gebhart/patrepeval huggingface dataset:
Molecular Cloning and Partial Characterization of a Novel Collagen Chain, αl(XVI), Consisting of Repetitive Collagenous Domains and Cysteine-Containing Non-Collagenous Segments (1992)

In an effort to identify new members of the collagen family, we screened a human placenta cDNA library with a collagenous probe. A novel 3.7 kb cDNA was identified encoding an open reading frame of 1,186 amino acids and containing a termination codon. The predicted polypeptide consists of 9 repetitive collagenous (stretches of Gly-X-Y) and several non-collagenous segments. Two cysteinyl residues separated by two amino acid residues (Cys-X-X-Cys) are regularly located in the N-terminal region of each non-collagenous segment. The deduced amino acid sequence described above is distinct from those of known types of collagen. Therefore, this novel collagen chain is designated alpha 1(XVI). Northern blot analysis revealed an alpha 1(XVI) mRNA of 5.2 kb, indicating that the overlapping cDNA clones isolated in this study covered nearly three-fourths of the mRNA. As a tool for further study on the expression of type XVI collagen, we prepared an antibody against the nonadecapeptide CFLSLERPRAEEARGDNSE, derived from the putative translation product of the cDNA. In immunoblot analysis, the antibody recognized a 160 kDa protein, which was bacterial collagenase-sensitive. Immunohistochemical stainings of human placental tissues with anti-peptide antibody revealed a positive reaction with amnion, the membranous tissue lining the amniotic cavity. The gene of alpha 1(XVI) chain, COL16A1, is mapped on the short arm of human chromosome 1 (1p13-p34).
Patient Considerations in the Management of Rheumatoid Arthritis: Role of Once-A-Month Golimumab Injection (2011)

Golimumab (GLM) is a fully human monoclonal antibody with amino acid sequences of the light and heavy chains identical to those of infliximab, that binds specifically to both the soluble and transmembrane bioactive forms of human TNF-α, thereby inhibiting the biological activity of TNF. GLM was studied in an extensive program of RCTs that included one study in phase I and one in phase II, and studies in phase III including patients failing MTX (GO-FORWARD), failing other anti TNF (GO-AFTER), MTX naïve patients (GO-BEFORE), and one study with IV GLM in patients that remained active in spite of receiving MTX. These studies showed that GLM is effective and safe for the treatment of RA, with a efficacy and safety profile very similar to the other classic anti TNF biologics, and determined the approval by the FDA in April 2009 for use in moderately-to-severely active RA in combination with methotrexate (MTX) when given to adults. In comparison to other biologics for RA, GLM has some advantages: first, it's less frequent administration (every 4 weeks); and second, its subcutaneous route of administration, which allows patients to self administer the drug at home. Currently, GLM represents an option to RA active patients desiring less frequent injections and to patients in whom the previous treatment with other TNF-α inhibitors failed.
Phenotypic comparison of periodontal ligament cells in vivo and in vitro (2001)

