gebhart/patrepeval huggingface dataset:
Accommodation measurements in a prepresbyopic and presbyopic population (2004)

Hartinger-measured accommodation provides more realistic measurement of accommodative amplitude than the subjective methods tested, especially in the presbyopic population. In presbyopic subjects, the subjective tests resulted in accommodative amplitudes up to 4.0 diopters greater than those measured with objective tests. Measurements of accommodative amplitude are best achieved with objective methods to stimulate and measure accommodation.
C60(g), C70(g), saturated carbon vapour and increase of cluster populations with temperature: A combined AM1 quantum-chemical and statistical-mechanical study (1987)

Saturated vapour above graphite and the content of C n ( g ) aggregates therein have been studied at various temperatures. The equilibrium constants of C( g ) into C n ( g ) association have been obtained for: (i) n = 1-5 from the available tabulated thermodynamical data, (ii) C 60 and C 70 from a quantum-chemical description in terms of the AM1 method as a source of molecular parameters for the construction of partition functions, and (iii) the other aggregates by linear inter- or extrapolation of the data sub (i) and (ii). The content of clusters with n ≥ 2 in the saturated vapour has been shown to increase steeply with temperature. This increase is due to small clusters ( n ~ 2-5), whereas the recently proved particular structures C 60 and C 70 are - according to these calculations – negligibly populated in the saturated vapour at all temperatures studied. At the conditions of saturated vapour the population of C 60 always exceeds that of C 70 by several orders of magnitude. The relations of these calculations to the recent observations of distinct populations of C 60 and C 70 are discussed.
Chronic neurological sequelae to organophosphate pesticide poisoning. (1994)

While these findings are limited by low response rates and by small sample sizes for specific pesticides, this study was based on a large surveillance database and is the largest study to date of the chronic effects of organophosphate pesticide poisoning. The evidence of some long-term effects of poisoning is consistent with two prior studies.
Response of a biologically inspired MEMS differential microphone diaphragm (2002)

The development of a novel, biologically inspired acoustic sensor is presented. The primary goal of this effort is to construct a miniature device that is capable of detecting the orientation of an incident sound source with an accuracy of 2&deg;. The design approach follows from our investigation of the mechanics of directional hearing in the parasitoid fly, Ormia ochracea. This animal has been shown to be able to detect changes in the line of bearing of an incident sound that are as small as 2&deg;. The tympanal structures of the ears of this animal suggest a novel approach to designing very small directionally sensitive microphones. A microphone diaphragm design is presented that has been fabricated using silicon microfabrication technology. Measurements of the static deflection due to intrinsic stress and of the response to sound are shown to be in excellent agreement with predictions. Predicted results indicate that this microphone concept could lead to a practical differential microphone with self-noise as low as 20 dBA.
Induction of specific immunoglobulin A in the small intestine, colon-rectum, and vagina measured by a new method for collection of secretions from local mucosal surfaces (1994)

In order study patterns of local antibody responses following mucosal immunization of mice via different routes, a method for collection of secretions directly from mucosal surfaces was developed. Mice were immunized on days 0, 10, 17, and 24 by administration of cholera toxin into the oral cavity, stomach, colon-rectum, or vagina. At sacrifice on day 32, absorbent wicks were placed in the oral cavity and, via an applicator tube, into the vagina and distal colon-rectum and along the entire small intestine after flushing of luminal contents. Protein was quantitatively extracted from wicks, and specific anti-cholera toxin immunoglobulin A (IgA) and IgG were measured by enzyme-linked immunosorbent assay. Concentrations of specific IgA in secretions at various mucosal sites were dramatically influenced by the route of immunization. Oral immunization effectively induced IgA in saliva, and the intragastric route was optimal for induction of IgA in the small intestine. High levels of specific IgA appeared on the colonic-rectal mucosal surface only after rectal delivery of antigen. Oral, gastric, and rectal immunizations also produced distant responses in the vagina. Following vaginal immunization, however, neither local nor distant IgA responses were detected. These results suggest that vaccines intended for protection of colonic-rectal and vaginal mucosal surfaces might best be administered by the rectal route.
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary (2005)

