gebhart/patrepeval huggingface dataset:
HAD, a Data Bank of Heavy-Atom Binding Sites in Protein Crystals: a Resource for Use in Multiple Isomorphous Replacement and Anomalous Scattering (1998)

Information on the preparation and characterization of heavy-atom derivatives of protein crystals has been collected, either from the literature or directly from protein crystallographers, and assembled in the form of a heavy-atom data bank (HAD). The data bank contains coordinate data for the heavy-atom positions in a form that is compatible with the crystallographic data in the Brookhaven Protein Data Bank, together with a wealth of information on the crystallization conditions, the nature of the heavy-atom reagent and references to relevant publications. Some statistical information derived from the data bank, such as the most popular heavy-atom derivatives, is also included. The information can be directly accessed and should be useful to protein crystallographers seeking to improve their success in preparing heavy-atom derivatives for the methods of isomorphous replacement and anomalous dispersion. The World Wide Web address of HAD is http://www.icnet.uk/bmm/had.
Identification and characterization of small RNAs involved in RNA silencing (2005)

Double-stranded RNA (dsRNA) is a potent trigger of sequence-specific gene silencing mechanisms known as RNA silencing or RNA interference. The recognition of the target sequences is mediated by ribonucleoprotein complexes that contain 21- to 28-nucleotide (nt) guide RNAs derived from processing of the trigger dsRNA. Here, we review the experimental and bioinformatic approaches that were used to identify and characterize these small RNAs isolated from cells and tissues. The identification and characterization of small RNAs and their expression patterns is important for elucidating gene regulatory networks.
DRM protected dynamic adaptive HTTP streaming (2011)

Dynamic adaptive HTTP streaming (DASH) is a new concept for video streaming using consecutive downloads of short video segments. 3GPP has developed the basic DASH standard which is further extended by the Open IPTV Forum (OIPF) and MPEG. In all versions available to date, only very simple content protection use cases are enabled. Extensions are needed to enable important advanced use cases like pay-per-view and license change in an ongoing video channel.
Neurocardiac Responses to Vagoafferent Electrostimulation in Humans (1992)

(1) A relationship exists between selective vagal nerve electrostimulation and the HRA; and (2) high stimulation frequency of the vagus nerve in man is associated with sustained augmentation of cardiac vagal tone throughout a 24-hour cycle.
Low Prevalence of Somatic TERT Promoter Mutations in Classic Papillary Thyroid Carcinoma (2016)

The prevalence of somatic TERT promoter mutations was low in Korean patients with classic PTC. Therefore, the prognostic role of TERT promoter mutations might be limited in this patient cohort.
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays (2000)

Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel method for genotyping single nucleotide polymorphisms (SNPs), using generic high-density oligonucleotide arrays that contain thousands of preselected 20-mer oligonucleotide tags. First, marker-specific primers are used in PCR amplifications of genomic regions containing SNPs. Second, the amplification products are used as templates in single base extension (SBE) reactions using chimeric primers with 3' complementarity to the specific SNP loci and 5' complementarity to specific probes, or tags, synthesized on the array. The SBE primers, terminating one base before the polymorphic site, are extended in the presence of labeled dideoxy NTPs, using a different label for each of the two SNP alleles, and hybridized to the tag array. Third, genotypes are deduced from the fluorescence intensity ratio of the two colors. This approach takes advantage of multiplexed sample preparation, hybridization, and analysis at each stage. We illustrate and test this method by genotyping 44 individuals for 142 human SNPs identified previously in 62 candidate hypertension genes. Because the hybridization results are quantitative, this method can also be used for allele-frequency estimation in pooled DNA samples.
In vivo targeting of SF/HGF and c‐met expression via U1snRNA/ribozymes inhibits glioma growth and angiogenesis and promotes apoptosis (2001)