The mammalian periodontal ligament contains heterogeneous populations of connective tissue cells, the precise function of which is poorly understood. Despite close proximity to bone and the application of high amplitude physical forces, cells in the periodontal ligament (PL) are capable of expressing regulatory factors that maintain PL width during adult life. The study of PL homeostasis and PL cell differentiation requires culture and phenotypic methods for precise characterization of PL cell populations, in particular those cells with an inherently osteogenic program. Currently it is unknown if cells cultured from the PL are phenotypically similar to the parental cells that are present in the tissues. We have compared the phenotype of cells in vivo with cells derived from the PL and expanded in vitro to assess the general validity of in vitro models for the study of phenotypic regulation in vivo. Rat PL cells were isolated by either scraping the root of the extracted first mandibular molars (Group A), or by scraping the alveolar socket following extraction of first mandibular molars (Group B), or by obtaining a mixture of cells after disaggregating a block of tissue consisting of first mandibular molar, PL and the surrounding alveolar bone (Group C). Cultured cells at confluence were fixed and immunostained for alpha-smooth muscle actin (alpha-SMA), osteopontin (OPN), alkaline phosphatase (AP), or bone sialoprotein (BSP). For in vivo assessments, frontal sections of rat first mandibular molar were immunostained for alpha-SMA, OPN, AP and BSP. We examined osteogenic differentiation of cultured PL cell cultures by bone nodule-forming assays. In vivo and at all examined sites, > 68% of PL cells were immunostained for AP; approximately 50% and approximately 51% for OPN and alpha-SMA (p = 0.3), respectively, while only approximately 8% were positively stained for BSP (p < 0.01). Analysis of cultured PL cells in Groups A, B and C showed 54%, 53%, and 56% positive staining for alpha-SMA respectively; 51%, 56%, 54% for OPN; 66%, 70%, 69% for AP and 2.2%, 1.4% and 2.8% for BSP. The mean percentage of PL cells in situ stained for the different markers was similar to that of cultured PL cells (Group A approximately Group B approximately Group C in situ for p > 0.2) except for BSP which was 3 to 4 fold higher in vitro (p < 0.01). PL cell cultures treated with dexamethasone showed mineralized tissue formation for all groups (A, B, C), but no mineralized tissue formation was detected in the absence of dexamethasone. As PL cells express quantitatively similar phenotypes in vitro and in vivo, we conclude that the in vitro models used here for assessment of PL cell differentiation appear to be appropriate and are independent of the cell sampling method. Further, dexamethasone-dependent progenitors are present both on the root and bone-related sides of the PL.
Patterning of Layer-by-Layer Self-Assembled Multiple Types of Nanoparticle Thin Films by Lithographic Technique (2002)

A lithographic approach to generate clean patterns of multiple types of nanoparticles on one 4-inch silicon wafer is demonstrated in this paper. Each type of nanoparticle is precisely directed to the desired location. The process is mainly based on conventional microelectronic techniques with extremely high reproducibility. This enables the possibility of industrial applications to fabricate devices made of nanocrystals. A thin film of polystyrene spheres, 150 nm in diameter, was first coated on the silicon wafer with layer-by-layer self-assembly, followed by a layer of aluminum deposited on the thin film. A layer of positive photoresist was spun on the surface of aluminum and then patterned by lithographic technique. The unprotected aluminum was removed by wet etching until the polystyrene thin film underneath was exposed to the air. Oxygen plasma was employed to etch the polystyrene thin film all the way to the silicon surface. Subsequently, a thin film of another type of nanoparticle, silica particle 78 nm in diameter, was adsorbed onto the surface with layer-by-layer self-assembly. Eventually, aluminum and photoresist were removed and each type of nanoparticle was located next to each other as the pattern was designed. A scanning electron microscope was used to produce the image of the pattern.
Introduction: A Principaled Approach (2018)

This introduction highlights the collaboration between Bank Street College and the New York City Board of Education who developed an approach to preparing principals that has proved highly effective. Wasley and Rizzo briefly describe the program's history and its evolution, and concludes by analyzing why it has worked so well and what they would do to further strengthen the approach.
A Molecular Switch Controlling Competence and Motility: Competence Regulatory Factors ComS, MecA, and ComK Control ς D -Dependent Gene Expression in Bacillus subtilis (1998)

Bacillus subtilis, like many bacteria, will choose among several response pathways when encountering a stressful environment. Among the processes activated under growth-restricting conditions are sporulation, establishment of motility, and competence development. Recent reports implicate ComK and MecA-ClpC as part of a system that regulates both motility and competence development. MecA, while negatively controlling competence by inhibiting ComK, stimulates sigmaD-dependent transcription of genes that function in motility and autolysin production. Both ComK-dependent and -independent pathways have been proposed for MecA's role in the regulation of motility. Mutations in mecA reduce the transcription of hag. encoding flagellin, and are partially suppressed by comK in both medium promoting motility and medium promoting competence. Reduced sigmaD levels are observed in mecA mutants grown in competence medium, but no change in sigmaD concentration is detected in a comK mutant. The comF operon, transcription of which requires ComK, is located immediately upstream of the operon that contains the flgM gene, encoding the sigmaD-specific antisigma factor. An insertion mutation that disrupts the putative comF-flgM transcription unit confers a phenotype identical to that of the comK mutant with respect to hag-lacZ expression. Expression of a flgM-lacZ operon fusion is reduced in both sigD and comK mutant cells but is abolished in the sigD comK double mutant. Reverse transcription-PCR examination of the comF-flgM transcript indicates that readthrough from comF into the flgM operon is dependent on ComK. ComK negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity. There likely exists another comK-independent mechanism of hag transcription that requires mecA and possibly affects the sigmaD concentration in cells undergoing competence development.
Investigations with monoclonal antibody drug (anthracycline) conjugates. (1988)

