gebhart/patrepeval huggingface dataset:
Absence of Porphyromonas asaccharolytica, Bacteroides fragilis and Chlamydia pneumoniae in human subgingival plaque (1997)

Little is known about the presence of common medical pathogens in the human oral cavity. Using a 16S rRNA-based PCR identification method, this study determined the occurrence of Porphyromonas asaccharolytica, Bacteroides fragilis and Chlamydia pneumoniae in subgingival plaque from 50 adults with advanced periodontitis. Each patient contributed samples from 3 deep periodontal pockets collected by paper points. The PCR primers were for P. asaccharolytica 5'-CTC TAG CTA GAG TGT ACT GG-3' and 5'-ATA GGG TTT ATA GAT TAG CTC TCT-3', for B. fragilis 5'-AAT GAT TCC GCA TGG TTT CAT TA-3' and 5'-GCG GTG ATT GCT CAC TGA CA-3', and for C. pneumoniae 5'- TGA CAA CTG TAG AAA TAC AGC-3' and 5'-CGC CTC TCT CCT ATA AAT-3'. The primers yielded a single amplicon with the respective reference strains and produced no amplicon with colonies of 25 groups of oral organisms. None of the three test species were detected in any of the 50 pooled subgingival samples tested. P. asaccharyolytica, B. fragilis and C. pneumoniae do not seem to be part of the periodontopathic microbiota in humans.
Accounting for Management (1985)

Accounting for management , Accounting for management , کتابخانه دیجیتالی دانشگاه علوم پزشکی و خدمات درمانی شهید بهشتی
ChemInform Abstract: Palladium Fluoride Complexes: One More Step Toward Metal‐Mediated C—F Bond Formation. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Redox-Neutral α-Arylation of Amines (2013)

The direct α-arylation/N-alkylation of cyclic amines was achieved in a redox-neutral fashion under mild conditions. Transformations occur in the absence of any additives or are promoted by simple carboxylic acids.
Genetic regulation of the immune response to hepatitis B surface antigen (HBsAg). VI. T cell fine specificity. (1985)

In the companion paper it was demonstrated that the T cell proliferative response to HBsAg was controlled by I region genes as was previously shown for in vivo anti-HBs production. In this paper, the structural requirements for T cell recognition of HBsAg were compared with B cell (antibody) recognition of HBsAg. Secondly, we attempted to map determinants on HBsAg required for activation of HBsAg-primed T cells, and we examined the influence of I region genotype on the observed T cell antigenic fine specificity. The results of these studies indicate clear differences between T cell and B cell recognition of HBsAg. T cell activation required significantly less native structure as compared with antibody binding to HBsAg. Reduced and alkylated HBsAg, the subunit polypeptide P25, tryptic fragments of P25, and synthetic peptide analogues of HBsAg were all capable of eliciting a T cell proliferative response, whereas these "denatured" forms of the antigen bind anti-HBs marginally or not at all. Furthermore, the results suggest that T cell recognition sites on HBsAg do not necessarily overlap with B cell recognition sites. Examination of T cell fine specificity in a series of H-2 congenic strains, with the use of HBsAg, P25, tryptic fragments of P25, and synthetic peptides, revealed multiple T cell recognition sites on HBsAg, and the particular site(s) recognized is dependent on the H-2 genotype of the responding strain. Finally, preliminary results indicate that the specificity of human, HBsAg-primed T cells appear to be variable among individuals.
Color Image to Grayscale Image Conversion (2010)

Conversion of a color image into a grayscale image inclusive of salient features is a complicated process. The converted grayscale image may lose contrasts, sharpness, shadow, and structure of the color image. To preserve contrasts, sharpness, shadow, and structure of the color image a new algorithm has proposed. To convert the color image into grayscale image the new algorithm performs RGB approximation, reduction, and addition of chrominance and luminance. The grayscale images generated using the algorithm in the experiment confirms that the algorithm has preserved the salient features of the color image such as contrasts, sharpness, shadow, and image structure.
Ultrashort low-loss optical multiquantum-well GaAs/GaAlAsvertical directional coupler switch (1996)

