gebhart/patrepeval huggingface dataset:
Dispersion-tolerant optical transmission system using duobinary transmitter and binary receiver (1997)

We propose a dispersion-tolerant optical duobinary transmission system which uses a binary intensity modulation direct detection (IM-DD) receiver. The proposed system also relaxes the fiber input power limitation due to stimulated Brillouin scattering (SBS). Tolerance to chromatic dispersion in the proposed system is estimated by a simulation. A 10 Gb/s optical duobinary signal can be transmitted over 200 km of standard single-mode fiber (SMF) with 1 dB dispersion penalty. The advantages of the proposed system are confirmed experimentally. The optical duobinary signal was successfully received by the binary IM-DD receiver at the same sensitivity as a binary IM signal. Power penalty due to chromatic dispersion over a 164-km standard SMF was about 1.8 dB at 10 Gb/s. The SBS threshold of the 10 Gb/s optical duobinary modulated light was more than +20 dBm.
Assessing the potential for AAV vector genotoxicity in a murine model (2010)

Gene transfer using adeno-associated virus (AAV) vectors has great potential for treating human disease. Recently, questions have arisen about the safety of AAV vectors, specifically, whether integration of vector DNA in transduced cell genomes promotes tumor formation. This study addresses these questions with high-dose liver-directed AAV-mediated gene transfer in the adult mouse as a model (80 AAV-injected mice and 52 controls). After 18 months of follow-up, AAV-injected mice did not show a significantly higher rate of hepatocellular carcinoma compared with controls. Tumors in mice treated with AAV vectors did not have significantly different amounts of vector DNA compared with adjacent normal tissue. A novel high-throughput method for identifying AAV vector integration sites was developed and used to clone 1029 integrants. Integration patterns in tumor tissue and adjacent normal tissue were similar to each other, showing preferences for active genes, cytosine-phosphate-guanosine islands, and guanosine/cytosine-rich regions. [corrected] Gene expression data showed that genes near integration sites did not show significant changes in expression patterns compared with genes more distal to integration sites. No integration events were identified as causing increased oncogene expression. Thus, we did not find evidence that AAV vectors cause insertional activation of oncogenes and subsequent tumor formation.
Wafer Level Hermetic Bonding Using Sn/In and Cu/Ti/Au Metallization (2008)

A low temperature hermetic wafer bonding using In/Sn interlayer and Cu/Ti/Au metallization was investigated for MEMS and sensor packaging application. Bonding was performed in a vacuum wafer bonder at 180°C and 150°C for 20 min under 5.5 MPa. It is found that bonding at 180°C, voids free joints composed of high temperature intermetallic compounds (IMCs) were obtained with good hermeticity and reliability. However, bonding at 150°C, voids were generated along the seal joint which caused poor hermeticity comparing with that bonded at 180°C. After four kinds of reliability tests, i. e., Pressure cooker test, high humidity storage, high temperature storage, temperature cycling test, dies bonded at 180°C showed good reliability properties by hermeticity test and shear tests. Present results proved that high yield and low temperature hermetic bonding can be achieved by using Sn/In/Cu metallization with thin Ti as a buffer layer.
Clarificação de extrato de Stevia rebaudiana (Bert.) Bertoni por adsorção em zeólitas modificadas (2001)

Selective adsorption on zeolites X and A was studied with Stevia rebaudiana (Bert.) Bertoni (Asteraceae) extract clarification. Ionic exchanges were made with calcium and barium ions in zeolites NaX and NaA and the effect of contact of aqueous extract of dry Stevia rebaudiana Bertoni leaves with CaX, BaX, CaA and BaA zeolites was evaluated. Stevia extract in contact with the zeolite CaX showed highest clarification and did not present alterations of initial characteristics in concentration, glycosides and flavor. In batch tests at room temperature, the contact of Stevia aqueous extract and CaX zeolite provided 70-80% clarification. Since zeolite may be reused, an approximate clarification of 65-70% is possible in regenerated zeolite.
Metabolite Profiling of Italian Tomato Landraces with Different Fruit Types (2016)

