gebhart/patrepeval huggingface dataset:
Life‐threatening human parvovirus B19 infection transmitted by intravenous immune globulin (2002)

Infection of human parvovirus B19 (B19) is usually a self-limiting febrile illness, but can sometimes be life-threatening under certain circumstances, such as aplastic crisis in patients with haemolytic anaemia, hydrops fetalis in pregnant women and fulminant hepatitis. B19 can be transmitted through respiratory secretions, transplacentally and by transfusion of blood or blood products. In the present case, administration of intravenous immune globulin (i.v.Ig) transmitted B19 infection and consequently caused pure red cell aplasia and aggravation of hepatitis to fulminant hepatitis. Our case may raise important questions as to the safety of i.v.Ig and possible contamination by B19.
Reduced depth of field in incoherent hybrid imaging systems (2002)

A hybrid imaging system combines a modified optical imaging module and a digital postprocessing step. We define what to our knowledge is a new metric to quantify the blurring of a defocused image that is more suitable than the defocus parameter for describing defocused hybrid imaging systems. We use this metric to design a pupil phase grating to reduce the depth of field, thereby increasing the axial resolution, of an incoherent hybrid imaging system using quasi-monochromatic illumination. By introducing this grating at the exit pupil and digitally processing the output of the detector, we reduce the depth of field by more than a factor of 2. Finally, we examine the effect of using a CCD optical detector, instead of an ideal optical detector, on the reduction of the depth of field.
Introduction to Concepts and Strategies for Molecular Imaging (2010)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTIntroduction to Concepts and Strategies for Molecular ImagingSamuel AchilefuView Author Information Department of Radiology, Washington University School of Medicine, 4525 Scott Ave, St. Louis, Missouri 63110Cite this: Chem. Rev. 2010, 110, 5, 2575–2578Publication Date (Web):April 26, 2010Publication History Received9 April 2010Published online26 April 2010Published inissue 12 May 2010https://pubs.acs.org/doi/10.1021/cr1001113https://doi.org/10.1021/cr1001113editorialACS PublicationsCopyright © 2010 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views8653Altmetric-Citations79LEARN 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 PDF (146 KB) Get e-AlertscloseSUBJECTS:Biological imaging,Fluorescence,Magnetic resonance imaging,Molecular imaging,Optical imaging Get e-Alerts
RDMA Capable iWARP over Datagrams (2011)

iWARP is a state of the art high-speed connection-based RDMA networking technology for Ethernet networks to provide InfiniBand-like zero-copy and one-sided communication capabilities over Ethernet. Despite the benefits offered by iWARP, many data center and web-based applications, such as stock-market trading and media-streaming applications, that rely on data gram-based semantics (mostly through UDP/IP) cannot take advantage of it because the iWARP standard is only defined over reliable, connection-oriented transports. This paper presents an RDMA model that functions over reliable and unreliable data grams. The ability to use data grams significantly expands the application space serviced by iWARP and can bring the scalability advantages of a connectionless transport to iWARP. In our previous work, we had developed an iWARP data gram solution using send/receive semantics showing excellent memory scalability and performance benefits over the current TCP-based iWARP. In this paper, we demonstrate an improved iWARP design that provides true RDMA semantics over data grams. Specifically, because traditional RDMA semantics do not map well to unreliable communication, we propose RDMA Write-Record, the first and the only method capable of supporting RDMA Write over both unreliable and reliable data grams. We demonstrate through a proof-of-concept software implementation that data gram-iWARP is feasible for real-world applications. Our proposed RDMA Write-Record method has been designed with data loss in mind and can provide superior performance under conditions of packet loss. It is shown through micro-benchmarks that by using RDMA capable data gram-iWARP a maximum of 256% increase in large message bandwidth and a maximum of 24.4\% improvement in small message latency can be achieved over traditional iWARP. For application results we focus on streaming applications, showing a 24% improvement in memory usage and up to a 74% improvement in performance, although the proposed approach is also applicable to the HPC domain.
Semi-automatic, self-adaptive control of garbage collection rates in object databases (1996)

A fundamental problem in automating object database storage reclamation is determining how often to perform garbage collection. We show that the choice of collection rate can have a significant impact on application performance and that the best rate depends on the dynamic behavior of the application, tempered by the particular performance goals of the user. We describe two semi-automatic, self-adaptive policies for controlling collection rate that we have developed to address the problem. Using trace-driven simulations, we evaluate the performance of the policies on a test database application that demonstrates two distinct reclustering behaviors. Our results show that the policies are effective at achieving user-specified levels of I/O operations and database garbage percentage. We also investigate the sensitivity of the policies over a range of object connectivities. The evaluation demonstrates that semi-automatic, self-adaptive policies are a practical means for flexibly controlling garbage collection rate.
The Laminin Response in Inflammatory Bowel Disease: Protection or Malignancy? (2014)

