Phe-Asn-Ala-Phe-DPro], comprised the hexa-peptide β-hairpin loop from AGRP cyclized through a DPro-Pro motif. A 20 compound library was synthesized from this scaffold for further structure-activity relationship studies. The most potent peptide from this library was an asparagine to diaminopropionic acid substitution that possessed sub-nanomolar antagonist activity at the mMC4R and was greater than 160-fold selective for the mMC4R versus the mMC3R. The reported ligands may serve as probes to characterize the melanocortin receptors in vivo and leads in the development of novel therapeutics.
High-speed modulation of vertical-cavity surface-emitting lasers (1991)

The IM (intensity modulation) and FM (frequency modulation) characteristics of vertical-cavity surface-emitting lasers are studied. The laser has high FM efficiency and broad IM bandwidth (near 8 GHz) at a very low bias (4.5 mA). Five Gb/s pseudorandom direct intensity modulation of this laser with open eyes is demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluating the Roomba: A low-cost, ubiquitous platform for robotics research and education (2007)

This paper presents the iRobot corporation's Roomba vacuum as a low-cost resource for robotics research and education.Sensor and actuation models for unmodified Roombas are presented in the context of both special-and general-purpose spatial-reasoning algorithms, including Monte Carlo Localization and FastSLAM.Further tests probe the feasibility of sensor extensions to the platform.Results demonstrate that, with some caveats, the Roomba is a viable foundation for both classroom and laboratory use, especially for work seeking to leverage robots to other ends, as well as robotics per se with a computational focus.
Ultimate Q of optical microsphere resonators (1996)

We demonstrate the quality factor Q - (0.8 +/- 0.1) x 10(10) of whispering-gallery modes in fused-silica microspheres at 633 nm, close to the ultimate level determined by fundamental material attenuation as measured in optical fibers. The lifetime of ultimate Q is limited by adsorption of atmospheric water. Monitoring of adsorption kinetics with submonolayer sensitivity by Q factors and frequencies of whispering-gallery modes is demonstrated. The possibility of supermaterial Q's owing to intrinsic suppression of scattering losses in micropheres is discussed.
341 nm emission from hydride vapor-phase epitaxy ultraviolet light-emitting diodes (2004)

Hydride vapor-phase epitaxy (HVPE) was used to grow aluminum gallium nitride-based p–n diode structures on sapphire (0001) substrates. In the diode structure, an n-type AlGaN photon-emitting layer was sandwiched between n-type and p-type AlGaN cladding layers that contained higher AlN concentrations. These diode structures were processed and subsequently packaged into transistor outline cans. The light-emitting diodes (LEDs) were characterized using a state-of-the-art spectroradiometer. LED spectral emission occurred at a peak wavelength of 341 nm with a typical full width at half-maximum of approximately 14 nm. Pulsed injection currents of 110 mA resulted in greater than 2 mW of optical output power at a wavelength of 341 nm. This HVPE-grown LED’s pulsed optical power output level is comparable to reported results on similar sized metalorganic chemical vapor deposition grown ultraviolet LEDs with emission wavelengths near 340 nm.
Formation of regular arrays of silicon microspikes by femtosecond laser irradiation through a mask (2003)

We report fabrication of regular arrays of silicon microspikes by femtosecond laser irradiation of a silicon wafer covered with a periodic mask. Without a mask, microspikes form, but they are less ordered. We believe that the mask imposes order by diffracting the laser beam and providing boundary conditions for capillary waves in the laser-melted silicon.
Periostin Promotes Invasion and Anchorage-Independent Growth in the Metastatic Process of Head and Neck Cancer (2006)

