gebhart/patrepeval huggingface dataset:
Treatment of Indolent, Nonencapsulated Cryptococcal Meningitis Associated with Hydrocephalus (2012)

Infection with cryptococcal meningitis is uncommon in immunocompetent patients. The major virulence factor is the polysaccharide capsule, while nonencapsulated mutants are generally considered nonpathogenic. The authors present a case of hydrocephalus caused by meningitis from an indolent, nonencapsulated Cryptococcus sp. requiring placement and multiple revisions of a ventriculoperitoneal shunt (VPS). The patient presented with progressively worsening occipital headaches. Computed tomography and magnetic resonance imaging showed significant hydrocephalus with no apparent cause. Her symptoms initially resolved after placement of a VPS, but returned four months later. Cultures of the shunt tubing and cerebrospinal fluid (CSF) showed no bacterial infection. When the symptoms failed to resolve, CSF fungal culture revealed Cryptococcus-like yeast, although the organisms were nonencapsulated, and the cryptococcal antigen was negative. After antibiotic therapy, the symptoms resolved. The unusual clinical presentation delayed the diagnosis, highlighting the importance of understanding the detection, diagnosis, and treatment of meningeal infections caused by C. neoformans.
Structural Data De-anonymization (2014)

In this paper, we study the quantification, practice, and implications of structural data (e.g., social data, mobility traces) De-Anonymization (DA). First, we address several open problems in structural data DA by quantifying perfect and (1-ε)-perfect structural data DA}, where ε is the error tolerated by a DA scheme. To the best of our knowledge, this is the first work on quantifying structural data DA under a general data model, which closes the gap between structural data DA practice and theory. Second, we conduct the first large-scale study on the de-anonymizability of 26 real world structural datasets, including Social Networks (SNs), Collaborations Networks, Communication Networks, Autonomous Systems, and Peer-to-Peer networks. We also quantitatively show the conditions for perfect and (1-ε)-perfect DA of the 26 datasets. Third, following our quantification, we design a practical and novel single-phase cold start Optimization based DA} (ODA) algorithm. Experimental analysis of ODA shows that about 77.7% - 83.3% of the users in Gowalla (.2M users and 1M edges) and 86.9% - 95.5% of the users in Google+ (4.7M users and 90.8M edges) are de-anonymizable in different scenarios, which implies optimization based DA is implementable and powerful in practice. Finally, we discuss the implications of our DA quantification and ODA and provide some general suggestions for future secure data publishing.
Incentive compatible mechanism for coordinated temperature control in multi-occupant buildings (2015)

Minimizing the total energy consumption (cost) and maximizing the aggregate comfort across all building occupants, are two major objectives that must be balanced for effective environmental control in multi-occupant buildings and other shared spaces. Energy cost function for a given building is generally available (or can be measured/estimated) but information on the comfort ranges/functions are held privately by the occupants. In this work we present a game-theoretic (auction) mechanism, that requires occupants to “purchase” their individualized comfort levels beyond what is provided by default by the building operator. The comfort pricing policy is incentive-compatible in the sense that it elicits truthful comfort feedback from rational occupants acting only in self-interest. The declared (or estimated) occupant comfort ranges (functions) are then utilized by the building operator (HVAC system operator) - along with the energy cost information - to set the environment controls to optimally balance the aggregate discomfort of the occupants and the energy cost of the building operator. We use realistic building model and parameters based on our test facility to demonstrate the convergence of the actual temperatures in different zones to the desired temperatures, and provide insight to the pricing structure necessary for truthful comfort feedback from the occupants.
Solution‐Processed Organic Tandem Solar Cells (2006)

Abstract A solution‐processed polymer tandem cell fabricated by stacking two single cells in series is demonstrated. The two bulk‐heterojunction subcells have complementary absorption maxima at λ max ∼ 850 nm and λ max ∼ 550 nm, respectively. A composite middle electrode is applied that serves both as a charge‐recombination center and as a protecting layer for the first cell during spin‐coating of the second cell. The subcells are electronically coupled in series, which leads to a high open‐circuit voltage of 1.4 V, equal to the sum of each subcell. The layer thickness of the first (bottom) cell is tuned to maximize the optical absorption of the second (top) cell. The performance of the tandem cell is presently limited by the relatively low photocurrent generation in the small‐bandgap polymer of the top cell. The combination of our tandem architecture with more efficient small‐bandgap materials will enable the realization of highly efficient organic solar cells in the near future.
Ty1 and Ty5 ofSaccharomyces cerevisiae (2007)

