gebhart/patrepeval huggingface dataset:
AGENT-BASED COMPUTER SIMULATION AND SIRS: BUILDING A BRIDGE BETWEEN BASIC SCIENCE AND CLINICAL TRIALS (2001)

The management of Systemic Inflammatory Response Syndrome (SIRS)/Multiple Organ Failure (MOF) remains the greatest challenge in the field of critical care. There has been uniform difficulty in translating the results of basic science research into effective therapeutic regimes. We propose that this is due in part to a failure to account for the complex, nonlinear nature of the inflammatory process of which SIRS/MOF represents a disordered state. Attempts to manipulate this process without an understanding of the dynamics of the system may potentially produce unintended consequences. Agent-Based Computer Simulation (ABCS) provides a means to synthesize the information acquired from the linear analysis of basic science into a model that preserves the complexity of the inflammatory system. We have constructed an abstracted version of the inflammatory process using an ABCS that is based at the cellular level. Despite its abstraction, the simulation produces non-linear behavior and reproduces the dynamic structure of the inflammatory response. Furthermore, adjustment of the simulation to model one of the unsuccessful initial anti-inflammatory trials of the 1990's demonstrates the adverse outcome that was observed in those clinical trials. It must be emphasized that the current model is extremely abstract and simplified. However, it is hoped that future ABCSs of sufficient sophistication eventually may provide an important bridging tool to translate basic science discoveries into clinical applications. Creating these simulations will require a large collaborative effort, and it is hoped that this paper will stimulate interest in this form of analysis.
Integration of Logic Functions and Sequential Operation of Gates at the Molecular-Scale (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTIntegration of Logic Functions and Sequential Operation of Gates at the Molecular-ScaleA. Prasanna de Silva, Isabelle M. Dixon, H. Q. Nimal Gunaratne, Thorfinnur Gunnlaugsson, Pamela R. S. Maxwell, and Terence E. RiceView Author Information School of Chemistry, Queen's University Belfast BT9 5AG, Northern Ireland Cite this: J. Am. Chem. Soc. 1999, 121, 6, 1393–1394Publication Date (Web):January 28, 1999Publication History Received13 August 1998Published online28 January 1999Published inissue 1 February 1999https://pubs.acs.org/doi/10.1021/ja982909bhttps://doi.org/10.1021/ja982909brapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1670Altmetric-Citations333LEARN 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:Fluorescence,Luminescence,Mercury,Phosphorescence,Receptors Get e-Alerts
Centrifugal extraction of plasma from whole blood on a rotating disk (2006)

We present a centrifugal process for the extraction of plasma from sediment by a decanting structure, terminating with metered plasma which is readily available for subsequent on-disk processing. Our technique supplies 2 microl plasma from 5 microl of whole blood at moderate spinning frequencies of 40 Hz within 20 s, only. The residual cell concentration in the purified plasma amounts to less than 0.11%, independent of the frequency of rotation. A capillary duct connects the extracted plasma to subsequent on-disk processing units.
Microencapsulation of a synthetic peptide epitope for HTLV-1 in biodegradable poly(D,L-lactide-co-glycolide) microspheres using a novel encapsulation technique (2001)

A novel procedure has been developed for the encapsulation of peptide antigens in poly(lactide-co-glycolide) (PLGA) microspheres, which employs trifluoro-acetic acid (TFA) as a carrier solvent for both the polymer and antigen. The antigen/polymer solution is emulsified in mineral oil containing sorbitan trioleate (Span 85) as an emulsifier and a low level of cottonseed oil to extract the TFA. Fluoresceinisothiocyanate-labelled bovine serum albumin (FITC-BSA) was used as a model antigen to characterize the microencapsulation. Microspheres were of the desired size (<10 microm) for targeting to antigen-presenting cells, and released the model antigen slowly after an initial burst release (11%) in PBS/0.02% Tween 80 at 37 degrees C. Subsequently, a potential peptide vaccine, designated MVFMF2, for the human T-lymphotropic virus type 1 (HTLV-1 ) was encapsulated at 4.7% loading using the novel oil-in-oil method. In vivo immune responses were examined in rabbits immunized with (i) encapsulated MVFMF2 together with encapsulated adjuvant (N-acetyl-glucosamine-3yl-acetyl-L-alanyl-D-isoglutamine, nor-MDP, (ii) encapsulated MVFMF2 without adjuvant, and (iii) free peptide with adjuvant. Inoculation of the encapsulated peptide produced an antibody response similar to that of the free peptide emulsified in adjuvant. Moreover, the elevated immune response elicited by the encapsulated peptide was observed without multiple booster immunizations and irrespective of whether an adjuvant was used. Additionally, the antibodies raised against both free and encapsulated MVFMF2 had similar affinities, as judged by competitive enzyme-linked immunosorbant assay (ELISA), indicating that the encapsulated peptide retained a significant fraction of its epitopes. Hence, these results demonstrate that peptide vaccines can be encapsulated in PLGA microspheres using a common carrier solvent for both the peptide and polymer, which produces a desirable immune response in the absence of an adjuvant.
Rapid rumor ramification: approximating the minimum broadcast time (2002)

