gebhart/patrepeval huggingface dataset:
The Golgi apparatus: Lessons from Drosophila (2009)

Historically, Drosophila has been a model organism for studying molecular and developmental biology leading to many important discoveries in this field. More recently, the fruit fly has started to be used to address cell biology issues including studies of the secretory pathway, and more specifically on the functional integrity of the Golgi apparatus. A number of advances have been made that are reviewed below. Furthermore, with the development of RNAi technology, Drosophila tissue culture cells have been used to perform genome-wide screens addressing similar issues. Last, the Golgi function has been involved in specific developmental processes, thus shedding new light on the functions of a number of Golgi proteins.
Excretion of FDG into saliva and its significance for PET imaging (2002)

The salivary FDG concentration is higher than expected from the low physiologic content of glucose. This may--similarly to renal excretion--reflect a different behavior of FDG and glucose during reabsorption processes. Nevertheless, the salivary concentration of FDG is so low that no relevant influence on PET imaging is to be expected. Accordingly, the drinking of water prior to the scan is of no benefit for FDG PET imaging of the head and the neck.
Seroprevalence of Pandemic 2009 (H1N1) Influenza A Virus among Schoolchildren and Their Parents in Tokyo, Japan (2011)

Since its emergence, the 2009 pandemic H1N1 virus has spread rapidly throughout the world. Previously, we reported that most individuals born after 1920 do not have cross-reactive virus-neutralizing antibodies against pandemic (H1N1) 2009 virus, indicating that they were immunologically naïve to the pandemic virus prior to its emergence. This finding provided us with an excellent opportunity for a seroepidemiological investigation of the transmission mode of the pandemic virus in the community. To gain insight into its transmission within communities, we performed a serosurvey for pandemic virus infection with schoolchildren at an elementary school in Tokyo, Japan, and their parents. We observed a high prevalence of neutralizing antibodies to the pandemic virus in the children at this school, although the percentage of children positive for the neutralizing antibodies varied among classrooms. While a much lower prevalence was observed among parents, seropositivity of the parents correlated with that of their schoolchildren. Moreover, many adults appeared to have experienced asymptomatic infection with the pandemic virus. These data suggest that the pandemic virus was readily transmitted among schoolchildren in elementary schools and that it was also transmitted from schoolchildren to their parents.
Virtual monochromatic imaging in dual‐source dual‐energy CT: Radiation dose and image quality (2011)

In dual-source dual-energy CT, optimal virtual monochromatic energy depends on patient size, dose partitioning, and the image quality metric optimized. With the optimal monochromatic energy, the noise level was similar to and the iodine CNR was better than that in 120 kV images for the same radiation dose. Compared to single-energy 80 kV images, the iodine CNR in virtual monochromatic images was lower for small to large phantom sizes.
Development of Vaccine Adjuvants Using Polymeric Nanoparticles and Their Potential Applications for Anti-HIV Vaccine (2007)

The development of a prophylactic/therapeutic HIV-1 vaccine based on recombinant proteins is needed for the control of the worldwide AIDS epidemic. Subunit protein and peptide vaccines are generally very safe, with well-defined components. However, these antigens are often poorly immunogenic, and thus require the use of adjuvants to induce adequate immunity. Particulate adjuvants (e.g. micro/nanoparticles, emulsions, ISCOMS, liposomes, virosomes, and virus-like particles) have been widely investigated as HIV-1 vaccine delivery systems. Antigen uptake by antigen-presenting cells (APC) is enhanced by the association of the antigens with polymeric micro/nanoparticles. The adjuvant effect of micro/nanoparticles appears to largely be a consequence of their uptake into APC. More importantly, particulate antigens have been shown to be more efficient than soluble antigens for the induction of immune responses. Over the past two decades, we have studied the synthesis and clinical applications of core-corona polymeric nanospheres composed of hydrophobic polystyrene and hydrophilic macromonomers. Core-corona type polymeric nanospheres have applications in various technological and biomedical fields, because their chemical structures and particle size can be easily controlled. In this study, we focused on the development of a HIV-1 vaccine using polymeric nanoparticles. We evaluated the immunization strategies for HIV-1-capturing core-corona type polystyrene nanospheres that would efficiently induce HIV-1-specific IgA responses in female mice and the macaque genital tract. Moreover, based on this research, we attempted to develop novel biodegradable nanoparticles composed of poly (gamma-glutamic acid) (gamma-PGA) for protein-based vaccine delivery. These HIV-1-capturing nanospheres and protein-loaded gamma-PGA nanoparticles have shown unique potential as vaccine carriers.
The worldwide societal costs of dementia: Estimates for 2009 (2010)