We demonstrated the use of the KEGG Orthology (KO), part of the KEGG suite of resources, as an alternative controlled vocabulary for automated annotation and pathway identification. We developed a KO-Based Annotation System (KOBAS) that can automatically annotate a set of sequences with KO terms and identify both the most frequent and the statistically significantly enriched pathways. Results from both whole genome and microarray gene cluster annotations with KOBAS are comparable and complementary to known annotations. KOBAS is a freely available stand-alone Python program that can contribute significantly to genome annotation and microarray analysis.
Cloning and Secondary Structure Analysis of Caleosin, a Unique Calcium-Binding Protein in Oil Bodies of Plant Seeds (1999)

Plant seed oil bodies comprise a matrix of triacylglycerols surrounded by a monolayer of phospholipids embedded with abundant oleosins and some minor proteins. Three minor proteins, temporarily termed Sops 1-3, have been identified in sesame oil bodies. A cDNA sequence of Sop1 was obtained by PCR cloning using degenerate primers derived from two partial amino acid sequences, and subsequently confirmed via immunological recognition of its over-expressed protein in Escherichia coli. Alignment with four published homologous sequences suggests Sop1 as a putative calcium-binding protein. Immunological cross-recognition implies that this protein, tentatively named caleosin, exists in diverse seed oil bodies. Caleosin migrated faster in SDS-PAGE when incubated with Ca2+. A single copy of caleosin gene was found in sesame genome based on Southern hybridization. Northern hybridization revealed that both caleosin and oleosin genes were concurrently transcribed in maturing seeds where oil bodies are actively assembled. Hydropathy plot and secondary structure analysis suggest that caleosin comprises three structural domains, i.e., an N-terminal hydrophilic calcium-binding domain, a central hydrophobic anchoring domain, and a C-terminal hydrophilic phosphorylation domain. Compared with oleosin, a conserved proline knot-like motif is located in the central hydrophobic domain of caleosin and assumed to involve in protein assembly onto oil bodies.
Advanced therapy of prostate disease (2000)

Advanced therapy of prostate disease , Advanced therapy of prostate disease , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Chymotrypsin inhibitory activity of normal C1‐inhibitor and a P1 Arg to His mutant: Evidence for the presence of overlapping reactive centers (1993)

C1-inhibitor is a serine proteinase inhibitor that is active against C1s, C1r, kallikrein, and factor XII. Recently, it has been shown that it also has inhibitory activity against chymotrypsin. We have investigated this activity of normal human C1-inhibitor, normal rabbit C1-inhibitor, and P1 Arg to His mutant human C1-inhibitors and find that all are able to inhibit chymotrypsin and form stable sodium dodecyl sulfate-resistant complexes. The Kass values show that the P1 His mutant is a slightly better inhibitor of chymotrypsin than normal human C1-inhibitor (3.4 x 10(4) compared with 7.3 x 10(3)). The carboxy-terminal peptide of normal human C1-inhibitor, derived from the dissociated protease-inhibitor complex, shows cleavage between the P2 and P1 residues. Therefore, as with alpha 2-antiplasmin, C1-inhibitor possesses two overlapping P1 residues, one for chymotrypsin and the other for Arg-specific proteinases. In contrast, with the P1 His mutant, the peptide generated from the dissociation of its complex with chymotrypsin demonstrated cleavage between the P1 and P'1 residues. Therefore, unlike alpha 2-antiplasmin, chymotrypsin utilizes the P2 residue as its reactive site in normal C1-inhibitor but utilizes the P1 residue as its reactive site in the P1 His mutant protein. This suggests that the reactive center loop allows a degree of induced fit and therefore must be relatively flexible.
Cilengitide: A Prototypic Integrin Inhibitor for the Treatment of Glioblastoma and Other Malignancies (2011)

