gebhart/patrepeval huggingface dataset:
Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society (2016)

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.These guidelines are intended for use by healthcare professionals who care for patients at risk for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), including specialists in infectious diseases, pulmonary diseases, critical care, and surgeons, anesthesiologists, hospitalists, and any clinicians and healthcare providers caring for hospitalized patients with nosocomial pneumonia. The panel's recommendations for the diagnosis and treatment of HAP and VAP are based upon evidence derived from topic-specific systematic literature reviews.
Balanced network flows. I. A unifying framework for design and analysis of matching algorithms (1999)

We discuss a wide range of matching problems in terms of a network flow model. More than this, we start up a matching theory which is very intuitive and independent from the original graph context. This first paper contains a standardized theory for the performance analysis of augmentation algorithms in a wide area of matching problems. Several optimality criteria are given which do not use cuts or barriers. As an application of our theory, the known cardinality matching algorithms of Edmonds, Kameda and Munro, and Micali and Vazirani, and the algorithm of Kocay and Stone for capacitated matching problems can be studied in their effects. From our theory a c-capacitated b-matching algorithm can be derived that behaves like the Dinic algorithm for the maximum flow problem. It will turn out that techniques for the maximum flow problem can be applied to matching problems much more explicitly than done before. A comprehensive duality theory depending on the network flow model used here will follow. Explicit algorithms for nonweighted problems will be presented in subsequent papers. © 1999 John Wiley & Sons, Inc. Networks 33: 1–28, 1999
Phase 2 Clinical Trial of a Recombinant Adeno-Associated Viral Vector Expressing α 1 -Antitrypsin: Interim Results (2011)

Recombinant adeno-associated virus (rAAV) vectors offer promise for the gene therapy of α(1)-antitrypsin (AAT) deficiency. In our prior trial, an rAAV vector expressing human AAT (rAAV1-CB-hAAT) provided sustained, vector-derived AAT expression for >1 year. In the current phase 2 clinical trial, this same vector, produced by a herpes simplex virus complementation method, was administered to nine AAT-deficient individuals by intramuscular injection at doses of 6.0×10(11), 1.9×10(12), and 6.0×10(12) vector genomes/kg (n=3 subjects/dose). Vector-derived expression of normal (M-type) AAT in serum was dose dependent, peaked on day 30, and persisted for at least 90 days. Vector administration was well tolerated, with only mild injection site reactions and no serious adverse events. Serum creatine kinase was transiently elevated on day 30 in five of six subjects in the two higher dose groups and normalized by day 45. As expected, all subjects developed anti-AAV antibodies and interferon-γ enzyme-linked immunospot responses to AAV peptides, and no subjects developed antibodies to AAT. One subject in the mid-dose group developed T cell responses to a single AAT peptide unassociated with any clinical effects. Muscle biopsies obtained on day 90 showed strong immunostaining for AAT and moderate to marked inflammatory cell infiltrates composed primarily of CD3-reactive T lymphocytes that were primarily of the CD8(+) subtype. These results support the feasibility and safety of AAV gene therapy for AAT deficiency, and indicate that serum levels of vector-derived normal human AAT >20 μg/ml can be achieved. However, further improvements in the design or delivery of rAAV-AAT vectors will be required to achieve therapeutic target serum AAT concentrations.
Maximum entropy models for natural language ambiguity resolution (1998)

The best aspect of a research environment, in my opinion, is the abundance of bright people with whom you argue, discuss, and nurture your ideas. I thank all of the people at Penn and elsewhere who have given me the feedback that has helped me to separate the good ideas from the bad ideas. I hope that Ihavekept the good ideas in this thesis, and left the bad ideas out! Iwould like toacknowledge the following people for their contribution to my education: I thank my advisor Mitch Marcus, who gave me the intellectual freedom to pursue what I believed to be the best way to approach natural language processing, and also gave me direction when necessary. I also thank Mitch for many fascinating conversations, both personal and professional, over the last four years at Penn. I thank all of my thesis committee members: John La erty from Carnegie Mellon University, Aravind Joshi, Lyle Ungar, and Mark Liberman, for their extremely valuable suggestions and comments about my thesis research. I thank Mike Collins, Jason Eisner, and Dan Melamed, with whom I&amp;apos;ve had many stimulating and impromptu discussions in the LINC lab. Iowe themmuch gratitude for their valuable feedback onnumerous rough drafts of papers and thesis chapters.
Identification and Characterization of Additional Members of the Cytochrome P450 Multigene Family CYP52 of Candida tropicalis (1992)