Ty1 and Ty5 of Saccharomyces cerevisiae are long terminal repeat (LTR) retrotransposons, members of a large and ubiquitous class of mobile genetic elements. Like the retroviruses, LTR retrotransposons replicate by reverse transcribing RNA into DNA and then integrating the DNA transposition intermediate into the genome of their host. This chapter begins with a description of Ty1 and Ty5, including their origins and genetic organization. Subsequent sections deal with four discrete steps in the LTR retrotransposon life cycle, namely, (i) transcription and transcriptional regulation; (ii) protein expression, processing, and virus-like particle assembly; (iii) reverse transcription; and (iv) integration. The study of activating mutations has unveiled a complex array of both positively and negatively acting factors responsible for Ty1's transcriptional regulation. The discussion of reverse transcription in the remainder of the chapter focuses on the native Ty1 enzyme. Negative post transcriptional regulation of Ty1 was suggested by the paradoxical observation that Ty1 mRNA is very abundant, yet mature Ty1 proteins are scarce and transposition infrequent. In the postgenomics era, S. cerevisiae is the proving ground for new technologies that are beginning to offer unprecedented insights into the complex regulatory and metabolic networks that underlie cellular biology. The development of the research tools and the accumulated knowledge that results from their use will undoubtedly greatly facilitate Ty1 and Ty5 research in the coming years.
Skeletal muscle anabolic response to resistance exercise and essential amino acids is delayed with aging (2008)

The loss of skeletal muscle during aging (sarcopenia) leads to an increased risk of falls, fractures and eventually loss of independence. Resistance exercise (RE) is a useful intervention to prevent sarcopenia, however, the response to RE is less when compared to young subjects. Essential amino acids (EAA) increase muscle protein synthesis (MPS) equally in both young and old subjects. We hypothesized that EAA ingestion following RE would restore anabolic signaling and MPS in aging muscle. Young and old men ingested 20g of EAA 1hr following a bout of leg‐RE. Muscle biopsies were obtained before, 1, 3, and 6hr post‐exercise to measure MPS and signaling pathways which regulate translation initiation. MPS increased early in young (1–3hr post‐exercise) and later in old (3–6hr post‐exercise). RE activated ERK1/2 and eIF2α signaling only in the young 1hr post‐exercise. mTOR/S6K1 signaling was similar between groups at all time points and AMPKα phosphorylation was higher in old 1–3hr post‐exercise. We conclude that MPS after RE and EAA ingestion is similar between young and old but delayed with aging. Unresponsive ERK1/2 signaling and AMPK activation in aging may explain the delayed activation of MPS. Notwithstanding, the combination of RE and EAA should be a useful strategy to combat sarcopenia. Supported by NIH/NIAMS grant # R01 AR049877 and NIH/NIA P30 AG024832
Preclinical In-Vivo Safety of a Novel Thyrotropin-Releasing Hormone-Loaded Biodegradable Nanoparticles After Intranasal Administration in Rats and Primates (2023)

Thyrotropin-releasing hormone (TRH) and TRH-like peptides carry a therapeutic potential for neurological conditions. Nanoparticles (NP) made of the biodegradable polymer, Poly(Sebacic Anhydride) (PSA), have been developed to carry TRH, intended for intranasal administration to patients. There is limited information on the safety of biodegradable polymers when given intranasally, and therefore, we have performed two preclinical safety and toxicity studies in cynomolgus monkeys and rats using TRH-PSA nanoparticles. The rats and monkeys were dosed intranasally for 42 days or 28 days, respectively, and several animals were followed for additional 14 days. Animals received either placebo, vehicle (PSA), or different concentrations of TRH-PSA. No systemic adverse effects were seen. Changes in T3 or T4 concentrations were observed in some TRH-PSA-treated animals, which did not have clinical or microscopic correlates. No effect was seen on TSH or prolactin concentrations. In the monkey study, microscopic changes in the nasal turbinates were observed, which were attributed to incidental mechanical trauma caused during administration. Taken together, the TRH-loaded PSA NPs have proven to be safe, with no local or systemic adverse effects attributed to the drug loaded nanoparticles. These findings provide additional support to the growing evidence of the safety of peptide-loaded NPs for intranasal delivery and pave the way for future clinical trials in humans.
Widely linear EDFA for analog radio-over-fiber transmission over a passive optical network configuration (2015)