Laminins (LM), basement membrane molecules and mediators of epithelial-stromal communication, are crucial in tissue homeostasis. Inflammatory Bowel Diseases (IBD) are multifactorial pathologies where the microenvironment and in particular LM play an important yet poorly understood role in tissue maintenance, and in cancer progression which represents an inherent risk of IBD. Here we showed first that in human IBD colonic samples and in murine colitis the LMα1 and LMα5 chains are specifically and ectopically overexpressed with a concomitant nuclear p53 accumulation. Linked to this observation, we provided a mechanism showing that p53 induces LMα1 expression at the promoter level by ChIP analysis and this was confirmed by knockdown in cell transfection experiments. To mimic the human disease, we induced colitis and colitis-associated cancer by chemical treatment (DSS) combined or not with a carcinogen (AOM) in transgenic mice overexpressing LMα1 or LMα5 specifically in the intestine. We demonstrated that high LMα1 or LMα5 expression decreased susceptibility towards experimentally DSS-induced colon inflammation as assessed by histological scoring and decrease of pro-inflammatory cytokines. Yet in a pro-oncogenic context, we showed that LM would favor tumorigenesis as revealed by enhanced tumor lesion formation in both LM transgenic mice. Altogether, our results showed that nuclear p53 and associated overexpression of LMα1 and LMα5 protect tissue from inflammation. But in a mutation setting, the same LM molecules favor progression of IBD into colitis-associated cancer. Our transgenic mice represent attractive new models to acquire knowledge about the paradoxical effect of LM that mediate either tissue reparation or cancer according to the microenvironment. In the early phases of IBD, reinforcing basement membrane stability/organization could be a promising therapeutic approach.
Implications of cell death regulation in the pathogenesis and treatment of prostate cancer. (1999)

Although the phenomenon of programed cell death, or apoptosis, has been recognized for many years, interest in the clinical implications of apoptotic cell death has not been widely apparent until recently. It is now established that the products of at least some oncogenes and tumor suppressor genes are able to regulate the rates of apoptosis as well as proliferation in tumor cell populations. In fact, it appears that evasion of deletion via apoptotic cell death may be a requisite event in the development of many malignant neoplasms. Molecular alterations that occur at high frequency in the pathogenesis of prostate cancer often involve genes implicated in the regulation of cell death. There is now ample reason to speculate that the susceptibility of individual malignant neoplasms to undergo apoptosis in response to a given therapeutic intervention may be a useful parameter in predicting therapeutic response. This realization has profound implications with respect to the design and implementation of treatment strategies for prostate cancer based on the biology of this disease.
Kinetics and mechanistic analysis of an extremely rapid carbon dioxide fixation reaction (2011)

Carbon dioxide may react with free or metal-bound hydroxide to afford products containing bicarbonate or carbonate, often captured as ligands bridging two or three metal sites. We report the kinetics and probable mechanism of an extremely rapid fixation reaction mediated by a planar nickel complex [Ni(II)(NNN)(OH)](1-) containing a tridentate 2,6-pyridinedicarboxamidate pincer ligand and a terminal hydroxide ligand. The minimal generalized reaction is M-OH + CO(2) → M-OCO(2)H; with variant M, previous rate constants are ≲10(3) M(-1) s(-1) in aqueous solution. For the present bimolecular reaction, the (extrapolated) rate constant is 9.5 × 10(5) M(-1) s(-1) in N,N'-dimethylformamide at 298 K, a value within the range of k(cat)/K(M)≈10(5)-10(8) M(-1) s(-1) for carbonic anhydrase, the most efficient catalyst of CO(2) fixation reactions. The enthalpy profile of the fixation reaction was calculated by density functional theory. The initial event is the formation of a weak precursor complex between the Ni-OH group and CO(2), followed by insertion of a CO(2) oxygen atom into the Ni-OH bond to generate a four center Ni(η(2)-OCO(2)H) transition state similar to that at the zinc site in carbonic anhydrase. Thereafter, the Ni-OH bond detaches to afford the Ni(η(1)-OCO(2)H) fragment, after which the molecule passes through a second, lower energy transition state as the bicarbonate ligand rearranges to a conformation very similar to that in the crystalline product. Theoretical values of metric parameters and activation enthalpy are in good agreement with experimental values [ΔH(‡) = 3.2(5) kcal/mol].
Recurrent neural networks for polyphonic sound event detection (2015)