Using different DNA probes from the first two previously described alkane-inducible cytochrome P450 genes of the Candida tropicalis CYP52 gene family, we isolated five independent additional members by screening a genomic library under low-stringency conditions. These genes are not allelic variants and, when taken gogether, constitute the largest gene family known in this organism. The seven members of this gene family are located on four different chromosomes and four of them are tandemly arranged on the C. tropicalis genome. The products of the seven genes, alk1 to alk7, were compared to each other and revealed a high degree of divergence: the two most diverged proteins exhibit a sequence identity of only 32%. Six of the seven genes were shown to be induced by a variety of different aliphatic carbon sources but repressed when the organism was grown on glucose. Three of the five additional CYP52 genes could be successfully expressed in Saccharomyces cerevisiae and display different substrate specificities in in vitro assays with model substrates: alk2 and alk3 exhibit a strong preference for hexadecane, while alk4 and alk5 preferentially hydroxylate lauric acid.
Factor XIIa Inhibitor Recombinant Human Albumin Infestin-4 Abolishes Occlusive Arterial Thrombus Formation Without Affecting Bleeding (2010)

These results identify rHA-Infestin-4 as a promising agent to achieve powerful protection from ischemic cardiovascular and cerebrovascular events without affecting hemostasis.
Mouse primordial germ cells lacking β1 integrins enter the germline but fail to migrate normally to the gonads (1999)

Primordial germ cells are the founder cells of the gametes. They are set aside at the initial stages of gastrulation in mammals, become embedded in the hind-gut endoderm, then actively migrate to the sites of gonad formation. The molecular basis of this migration is poorly understood. Here we sought to determine if members of the integrin family of cell surface receptors are required for primordial germ cell migration, as integrins have been implicated in the migration of several other motile cell types. We have established a line of mice which express green fluorescent protein in germline cells that has enabled us to efficiently purify primordial germ cells at different stages by flow cytometry. We have catalogued the spectrum of integrin subunit expression by primordial germ cells during and after migration, using flow cytometry, immunocytochemistry and RT-PCR. Through analysis of integrin beta1(-/-)-->wild-type chimeras, we show that embryonic cells lacking beta1 integrins can enter the germline. However, integrin beta1(-/-) primordial germ cells do not colonize the gonad efficiently. Embryos with targeted deletion of integrin subunit alpha3, alpha6, or alphaV show no major defects in primordial germ cell migration. These results demonstrate a role for beta1-containing integrins in the development of the germline, although an equivalent role for * integrin subunit(s) has yet to be established.
The influence of drug input rate on the development of tolerance to frusemide (1998)

The direction of the hysteresis loop is dependent on the input rate of frusemide. After the administration of a single low dose of frusemide, the time course of tolerance, rather than the integrated time course of tolerance, is influenced by the drug input rate.
Calibration of vision systems based on pseudo-random patterns (2009)

Solving visual features' correspondence and dealing with missing data are two factors of limitations for points registration techniques. To tackle this problem, we conceived a pattern, primarily designed for structured lighting vision systems, which may also be used for camera calibration purposes. The pattern design previously presented provides a huge of benefits. Among them, we firstly present a new calibration technique of a structured lighting system and secondly an automatic distortion compensation based on a printed pattern. These two well-known issues are very useful in 3D vision-based metrology with range data, for instance for model-based visual robot control, especially when the model is incrementally built with a real-time 3D reconstruction of moving surfaces. Perhaps, one of the most significant profit with a high Hamming distance pattern is the ability to reliably decode its projected individual elements even if several of items are missing, as it greatly extends the range of measurements volume. A technique which solves the distortion parameters by means of a robust M-estimator algorithm is presented. It uses a printed pattern and it allows the distortion be corrected with a single view and without the computation of other (intrinsic/extrinsic) parameters, even in presence of occlusions. Experimental results, in one hand by means of a printed pattern for the distortion compensation of a rigid endoscope and on the other hand by means of a projected pattern for the calibration of the structured lighting system, show very good performance for the 3-D reconstruction.
Progesterone Receptor Induces ErbB-2 Nuclear Translocation To Promote Breast Cancer Growth via a Novel Transcriptional Effect: ErbB-2 Function as a Coactivator of Stat3 (2010)

Progesterone receptor (PR) and ErbB-2 bidirectional cross talk participates in breast cancer development. Here, we identified a new mechanism of the PR and ErbB-2 interaction involving the PR induction of ErbB-2 nuclear translocation and the assembly of a transcriptional complex in which ErbB-2 acts as a coactivator of Stat3. We also highlighted that the function of ErbB-2 as a Stat3 coactivator drives progestin-induced cyclin D1 promoter activation. Notably, PR is also recruited together with Stat3 and ErbB-2 to the cyclin D1 promoter, unraveling a new and unexpected nonclassical PR genomic mechanism. The assembly of the nuclear Stat3/ErbB-2 transcriptional complex plays a key role in the proliferation of breast tumors with functional PR and ErbB-2. Our findings reveal a novel therapeutic intervention for PR- and ErbB-2-positive breast tumors via the specific blockage of ErbB-2 nuclear translocation.
Temporal representations with cochlear implants. (1997)