Increased interest toward traditional tomato varieties is fueled by the need to rescue desirable organoleptic traits and to improve the quality of fresh and processed tomatoes in the market. In addition, the phenotypic and genetic variation preserved in tomato landraces represents a means to understand the genetic basis of traits related to health and organoleptic aspects and improve them in modern varieties. To establish a framework for this approach, we studied the content of several metabolites in a panel of Italian tomato landraces categorized into three broad fruit type classes (flattened/ribbed, pear/oxheart, round/elongate). Three modern hybrids, corresponding to the three fruit shape typologies, were included as reference. Red ripe fruits were morphologically characterized and biochemically analyzed for their content in glycoalkaloids, phenols, amino acids, and Amadori products. The round/elongate types showed a higher content in glycoalkaloids, whereas flattened types had higher levels of phenolic compounds. Flattened tomatoes were also rich in total amino acids and in particular in glutamic acid. Multivariate analysis of amino acid content clearly separated the three classes of fruit types. Making allowance of the very low number of genotypes, phenotype-marker relationships were analyzed after retrieving single nucleotide polymorphisms (SNPs) among the landraces available in the literature. Sixty-six markers were significantly associated with the studied traits. The positions of several of these SNPs showed correspondence with already described genomic regions and QTLs supporting the reliability of the association. Overall the data indicated that significant changes in quality-related metabolites occur depending on the genetic background in traditional tomato germplasm, frequently according to specific fruit shape categories. Such a variability is suitable to harness association mapping for metabolic quality traits using this germplasm as an experimental population, paving the way for investigating their genetic/molecular basis, and facilitating breeding for quality-related compounds in tomato fruits.
PlnTFDB: updated content and new features of the plant transcription factor database (2009)

The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.
Chlamydophila Pneumoniae and the Etiology of Late-Onset Alzheimer's Disease (2008)

Sporadic, late-onset Alzheimer's disease (LOAD) is a non-familial, progressive neurodegenerative disease that is now the most common and severe form of dementia in the elderly. That dementia is a direct result of neuronal damage and loss associated with accumulations of abnormal protein deposits in the brain. Great strides have been made in the past 20 years with regard to understanding the pathological entities that arise in the AD brain, both for familial AD ( approximately 5% of all cases) and LOAD ( approximately 95% of all cases). The neuropathology observed includes: neuritic senile plaques (NSPs), neurofibrillary tangles (NFTs), neuropil threads (NPs), and often deposits of cerebrovascular amyloid. Genetic, biochemical, and immunological analyses have provided a relatively detailed knowledge of these entities, but our understanding of the "trigger" events leading to the many cascades resulting in this pathology and neurodegeneration is still quite limited. For this reason, the etiology of AD, in particular LOAD, has remained elusive. However, a number of recent and ongoing studies have implicated infection in the etiology and pathogenesis of LOAD. This review focuses specifically on infection with Chlamydophila (Chlamydia) pneumoniae in LOAD and how this infection may function as a "trigger or initiator" in the pathogenesis of this disease.
CORRELATION OF SERUM LEVELS OF MACROPHAGE MIGRATION INHIBITORY FACTOR WITH DISEASE SEVERITY AND CLINICAL OUTCOME IN DENGUE PATIENTS (2006)

Dengue virus infection can cause mild dengue fever (DF) or severe dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Cytokines are believed to be involved in the pathogenesis of dengue infection. However, the role of the pro-inflammatory cytokine macrophage migration inhibitory factor (MIF) in dengue infection is unclear. In this study, serum levels of MIF in adult dengue patients with different disease severity and clinical outcome were determined and compared with the levels of other cytokines, tumor necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), IL-10, and interferon gamma (IFN-gamma), in the same patients. Serum levels of MIF, IL-6, and IL-10, but not IFN-gamma or TNF-alpha, were higher in all DHF patients who died than in DHF survivors and DF patients. We conclude that in addition to IL-6 and IL-10, elevated levels of serum MIF are a potential predictor of disease severity and clinical outcome in dengue patients.
Detection of Chlamydia trachomatis by Isothermal Ramification Amplification Method: a Feasibility Study (2002)