Head and neck squamous cell carcinoma (HNSCC) is one of the most common types of human cancer. Typically, HNSCC cells show persistent invasion that frequently leads to local recurrence and distant lymphatic metastasis. However, molecular mechanisms associated with the invasion and metastasis of HNSCC remain poorly understood. Here, we identified periostin as an invasion-promoting factor in HNSCC by comparing the gene expression profiles between parent HNSCC cells and a highly invasive clone. Indeed, periostin overexpression promoted invasion and anchorage-independent growth both in vitro and in vivo in HNSCC cells. Moreover, periostin-overexpressing cells spontaneously metastasized to cervical lymph nodes and to the lung through their aggressive invasiveness in an orthotopic mouse model of HNSCC. Interestingly, periostin was highly expressed in HNSCCs in comparison with normal tissues, and the level of periostin expression was well correlated with the invasiveness of HNSCC cases. In summary, these findings suggest that periostin plays an important role in the invasion and anchorage-independent growth of HNSCC.
Bone Health in Patients with Breast Cancer: Recommendations from an Evidence-Based Canadian Guideline (2013)

Bone loss is common in patients with breast cancer. Bone modifying agents (BMAs), such as bisphosphonates and denosumab, have been shown to reverse or stabilize bone loss and may be useful in the primary and metastatic settings. The purpose of this review is to provide clear evidence-based strategies for the management of bone loss and its symptoms in breast cancer. A systematic review of clinical trials and meta-analyses published between 1996 and 2012 was conducted of MEDLINE and EMBASE. Reference lists were hand-searched for additional publications. Recommendations were developed based on the best available evidence. Zoledronate, pamidronate, clodronate, and denosumab are recommended for metastatic breast cancer patients; however, no one agent can be recommended over another. Zoledronate or any oral bisphosphonate and denosumab should be considered in primary breast cancer patients who are postmenopausal on aromatase inhibitor therapy and have a high risk of fracture and/or a low bone mineral density and in premenopausal primary breast cancer patients who become amenorrheic after therapy. No one agent can be recommended over another. BMAs are not currently recommended as adjuvant therapy in primary breast cancer for the purpose of improving survival, although a major Early Breast Cancer Cooperative Trialists' Group meta-analysis is underway which may impact future practice. Adverse events can be managed with appropriate supportive care.
Procedures for the purification of interleukin 3 to homogeneity. (1982)

A procedure is described for the routine purification of IL 3 to homogeneity from WEHI-3-conditioned media. The techniques employed include ammonium sulfate fractionation, DEAE-cellulose, hydroxylapatite, and G-75 Sephadex column chromatography. The last step in purification involves chromatography on C18 hydrophobic supports in RP-HPLC systems, which results in the coelution of a protein peak and IL 3 activity. This purification sequence results in approximately a 1,000,000-fold purification from the initial starting material with yields of 5 to 10% of the initial activity. typically, 150 liters of conditioned media yields 2 to 10 micrograms of IL 3. The purified material was homogeneous by SDS-PAGE analysis and had an apparent m.w. of 28,000. Purified IL 3 had a specific activity of approximately 0.05 ng/unit of activity. Additional criteria used to establish the relationship of the 28,000-dalton protein to IL 3 include the ability of an antiserum against IL 3 to concomitantly immunoprecipitate the iodinated protein and to inhibit its biologic activity as well as the ability of the iodinated protein to bind specifically to cell lines known to require IL 3 for growth.
Generation of cDNA expression libraries enriched for in-frame sequences (1997)

Bacterial cDNA expression libraries are made to reproduce protein sequences present in the mRNA source tissue. However, there is no control over which frame of the cDNA is translated, because translation of the cDNA must be initiated on vector sequence. In a library of nondirectionally cloned cDNAs, only some 8% of the protein sequences produced are expected to be correct. Directional cloning can increase this by a factor of two, but it does not solve the frame problem. We have therefore developed and tested a library construction methodology using a novel vector, pKE-1, with which translation in the correct reading frame confers kanamycin resistance on the host. Following kanamycin selection, the cDNA libraries contained 60-80% open, in-frame clones. These, compared with unselected libraries, showed a 10-fold increase in the number of matches between the cDNA-encoded proteins made by the bacteria and database protein sequences. cDNA sequencing programs will benefit from the enrichment for correct coding sequences, and screening methods requiring protein expression will benefit from the enrichment for authentic translation products.
Timing of Recanalization After Tissue Plasminogen Activator Therapy Determined by Transcranial Doppler Correlates With Clinical Recovery From Ischemic Stroke (2000)