The objective of this thesis is to investigate how a deep learning model called recurrent neural network (RNN) performs in the task of detecting overlapping sound events in real life environments. Examples of such sound events include dog barking, footsteps, and crowd applauding. When several sound sources are active simultaneously, as it is often the case in everyday contexts, identifying individual sound events from their polyphonic mixture is a challenging task. Other factors such as noise and distortions contribute to making even more difficult to explicitly implement a computer program to solve the detection task.\nWe present an approach to polyphonic sound event detection in real life recordings based on a RNN architecture called bidirectional long short term memory (BLSTM). A multilabel BLSTM RNN is trained to map the time-frequency representation of a mixture signal consisting of sounds from multiple sources, to binary activity indicators of each event class. Our method is tested on two large databases of recordings, both containing sound events from more than 60 different classes, and in one case from 10 different everyday contexts. Furthermore, in order to reduce overfitting we propose to use several data augmentation techniques: time stretching, sub-frame time shifting, and block mixing.\nThe proposed approach outperforms the previous state-of-the-art method, despite using half of the parameters, and the results are further largely improved using the block mixing data augmentation technique. Overall, for the first dataset our approach reports an average F1-score of 65.5% on 1 second blocks and 64.7% on single frames, a relative improvement over previous state-of-the-art approach of 6.8% and 15.1% respectively. For the second dataset our system reports an average F1- score of 84.4% on 1 second blocks and 85.1% on single frames, a relative improvement over the baseline approach of 38.4% and 35.9% respectively.
<i>KiSS‐1</i>: A Likely Candidate for the Photoperiodic Control of Reproduction in Seasonal Breeders (2006)

In seasonal species, photoperiod exerts tight regulation of reproduction to ensure that birth occurs at the most favorable time of yr. A distinct photoneuroendocrine circuit composed of the retina, suprachiasmatic nucleus (SCN) of the hypothalamus, and pineal gland transduces daylength into a rhythmic secretion of melatonin. The duration of the night-time rise of this hormone conveys daylength information to the organism. Melatonin is known to mediate the control of seasonal reproduction, but how it modulates sexual activity is far from understood. Recent data indicate that the product of the KiSS-1 gene is a potent stimulator of the hypothalamic-pituitary-gonadal axis and may play, together with its receptor GPR54, a central role in the neuroendocrine regulation of gonadotropin secretion. This article briefly reviews these findings and presents arguments that KiSS-1 could take part in the seasonal control of reproduction.
Flow cytometric assessment of Escherichia coli and Salmonella typhimurium starvation-survival in seawater using rhodamine 123, propidium iodide, and oxonol (1995)

The use of flow cytometry in microbiology allows rapid characterization of cells from a nonhomogeneous population. A method based on flow cytometry to assess the effects of lethal agents and the bacterial survival in starved cultures through the use of membrane potential-sensitive dyes and a nucleic acid marker is presented. The use of propidium iodide, rhodamine, and oxonol has facilitated the differentiation of cells of Escherichia coli and Salmonella typhimurium of various states of vitality following various treatments (heat, sonication, electroporation, and incubation with gramicidin) and during starvation in artificial seawater. The fluorescence intensity is directly correlated with viable cell counts for rhodamine 123 labelling, whereas oxonol and propidium iodide labelling is inversely correlated with viable counts. The distribution of rhodamine and oxonol uptake during starvation-survival clearly indicates that single-species starved bacteria are heterogeneous populations, and flow cytometry can be a fundamental tool for quantifying this heterogeneity.
A system for pattern matching applications on biosequences (1993)

ANREP is a system for finding matches to patterns composed of (i) spacing constraints called 'spacers', and (ii) approximate matches to 'motifs' that are, recursively, patterns composed of 'atomic' symbols. A user specifies such patterns via a declarative, free-format and strongly typed language called A that is presented here in a tutorial style through a series of progressively more complex examples. The sample patterns are for protein and DNA sequences, the application domain for which ANREP was specifically created. ANREP provides a unified framework for almost all previously proposed biosequence patterns and extends them by providing approximate matching, a feature heretofore unavailable except for the limited case of individual sequences. The performance of ANREP is discussed and an appendix gives a concise specification of syntax and semantics. A portable C software package implementing ANREP is available via anonymous remote file transfer.
Mixed sulfonic-carboxylic anhydrides. II. Reactions with aliphatic ethers and amines (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMixed sulfonic-carboxylic anhydrides. II. Reactions with aliphatic ethers and aminesYehuda Mazur and Michael H. KargerCite this: J. Org. Chem. 1971, 36, 4, 532–540Publication Date (Print):February 1, 1971Publication History Published online1 May 2002Published inissue 1 February 1971https://doi.org/10.1021/jo00803a010RIGHTS & PERMISSIONSArticle Views628Altmetric-Citations43LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
An economical minichamber for immunohistochemical incubation. (1985)