Population responses of the human auditory nerve, as indicated by EP magnitudes, reflect the amplitudes of electrical pulses for pulse rates below about 200/s and above about 3000/s. Use of intermediate rates may introduce distortions in the transmission of stimulus information with cochlear implants.
Divergence in the anti-apoptotic signalling pathways used by nerve growth factor and basic fibroblast growth factor (bFGF) in PC12 cells: rescue by bFGF involves protein kinase Cδ (2000)

The mechanisms whereby nerve growth factor (NGF) and basic fibroblast growth factor (bFGF) block apoptosis in serum-deprived PC12 cells were investigated. NGF, but not bFGF, strongly activated Akt/protein kinase B, a downstream effector of phosphoinositide (phosphatidylinositol) 3-kinase (PI 3-kinase). In addition, inhibition of PI 3-kinase by LY294002 partially blocked inhibition of apoptosis by NGF, but not that by bFGF, suggesting divergence in NGF and bFGF anti-apoptotic signalling pathways. Both growth factors strongly activated mitogen-activated protein (MAP) kinases, but blockade of signalling through this pathway, either by the expression of dominant-negative Ras or by treatment with the MAP kinase/ERK kinase (MEK) inhibitor U0126, partially inhibited only bFGF, but not NGF, anti-apoptotic signalling. Use of isoform-specific protein kinase C (PKC) inhibitors such as bisindoylmaleimide-I and Gö 6983 suggested that PKC delta is a likely component of bFGF trophic signalling. A role for PKC delta was confirmed in PC12 cells expressing a dominant-negative PKCdelta fragment, in which reversal of apoptosis by bFGF was partially blocked. The PKC delta signal was not mediated by the MAP kinase cascade, as bFGF activation of this pathway was not affected in cells expressing the dominant-negative PKC delta fragment. Full inhibition of bFGF anti-apoptotic signalling occurred when both the PKCdelta and Ras/MAP kinase pathways were inhibited. Together, these data demonstrate that inhibition of apoptosis by bFGF in PC12 cells operates differently from that mediated by NGF, requiring the addition of signals from both the Ras/MAP kinase and PKC signalling pathways.
8446-Angstrom observations of neutral oxygen with the Spatial Heterodyne Spectrometer at Millstone Hill (2009)

Neutral oxygen (O I) is a dominant species between about 250 and 500 km in the thermosphere. A complete thermospheric model requires measurements of the species density ([O]) to incorporate into forward models. One way to measure [O] is to detect Bowen fluorescence at triplet 8446 &Aring;. Bowen fluorescence is generated when thermospheric oxygen absorbs Solar Lyman-&beta; and de-excites through a path eventually leading to 8446 emission. This emission must be distinguished from the brighter 8446 emission caused by photoelectron (PE) impact, which can be done by measuring the intensity ratio between two branches of the 8446 triplet. An instrument to measure Mid-latitude Bowen fluorescence has been installed at Millstone Hill Observatory. The instrument is a Spatial Heterodyne Spectrometer (SHS), a novel type of Fourier transform spectrometer. This SHS was first used to observe Na Fraunhofer lines from dayglow at 589 nm, and then observed the 8446 region in an oxygen spectrum tube. Modifications to the system will allow it to observe 8446 emissions from the evening sky.
Phenobarbital-Induced Alterations in Vitamin D Metabolism (1972)

The metabolic fate of intravenously injected vitamin D(3)-1,2-(3)H (D(3)-(3)H) was studied in two normal individuals on chronic phenobarbital therapy. Silicic acid column chromatography of lipid-soluble plasma extracts obtained serially for 96 hr after D(3)-(3)H injection demonstrated a decreased plasma D(3)-(3)H half-life and increased conversion to more polar metabolites. The polar metabolites formed included several with chromatographic mobility similar to known biologically inactive vitamin D metabolites and one with chromatographic mobility identical to 25-hydroxycholecalciferol. Disappearance of this latter material was also accelerated. A child with rickets and a normal volunteer studied before and after a 2 wk course of phenobarbital therapy demonstrated similar alterations in D(3)-(3)H metabolism. When liver microsomes from 3-wk-old Sprague-Dawley rats treated with phenobarbital were incubated with D(3)-(3)H, polar metabolites were produced with chromatographic mobility similar to the plasma D(3)-(3)H metabolites from phenobarbital-treated humans. Similar incubations employing 25-hydroxy-cholecalciferol-26-27-(3)H as the substrate also demonstrated an increased conversion to polar metabolites. The data suggest that the reported increased incidence of osteomalacia observed in patients on chronic anticonvulsant therapy may be the result of an accelerated conversion of vitamin D and its active metabolite, 25-hydroxycholecalciferol, to polar metabolites by druginduced liver microsomal enzymes.
Clinical and Clinicopathologic Characteristics of Ovine GM-1 Gangliosidosis (1994)