An analog radio-over-fiber signal transmission over a passive-optical-network using a widely-linear erbium-doped fiber amplifier with a capability of 256 subscribers is demonstrated with an observed error vector magnitude less than 4% rms.
Site-Specific 18F-Labeling of the Protein Hormone Leptin Using a General Two-Step Ligation Procedure (2008)

The protein hormone leptin acts to regulate body fat and energy expenditure. Resistance to this hormone is implicated in human obesity and its pathophysiological consequences. In order to gain insight into the mechanism of leptin resistance, an (18)F-labeled derivative was developed to study the biodistribution of the hormone using positron emission tomography (PET). A two-step, site specific ligation approach was developed for this purpose, in which an aminooxy-reactive group was incorporated at the C-terminus of leptin using expressed protein ligation (EPL), which was subsequently derivatized with [ (18)F]fluorobenzaldehyde using an aniline-accelerated radiochemical oximation reaction. The modified hormone was shown to be biologically active in vitro and in vivo, and it was applied to PET imaging in ob/ ob mice. These protocols will allow for the routine production of site-specifically (18)F radiolabeled leptin, as well as other proteins, for use in PET imaging in systems from mouse to man.
Acute Phase Protein Lipocalin-2 Is Associated with Formalin-induced Nociception and Pathological Pain (2013)

Lipocalin-2 (LCN2) is an acute-phase protein induced by injury, infection, or other inflammatory stimuli. LCN2 binds small hydrophobic ligands and interacts with cell surface receptor to regulate diverse cellular processes. The role of LCN2 as a chemokine inducer in the central nervous system (CNS) has been previously reported. Based on the previous participation of LCN2 in neuroinflammation, we investigated the role of LCN2 in formalin-induced nociception and pathological pain. Formalin-induced nociceptive behaviors (licking/biting) and spinal microglial activation were significantly reduced in the second or late phase of the formalin test in Lcn2 knockout mice. Likewise, antibody-mediated neutralization of spinal LCN2 attenuated the mechanical hypersensitivity induced by peripheral nerve injury in mice. Taken together, our results suggest that LCN2 can be therapeutically targeted, presumably for both prevention and reversal of acute inflammatory pain as well as pathological pain.
Reconstruction of Large, Complicated Trunk Defects Using Alloderm and Flaps in Cancer Patients (2005)

Complication rates are increased in pelvic, chest, and abdominal-wall reconstructions with polypropylene mesh when the mesh is placed directly over viscera or the operative site has been irradiated or contaminated with bacteria. An alternative mesh material is Alloderm (decellularized allodermis), which becomes vascularized and remodeled into autologous tissue after implantation. When used for fascial reconstruction, it forms a strong repair, causes minimal abdominal adhesions, and resists infection.
Supplementary Figure 4 from Cross-Species Functional Analysis of Cancer-Associated Fibroblasts Identifies a Critical Role for CLCF1 and IL-6 in Non–Small Cell Lung Cancer <i>In Vivo</i> (2023)

&lt;p&gt;PDF file - 85K, Lung tumor cells and CAFs induce a of CAF-like phenotype in NFs&lt;/p&gt;
Flat‐panel detectors in the cardiac catheterization laboratory: Revolution or evolution—what are the issues? (2004)

Continuous developments in digital imaging technology have contributed to the vital role held today by digital X-ray imaging in the cardiac catheterization laboratory. Foremost among these developments is the replacement of cine film with digital data equivalents as the procedure record. Other improvements include software innovations and processing algorithms, along with new types of hardware capable of delivering required functionality more rapidly. A significant recent development is that of the flat-panel X-ray detector as a replacement for the image intensifier, which has served the needs of the cardiac catheterization laboratory for nearly 5 decades. Clinical users must evaluate the respective technologies and determine whether one or the other meets the needs of their own laboratories. In this review, the two competing detector technologies are reviewed and a summary of general advantages and disadvantages of each is provided. A qualitative description is provided of parameters that can be used to assess quantitatively the performance of detectors and imaging systems. Using such objective measurements, together with standard techniques for evaluating imaging systems, angiographers and managers can better arrive at informed decisions for their own situation.
Getting Knit-PI3Ky: PIK3CA Mutation Status to Direct Multimodality Therapy? (2009)