The worldwide cost of dementia has increased by 34% (18% in fixed prices) between 2005 and 2009.
Hydrogen Spillover Enhanced Hydriding Kinetics of Palladium-Doped Lithium Nitride to Lithium Imide (2009)

Hydrogen storage in complex metal hydrides often suffers from unsatisfied hydriding kinetics of the corresponding complex metals under moderated conditions, partly due to the kinetic barrier associated with the breaking of the H−H bond. Therefore, doping catalysts for H−H bond breakage become a feasible strategy to improve the hydriding kinetics because hydrogen adatoms can efficiently spill over from catalyst to complex metals. To realize this strategy, we developed a unique method to uniformly dope catalytic metal in the storage complex metals via synthesis of the eutectic of the catalytic metal and the precursory storage metal. This method eliminates the use of support materials for catalysts, while still maintaining the large surface area and uniformity of the catalysts. We demonstrated that Li3NPd0.03 with nanoscopic Pd uniformity can be prepared through nitridization of LiPd0.01 eutectic. The resulting Li3NPd0.03 exhibits enhanced hydriding kinetics over pure Li3N for the reaction Li3N + H2 ↔ Li2NH + LiH under moderate conditions. The activation barrier for the hydriding of Li3NPd0.03 was measured to be ∼28 kJ/mol. DFT calculation reveals that the hydrogen adatom migration barrier from the palladium to the nitrogen atom is ∼25 kJ/mol. These results indicate that the Pd-doped LiN3 is hydrided by hydrogen adatoms that migrate from the Pd catalyst and the kinetic barrier for such a hydriding process is mainly ascribed to the diffusion barrier of the H adatom from the palladium to the nitrogen atom.
P1‐342: Relationship between cardiovascular disease risk factors and Alzheimer's disease Aβ protein in subjective memory complainers (2008)

Current research indicates a strong link between obesity and overweight, cardiovascular disease (CVD) and risk for developing Alzheimer's disease (AD). This may be exacerbated in people who possess the major AD genetic risk factor apolipoprotein Eϵ4 (APOEϵ4). The biological mechanisms underlying these associations are still unclear. Since subjective memory complaint (SMC) may be a potential early indicator for cognitive decline, it was pertinent to examine these risk factors in a cohort of SMC to determine their clinical significance. As beta amyloid (Aβ) is considered to play a central role in AD, we hypothesized that the CVD risk profile (increased low density lipoprotein-LDL and reduced high density lipoprotein-HDL) may be associated with raised plasma Aβ levels. We also hypothesized that the CVD risk profile may be associated with poorer cognition, as assessed using a neuropsychological battery. We explored this association in 198 individuals from a study of SMC (average age= 63 years). A positive correlation between Aβ40 and triglycerides (rho= 0.147, p= 0.020) and a negative correlation between Aβ40 and HDL was observed. The latter was stronger in those who do not possess the APOEϵ4 allele (rho= -0.315, p=0.00). Age and HDL remained predictive for plasma Aβ40 using multivariate regression analysis. HDL levels were also positively correlated with cognitive performance. The negative association between HDL and Aβ is reported here for the first time and has implications for the development of novel therapeutics that complement LDL lowering approaches. Our findings confirm the close association between lipid and Aβ metabolism and emphasize the importance of the APOEϵ4 allele in modulating AD risk. The role of HDL as a predictor of cognitive decline needs to be assessed in a larger longitudinal study.
Amino acid sequence of Escherichia coli citrate synthase (1984)