The timing of arterial recanalization after tPA therapy as determined with TCD correlates with clinical recovery from stroke and demonstrates a 300-minute window to achieve early complete recovery. These data parallel findings in animal models of cerebral ischemia and confirm the relevance of these models in the prediction of response to reperfusion therapy.
CD40 translocation to lipid rafts: Signaling requirements and downstream biological events (2011)

CD40, a member of the TNF receptor family, is expressed on a variety of immune and non-immune cells. Its interaction with its ligand, CD154, plays a pivotal role in humoral and cell-mediated immunity. A low level of CD40 is constitutively associated within membrane lipid rafts and, upon engagement, this level is significantly enhanced. In this study, our objective is to evaluate the process of CD40/lipid raft association in terms of the signals required for its initiation and the resulting biological outcomes. Here, we show the CD40/lipid raft association to be independent of PI-3-kinase, Src family kinases and p38 MAPK pathways. Moreover, CD40 lacking its intracellular domain, which is usually required for CD40-mediated signaling, still localizes to lipid rafts upon engagement, confirming that the CD40/lipid raft association is independent of signaling events. As to the biological outcomes of the CD40/lipid raft association, we show that disrupting lipid raft integrity selectively abolishes CD40-mediated Akt phosphorylation. In addition, replacing the transmembrane domain of CD40 with that of CD45 (a protein excluded from lipid rafts) dramatically reduced CD40-mediated Akt phosphorylation and B7.1 upregulation, while not influencing p38, ERK and JNK activation. Together, these findings clarify the requirements for CD40/lipid raft association and the signals triggered upon CD40 engagement by CD154.
Activity of T-DNA borders in plant cell transformation by mini-T plasmids (1986)

By using a binary vector system, we examined the requirements for border sequences in T-DNA transformation of plant genomes. Mini-T plasmids consisting of small replicons with different extents of pTiT37 T-DNA were tested for plant tumor-inducing ability in Agrobacterium tumefaciens strain LBA4404 containing helper plasmid pAL4404 (which encodes virulence genes needed for T-DNA transfer). Assays of these bacteria on carrot disks, Kalanchoë leaves, and SR1 Nicotiana tabacum plantlets showed that mini-T plasmid containing full length T-DNA including left and right borders was highly virulent, as were mini-T plasmids containing all onc (oncogenicity) genes and only the right border. In contrast, mini-T plasmids containing all onc genes and only the left border induced tumors only rarely, and a mini-T plasmid containing all onc genes but no T-DNA borders was completely avirulent. Southern hybridization analyses of tumor DNA showed that T-DNA border sequences delimited the extent of the two-border mini-T plasmid transferred and integrated into the plant genome. When only one T-DNA border was present, it formed one end of the transferred DNA, and the other end mapped in the vector sequences. The implications of these results for the mechanism of T-DNA transfer and integration are discussed.
Optical NP problem solver on laser-written waveguide platform (2018)

Cognitive photonic networks are researched to efficiently solve computationally hard problems. Flexible fabrication techniques for the implementation of such networks into compact and scalable chips are desirable for the study of new optical computing schemes and algorithm optimization. Here we demonstrate a femtosecond laser-written optical oracle based on cascaded directional couplers in glass, for the solution of the Hamiltonian path problem. By interrogating the integrated photonic chip with ultrashort laser pulses, we were able to distinguish the different paths traveled by light pulses, and thus infer the existence or the absence of the Hamiltonian path in the network by using an optical correlator. This work proves that graph theory problems may be easily implemented in integrated photonic networks, down scaling the net size and speeding up execution times.
N-Acetylglutamate and its changing role through evolution (2003)