There is high morbidity associated with local recurrence of rectal cancer. However, the adjuvant therapies given to prevent such recurrences also have significant side effects and associated risks. The ability to select patients with the highest risk of recurrence and greatest therapeutic response will improve rectal cancer care.
Sum Frequency Generation on Surfactant-Coated Gold Nanoparticles (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSum Frequency Generation on Surfactant-Coated Gold NanoparticlesTakeshi Kawai, David J. Neivandt, and Paul B. DaviesView Author Information Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK Cite this: J. Am. Chem. Soc. 2000, 122, 48, 12031–12032Publication Date (Web):November 14, 2000Publication History Received28 July 2000Published online14 November 2000Published inissue 1 December 2000https://pubs.acs.org/doi/10.1021/ja002785ehttps://doi.org/10.1021/ja002785erapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1108Altmetric-Citations51LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Gold,Metal nanoparticles,Nanoparticles,Silicon,Surfactants Get e-Alerts
A feasibility evaluation of an automated bloodcomponent collection system platelets and red cells (1999)

Both in vitro and in vivo testing for the packed RBCs collected and stored for 42 days met the standards for both hemolysis and percentage of 51Cr 24-hour RBC recovery. The in vitro results and transfusion data on white cell-reduced platelet components transfused to thrombocytopenic patients were comparable to those on available platelet components.
Chemical Identity and Mechanism of Action and Formation of a Cell Growth Inhibitory Compound from Polycarbonate Flasks (2018)

This paper reports the chemical identity and mechanism of action and formation of a cell growth inhibitory compound leached from some single-use Erlenmeyer polycarbonate shaker flasks under routine cell culture conditions. Single-use cell culture vessels have been increasingly used for the production of biopharmaceuticals; however, they often suffer from issues associated with leachables that may interfere with cell growth and protein stability. Here, high-performance liquid-chromatography preparations and cell proliferation assays led to identification of a compound from the water extracts of some polycarbonate flasks, which exhibited subline- and seeding density-dependent growth inhibition of CHO cells in suspension culture. Mass spectroscopy, nuclear magnetic resonance spectroscopy, and chemical synthesis confirmed that this compound is 3,5-dinitro-bisphenol A. Cell cycle analysis suggests that 3,5-dinitro-bisphenol A arrests CHO-S cells at the G<sub>1</sub>/G<sub>o</sub> phase. Dynamic mass redistribution assays showed that 3,5-dinitro-bisphenol A is a weak GPR35 agonist. Analysis of the flask manufacturing process suggests that 3,5-dinitro-bisphenol A is formed via the combination of molding process with γ-sterilization. This is the first report of a cell culture/assay interfering leachable compound that is formed through γ-irradiation-mediated nitric oxide free radical reaction.
Pulsed-Laser-Induced Modification of Gold Nanorods: Damage Thresholds and Impact on Photoacoustic Imaging in Turbid Media (2018)

Nanorod reshaping during photoacoustic imaging (PAI) may severely impact performance. Nanorod damage thresholds were studied with electron microscopy and spectrophotometry, and the effect of laser exposure on PAI was studied in a turbid phantom.
B G@Sbase--a microbial gene expression and comparative genomic database (2011)

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future.
The Role of Private Prayer in Psychological Recovery Among Midlife and Aged Patients Following Cardiac Surgery (1998)

Issues related to psychological recovery following coronary bypass surgeries (CABG) have emerged in recent years. Other research has shown the effects of spiritual or religious activities on health and aging. However, little is known about the relationship of spiritual coping, including religious coping, to post-CABG adjustment. This study addressed multifactorial determinants of postoperative psychological recovery and the effects of private prayer, a form of spiritual coping, on the recovery of 151 older patients. Results show that most patients pray about their postoperative problems and that private prayer appears to significantly decrease depression and general distress one year post-CABG.
Crystallization and preliminary X-ray analysis of LipL32 fromLeptospira interrogansserovar Copenhageni (2009)

LipL32 is a major surface protein that is expressed during infection by pathogenic Leptospira. Here, the crystallization of recombinant LipL32(21-272), which corresponds to the mature LipL32 protein minus its N-terminal lipid-anchored cysteine residue, is described. Selenomethionine-labelled LipL32(21-272) crystals diffracted to 2.25 A resolution at a synchrotron source. The space group was P3(1)21 or P3(2)21 and the unit-cell parameters were a = b = 126.7, c = 96.0 A.
Serum IP-10 Levels Correlate with the Severity of Liver Histopathology in Patients Infected with Genotype-1 HCV (2011)

Serum IP-10 concentration was significantly correlated with the severity of liver histology in genotype 1 HCV infection.
Structure, function and diversity of the healthy human microbiome (2012)

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.