An optical GaAs/GaAlAs multiquantum-well vertical directional coupler switch with a device length of 85 µm is presented. At a wavelength of 854 nm the voltage necessary for switching was 5 V, associated with a transmission loss of only 2 dB in the switched state and an extinction ratio of greater than 10 dB. The device parameters were chosen so as to enable monolithic integration.
Effect of povidone-iodine on anastomotic tumor growth in an experimental model of colorectal cancer surgery. (1999)

Implantation of viable exfoliated tumor cells may be responsible for the local recurrence of colorectal cancer. Intraluminal colon cancer cells derived from chemically induced colon cancer in syngenic F344 rats, were introduced 2 cm proximally to a colonic anastomosis and anastomotic tumor growth was observed. Anastomotic tumor growth was found in about 30% of the animals, when sacrificed on the 3rd postoperative week. The cytotoxic efficacy of povidone-iodine (PVP-I) was tested with the same model. The administration of 10% PVP-I solution significantly reduced the incidence of tumor growth. Viable intraluminal tumor cells cause anastomotic tumor growth by becoming implanted on an anastomosis and PVP-I had effective cytotoxicity.
Quantitative Importance of Changes in Postglomerular Colloid Osmotic Pressure in Mediating Glomerulotubular Balance in the Rat (1973)

In recent studies in this laboratory employing normal hydropenic rats we have demonstrated that the reduction in absolute proximal reabsorption that attends the experimental reduction of single nephron glomerular filtration rate (SNGFR) (glomerulotubular balance) is mediated, at least in part, by the accompanying decline in postglomerular vascular protein concentration, and therefore, postglomerular colloid osmotic pressure (piEA). The present study was undertaken to define the quantitative contribution of these changes in piEA to the changes in absolute proximal reabsorption measured under these conditions. A protocol was employed which enabled us to examine the effects on absolute proximal reabsorption of reductions in filtered load brought about under conditions in which piEA remained essentially unchanged. Thus, after partial aortic constriction in 16 plasma-loaded rats, near constancy of piEA was observed in 10 (a change in efferent arteriolar protein concentration of 0.4 g/100 ml or less) and in these, uniform reductions in SNGFR averaging 16.7 nl/min were attended by reductions in absolute proximal reabsorption averaging only 1.7 nl/min, or 7% of preconstriction values. These findings, taken together with previous observations from this laboratory, suggest that the proximal reabsorptive adjustment that characterizes glomerulotubular balance in the rat is markedly blunted when changes in piEA are prevented. In the remaining six rats, a mean reduction in filtered load comparable to that observed in the above group was attended by slightly to moderately greater reductions in efferent arteriolar protein concentration, thereby fulfilling less well the stated aim of this study. Nevertheless, in accord with the above conclusion, these relatively greater reductions in piEA were accompanied by correspondingly greater reductions in absolute proximal reabsorption.
Development of A Microchamber Array for Picoliter PCR (2000)

A microchamber array for PCR was developed by semiconductor microfabrication technology. The microchambers were designed to be of picoliter quantity. To optimize fluid retention, the surface states of the substrate and the inner walls were examine for four different types of microchamber. The substrate was silicon, while silicon dioxide was selected for the inner walls. PCR was performed in the microchamber array, and the amplification of DNA was detected using a technique based on the energy transfer of fluorescent dyes. The lower volume limit for PCR was investigated using various sizes of microchambers. Microchambers with volume greater than 86 pL gave successful PCR. In addition, the system was improved in order to take up the PCR product. To prevent mixing of the samples, the samples were dried after PCR using a membrane that permeates only vapor.
Swapping of the β-Hairpin Region between Sp1 and GLI Zinc Fingers:  Significant Role of the β-Hairpin Region in DNA Binding Properties of C2H2-type Zinc Finger Peptides (2005)

The recent design strategy of zinc finger peptides has mainly focused on the alpha-helix region, which plays a direct role in DNA recognition. On the other hand, the study of non-DNA-contacting regions is extremely scarce. By swapping the beta-hairpin regions between the Sp1 and GLI zinc fingers, in this study, we investigated how the beta-hairpin region of the C(2)H(2)-type zinc finger peptides contributes to the DNA binding properties. Surprisingly, the Sp1 mutant with the GLI-type beta-hairpin had a higher DNA binding affinity than that of the wild-type Sp1. The result of the DNase I footprinting analyses also showed the change in the DNA binding pattern. In contrast, the GLI zinc finger completely lost DNA binding ability as a result of exchanging the beta-hairpin region. These results strongly indicate that the beta-hairpin region appears to function as a scaffold and has an important effect on the DNA binding properties of the C(2)H(2)-type zinc finger peptides.
Challenges of drug-resistant malaria (2014)