Detailed evidence for the amino acid sequence of allosteric citrate synthase from Escherichia coli is presented. The evidence confirms all but 11 of the residues inferred from the sequence of the gene as reported previously [Ner, S. S., Bhayana, V., Bell, A. W., Giles, I. G., Duckworth, H. W., & Bloxham, D. P. (1983) Biochemistry 22, 5243]; no information has been obtained about 10 of these (residues 101-108 and 217-218), and we find aspartic acid rather than asparagine at position 10. Substantial regions of sequence homology are noted between the E. coli enzyme and citrate synthase from pig heart, especially near residues thought to be involved in the active site. Deletions or insertions must be assumed in a number of places in order to maximize homology. Either of two lysines, at positions 355 and 356, could be formally homologous to the trimethyllysine of pig heart enzyme, but neither of these is methylated. It appears that E. coli and pig heart citrate synthases are formed of basically similar subunits but that considerable differences exist, which must explain why the E. coli enzyme is hexameric and allosterically inhibited by NADH, while the pig heart enzyme is dimeric and insensitive to that nucleotide.
Quantitative analysis of p185HER2neu protein in breast cancer and its association with other prognostic factors (1997)

The total cellular p185HER-2/neu protein (p185) content was measured by ELISA in 346 invasive primary breast cancers, and the results were compared with those of estrogen (ER) and progesterone (PR) receptors, pS2 and Cathepsin D (Cat D) content. At a cut-off level of 260 fmol/mg protein, 53 of the 346 tumors (15%) were p185-positive. A significant positive correlation was observed between p185 levels and those of Cat D, and a weaker, though significant, positive correlation with ER, and pS2 levels, but not with those of PR. However, when only the 293 p185-negative tumors were considered, the correlation between p185 and ER improved substantially, and statistical significance was reached for PR. p185-positive tumors exhibited lower ER and PR content and higher Cat D content than p185-negative tumors. The pS2 content, in contrast, did not undergo significant variation. Tumors considered to be p185-positive were significantly more frequently positive for Cat D at the cut-off of 45 pmol/mg protein, and were more frequently negative for ER and/or PR, but only significant at the cut-off of 15 fmol/mg or higher for both steroid receptors. Finally, p185 status was not associated with menopausal status, tumor size, axillary-lymph-node invasiveness or distant metastases. These results suggest that 260 fmol/mg protein as the cut-off for p185 allows the identification of a tumoral sub-population with a more aggresive phenotype.Int. J. Cancer 74:175–179, 1997. © 1997 Wiley-Liss, Inc.
The Promotion and Marketing of OxyContin: Commercial Triumph, Public Health Tragedy (2008)

I focus on issues surrounding the promotion and marketing of controlled drugs and their regulatory oversight. Compared with noncontrolled drugs, controlled drugs, with their potential for abuse and diversion, pose different public health risks when they are overpromoted and highly prescribed. An in-depth analysis of the promotion and marketing of OxyContin illustrates some of the associated issues. Modifications of the promotion and marketing of controlled drugs by the pharmaceutical industry and an enhanced capacity of the Food and Drug Administration to regulate and monitor such promotion can have a positive impact on the public health.
The Coevolution of Cooperation and Trait Distinction (2008)

본 논문은 국지적 상호작용 하에서 행위자들간에 특성의 차이에 근거한 구별짓기가 협조적 행위의 진화에 미치는 영 향을 분석한다. 이 논문에서는 이러한 구별짓기의 성향이 왜, 그리고 어떤 메커니즘을 통해서 진화해나가는지를 보이고 자 시도할 것이다. 아울러 구별짓기 성향과 함께 내부인과 외부인을 향한 행동을 다르게 함으로써 어떻게 내부인에 대한 이타적 협조행동을 발생시키는지, 더 나아가 구별짓기의 근거가 되는 행위자들의 여러 특성들(생물학적 혹은 문화적)은 어떻게 변화해 나가고 이들 특성의 변화가 구별짓기와 협조적 행동에 어떤 효과를 가져오는지를 살펴보고자 한다. 더 나 아가 본 논문에서는 구별짓기가 협조적 행위의 진화에 영향을 미치는 과정을 장/단기로 구분함으로써 구별짓기의 효과를 보다 명확히 규명하고자 한다
Effect ofallergen avoidance athighaltitude on direct andindirect bronchial hyperresponsiveness andmarkers of inflammation inchildren withallergic asthma (1996)