Given an undirected graph representing a network of processors, and a source node containing a message that must be broadcast to all the nodes, find a scheme that accomplishes the broadcast in the minimum number of time steps. At each time step, any processor that has received the message is allowed to communicate the message to at most one of its neighbors in the network, i.e. can communicate via a telephone call to a neighbor. This has been termed the minimum broadcast time problem under the telephone model and is known to be NP-complete. The minimum broadcast time in a graph is closely related to the poise of the graph. The poise of a tree is defined to be the quantity (maximum degree of any node in the tree+diameter of the tree). The poise of a graph is the minimum poise of any of its spanning trees. Computing the poise of a graph is shown to be NP-hard and an algorithm for computing a spanning tree of approximately minimum poise is derived. This algorithm is then used to derive an O(log/sup 2/n/log log n)-approximation for the minimum broadcast time problem on an n-node graph. Our algorithm extends to many generalizations of the problem such as the multicast problem, a telephone model allowing conference calls, and to the closely related minimum gossip time problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
EVIDENCE FOR A SINGLE-STRANDED ADENOVIRUS-ASSOCIATED VIRUS GENOME: FORMATION OF A DNA DENSITY HYBRID ON RELEASE OF VIRAL DNA (1969)

Extracted adenovirus-associated virus DNA is known to be double-stranded, and, therefore, it has been assumed that these virus particles contain a double-stranded genome. Recent findings, however, have suggested that the DNA in virus particles is equivalent to only half the molecular weight of extracted molecules. A density analysis of DNA extracted from a mixture of virus particles containing either bromodeoxyuridine-substituted or unsubstituted DNA shows that virions contain single-stranded DNA which, when released, forms duplex structures. A similar circumstance is as yet unknown among other viruses.
431 (2012)

Introduction: Outcomes of obese patients in critical care unit has been subjected to debate with many studies showing obesity to be associated with decreased mortality - a phenomenon known as ‘obesity paradox’. Obese patients have limited cardiopulmonary reserve and thus should have worse outcomes, especially as severity of disease increases. Hypothesis: Morbidly obese (BMI?40) persons undergoing Invasive mechanical ventilation(IMV) have higher mortality and the risk increases with severity of disease. Methods: Using the Nationwide Inpatient Sample 2004-2008, patients?18 years, undergoing IMV were identified using ICD-9-CM code 96.70-72. The morbidly obese were similarly identified using ICD-9-CM code 278.01. The severity of disease was defined by the number of organ failures. Outcome variables included in-hospital mortality and rates of tracheostomy (surrogateof prolonged IMV and failure to wean). Multivariate logistic regression model was developed to examine if morbid obesity was independent predictor of mortality. The model adjusted for demographic and hospital characteristics, Charlson’s co-morbidity index and severity of disease. Results: Of the 4,159,342 adult discharges requiring IMV, 2.9% were morbidly obese. The severity of disease was significantly lower in morbidly obese persons (e.g. The number of 2 or more organ failing 17.8% vs. 25.5%, p<0.001). Similarly, the mean age (56.5 years vs. 63.0, p<0.001) and Charlson’s Co-morbid index(score?7: 1.8% vs. 4.75, p<0.001) were also lower in morbidly obese.There was a step wise increment in the odds ratio for mortality relative to non-obese persons with increasing number of organ failures in morbidly obese(OR 0.77 (95% CI 0.58–1.01)for one organ failing to OR 4.14(95% CI 1.11–15.3) for five or more organs failing). The odds of tracheostomy was 2.8 times(95%CI 2.22-3.40) higher in morbidly obese. Conclusions: Mechanically ventilated patients with morbid obesity do not have lower odds of mortality (compared to non-obese) in less severe form of disease; but as the severity of illness increases, the risk of death increases. Morbid obesity is also associated with higher rates of tracheostomy.
Can Man-Made Nanomachines Compete with Nature Biomotors? (2009)