Over the past six decades, the drug resistance of Plasmodium falciparum has become an issue of utmost concern. Despite the remarkable progress that has been made in recent years in reducing the mortality rate to about 30% with the scaling-up of vector control, introduction of artemisinin-based combination therapies and other malaria control strategies, the confirmation of artemisinin resistance on the Cambodia-Thailand border threatened all the previous success. This review addresses the global scenario of antimalarial resistance and factors associated with it, with the main emphasis on futuristic approaches like nanotechnology and stem cell therapy that may impede resistant malaria, along with novel medications which are preparing to enter the global antimalarial market. These novel studies are likely to escalate over the coming years and will hopefully help to reduce the burden of malaria.
The basis for disease‐modifying treatments for Alzheimer's disease: The Sixth Annual Mild Cognitive Impairment Symposium (2008)

At the Sixth Annual Mild Cognitive Impairment Symposium in Miami Beach, Florida, a multidisciplinary group of experts from the Alzheimer's disease (AD) community met to discuss the current status of AD intervention trials and future plans for designing trials of prodromal AD and/or mild cognitive impairment. There is no agreement regarding a single pathogenic mechanism to be targeted, although a consensus seems to be emerging that effective treatment will require attacking multiple targets. These targets include beta amyloid (Ass) aggregates (including different isoforms and different aggregation species), neurofibrillary tangles composed of hyperphosphorylated tau, neuronal and synaptic loss, and mechanisms that contribute to Ass deposition-induced inflammation and immune dysregulation. Vascular disease, which is very common in the elderly, also appears to be a contributor to AD pathogenesis and might be modifiable through pharmacologic and lifestyle interventions to reduce the impact of conditions such as hypertension and metabolic syndrome. Potential disease-modifying approaches that were discussed, including pharmacologic agents that target Abeta, immunotherapy to eliminate plaques in the brain, passive immunotherapy, and secretase inhibitors. Nonpharmacologic approaches included stimulation of endogenous bone marrow cells, which can enter the brain and remove amyloid deposits, and cognitive and exercise training. Innovative trial designs are required that will allow a drug's effectiveness to be determined efficiently in the transition from normal to mild cognitive impairment to probable AD. This might be achieved through the use of various forms of imaging and measurement of biochemical markers in the blood or cerebrospinal fluid, as well as measures that assess very early cognitive and behavioral changes. In the absence of effective treatments for AD, clinicians are faced with a dilemma about why, when, and how to disclose the diagnosis to patients and their family members and/or caregivers. The issues were discussed from multiple perspectives by a panel that included a lay representative, neurologist, psychiatrist, primary care physician, and a psychosocial researcher.
Comparison of Bayesian Discriminative and Generative Models for Dialogue State Tracking (2013)

In this paper, we describe two dialogue state tracking models competing in the 2012 Dialogue State Tracking Challenge (DSTC). First, we detail a novel discriminative dialogue state tracker which directly estimates slot-level beliefs using deterministic state transition probability distribution. Second, we present a generative model employing a simple dependency structure to achieve fast inference. The models are evaluated on the DSTC data, and both significantly outperform the baseline DSTC tracker.
RNAi in C. elegans : Soaking in the Genome Sequence (1998)

T he completion of the Caenorhabditis elegans genome sequence represents a major milestone in a journey initiated by Sydney Brenner some 30 years ago. The goal then as now was to discover how genetic information specifies the development, anatomy, and behavior of a simple animal. Bringing the full
Beneficial effects of tumour necrosis factor-alpha (TNF-α) blockade in rheumatoid arthritis (RA) (1995)