The multifunctional growth factor scatter factor/hepatocyte growth factor (SF/HGF) and its receptor c-met have been implicated in the genesis, malignant progression, and chemo/radioresistance of multiple human malignancies, including gliomas. We examined the antitumor effects of targeting SF/HGF and c-met expression in pre-established glioma xenografts by using novel chimeric U1snRNA/ribozymes. Transient expression of anti-SF/HGF and anti-c-met U1snRNA/ribozymes inhibited SF/HGF and c-met expression, c-met receptor activation, tumor cell migration, and anchorage-independent colony formation in vitro. Delivery of U1snRNA/ribozymes to established subcutaneous glioma xenografts via liposome-DNA complexes significantly inhibited tumor growth as well as tumor SF/HGF and c-met expression levels. Histologic analysis of tumors treated with U1snRNA/ribozymes showed a significant decrease in blood vessel density, an increase in activation of the pro-apoptotic enzyme caspase-3, and an increase in tumor cell apoptosis. Treatment of animals bearing intracranial glioma xenografts with anti-SF/HGF and anti-c-met U1snRNA/ribozymes by either intratumoral injections of adenoviruses expressing the transgenes or intravenous injections of U1snRNA/ribozyme-liposome complexes substantially inhibited tumor growth and promoted animal survival. We demonstrate that SF/HGF and/or c-met expression can be targeted in vivo to inhibit tumor growth. In addition, our findings represent the first in vivo application of chimeric U1snRNA/ribozymes, which have numerous potential therapeutic gene-targeting applications.
Isolation and Characterization of Tetracycline-Resistant Clinical Isolates of Helicobacter pylori (2000)

Tetracycline is an important component of combination therapies for Helicobacter pylori eradication. Twenty-nine tetracycline-resistant isolates requiring MICs ranging from 4 to 16 microgram/ml were isolated from Korean (22 of 460) and Japanese (7 of 105) patients. Interestingly, all of the 29 tetracycline-resistant isolates exhibited cross-resistance to metronidazole, and the cross-resistance was transferred to tetracycline-sensitive H. pylori strains.
Antigen 43-Mediated Autotransporter Display, a Versatile Bacterial Cell Surface Presentation System (2002)

Antigen 43 (Ag43), a self-recognizing outer membrane protein of Escherichia coli, has been converted into an efficient and versatile tool for surface display of foreign protein segments. Ag43 is an autotransporter protein characterized by the feature that all information required for transport to the outer membrane and secretion through the cell envelope is contained within the protein itself. Ag43 consists of two subunits (alpha and beta), where the beta-subunit forms an integral outer membrane translocator to which the alpha-subunit is noncovalently attached. The simplicity of the Ag43 system makes it ideally suited as a surface display scaffold. Here we demonstrate that the Ag43 alpha-module can accommodate and display correctly folded inserts and has the ability to display entire functional protein domains, exemplified by the FimH lectin domain. The presence of heterologous cysteine bridges does not interfere with surface display, and Ag43 chimeras are correctly processed into alpha- and beta-modules, offering optional and easy release of the chimeric alpha-subunits. Furthermore, Ag43 can be displayed in many gram-negative bacteria. This feature is exploited for display of our chimeras in an attenuated Salmonella strain.
Multicarbocycle Formation Mediated by Arenoporphyrin 1,4-Diradicals: Synthesis of Picenoporphyrins (2001)

Bergman cyclization of 2,3-dialkynyl-meso-tetraphenylporphyrins and carbon-carbon bond formation (mediated by 1,4-diradicals) with the adjacent meso-phenyl rings lead to formation of an unprecedented multicarbocycle fused onto the porphyrin periphery. The highly π-extended parent molecules (1; R = Bu, H, Ph) are described and are named picenoporphyrins after their [5]phenacene structure.
Effects of Heat Shock on Amino Acid Metabolism of Cowpea Cells (1990)

When cowpea (Vigna unguiculata) cells maintained at 26 degrees C are transferred to 42 degrees C, rapid accumulation of gamma-aminobutyrate (>10-fold) is induced. Several other amino acids (including beta-alanine, alanine, and proline) are also accumulated, but less extensively than gamma-aminobutyrate. Total free amino acid levels are increased approximately 1.5-fold after 24 hours at 42 degrees C. Heat shock also leads to release of amino acids into the medium, indicating heat shock damage to the integrity of the plasmalemma. Some of the changes in metabolic rates associated with heat shock were estimated by monitoring the (15)N labeling kinetics of free intracellular, extracellular and protein-bound amino acids of cultures supplied with (15)NH(4) (+), and analyzing the labeling data by computer simulation. Preliminary computer simulation models of nitrogen flux suggest that heat shock induces an increase in the gamma-aminobutyrate synthesis rate from 12.5 nanomoles per hour per gram fresh weight in control cells maintained at 26 degrees C, to as high as 800 nanomoles per hour per gram fresh weight within the first 2 hours of heat shock. This 64-fold increase in the gamma-aminobutyrate synthesis rate greatly exceeds the expected (Q(10)) change of metabolic rate of 2.5- to 3-fold due to a 16 degrees C increase in temperature. We suggest that this metabolic response may in part involve an activation of glutamate decarboxylase in vivo, perhaps mediated by a transient cytoplasmic acidification. Proline appears to be synthesized from glutamate and not from ornithine in cowpea cells. Proline became severalfold more heavily labeled than ornithine, citrulline and arginine in both control and heat-shocked cultures. Proline synthesis rate was increased 2.7-fold by heat shock. Alanine, beta-alanine, valine, leucine, and isoleucine synthesis rates were increased 1.6-, 3.5-, 2.0-, 5.0-, and 6.0-fold, respectively, by heat shock. In contrast, the phenylalanine synthesis rate was decreased by 50% in response to heat shock. The differential effects of heat stress on metabolic rates lead to flux and pool size redistributions throughout the entire network of amino acid metabolism.
Improvements of ModalMax High-Fidelity Piezoelectric Audio Device (2005)