Ovine GM-1 gangliosidosis is an inherited lysosomal storage disease. Nine lambs affected with the disease were studied to characterize clinical signs and to determine if there were any pathognomonic clinicopathologic abnormalities. Evaluation included physical, ophthalmic, and neurologic examinations, complete blood counts, serum enzyme and electrolyte analyses, urinalyses, cerebrospinal fluid analyses, blood gas analyses, roentgenograms, electromyograms, and electrocardiograms. Two affected lambs had clinicopathologic tests performed before and after the onset of clinical signs. The only consistent abnormalities recognized were nonspecific signs referable to the central nervous system; predominantly ataxia, conscious proprioceptive deficit most severe in the hind limbs, blindness, and recumbency. Lambs continued to eat and drink, though at diminished levels and with loss of body condition. It was concluded that there are no pathognomonic clinicopathologic abnormalities associated with ovine GM-1 gangliosidosis, and antemortem diagnosis requires enzyme assay of leukocytes or cultured fibroblasts, or lectin histochemistry of tissues obtained by biopsy. Lysosomal storage diseases should be considered among the differential diagnoses in young animals presenting with early neonatal death or with nonspecific neurological signs, in concert with an absence of diagnostic clinicopathologic findings.
Are procalcitonin or other infection markers useful in the detection of group A streptococcal acute tonsillitis? (2014)

The sensitivity, specificity, and area under the curve of the RADT were higher than those of the 4 measured infection markers in the differentiation between GAS and non-GAS acute tonsillitis patients. The infection markers did not increase the diagnostic accuracy when added to the Centor score and RADT. When RADT is not available, measurement of CRP or ANC may increase the diagnostic accuracy in the detection of GAS-positive patients.
Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle) (2000)

Restriction enzymes are well known as reagents widely used by molecular biologists for genetic manipulation and analysis, but these reagents represent only one class (type II) of a wider range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the provenance of the DNA on the basis of specific modifications to their target sequence. Type I restriction and modification (R-M) systems are complex; a single multifunctional enzyme can respond to the modification state of its target sequence with the alternative activities of modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves like a molecular motor, translocating vast stretches of DNA towards itself before eventually breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which will emphasize those aspects that give insights into more general problems of molecular and microbial biology. Current molecular experiments explore target recognition, intramolecular communication, and enzyme activities, including DNA translocation. Type I R-M systems are notable for their ability to evolve new specificities, even in laboratory cultures. This observation raises the important question of how bacteria protect their chromosomes from destruction by newly acquired restriction specifities. Recent experiments demonstrate proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory.
Antiarrhythmic drug research (2006)

This article was written as part of the 75th anniversary celebration of the British Pharmacological Society (BPS). It discusses antiarrhythmic drug research conducted by members of BPS, and as published in the British Journal of Pharmacology (BJP). BPS members, past and present, as well as antiarrhythmic manuscripts published in the BJP have been identified. From these data, the article attempts to semiquantitatively summarize results published in the journal, but only quotes selected manuscripts and individuals. Apologies are offered for omissions and errors, but as in any history, a writer's biases and opinions are unavoidable.
Screening, cloning, and sequence analysis of random MARs in the genome of human T cells (2004)

Objective To screen and clone the fragment the random matrix association regions (MARs) in human genome and analyze the characteristics of their sequences in order to provide proof for further investigation of the molecular mechanisms of MARs in the regulation of eukaryotes gene expression. Methods The fragment of functions and the random MARs of human genome, isolated by treatment of the nuclei using DNase I, high salt, and protein K, was cloned into the PUC19 vector. MARs which could bind with nuclear matrix proteins were identified by binding assay in vitro and sequenced consequently. The characteristics were analyzed by the bioinformatic method. Results A large number of MARs fragments were screened and obtained from human T cells successfully. A MARs library was constructed and 58 clones were selected randomly from the library. The results of the binding assay in vitro showed that the random MARs had binding activity with nuclear matrix proteins, and sequence analysis of one of the clones showed that it was consisted of rich A and T base pair, AC rich elements and ATAT motifs, many origin points of transcription/replication, enhancer, curved DNA, kinked DNA regions, and numerous reverse repeated base sequences. Conclusion The obtained DNA fragments have the characteristics of MARs and multiple cis function elements in a DNA sequence, suggesting that the functions of MARs in regulation of gene expression are complicated and multiform.