The biological properties of TNF-alpha make it a candidate therapeutic target in RA. Our studies have demonstrated that TNF-alpha and its receptors are up-regulated and co-expressed in the synovium and cartilage-pannus junction of RA joints. Neutralizing TNF-alpha antibodies reduce the production of the many pro-inflammatory cytokines, including IL-1 and granulocyte-macrophage colony-stimulating factor (GM-CSF), produced by mononuclear cells from RA in culture. When injected into DBA/1 mice with collagen-induced arthritis and TNF-alpha transgenic mice with arthritis, anti-TNF MoAbs decrease inflammatory damage of joints. Clinical trials employing cA2, a chimaeric anti-TNF-alpha MoAb, in open-label and randomized placebo-controlled studies have demonstrated a dose-dependent efficacy with impressive improvement in disease activity and acute-phase responses lasting several weeks. We conclude that TNF-alpha is a critical mediator of inflammation in RA, and is an important therapeutic target in this disease.
Expression of maize KNOTTED1 related homeobox genes in the shoot apical meristem predicts patterns of morphogenesis in the vegetative shoot (1994)

ABSTRACT In this paper we describe the expression patterns of a family of homeobox genes in maize and their relationship to organogenic domains in the vegetative shoot apical meristem. These genes are related by sequence to KNOTTED1, a gene characterized by dominant neomorphic mutations which perturb specific aspects of maize leaf development. Four members of this gene family are expressed in shoot meristems and the developing stem, but not in determinate lateral organs such as leaves or floral organs. The genes show distinct expression patterns in the vegetative shoot apical meristem that together predict the site of leaf initiation and the basal limit of the vegetative ‘phytomer’ or segmentation unit of the shoot. These genes are also expressed in the inflorescence and floral meristems, where their patterns of expression are more similar, and they are not expressed in root apical meristems. These findings are discussed in relation to other studies of shoot apical meristem organization as well as possible commonality of homeobox gene function in the animal and plant kingdoms.
Scan chain design for test time reduction in core-based ICs (2002)

The size of the test vector set forms a significant factor in the overall production costs of ICs, as it defines the test application time and the required pin memory size of the test equipment. Large core-based ICs often require a very large test vector set for a high test coverage. This paper deals with the design of scan chains as transport mechanism for test patterns from IC pins to embedded cores and vice versa. The number of pins available to accommodate scan test is given, as well as the number of scan test patterns and scannable flip flops of each core. We present and analyze three scan chain architectures for core-based ICs, which aim at a minimum test vector set size. We give experimental results of the three architectures for an industrial IC. Furthermore we analyze the test time consequences of reusing cores with fixed internal scan chains in multiple ICs with varying design parameters.
A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform (2015)

Writing DNA plays a significant role in the fields of synthetic biology, functional genomics and bioengineering. DNA clones on next-generation sequencing (NGS) platforms have the potential to be a rich and cost-effective source of sequence-verified DNAs as a precursor for DNA writing. However, it is still very challenging to retrieve target clonal DNA from high-density NGS platforms. Here we propose an enabling technology called 'Sniper Cloning' that enables the precise mapping of target clone features on NGS platforms and non-contact rapid retrieval of targets for the full utilization of DNA clones. By merging the three cutting-edge technologies of NGS, DNA microarray and our pulse laser retrieval system, Sniper Cloning is a week-long process that produces 5,188 error-free synthetic DNAs in a single run of NGS with a single microarray DNA pool. We believe that this technology has potential as a universal tool for DNA writing in biological sciences.
A 0.4-4-Gb/s CMOS quad transceiver cell using on-chip regulated dual-loop PLLs (2003)

This paper describes the design and implementation of a quad high-speed transceiver cell fabricated in 0.13-μm CMOS technology. The clocking circuit of the cell employs a dual-loop architecture with a high-bandwidth core phase-locked loop (PLL) and low-bandwidth digitally controlled interpolators. To achieve low jitter while maintaining low power consumption, the dual-loop PLL uses two on-chip linear regulators of different bandwidths, one for the core and the other for the interpolator loop. The prototype chip operates from 400 Mb/s to 4 Gb/s with a bit error rate of <10/sup -14/. The quad cell consumes 390 mW at 2.5 Gb/s (95 mW/link) under typical operating conditions with a 400-mV output swing driving double terminated links.
RDE Measurements of ORR Activity of Pt[sub 1−x]Ir[sub x] (0<x<0.3) on High Surface Area NSTF-Coated Glassy Carbon Disks (2009)