Chlamydia trachomatis is the leading cause of sexually transmitted disease in the United States. Effective screening for this agent can facilitate prompt treatment and prevent its sequelae. The recent introduction of liquid-based cytology has made possible the simultaneous screening of cervical intraepithelial lesions and detection of C. trachomatis in a single collection vial. In this study we determined whether cytological fluid could support DNA-based amplification for the detection of C. trachomatis. Three methods were compared, including ramification amplification (RAM), real-time PCR with molecular beacon, and Abbott's ligase chain reaction (LCx). RAM is a novel, recently introduced, isothermal DNA amplification technique that utilizes a circular probe for target detection and achieves exponential amplification through the mechanism of primer extension, strand displacement, and ramification. Our results show that RAM can detect as few as 10 C. trachomatis elementary bodies in less than 2 h, comparable to results with real-time PCR. Thirty clinical specimens collected in PreservCyt solution were tested by LCx, real-time PCR, and RAM. Among 30 specimens, 15 were positive by PCR and LCx and 14 were positive by RAM. One specimen missed by RAM had an inadequate amount of residual cellular material. Our results show that nucleic acid amplification methods can serve to detect C. trachomatis and presumably other sexually transmitted agents in cytological fluid and that the RAM assay can be an alternative to PCR and LCx because of its simplicity and isothermal amplification.
Wafer-Scale Graphene Integrated Circuit (2011)

A wafer-scale graphene circuit was demonstrated in which all circuit components, including graphene field-effect transistor and inductors, were monolithically integrated on a single silicon carbide wafer. The integrated circuit operates as a broadband radio-frequency mixer at frequencies up to 10 gigahertz. These graphene circuits exhibit outstanding thermal stability with little reduction in performance (less than 1 decibel) between 300 and 400 kelvin. These results open up possibilities of achieving practical graphene technology with more complex functionality and performance.
Photoelectron study of Yb/C60bilayers and the Yb fullerides formed at the interfaces (1993)

Photoelectron measurements were obtained for Yb-${\mathrm{C}}_{60}$ and the results are compared to those reported for alkali-metal fullerides and Yb isolated in xenon or solid ${\mathrm{NH}}_{3}$. The valence photoelectron spectra for Yb deposited on ${\mathrm{C}}_{60}$ and ${\mathrm{C}}_{60}$ on Yb show changes in the Yb 4f peaks, and in the ${\mathrm{C}}_{60}$ valence states and a metal-induced state just above the Yb 4f bands. The position of this valence feature is near to that found for an analogous feature in the nonsuperconducting ${\mathrm{K}}_{6}$${\mathrm{C}}_{60}$ fulleride. Similar features also appear when Yb is solvated in condensed ammonia. The appearance and binding energy of the Yb 4f levels argue that the Yb is largely divalent but has a small trivalent component. A comparison of the data for Yb-${\mathrm{C}}_{60}$ with that for Yb clusters in xenon shows that the changes in the electronic state of the Yb are not those found for small Yb particles in a nonreactive matrix.
Megalin/gp330 mediates uptake of albumin in renal proximal tubule (1996)