ModalMax audio speakers have been enhanced by innovative means of tailoring the vibration response of thin piezoelectric plates to produce a high-fidelity audio response. The ModalMax audio speakers are 1 mm in thickness. The device completely supplants the need to have a separate driver and speaker cone. ModalMax speakers can perform the same applications of cone speakers, but unlike cone speakers, ModalMax speakers can function in harsh environments such as high humidity or extreme wetness. New design features allow the speakers to be completely submersed in salt water, making them well suited for maritime applications. The sound produced from the ModalMax audio speakers has sound spatial resolution that is readily discernable for headset users.
Mapping of the Interaction Site between Sortilin and the p75 Neurotrophin Receptor Reveals a Regulatory Role for the Sortilin Intracellular Domain in p75 Neurotrophin Receptor Shedding and Apoptosis (2012)

Neurotrophins comprise a group of neuronal growth factors that are essential for the development and maintenance of the nervous system. However, the immature pro-neurotrophins promote apoptosis by engaging in a complex with sortilin and the p75 neurotrophin receptor (p75(NTR)). To identify the interaction site between sortilin and p75(NTR), we analyzed binding between chimeric receptor constructs and truncated p75(NTR) variants by co-immunoprecipitation experiments, surface plasmon resonance analysis, and FRET. We found that complex formation between sortilin and p75(NTR) relies on contact points in the extracellular domains of the receptors. We also determined that the interaction critically depends on an extracellular juxtamembrane 23-amino acid sequence of p75(NTR). Functional studies further revealed an important regulatory function of the sortilin intracellular domain in p75(NTR)-regulated intramembrane proteolysis and apoptosis. Thus, although the intracellular domain of sortilin does not contribute to p75(NTR) binding, it does regulate the rates of p75(NTR) cleavage, which is required to mediate pro-neurotrophin-stimulated cell death.
XPAND: an efficient test stimulus compression technique (2006)

Combinational circuits implemented with exclusive-or gates are used for on-chip generation of deterministic test patterns from compressed seeds. Unlike major test compression techniques, this technique doesn't require test pattern generation with don't cares. Experimental results on industrial designs demonstrate that this new XPAND technique achieves exponential reduction in test data volume and test time compared to traditional scan and significantly outperforms existing test compression tools. The XPAND technique is currently being used by several industrial designs.
Fcγreceptor-mediated phagocytosis ofPlasmodium falciparum-infected erythrocytesin vitro (2002)

Although convincing evidence exists for the role of immunoglobulin G (IgG) antibodies in immunity to malaria, antibody titres do not usually predict protection. In this study we have assessed the interaction between Plasmodium falciparum-infected erythrocytes (PE), opsonized with immune serum containing different amounts of IgG antibody isotypes, with either THP-1 cells, ex-vivo human monocytes or IIAI.6 transfectant cells expressing Fc(gamma)RIIa-Arg/Arg131 or -His/His131 allotypes. Our results show that PMA-treated THP-1 cells were capable of phagocytosing serum-opsonized PE by Fc(gamma)RI (CD64) and Fc(gamma)RIIa (CD32), acting synergistically. The known Fc(gamma)RIIa polymorphism motivated us to examine its influence on IgG isotype-mediated phagocytosis of opsonized PE with human monocytes and the IIAI.6 transfectant cells expressing either allelic forms. Regardless of the cell type, PE phagocytosis with Fc(gamma)RIIa-His/His131 was highest following opsonization with a predominantly IgG3-containing immune serum pool. In contrast, PE phagocytosis with Fc(gamma)RIIa-Arg/Arg131 tended to be higher with an IgG1-containing pool. These results suggest a genetically determined influence of effector cell phenotype on IgG antibody-pathogen interaction in P. falciparum malaria.
Molecular magnetic materials based on 4d and 5d transition metals (2011)