Layered and Pt films were sputtered onto mirror-polished and nanostructured thin film (NSTF)-coated glassy carbon (GC) disks. Rotating disk electrode (RDE) studies of oxygen reduction reaction (ORR) activity were completed for all prepared disks. The film was prepared by depositing alternating layers of Pt (constant thickness) and Ir (gradient), finished with a Pt top layer. The NSTF-supported catalysts had much higher active surface areas and reached the diffusion-limited current at higher potentials than the bare GC supported catalysts. The surface enhancement factor (SEF) of Pt on NSTF-coated disks was approximately 14. The SEF increased (reaching a maximum of 22 at in ) as the Ir content increased for the samples on NSTF. The kinetic ORR current density also increased with increasing Ir content. A similar trend was not observed for the same catalyst coated onto bare GC disks. All of the catalyst/support combinations had identical Tafel slopes and area-specific current densities, suggesting that Pt is the active catalytic ingredient. Catalysts coated on NSTF-coated GC disks can be used to accurately examine both catalytic activities and the effects of high surface area supports in a single measurement.
Tau-Derived-Hexapeptide 306VQIVYK311 Aggregation Inhibitors: Nitrocatechol Moiety as A Pharmacophore In Drug Design (2013)

The nitrocatechol derivatives tolcapone (1) and entacapone (2), used as adjunctive therapy in the treatment of Parkinson's disease, were investigated for their potential to inhibit the tau-derived-hexapeptide 306VQIVYK311. They were compared to small molecules that contain similar pharmacophores including the catechol derivatives (dopamine 3 and epinephrine 4), nitroderivatives (nifedipine 5 and chloramphenicol 6), nitrocatechol isomers (7 and 8), and a tolcapone derivative (13) lacking the nitrocatechol moiety. The aggregation kinetics by thioflavin S fluorescence assay indicates that both tolcapone (1) and entacapone (2) exhibit antiaggregation properties. These findings were supported by transmission electron microscopy (TEM) and circular dichroism (CD) spectroscopy measurements which suggest that the nitrocatechol (3,4-dihydroxy-5-nitrophenyl) moiety is a suitable pharmacophore in the design of new tau-aggregation inhibitors. Furthermore, tolcapone (1) was identified as most active compound with antiaggregation activity (46% inhibition of fluorescence intensity at 50 μM), which was supported by TEM data. The in silico steric zipper model of the tau-derived-hexapeptide 306VQIVYK311 indicates that the 3,4-dihydroxy-substituent present in tolcapone (1) and entacapone (2) underwent polar contacts with lysine side chains (VQIVYK), whereas the charged 5-nitrosubstituent was in close contact with lysine side chain present in the steric zipper region suggesting the critical role of a nitrocatechol (3,4-dihydroxy-5-nitrophenyl) pharmacophore present in tolcapone (1) and entacapone (2) in tau-hexapeptide binding and prevention of β-sheet assembly. Our results have significant implications in the design and development of tau-aggregation inhibitors.
Color My Nanoworld (2004)

In this activity, students are introduced to the unique properties of nanoscale materials. The activity begins with the synthesis of 13 nm-diameter gold nanoparticles by reduction of a gold salt. The students use the resulting nanoparticle solution to explore the size-dependent optical properties of gold nanoparticles. Specifically, they determine that the nanoparticle solution functions as an electrolyte sensor because electrolyte-induced aggregation of the nanoparticles results in a dramatic color change.
Magnetic characterization of CoFeB∕MgO and CoFe∕MgO interfaces (2007)

The use of CoFeB ferromagnetic electrodes in place of CoFe has been shown to significantly increase the tunneling magnetoresistance (TMR) of MgO based magnetic tunnel junctions (MTJs). By using soft x-ray scattering techniques, we show that the behavior of the magnetic moments located at the CoFe–MgO interface are drastically different from the rest of the CoFe film, whereas the magnetic response of the CoFeB–MgO interfacial moments is coherent with the film’s bulk. Our results support the view that the high TMR values observed in MgO based MTJs with CoFeB electrodes are due to the uniform magnetic response of the entire CoFeB electrode including the MgO interfacial moments.