Background - Improvementofallergic asthmaisseenathighaltitude partly becauseoflowconcentrations ofallergen, especially housedustmite.Toinvestigate theeffect ofahypoallergenic environment (Davos, 1560m)onairways inflammation, thechanges inbronchial hyperresponsivenessmeasured withmethacholine andadenosine5'-monophosphate (AMP),blood eosinophils, eosinophil cationic protein (ECP),andserumIgEwerestudied. Methods -In16allergic asthmatic children testswereperformed on admission and after onemonth.Medication waskeptunchangedduring themonthofinvestigation and thepatients performedpeakexpiratory flow(PEF)measurements twice daily. Results -Afteronemonthathighaltitude a considerable improvement wasseenin theprovocative concentration ofAMP causing a 20%fall inforcedexpiratory volumeinonesecond(PC20AMP),but notwithmethacholine. Therewasalsoa reduction intotal bloodeosinophils and ECP.No changeinserumIgEwasobserved. Peakflowvariability decreased. Conclusions - Afteronemonthathigh altitude a reductionin airwaysinflammation occurs.Theresults indicate thatAMP responsiveness isa more accuratemarkerofdisease activity inrelation toinflammation inasthmathan methacholine. The benefits ofallergen avoidance athighaltitude haveimportant clinical implications forchildren withallergic asthma. (Thorax 1996;51:582-584)
Evidence for nitric oxide‐mediated oxidative damage in chronic inflammation Nitrotyrosine in serum and synovial fluid from rheumatoid patients (1994)

Reaction of nitric oxide (NO.) with superoxide radical generates peroxy-nitrite, which can decompose to products that nitrate aromatic amino acids. Such nitro-aromatics may be 'markers' of NO.-dependent oxidative damage. Blood serum and synovial fluid from patients with the inflammatory joint disease rheumatoid arthritis contain 3-nitrotyrosine. By contrast, body fluids from normal subjects and patients with osteoarthritis contain no detectable 3-nitrotyrosine; much lower levels were found in serum from patients in the early stages of rheumatoid arthritis. This is evidence that NO. plays a role in joint damage in rheumatoid arthritis.
Endothelial cells and hyperthermia (1994)

Most radiation oncologists are aware of the effects of clinical hyperthermia on neoplastic cells. Its effects on blood vessels, however, are not as well recognized. Yet, since the 1960s a number of investigators have described and categorized the effects of hyperthermia on microvessels (in vivo), and on cultured endothelial cells (EC) (in vitro). Both EC and microvessels can be lethally damaged by the hyperthermia doses used as antineoplastic therapy. In vitro data indicate that capillary EC are moderately sensitive to hyperthermia. Proliferating EC are more thermosensitive suggesting that microvessels of malignant neoplasms (which contain many proliferating EC) are more affected than microvessels of normal tissues. This differential sensitivity of microvessels has also been observed in blood flow studies. Furthermore, hyperthermia inhibits angiogenesis. Thus, some of the antineoplastic effects of heat are caused by ischaemia due to obstruction or destruction of the tumour vessels or to inability to form new vessels. Sublethal EC damage can also be demonstrated, resulting in decreased synthesis of most proteins including adhesion molecules (as well as increased expression of a few such as heat shock proteins) and producing reversible loss of cytoskeletal elements. The therapeutic advantage provided by the higher thermal sensitivity of neoplastic vessels should be exploited further, perhaps by developing strategies specifically aimed to the tumour microvasculature.
Methylation induced premeiotically in Ascobolus: coextension with DNA repeat lengths and effect on transcript elongation. (1993)

The effect of duplications of gene fragments on the triggering of DNA methylation induced premeiotically (MIP) was studied in the sexual progeny of strains harboring, in addition to the resident met2 gene, a fragment of this gene inserted at an ectopic position. Cytosine methylation of the resident gene was checked for each of the eight duplications tested. Methylation was always found and it was coextensive with the length of the duplications. Silencing of the resident gene was triggered by duplications of segments corresponding to the region 5' to the open reading frame, to only the open reading frame, or to segments beginning 0.87-1.2 kb downstream from the transcription start. Silencing was accompanied by either the absence of transcripts or the presence of truncated transcripts, which suggests that methylation acts on transcript elongation.
Nanostructure of Native Pectin Sugar Acid Gels Visualized by Atomic Force Microscopy (2004)