Biological nanomotors have evolved over million years to perform specific tasks with high efficiency. The remarkable performance of biomotors is inspiring scientists to create synthetic nanomachines that mimic the function of these amazing natural systems. This review discusses the challenges and opportunities facing artificial nanomotors and summarizes recent progress toward the development of such man-made nanomachines. Particular attention is given to catalytic nanowire motors propelled by the electrocatalytic decomposition of a chemical fuel. While artificial nanomotors pale compared to nature biomotors, recent advances indicate their great potential to perform diverse applications and demanding tasks. Such advances include significant improvements in the velocity, motion control, cargo-towing force, and lifetime of such catalytic nanomotors. As a result, artificial nanomotors can have velocities as large as 100 body lengths per second and relatively high powers to transport a "heavy" cargo within complex microchannel networks. Despite this impressive progress, man-made nanomachines still lack the efficiency, functionality, and force of their biological counterparts and are limited to a very narrow range of environments and fuels. Improved understanding of the behavior of catalytic nanomotors will facilitate the design of highly efficient and powerful artificial nanomachines for complex operations in diverse realistic environments, leading to practical nanoscale applications in the not-so-distant future.
Transgenic rat model of Huntington's disease (2003)

Huntington's disease (HD) is a late manifesting neurodegenerative disorder in humans caused by an expansion of a CAG trinucleotide repeat of more than 39 units in a gene of unknown function. Several mouse models have been reported which show rapid progression of a phenotype leading to death within 3-5 months (transgenic models) resembling the rare juvenile course of HD (Westphal variant) or which do not present with any symptoms (knock-in mice). Owing to the small size of the brain, mice are not suitable for repetitive in vivo imaging studies. Also, rapid progression of the disease in the transgenic models limits their usefulness for neurotransplantation. We therefore generated a rat model transgenic of HD, which carries a truncated huntingtin cDNA fragment with 51 CAG repeats under control of the native rat huntingtin promoter. This is the first transgenic rat model of a neurodegenerative disorder of the brain. These rats exhibit adult-onset neurological phenotypes with reduced anxiety, cognitive impairments, and slowly progressive motor dysfunction as well as typical histopathological alterations in the form of neuronal nuclear inclusions in the brain. As in HD patients, in vivo imaging demonstrates striatal shrinkage in magnetic resonance images and a reduced brain glucose metabolism in high-resolution fluor-deoxy-glucose positron emission tomography studies. This model allows longitudinal in vivo imaging studies and is therefore ideally suited for the evaluation of novel therapeutic approaches such as neurotransplantation.
SIRT1 Activation by Small Molecules (2010)

SIRT1 is a protein deacetylase that has emerged as a therapeutic target for the development of activators to treat diseases of aging. SIRT1-activating compounds (STACs) have been developed that produce biological effects consistent with direct SIRT1 activation. At the molecular level, the mechanism by which STACs activate SIRT1 remains elusive. In the studies reported herein, the mechanism of SIRT1 activation is examined using representative compounds chosen from a collection of STACs. These studies reveal that activation of SIRT1 by STACs is strongly dependent on structural features of the peptide substrate. Significantly, and in contrast to studies reporting that peptides must bear a fluorophore for their deacetylation to be accelerated, we find that some STACs can accelerate the SIRT1-catalyzed deacetylation of specific unlabeled peptides composed only of natural amino acids. These results, together with others of this study, are at odds with a recent claim that complex formation between STACs and fluorophore-labeled peptides plays a role in the activation of SIRT1 (Pacholec, M., Chrunyk, B., Cunningham, D., Flynn, D., Griffith, D., Griffor, M., Loulakis, P., Pabst, B., Qiu, X., Stockman, B., Thanabal, V., Varghese, A., Ward, J., Withka, J., and Ahn, K. (2010) J. Biol. Chem. 285, 8340-8351). Rather, the data suggest that STACs interact directly with SIRT1 and activate SIRT1-catalyzed deacetylation through an allosteric mechanism.
CLUSTAL V: improved software for multiple sequence alignment (1992)

The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate phylogenetic trees after alignment. The program is simple to use, completely menu driven and on-line help is provided.
Diabetes-Related Microvascular and Macrovascular Diseases in the Physical Therapy Setting (2008)

Physical therapists commonly treat people with diabetes for a wide variety of diabetes-associated impairments, including those from diabetes-related vascular disease. Diabetes is associated with both microvascular and macrovascular diseases affecting several organs, including muscle, skin, heart, brain, and kidneys. A common etiology links the different types of diabetes-associated vascular disease. Common risk factors for vascular disease in people with diabetes, specifically type 2 diabetes, include hyperglycemia, insulin resistance, dyslipidemia, hypertension, tobacco use, and obesity. Mechanisms for vascular disease in diabetes include the pathologic effects of advanced glycation end product accumulation, impaired vasodilatory response attributable to nitric oxide inhibition, smooth muscle cell dysfunction, overproduction of endothelial growth factors, chronic inflammation, hemodynamic dysregulation, impaired fibrinolytic ability, and enhanced platelet aggregation. It is becoming increasingly important for physical therapists to be aware of diabetes-related vascular complications as more patients present with insulin resistance and diabetes. The opportunities for effective physical therapy interventions (such as exercise) are significant.
Analysis of the effects of water on the ACTS propagation terminal antenna (2002)