The development of monoclonal antibody-drug (anthracycline) conjugates (immunocytostatics) that has emerged during the last decade is briefly reviewed. Stress is layed on the various procedures that have been employed for the chemical attachment of daunorubicin (daunomycin) and doxorubicin (adriamycin) to spacers, high-molecular weight carrier molecules, and immunoglobulins. Anthracycline conjugates that have proved effective in mice with respect to the treatment of cancer are especially evaluated. Also a new method developed for the conjugation of rhodosaminyl anthracyclinones via a hydrolysable spacer, developed in our laboratories, is briefly communicated. Finally, import aspects for further developments of monoclonal antibody-drug conjugates are discussed.
Human promyelocytic leukemia HL-60 cell proliferation and c-myc protein expression are inhibited by an antisense pentadecadeoxynucleotide targeted against c-myc mRNA. (1988)

The human promyelocytic leukemia cell line HL-60 overexpresses the c-myc protooncogene. A calculated secondary structure for c-myc mRNA placed the initiation codon in a bulge of a weakly base-paired region. Treatment of HL-60 cells with 5' d(AACGTTGAGGGGCAT) 3', complementary to the initiation codon and the next four codons of c-myc mRNA, inhibited c-myc protein expression in a dose-dependent manner. However, treatment of HL-60 cells with 5' d(TTGGGATAACACTTA) 3', complementary to nucleotides 17-31 of vesicular stomatitis virus matrix protein mRNA, displayed no such effects. These results agree with analogous studies of normal human T lymphocytes [Heikkila, R., Schwab, G., Wickstrom, E., Loke, S. L., Pluznik, D. H., Watt, R. & Neckers, L. M. (1987) Nature (London) 328, 445-449], except that only one-third as much oligomer was needed for a comparable effect. Proliferation of HL-60 cells in culture was inhibited in a sequence-specific, dose-dependent manner by the c-myc-complementary oligomer, but neither the oligomer complementary to vesicular stomatitis virus matrix protein mRNA nor 5' d(CATTTCTTGCTCTCC) 3', complementary to nucleotides 5399-5413 of human immunodeficiency virus tat gene mRNA, inhibited proliferation. It thus appears that antisense oligodeoxynucleotides added to myc-transformed cells via culture medium are capable of eliciting sequence-specific, dose-dependent inhibition of c-myc protein expression and cell proliferation.
The Recombinational Anatomy of a Mouse Chromosome (2008)

Among mammals, genetic recombination occurs at highly delimited sites known as recombination hotspots. They are typically 1-2 kb long and vary as much as a 1,000-fold or more in recombination activity. Although much is known about the molecular details of the recombination process itself, the factors determining the location and relative activity of hotspots are poorly understood. To further our understanding, we have collected and mapped the locations of 5,472 crossover events along mouse Chromosome 1 arising in 6,028 meioses of male and female reciprocal F1 hybrids of C57BL/6J and CAST/EiJ mice. Crossovers were mapped to a minimum resolution of 225 kb, and those in the telomere-proximal 24.7 Mb were further mapped to resolve individual hotspots. Recombination rates were evolutionarily conserved on a regional scale, but not at the local level. There was a clear negative-exponential relationship between the relative activity and abundance of hotspot activity classes, such that a small number of the most active hotspots account for the majority of recombination. Females had 1.2x higher overall recombination than males did, although the sex ratio showed considerable regional variation. Locally, entirely sex-specific hotspots were rare. The initiation of recombination at the most active hotspot was regulated independently on the two parental chromatids, and analysis of reciprocal crosses indicated that parental imprinting has subtle effects on recombination rates. It appears that the regulation of mammalian recombination is a complex, dynamic process involving multiple factors reflecting species, sex, individual variation within species, and the properties of individual hotspots.
Effect of hepcidin on intestinal iron absorption in mice (2004)