The study of paramagnetic compounds based on 4d and 5d transition metals is an emerging research topic in the field of molecular magnetism. An essential driving force for the interest in this area is the fact that heavier metal ions introduce important attributes to the physical properties of paramagnetic compounds. Among the attractive characteristics of heavier elements vis-à-vis magnetism are the diffuse nature of their d orbitals, their strong magnetic anisotropy owing to enhanced spin-orbit coupling, and their diverse structural and redox properties. This critical review is intended to introduce readers to the topic and to report recent progress in this area. It is not fully comprehensive in scope although we strived to include all relevant topics and a large subset of references in the area. Herein we provide a survey of the history and current status of research that has been conducted on the topic of second and third row transition metal molecular magnetism. The article is organized according to the nature of the precursor building blocks with special topics being highlighted as illustrations of the special role of heavier transition metal ions in the field. This paper is addressed to readers who are interested in molecular magnetism and the application of coordination chemistry principles to materials synthesis (231 references).
High-Yield Assembly of Individual Single-Walled Carbon Nanotube Tips for Scanning Probe Microscopies (2001)

The structural and mechanical properties of single-walled carbon nanotubes (SWNTs) make them ideal tips for scanning probe microscopies such as atomic force microscopy (AFM). However, the ideal nanotube probe, which corresponds to an individual SWNT, has been difficult to produce in high yield. To overcome this difficulty, a straightforward and easily implemented method that enables very high-yield fabrication of individual SWNT probes has been developed. This new method is based upon the observation that microfabricated tips can “pick up” vertically aligned SWNTs grown from planar substrate surfaces. Substrates with isolated, vertically aligned SWNT are first prepared by chemical vapor deposition and then imaged with commercial microfabricated silicon AFM tips. The silicon tips pick up individual SWNTs from the substrate during imaging to create well-aligned SWNT probes. The SWNT tips have been etched using a procedure that allows variation of the nanotube length with 2 nm control. Studies of gold nanocluster standards demonstrate that these individual SWNT tips are capable of high resolution and robust imaging in air and fluids, and thus these tips are expected to open up new opportunities in nanoscale science and technology.
Autologous Bone Marrow Transplantation in Patients With Cancer (1980)

TOXICITY to the hemopoietic cells of the bone marrow is a common doselimiting factor in cancer therapy. It has long been known that animals could be rescued from lethal doses of drugs or radiation by the infusion of their own or genetically identical bone marrow. Recently, there has been renewed interest in bone marrow transplantation in leukemia, aplastic anemia, and immunodeficiency diseases, and an increasing number of transplants are now being performed in lymphomas and solid tumors. I shall review recent progress in marrow transplantation in cancer. There are two potential sources of bone marrow for transplantation of patients with cancer: the patient's own marrow or marrow from a histocompatible donor, usually an HLA-identical sibling. The former procedure is referred to as autologous and the latter as allogeneic transplantation. An autologous or autotransplant may use marrow obtained either just before the transplant or cryopreserved marrow obtained months to years earlier.
Rapid stimulation of hepatic oxygen consumption by 3,5-di-iodo-l-thyronine (1989)

Tri-iodothyronine (T3) and thyroxine (T4) as well as 3,5-di-iodothyronine (T2) stimulated O2 consumption by isolated perfused livers from hypothyroid rats at a concentration as low as 1 pM by about 30% within 90 min. Application of T2 resulted in a faster stimulation than with application of T3 or T4. Inhibition of iodothyronine monodeiodinase by propylthiouracil, thereby blocking the degradation of T4 to T3 and of T3 to T2, demonstrated that only T2 is the active hormone for the rapid stimulation of hepatic O2 consumption: T3 and T4 lost all of their stimulative activity, whereas T2 was as potent as in the absence of propylthiouracil. Perfusion experiments with thyroid-hormone analogues confirmed the specificity of the T2 effect. The nucleus is unlikely to contribute to the rapid T2 effect, as can be deduced from perfusion experiments with cycloheximide and lack of induction of malic enzyme by T2. In conclusion, a new scheme of regulation of mitochondrial activity is proposed: T2 acts rapidly and directly via a mitochondrial pathway, whereas T3 exerts its long-term action indirectly by induction of specific enzymes.
A Case of Primary Hepatic Squamous Cell Carcinoma. (1999)