Integrins are critical intermediaries in a wide spectrum of cancer cell activities and thus represent a highly attractive target in oncology therapy. Nonetheless, successful exploitation of anti-integrin therapeutics has proven challenging to date for cancer patients. In this review, we will focus on cilengitide, an RGD pentapeptide inhibitor of α V integrins. Although several integrin inhibitors are under clinical evaluation, cilengitide is the most clinically advanced and is emerging as a prototype for this class of anticancer therapy. A foundation of encouraging preclinical studies led to a well-designed clinical development plan that culminated in a pivotal phase III study of cilengitide in combination with radiation therapy and temozolomide chemotherapy for newly diagnosed glioblastoma patients. Accrual to this study recently completed, while phase II studies of cilengitide are ongoing for head and neck cancer as well as lung cancer. Important future considerations for cilengitide and other integrin-targeting agents will likely include the identification of optimal combinatorial regimens and the delineation of biomarkers associated with efficacy.
The design and analysis of MIMO antenna (2011)

This paper puts forward a design of MIMO antenna and simulates the antenna's characteristics. By adjusting the dimensions of the upper patch, an wide bandwidth omni-directional micro-strip antenna has been achieved, whose center frequency is 5GHz and its bandwidth reaches 2.2GHz with the VSWR below 1.4. Based on it, two types of array also have been analyzed, the one is planar antenna array include four elements, the other is ring-type four-cell antenna array, and achieved lots of valuable results.
Expression of hepatitis E virus putative structural proteins in recombinant vaccinia viruses (1994)

Hepatitis E virus (HEV) is a polyadenylated, positive-stranded RNA virus which is a major cause of enterically transmitted non-A, non-B hepatitis in many developing countries. The viral genome contains three different open reading frames (ORFs): ORF1, which is believed to encode nonstructural proteins, and ORF2 and ORF3, which are believed to encode structural proteins. The full-length putative structural proteins encoded by ORF2 and ORF3 of HEV have been cloned and expressed in recombinant vaccinia virus. Proteins encoded by ORF2 and ORF3 when expressed in vaccinia virus are recognized by pooled sera obtained from individuals with acute hepatitis E. Vaccinia-expressed viral gene products of HEV will have utility in characterizing the cell-mediated immune response to HEV.
Genomic structure and inducible expression of the IL-22 receptor alpha chain in mice. (2003)

IL-22 is a newly identified member of the interferon/IL-10 family. In humans, IL-22 signals through a heteroduplex receptor consisting of IL-22R and CRF2-4/IL-10Rbeta. To investigate the physiological function of IL-22 and IL-22R, we isolated a cDNA encoding the mouse IL-22R, which has been a missing component of the functional receptor complex for mouse IL-22. Subsequently, we identified the genomic sequence of the mouse IL-22R gene by a database search. The gene consists of about 24 kb and is split into seven exons. Interestingly, intron 2 begins with a GC dinucleotide instead of the consensus GT, although otherwise the overall structure of the mouse IL-22R gene is strikingly similar to its human counterpart. The gene was mapped to mouse chromosome 4 in the region syntenic to the human IL-22R gene locus. In normal mice, IL-22R mRNA is detected at very low levels in restricted organs such as the kidney, liver, and lung. However, upon lipopolysaccharide stimulation, IL-22R mRNA expression is highly upregulated in the liver, in contrast to CRF2-4, which is expressed constitutively in a variety of tissues. Thus, the expression of the functional IL-22 receptor in the liver is regulated at the gene transcription level.
Genes for Breakfast: The Have-Your-Cake and-Eat-lt-Too of Bacterial Transformation (1993)

Bacterial transformation, in which cells take up and recombine free strands of DNA, is the simplest process thought to have evolved for genetic exchange, i.e., because of the potential benefits of producing progeny with recombinant genotypes. However, two other functions are equally plausible: acquisition of intact DNA strands to use for recombinational repair of DNA damage, and acquisition of the nutrients contained in DNA molecules. Although the recombinant progeny produced by transformation can be beneficial, the success of genes causing transformation is limited by other factors, especially by the genetic quality of DNA derived from dead cells. Our recent experiments in the naturally transformable bacteria Haemophilus influenzae and Bacillus subtilis suggest that the DNA-repair hypothesis is unlikely to be correct. In H. influenzae, transformation does not detectably increase the cells' ability to survive DNA damage. More importantly, we have found that, although competence (the ability to take up DNA) is induced by nutritional limitation in both H. influenzae and B. subtilis, it is not induced by DNA damage in either. Thus we favor the hypothesis that transformation evolved as a nutrient-uptake system, especially because unrelated DNA is abundant in the environments of many naturally transformable bacteria.
Atomic force microscopy of DNA on mica and chemically modified mica. (1992)