Height and phase shift images of high methoxyl sugar acid gels (HMSAG) of pectin were obtained by atomic force microscopy in the tapping mode. Images revealed that pores in these gels were fluid and flattened out when measured as a function of time. These images revealed for the first time the structure of adsorbed sugar on pectin in the hydrated native gels and how the pectin framework is organized within these gels. Segmentation of images revealed that the underlying pectin framework contained combinations of rods, segmented rods, and kinked rods connected end to end and laterally. The open network of strands was similar to pectin aggregates from 5 mM NaCl solution imaged earlier by electron microscopy (Fishman et al., Arch. Biochem. Biophys. 1992, 294, 253). Area measurements revealed that the ratio of bound sugar to pectin was in excess of 100 to 1 (w/w). Furthermore, images indicated relatively small differences in the organization of native commercial citrus pectin, orange albedo pectin, and lime albedo pectin gels at optimal pH as determined in this study. The findings are consistent with earlier gel strength measurements of these gels. In addition, values of gel strength were consistent with values of molar mass and viscosity of the constituent pectins in that they increased in the same order. Finally, we demonstrated the advantage of simultaneous visualization of height and phase shift images for observing and quantitating the nanostructure of relatively soft gels which are fully hydrated with a buffer.
Bio-inspired topology control mechanism for autonomous underwater vehicles used in maritime surveillance (2013)

Autonomous underwater vehicles (AUVs) are increasingly used in maritime applications to acquire underwater information. With the guidance of intelligent topology control algorithms, AUVs adjust their positions efficiently such that they achieve desired underwater wireless sensor network (UWSN) configurations. A suitable application can be using AUVs in surveillance tasks, where they uniformly spread throughout a harbor entry or around a large civilian or military maritime vessel (e.g., an aircraft carrier) to detect any hostile or unexpected underwater intrusions. Since geographical characteristics are different for each port (shape, depth, etc.) and underwater currents constantly change, manually controlling underwater vehicles for these tasks is not feasible. In this paper, we present a particle swarm optimization (PSO) based topology control mechanism, called 3D-PSO, for AUVs operating in unknown 3D underwater spaces. 3D-PSO uses limited information collected from an AUV's neighborhood to make movement decisions over an unknown 3D space. Each AUV, using our 3D-PSO, is able to adjust its movement speed and direction to achieve a better location towards obtaining a uniform distribution. Simulation experiments demonstrate that, despite the significant variance of topographies of harbor entrances and the undersides of ships, 3D-PSO is an efficient tool to guide AUVs in creating a protection area for a harbor or a maritime vessel.
Toward individualized SAR models and in vivo validation (2011)

The specific absorption rate (SAR) is a limiting constraint in sequence design for high-field MRI. SAR estimation is typically performed by numerical simulations using generic human body models. This entails an intrinsic uncertainty in present SAR prediction. This study first investigates the required detail of human body models in terms of spatial resolution and the number of soft tissue classes required, based on finite-differences time-domain simulations of a 3 T body coil. The numerical results indicate that a resolution of 5 mm is sufficient for local SAR estimation. Moreover, a differentiation between fatty tissues, water-rich tissues, and the lungs was found to be essential to represent eddy current paths inside the human body. This study then proposes a novel approach for generating individualized body models from whole-body water-fat-separated MR data and applies it to volunteers. The SAR hotspots consistently occurred in the arms due to proximity to the body coil as well as in narrow regions of the muscles. An initial in vivo validation of the simulated fields in comparison with measured B(1)-field maps showed good qualitative and quantitative agreement.
Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search (2002)

We present a statistical model to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST. Employing the expectation maximization algorithm, the analysis learns to distinguish correct from incorrect database search results, computing probabilities that peptide assignments to spectra are correct based upon database search scores and the number of tryptic termini of peptides. Using SEQUEST search results for spectra generated from a sample of known protein components, we demonstrate that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides. This analysis makes it possible to filter large volumes of MS/MS database search results with predictable false identification error rates and can serve as a common standard by which the results of different research groups are compared.