The effect of the putative iron regulatory peptide hepcidin on iron absorption was investigated in mice. Hepcidin peptide was synthesized and injected into mice for up to 3 days, and in vivo iron absorption was measured with tied-off segments of duodenum. Liver hepcidin expression was measured by reverse transcriptase-polymerase chain reaction. Hepcidin significantly reduced mucosal iron uptake and transfer to the carcass at doses of at least 10 microg/mouse per day, the reduction in transfer to the carcass being proportional to the reduction in iron uptake. Synthetic hepcidin injections down-regulated endogenous liver hepcidin expression excluding the possibility that synthetic hepcidin was functioning by a secondary induction of endogenous hepcidin. The effect of hepcidin was significant at least 24 hours after injection of hepcidin. Liver iron stores and hemoglobin levels were unaffected by hepcidin injection. Similar effects of hepcidin on iron absorption were seen in iron-deficient and Hfe knockout mice. Hepcidin inhibited the uptake step of duodenal iron absorption but did not affect the proportion of iron transferred to the circulation. The effect was independent of iron status of mice and did not require Hfe gene product. The data support a key role for hepcidin in the regulation of intestinal iron uptake.
Modelling of Viscous Squeeze-Film Damping and the Edge Correction for Perforated Microstructures Having a Special Pattern of Holes (2007)

This paper contains an analysis of the squeeze-film damping in micro-electromechanical devices having a planar microstructure containing a repetitive pattern of oval holes. The planar microstructures containing oval holes assure a better protection against dust particles and water drops than the microstructures having circular holes. Consequently, they should be preferred in designing protective surfaces for microphones working in natural environment. Analytical formulas are provided for designing a planar microstructure with a periodic system of staggered holes to create a structure having minimum squeeze-film damping with an assigned open area. For the planar microstructures containing aligned oval holes an edge correction is given which accounts for the finite size of real structures.
Reconstruction of the Characteristic Modes on an Antenna Based on the Radiated Far Field (2013)

In this paper, we present a method to reconstruct the modal current distribution on an antenna from the radiated far field and general knowledge about the modes involved. The method leads to good results if the radiation mechanism of the antenna can be approximated by the current distribution on a simplified structure. The current distribution of the simplified structure is decomposed into its characteristic modes and the related modal far field is calculated. Assuming that the far field of the actual antenna contains the same modes, their weighting coefficients are calculated by comparing the far field of the actual antenna to the modal far field of the simplified structure. It can be shown that the weighting coefficients of all significant modes can be reconstructed with good accuracy even for complex real structures such as mobile phones.
Antisense RNA to eIF4E Suppresses Oncogenic Properties of a Head and Neck Squamous Cell Carcinoma Cell Line (2000)

Antisense RNA therapy to eIF4E can potentially be used as adjuvant therapy for head and neck cancers, particularly in cases in which elevated eIF4E is found in the surgical margins.
DNA Fingerprinting ofMycobacterium tuberculosis: Lessons Learned and Implications for the Future (2002)

DNA fingerprinting of Mycobacterium tuberculosis--a relatively new laboratory technique--offers promise as a powerful aid in the prevention and control of tuberculosis (TB). Established in 1996 by the Centers for Disease Control and Prevention (CDC), the National Tuberculosis Genotyping and Surveillance Network was a 5-year prospective, population-based study of DNA fingerprinting conducted from 1996 to 2000. The data from this study suggest multiple molecular epidemiologic and program management uses for DNA fingerprinting in TB public health practice. From these data, we also gain a clearer understanding of the overall diversity of M. tuberculosis strains as well as the presence of endemic strains in the United States. We summarize the key findings and the impact that DNA fingerprinting may have on future approaches to TB control. Although challenges and limitations to the use of DNA fingerprinting exist, the widespread implementation of the technique into routine TB prevention and control practices appears scientifically justified.
Update and Analysis of the University College London Low Density Lipoprotein Receptor Familial Hypercholesterolemia Database (2008)