Serum albumin filtered in renal glomeruli is reabsorbed very efficiently in the proximal tubule by endocytosis. The present study was undertaken to determine whether megalin/gp330 binds and mediates endocytosis of albumin. Rat serum albumin (RSA) labeled with 125I and colloidal gold particles labeled with bovine serum albumin (BSA) were microinfused into rat surface proximal tubules in vivo, and tubular uptake was determined in the presence or absence of different substances known to interfere with ligand binding to megalin. Binding of 125I-BSA and 125I-RSA to purified megalin was also determined directly using Sepharose columns. The results revealed that the tubular uptake of 125I-labeled RSA was significantly inhibited by receptor-associated protein (RAP), which reduced the uptake by > 50% and by cold RSA. The uptake of BSA gold by the proximal tubule was very intensive. BSA gold was found in small and large endocytic vacuoles, dense apical tubules, and in lysosomes. The uptake was reduced by RAP to 17%, by EDTA to 19%, by BSA to 16%, by megalin to 35%, by cytochrome c to 49%, and, together with gentamicin, there was virtually no uptake. Megalin-Sepharose columns bound 125I-labeled BSA as well as 125I-RSA, the binding was inhibited by RAP and EDTA, and analysis of the eluate revealed the bound tracer to be albumin. In conclusion, the present study demonstrates that megalin is a mediator of albumin reabsorption in renal proximal tubules.
Detection and strain identification of Actinobacillus actinomycetemcomitans by nested PCR (1994)

By using PCR, Actinobacillus actinomycetemcomitans strains were identified directly from plaque samples without the need to isolate or culture bacteria. DNA fragments were generated by a nested, two-step PCR amplification of the ribosomal spacer region between the 16S and 23S rRNA genes. For the first amplification, primers homologous to sequences common to all bacterial species were used. This was followed by a second amplification with primers specific to A. actinomycetemcomitans. The ribosomal DNA spacer region was amplified from as few as 10 bacterial cells within a total population of 10(8) cells (0.00001%), and cross-reactivity between species was not observed. DNA fragments specific for Porphyromonas gingivalis were generated from the same samples by using a P. gingivalis-specific primer, and equivalent sensitivity and specificity were observed. A. actinomycetemcomitans was detected in 60% and P. gingivalis was detected in 79% of 52 subjects tested. Sequence analysis of the spacer region DNA fragment for A. actinomycetemcomitans gave precise strain identification, producing unique sequences for seven reference strains and identification of nine plaque-derived isolates. A phylogenetic tree based on quantitative sequence relationships was constructed. Two-step PCR amplification directly from plaque samples combined with sequence analysis of the ribosomal DNA spacer region provides a sensitive assay for detection and strain identification of multiple species directly from a single plaque sample. This simplified approach provides a practical method for large-scale studies on the transmission and pathogenicity of periodontitis-associated bacteria.
Effects of an acute saline infusion on fluid and electrolyte metabolism in humans (1992)

Several hormonal systems participating in body fluid and electrolyte homeostasis were investigated in six healthy volunteers in a supine body position during a period of 9 days and nights. Under strictly controlled conditions, striking circadian rhythms were observed for plasma levels of vasopressin, renin, aldosterone, guanosine 3',5'-cyclic monophosphate, cortisol, and epinephrine. Nocturnal decreases and diurnal increases in urine flow rate and urinary excretion of electrolytes were observed and closely paralleled the urinary excretion of urodilatin. During 48 h after an acute isotonic saline infusion (2 liters within 25 min) and after a 48-h control experiment the urinary excretion of H2O and electrolytes, and simultaneously the alterations in endocrine systems participating in body fluid homeostasis, were determined. Urine flow and urinary electrolyte excretion rates were significantly increased during 2 days after the saline infusion. The largest increase in urinary fluid and electrolyte excretion was observed between 3 and 22 h postinfusion. These long-term changes were paralleled by altered H2O and Na balances and also by elevated body weights that returned to baseline values with an approximate half-life of 7 h. These data suggest that vasopressin, atrial natriuretic peptide, and catecholamines are unlikely to be of major importance for the renal response to this hypervolemic stimulus. The renin-aldosterone system was suppressed during 2 days postinfusion. This suppression correlated with the effects of saline load on Na excretion. However, the closest relation with Na excretion was observed for the kidney-derived member of the atrial natriuretic peptide family, urodilatin, which was considerably increased during the long-term period up to 22 h postinfusion. Thus these data show that the human body in supine position requires approximately 2 days to regulate the amount of Na and H2O provided by an acute saline infusion. The data also suggest that urodilatin and the renin-aldosterone system might participate in the long-term renal response to an acute saline infusion and also in the mediation of circadian urinary excretion rhythms.
The effect of a growth promoting drug, clenbuterol, on fibre frequency and area in hind limb muscles from young male rats (1986)