肝原発扁平上皮癌の1例を経験したので, 若干の文献的考察を加え報告する. 症例は73歳の男性.糖尿病・高血圧で当院通院中, 上腹部痛にて胃内視鏡検査施行し胃粘膜下腫瘍を認め精査目的に入院した. 理学所見, 血液検査では特記すべき異常は認められなかった. 胃内視鏡検査時の生検結果はグループIであった. CTでは肝外側区と胃小弯前壁間に直径7cmの不整形の腫瘤を認め, また, 下大静脈欠損も認めた. 血管造影検査では左胃動脈・短胃動脈・後胃動脈より腫瘍血管が認められた. 以上より胃粘膜下腫瘍+肝浸潤の診断で胃全摘+肝外側区部分切除術を行った. 病理組織学的には肝扁平上皮癌であった. 今回, 肝原発を積極的に示唆する扁平上皮化生は見られなかったが, 術後, 転移性肝癌の可能性も考慮し全身検索を行い, 他に原発巣となりうる病変が認められなかったことより, 肝原発扁平上皮癌と診断した.
Faraday rotation and optical absorption of a single crystal of bismuth-substituted gadolinium iron garnet (1973)

Faraday rotation and optical absorption of a single crystal of bismuth-substituted gadolinium iron garnet were measured in the near-infrared region. In spite of the remarkable increase of rotation by the bismuth substitution, no appreciable increase of absorption coefficient was observed in this wavelength region.
Expression of Cox-2, CD34, Bcl-2, and p53 and Survival in Patients with Primary Peritoneal Serous Carcinoma and Primary Ovarian Serous Carcinoma (2004)

The objective of this study was to compare the immunohistochemical profile and clinical course of primary peritoneal serous carcinoma (PPC) and primary ovarian serous carcinoma (OSC). These entities are virtually indistinguishable morphologically, but their differential molecular and clinical features are incompletely characterized. Twenty-nine cases of high-grade, high-stage PPC and 96 cases of stage matched OSCs were compared. PPC was identified based on the criteria proposed by the Gynecologic Oncology Group. The tumors were staged according to International Federation of Gynecology and Obstetrics criteria for ovarian cancer and graded according to World Health Organization criteria. Expression of Cox-2, CD-34, bcl-2, and p53 was compared in the two tumors and correlated with clinical data including stage, age, race, and overall survival. Although the median survival, using Kaplan-Meier test, of patients with OSC (1060 days, 35.3 months) was longer than those with PPC (708 days, 23.6 months) the difference was not statistically significant. However, Cox-2 expression was correlated with microvessel density in PPC (p=0.026) and OSC cases (p=0.005), and high expression of Cox-2 correlated with lower survival rate in OSC cases (p=0.045) but not in PPC cases (p=0.12). These findings, coupled with the morphologic overlap existing between OSC and PPC, support the view that they represent related pathologic entities.
Serum erythropoietin levels in healthy humans after a short period of normobaric and hyperbaric oxygen breathing: the “normobaric oxygen paradox” (2005)

Renal (peritubular) tissue hypoxia is a well-known physiological trigger for erythropoietin (EPO) production. We investigated the effect of rebound relative hypoxia after hyperoxia obtained under normo- and hyperbaric oxygen breathing conditions. A group of 16 healthy volunteers were investigated before and after a period of breathing 100% normobaric oxygen for 2 h and a period of breathing 100% oxygen at 2.5 ATA for 90 min (hyperbaric oxygen). Serum EPO concentration was measured using a radioimmunoassay at various time points during 24-36 h. A 60% increase (P < 0.001) in serum EPO was observed 36 h after normobaric oxygen. In contrast, a 53% decrease in serum EPO was observed at 24 h after hyperbaric oxygen. Those changes were not related to the circadian rhythm of serum EPO of the subjects. These results indicate that a sudden and sustained decrease in tissue oxygen tension, even above hypoxia thresholds (e.g., after a period of normobaric oxygen breathing), may act as a trigger for EPO serum level. This EPO trigger, the "normobaric oxygen paradox," does not appear to be present after hyperbaric oxygen breathing.