Familial hypercholesterolemia (FH) (OMIM 143890) is most commonly caused by variations in the LDLR gene which encodes the receptor for Low Density Lipoprotein (LDL) cholesterol particles. We have updated the University College London (UCL) LDLR FH database (http://www.ucl.ac.uk/ldlr) by adding variants reported in the literature since 2001, converting existing entries to standard nomenclature, and transferring the database to the Leiden Open Source Variation Database (LOVD) platform. As of July 2007 the database listed 1066 unique LDLR gene events. Sixty five percent (n = 689) of the variants are DNA substitutions, 24% (n = 260) small DNA rearrangements (<100bp) and 11% (n = 117) large DNA rearrangements (>100bp), proportions which are similar to those reported in the 2001 database (n = 683, 62%, 24% and 14% respectively). The DNA substitutions and small rearrangements occur along the length of the gene, with 24 in the promoter region, 86 in intronic sequences and 839 in the exons (93 nonsense variants, 499 missense variants and 247 small rearrangements). These occur in all exons, with the highest proportion (20%) in exon 4 (186/949); this exon is the largest and codes for the critical ligand binding region, where any missense variant is likely to be pathogenic. Using the PolyPhen and SIFT prediction computer programmes 87% of the missense variants are predicted to have a deleterious effect on LDLR activity, and it is probable that at least 48% of the remainder are also pathogenic, but their role in FH causation requires confirmation by in vitro or family studies.
ISO/IEC MPEG-4 High-Definition Scalable Advanced Audio Coding (2007)

Recently the MPEG Audio standardization group has successfully concluded the standardization process on technology for lossless coding of audio signals. A summary of the scalable lossless coding (SLS) technology as one of the results of this standardization work is given. MPEG-4 scalable lossless coding provides a fine-grain scalable lossless extension of the well-known MPEG-4 AAC perceptual audio coder up to fully lossless reconstruction at word lengths and sampling rates typically used for high-resolution audio. The underlying innovative technology is described in detail and its performance is characterized for lossless and near lossless representation, both in conjunction with an AAC coder and as a stand-alone compression engine. A number of application scenarios for the new technology are discussed.
The Immunosuppressant Rapamycin Mimics a Starvation-Like Signal Distinct from Amino Acid and Glucose Deprivation (2002)

RAFT1/FRAP/mTOR is a key regulator of cell growth and division and the mammalian target of rapamycin, an immunosuppressive and anticancer drug. Rapamycin deprivation and nutrient deprivation have similar effects on the activity of S6 kinase 1 (S6K1) and 4E-BP1, two downstream effectors of RAFT1, but the relationship between nutrient- and rapamycin-sensitive pathways is unknown. Using transcriptional profiling, we show that, in human BJAB B-lymphoma cells and murine CTLL-2 T lymphocytes, rapamycin treatment affects the expression of many genes involved in nutrient and protein metabolism. The rapamycin-induced transcriptional profile is distinct from those induced by glucose, glutamine, or leucine deprivation but is most similar to that induced by amino acid deprivation. In particular, rapamycin treatment and amino acid deprivation up-regulate genes involved in nutrient catabolism and energy production and down-regulate genes participating in lipid and nucleotide synthesis and in protein synthesis, turnover, and folding. Surprisingly, however, rapamycin had effects opposite from those of amino acid starvation on the expression of a large group of genes involved in the synthesis, transport, and use of amino acids. Supported by measurements of nutrient use, the data suggest that RAFT1 is an energy and nutrient sensor and that rapamycin mimics a signal generated by the starvation of amino acids but that the signal is unlikely to be the absence of amino acids themselves. These observations underscore the importance of metabolism in controlling lymphocyte proliferation and offer a novel explanation for immunosuppression by rapamycin.