Atomic force microscopy (AFM) was used to image circular DNA adsorbed on freshly cleaved mica and mica chemically modified with Mg(II), Co(II), La(III), and Zr(IV). Images obtained on unmodified mica show coiling of DNA due to forces involved during the drying process. The coiling or super twisting appeared to be right handed and the extent of super twisting could be controlled by the drying conditions. Images of DNA observed on chemically modified surfaces show isolated open circular DNA that is free from super twisting, presumably due to strong binding of DNA on chemically modified surfaces.
Adapting inverse planning to patient and organ geometrical variation: algorithm and implementation (2003)

Image guided radiotherapy has the potential to improve both tumour control and normal tissue sparing by including temporal patient specific geometry information into the adaptive planning process. In this study we present a practical method of image guided adaptive inverse planning based on computed tomography (CT) and portal image feedback during the treatment course. The method is based on a general description of the radiotherapy optimization problem subject to dynamic geometrical variations of the patient/organs. We will demonstrate the feasibility of off-line image feedback into the inverse planning process with the example of three prostate cancer patients. CT and portal images acquired during the early course of the treatment are used to predict the geometrical variation distribution of a patient and to re-optimize the treatment plan accordingly. We will study the convergence of the optimization problem with respect to the number of image measurements and adaptive feedback loops.
Behavioral correlates of soman-induced neuropathology: deficits in DRL acquisition. (1986)

Rats (N = 45) pretrained to lever press for milk reinforcement on a continuous reinforcement (CRF) schedule were injected with 100-110 micrograms/kg of the anticholinesterase soman (N = 24) or saline (N = 21) SC. Subjects exposed to soman experienced moderate to severe acute symptoms of anticholinesterase intoxication. After a 3 week recovery period, all surviving subjects were retrained on CRF, then given 45 training sessions on a differential reinforcement of low rates (DRL) 20 sec schedule, followed by 10 sessions of extinction. Brains of all subjects were then examined for evidence of neuropathology. Subjects exposed to soman showed no improvement over sessions in the number of reinforcements earned on the DRL schedule due to an inefficient patterning of responses. There were no differences between groups in the number of total DRL responses or terminal extinction responses. Neuropathology was most evident in dorsal thalamic areas, primary olfactory/piriform cortex and amygdala of subjects exposed to soman. There were significant correlations between the severity of acute intoxication scores, degree of neuropathology, and deficits in DRL performance. The results demonstrate that exposure to high doses of this anticholinesterase agent can result in neural damage and persistent decrements in performance of certain operant tasks.
The amino‐terminal domain of the P‐pilus adhesin determines receptor specificity (1994)

Summary Pyelonephritic isolates of Escherichia coli commonly express P‐pili, which mediate bacterial attachment to glycolipids on epithelial cell surfaces. Three classes of P‐pili have been defined, based on varying specificity for galabiose‐containing glycolipids. Variation in adhesive capacity is correlated with a shift in preferred host, suggesting that host tropism depends largely on detailed specificity for the globoseries glycolipids. In this study we examined the importance of the PapG adhesin in determining receptor specificity. Translational fusions were constructed between the ammo‐terminus of the PapG adhesin from each of the three pilus classes and a reporter protein. The binding specificity of the purified fusion proteins in vitro was identical to that seen with whole bacteria. Adherence of intact bacteria to cultured kidney cells was markedly reduced by a monoclonal antibody specific for the Class III adhesin (previously denoted PrsG ), confirming the importance of the ammo‐terminus of PapG in mediating attachment to a receptor when presented on the eukaryotic cell surface. These results suggest that the detailed receptor specificity resides solely within the amino‐terminus of the PapG adhesin and is independent of the complex pilus architecture.
The Escherichia coli Yej Transporter Is Required for the Uptake of Translation Inhibitor Microcin C (2007)