A simple and economical "slide-minichamber" method for incubating tissue sections with antisera in immunohistochemical (peroxidase-antiperoxidase) staining procedures is described. The technique requires only materials routinely used in the laboratory. The method permits prolonged incubation of tissue sections with antiserum at 4 degrees C or at room temperature, use of small quantities of antiserum, and simultaneous incubation of two tissue sections with the same small quantity of antiserum, thereby allowing use of very dilute antisera and conservation of antisera when availability is limited.
Sustained Oscillations of NF-κB Produce Distinct Genome Scanning and Gene Expression Profiles (2009)

NF-kappaB is a prototypic stress-responsive transcription factor that acts within a complex regulatory network. The signaling dynamics of endogenous NF-kappaB in single cells remain poorly understood. To examine real time dynamics in living cells, we monitored NF-kappaB activities at multiple timescales using GFP-p65 knock-in mouse embryonic fibroblasts. Oscillations in NF-kappaB were sustained in most cells, with several cycles of transient nuclear translocation after TNF-alpha stimulation. Mathematical modeling suggests that NF-kappaB oscillations are selected over other non-oscillatory dynamics by fine-tuning the relative strengths of feedback loops like IkappaBalpha. The ability of NF-kappaB to scan and interact with the genome in vivo remained remarkably constant from early to late cycles, as observed by fluorescence recovery after photobleaching (FRAP). Perturbation of long-term NF-kappaB oscillations interfered with its short-term interaction with chromatin and balanced transcriptional output, as predicted by the mathematical model. We propose that negative feedback loops do not simply terminate signaling, but rather promote oscillations of NF-kappaB in the nucleus, and these oscillations are functionally advantageous.
Anionic Polymerization of Styrenic Macromonomers (2003)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTADDITION / CORRECTIONThis article has been corrected. View the notice.Anionic Polymerization of Styrenic MacromonomersDimitris Pantazis, Ioanna Chalari, and Nikos HadjichristidisView Author Information Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece Cite this: Macromolecules 2003, 36, 11, 3783–3785Publication Date (Web):May 7, 2003Publication History Received2 December 2002Revised26 March 2003Published online7 May 2003Published inissue 1 June 2003https://doi.org/10.1021/ma025898mCopyright © 2003 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1398Altmetric-Citations91LEARN 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 InReddit Read OnlinePDF (73 KB) Get e-AlertsSUBJECTS:Anionic polymerization,Anions,Color,Polymerization,Vacuum Get e-Alerts
Localized minimum spanning tree based multicast routing with energy-efficient guaranteed delivery in ad hoc and sensor networks (2008)

We present a localized geographic multicast scheme, MSTEAM, based on the construction of local minimum spanning trees (MSTs), that requires information only on 1-hop neighbors. A message replication occurs when the MST spanning the current node and the set of destinations has multiple edges originated at the current node. Destinations spanned by these edges are grouped together, and for each of these subsets the best neighbor is selected as the next hop. This selection is based on a cost over progress metric, where the progress is approximated by subtracting the weight of the MST over a given neighbor and the subset of destinations to the weight of the MST over the current node and the subset of destinations. Since such greedy scheme may lead the message to a void area (i.e., no neighbor providing positive progress), we propose a new multicast generalization of the well-known face recovery mechanism. We provide a theoretical analysis proving that MSTEAM is loop-free, and achieves delivery of the multicast message as long as a path to the destinations exists. Our results demonstrate that MSTEAM outperforms the best existing localized multicast scheme, and is almost as efficient as a centralized scheme in high densities.
Treatment of Acute Lymphoblastic Leukemia -- 30 Years' Experience at St. Jude Children's Research Hospital (1993)

The development and successful application of preventive therapy for meningeal leukemia, followed by the intensification of systemic chemotherapy, has progressively improved the rate of cure of childhood lymphoblastic leukemia, with relatively few adverse sequelae.