N -Acetylglutamate (NAG) fulfils distinct biological roles in lower and higher organisms. In prokaryotes, lower eukaryotes and plants it is the first intermediate in the biosynthesis of arginine, whereas in ureotelic (excreting nitrogen mostly in the form of urea) vertebrates, it is an essential allosteric cofactor for carbamyl phosphate synthetase I (CPSI), the first enzyme of the urea cycle. The pathway that leads from glutamate to arginine in lower organisms employs eight steps, starting with the acetylation of glutamate to form NAG. In these species, NAG can be produced by two enzymic reactions: one catalysed by NAG synthase (NAGS) and the other by ornithine acetyltransferase (OAT). In ureotelic species, NAG is produced exclusively by NAGS. In lower organisms, NAGS is feedback-inhibited by L-arginine, whereas mammalian NAGS activity is significantly enhanced by this amino acid. The NAGS genes of bacteria, fungi and mammals are more diverse than other arginine-biosynthesis and urea-cycle genes. The evolutionary relationship between the distinctly different roles of NAG and its metabolism in lower and higher organisms remains to be determined. In humans, inherited NAGS deficiency is an autosomal recessive disorder causing hyperammonaemia and a phenotype similar to CPSI deficiency. Several mutations have been recently identified in the NAGS genes of families affected with this disorder.
Phytochrome A, phytochrome B and other phytochrome(s) regulate ATHB‐2 gene expression in etiolated and green Arabidopsis plants (1997)

ABSTRACT The expression of the Arabidopsis ATHB‐2 gene is light‐regulated both in seedlings and in adult plants. The gene is expressed at high levels in rapidly elongating etiolated seedlings and is down‐regulated by a pulse of red light (R) through the action of a phytochrome other than phytochrome A or B, or by a pulse of far‐red light (FR) through the action of phytochrome A. In green plants, the expression of the ATHB‐2 gene is rapidly and strongly enhanced by lowering the R:FR ratio perceived by a phytochrome other than A or B. Returning the plant to a high R:FR ratio results in an equally rapid decrease of the ATHB‐2 mRNA. Consistently, plants overproducing ATHB‐2 show developmental phenotypes characteristic of plants grown in low R:FR: elongated petioles, reduced leaf area, early flowering, and reduced number of rosette leaves. Taken together, the data strongly suggest a direct involvement of ATHB‐2 in light‐regulated growth phenomena throughout Arabidopsis development.
Cyclosporin A, FK-506, and Rapamycin: Pharmacologic Probes of Lymphocyte Signal Transduction (1992)

CsA, FK-506, and rapamycin are microbial products with potent immunosuppressive properties that result primarily from a selective inhibition of T lymphocyte activation. Although chemically unrelated, CsA and FK-506 affect a similar subset of calcium-associated signaling events involved in the regulation of lymphokine gene expression, activation-driven T-cell death and exocytosis. Rapamycin has structural similarity with FK-506 but suppresses T-cell activation at a different level, mainly through inhibition of proliferation induced by growth-promoting lymphokines. CsA interacts with an abundant 17 kDa protein, termed cyclophilin, that possesses peptidyl-prolyl cis-trans isomerase (PPIase) activity. Additional, minor cyclophilin-like molecules have been identified. Both FK-506 and rapamycin interact with FKBP, a 12 kDa protein, which, although unrelated to cyclophilin, is also abundant and ubiquitous, has a similar enzymatic activity, and is a member of a larger family of FKBPs. All three immunosuppressants inhibit the PPIase activity of their respective binding proteins. However, nonimmunosuppressive analogs of CsA and FK-506 are also inhibitory, indicating that inhibition of PPIase activity is not directly implicated in immunosuppression. Moreover, only a small fraction of the cellular pool of the major forms of cyclophilin or FKBP needs to be occupied by the drugs in order to achieve maximal immunosuppression. These observations suggest that complexes formed between the drugs and their major binding proteins may affect the function of other, unidentified, molecules or, alternatively, that minor binding proteins may play a role in the drugs' action. Further characterization of the biochemical processes altered by CsA, FK-506, and rapamycin should yield important insights into the signal transduction pathways involved in T-cell activation and should help in the development of novel immunosuppressive agents.