Microcin C (McC), a peptide-nucleotide antibiotic, targets aspartyl-tRNA synthetase. By analyzing a random transposon library, we identified Escherichia coli mutants resistant to McC. Transposon insertions were localized to a single locus, yejABEF, which encodes components of a putative inner membrane ABC transporter. Analysis of site-specific mutants established that all four components of the transporter are required for McC sensitivity. Since aspartyl-tRNA synthetase in yej mutant extracts was fully sensitive to McC, we conclude that yej mutations interfere with McC uptake and that YejABEF is the only inner membrane transporter responsible for McC uptake in E. coli. Other substrates of YejABEF remain to be identified.
Distance Is Not Dead: Social Interaction and Geographical Distance in the Internet Era (2009)

The Internet revolution has made long-distance communication dramatically faster, easier, and cheaper than ever before. This, it has been argued, has decreased the importance of geographic proximity in social interactions, transforming our world into a global village with a borderless society. We argue for the opposite: while technology has undoubtedly increased the overall level of communication, this increase has been most pronounced for local social ties. We show that the volume of electronic communications is inversely proportional to geographic distance, following a Power Law. We directly study the importance of physical proximity in social interactions by analyzing the spatial dissemination of new baby names. Counter-intuitively, and in line with the above argument, the importance of geographic proximity has dramatically increased with the internet revolution.
CARD15 polymorphisms are associated with anti-Saccharomyces cerevisiae antibodies in caucasian Crohn's disease patients (2005)

Carriage of CARD15 gene polymorphisms and the serological marker anti-Saccharomyces cerevisiae antibodies (ASCA) are two markers for Crohn's disease (CD). Similar phenotypes have been associated with both markers. In the present study we analysed whether both markers were associated with each other and, if so, whether this association could be explained by a direct link or by an indirect association with those phenotypes. Therefore, we included 156 consecutive Caucasian CD patients and assessed the prevalence of the three common single nucleotide polymorphisms in the CARD15 gene. Serum samples were analysed for IgA and IgG ASCA by ELISA. CD patients with CARD15 polymorphisms were more frequently ASCA positive (OR 2.7 (1.4-5.2); P = 0.002) and had higher titres for ASCA IgA (P = 0.005) and ASCA IgG (P < 0.001) compared to patients carrying the wild type polymorphisms. Multivariate analysis demonstrated that this association was independent from ileal disease, penetrating disease and stricturing disease, the need for resective bowel surgery, familial cases, smoking habits and early age at onset. Homozygotes or compound heterozygotes for CARD15 polymorphisms had significantly more frequent ASCA positivity compared to single heterozygotes (OR 9.1 (1.1-74.2), P(c) (corrected P-value) = 0.030). These data indicate that there is a significant association between the carriage of CARD15 polymorphisms and ASCA, independent of the described phenotypes. Moreover, ASCA positivity is more frequent in CD patients carrying 2 CARD15 polymorphisms compared to single heterozygotes.
Current status of cancer immunotherapy (2014)

To prove clinical benefits of cancer vaccine is currently difficult, except for one phase III trial has documented improved overall survival with the vaccine, Sipuleucel-T, although induction of anti-tumor immune responses through cancer vaccine is theoretically promising and would be straightforward. In contrast, immune checkpoint blockade with anti-CTLA4 mAb and anti-PD-1 mAb has demonstrated clear evidence of objective responses including improved overall survival and tumor shrinkage, driving renewed enthusiasm for cancer immunotherapy in multiple cancer types. In addition, there is a promising novel cancer immunotherapy, CAR therapy-a personalized treatment that involves genetically modifying a patient's T-cells to make them target tumor cells. We are now facing new era of cancer immunotherapy.