The effect of dietary administration of clenbuterol on soleus and extensor digitorum longus muscles was studied after 4 and 21 days. Both muscles showed an increase in wet weight with no significant change in total fibre number. After 4 days fibre cross-sectional areas were increased in soleus, but not in extensor digitorum longus, and after 21 days there was a change in fibre frequencies in extensor digitorum longus but not soleus muscles.
NVP-AUY922: A novel small molecule HSP90 inhibitor with potent in vivo antitumor efficacy (2007)

B279 Heat Shock Protein 90 (HSP90) is a ubiquitously expressed molecular chaperone with ATPase activity which plays an important role in the conformational maturation and activation of a large number of client proteins that have been implicated in oncogenesis. HSP90 has attracted considerable interest as a therapeutic target for anticancer drugs since HSP90 ATPase inhibition induces simultaneous degradation of multiple oncogenic proteins. The most advanced HSP90 inhibitors are of the benzoquinone ansamycin class which have shown promising activity in human tumor xenograft models. NVP-AUY922, is a novel synthetic resorcinylic isoxazole HSP90 inhibitor which recently entered Phase I clinical trials. In a competitive fluorescent polarization assay, NVP-AUY922 inhibited Hsp90β with an IC50 of 21nM and a Ki of 9nM. Inhibition of HSP90 translates into anti-proliferative effect of human breast cancer tumor cells with GI50 values in the range of 3-10 nM. Importantly, treatment of cell lines with NVP-AUY922 consistently induced dissociation of p23/Hsp90, HSP72 upregulation and client protein depletion - hallmarks of HSP90 inhibition. Intravenous administration of NVP-AUY922 to athymic mice (25 mg/kg) resulted in drug levels exceeding 1000-fold cellular GI50 for about 2 days in BT-474 breast cancer xenografts. Tumor stasis was observed when the compound was administered once per week and was accompanied by apoptosis. Therapeutic effects were also concordant with changes in pharmacodynamic markers including p23/Hsp90 dissociation, decreases in ERBB2 and P-AKT as well as increased HSP72. Overall, we demonstrate that NVP-AUY922 is a potent, novel HSP90 inhibitor with long lasting tumor retention and rapid organ clearance. This translates into potent anti-tumor effect with concurrent effects on client proteins when administered once weekly to nude mice bearing human breast cancer xenograft tumors.
T Cell Epitopes of Human Myelin Oligodendrocyte Glycoprotein Identified in HLA-DR4 (DRB1*0401) Transgenic Mice Are Encephalitogenic and Are Presented by Human B Cells (2001)

Myelin oligodendrocyte glycoprotein (MOG) is an Ag present in the myelin sheath of the CNS thought to be targeted by the autoimmune T cell response in multiple sclerosis (MS). In this study, we have for the first time characterized the T cell epitopes of human MOG restricted by HLA-DR4 (DRB1*0401), an MHC class II allele associated with MS in a subpopulation of patients. Using MHC binding algorithms, we have predicted MOG peptide binding to HLA-DR4 (DRB1*0401) and subsequently defined the in vivo T cell reactivity to overlapping MOG peptides by testing HLA-DR4 (DRB1*0401) transgenic mice immunized with recombinant human (rh)MOG. The data indicated that MOG peptide 97-108 (core 99-107, FFRDHSYQE) was the immunodominant HLA-DR4-restricted T cell epitope in vivo. This peptide has a high in vitro binding affinity for HLA-DR4 (DRB1*0401) and upon immunization induced severe experimental autoimmune encephalomyelitis in the HLA-DR4 transgenic mice. Interestingly, the same peptide was presented by human B cells expressing HLA-DR4 (DRB1*0401), suggesting a role for the identified MOG epitopes in the pathogenesis of human MS.