The NASA advanced communications technology satellite (ACTS) propagation experiment was designed to observe the attenuation produced by rain on Earth-satellite paths operating in the Ka-band. Unwanted effects of water on the antenna reflector surface were noted. Wet-antenna attenuation could be attributed to the combined effect of a water layer on the reflector surface and water wetting the feed window surface. A model was developed to calculate the antenna reflector and feed surface water layer thickness values as a function of position on each surface. The thickness values were used to calculate the additional attenuation produced by the water layers as a function of rain rate on the antenna. The wet-antenna-attenuation prediction model was verified by sprayer tests. The goal of the ACTS propagation experiment was to obtain path attenuation statistics, statistics that represent the effects of rain on the Earth-satellite path but not on the antenna itself. The wet-antenna attenuation prediction model was used to remove the effects of water on the antenna from the combined antenna-plus-path attenuation statistics produced by the experiment. The overall efficacy of the model was demonstrated by comparing the corrected path loss statistics from two ACTS propagation experiment sites with earlier COMSTAR path loss measurements made at or near those sites. The empirical distribution functions from both the ACTS and COMSTAR experiments were identical within the expected uncertainty of an empirical annual distribution of attenuation by rain.
Suppression of allogeneic T-cell proliferation by human marrow stromal cells: implications in transplantation (2003)

Human MSC fail to stimulate allogeneic PBMC or T-cell proliferation in mixed cell cultures. Unlike other nonprofessional APC, this failure of function is not reversed by provision of CD28-mediated costimulation nor gamma-interferon pretreatment. Rather, MSC actively inhibit T-cell proliferation, suggesting that allogeneic MSC transplantation might be accomplished without the need for significant host immunosuppression.
Economics of Utilizing Sagebrush Ranges (1968)

Individual ranchers want to know if it is profitable to make investments in range improvement. Public land agencies are also interested in the economics of range improvements, especially with the pressure for economic justification by Public Programs Budget System (P.P.B.S.). Several alternative approaches to economic justification of range improvements will be discussed in this paper.
Combined Modality Therapy of A431 Human Epidermoid Cancer Using Anti-EGFr Antibody C225 and Radiation (1999)

These data demonstrate an interaction between C225 and RT. C225-mediated apoptosis and inhibition of EGFr phosphorylation may be critical in the interaction. Studies to define the precise influence of combined modality treatment on the EGFr signal transduction cascade need to be pursued. The combination of growth factor receptor antibodies and RT has potential application in clinical oncology.
Formation of Pseudoislets from Human Pancreatic Cultures (1992)

We have successfully developed a technique for culturing human islet cells obtained from the cadaveric pancreata of children. Within 24-48 h of in vitro culture, collagenase-digested human pancreatic tissue formed epithelioid monolayers. Scattered within these monolayers were insulin-positive cells, as detected by immunocytochemical and dithizone staining. Treatment of the beta cell-containing epithelioid-cell monolayers with EDTA resulted in the formation of spherical cellular clusters, i.e., pseudoislets. These pseudoislets differed from isolated islets of Langerhans in that they showed a more peripheral distribution of insulin-positive cells. Our studies have demonstrated that insulin-positive cells can be detected in monolayers obtained from human pancreata 3-4 weeks after culture. When exposed to varying concentrations of glucose, these cells secreted insulin. The development of this in vitro technique for culturing human pancreatic islet tissue could provide a model for systematically studying in vitro islet function.
Structure, dynamics, and Hck interaction of full‐length HIV‐1 Nef (2011)

Nef is an HIV accessory protein that plays an important role in the progression of disease after viral infection. It interferes with numerous signaling pathways, one of which involves serine/threonine kinases. Here, we report the results of an NMR structural investigation on full-length Nef and its interaction with the entire regulatory domain of Hck (residues 72-256; Hck32L). A helical conformation was found at the N-terminus for residues 14-22, preceding the folded core domain. In contrast to the previously studied truncated Nef (Nef Δ1-39), the full-length Nef did not show any interactions of Trp57/Leu58 with the hydrophobic patch formed by helices α1 and α2. Upon Hck32L binding, the N-terminal anchor domain as well as the well-known SH3-binding site of Nef exhibited significant chemical shift changes. Upon Nef binding, resonance changes in the Hck spectrum were confined mostly to the SH3 domain, with additional effects seen for the connector between SH3 and SH2, the N-terminal region of SH2 and the linker region that contains the regulatory polyproline motif. The binding data suggest that in full-length Nef more than the core domain partakes in the interaction. The solution conformation of Hck32L was modeled using RDC data and compared with the crystal structure of the equivalent region in the inactivated, full-length Hck, revealing a notable difference in the relative orientations of the SH3 and SH2 domains. The RDC-based model combined with (15)N backbone dynamics data suggest that Hck32L adopts an open conformation without binding of the polyproline motif in the linker to the SH3 domain.