gebhart/patrepeval huggingface dataset:
Transfusing blood safely and appropriately (2013)

#### Summary points 

Blood transfusion is an essential part of modern healthcare and can be life saving when used appropriately. Blood services worldwide strive to provide a safe supply and work with hospitals to ensure that blood products are readily available for patients. Blood components such as red cells, platelets, fresh frozen plasma, cryoprecipitate, and granulocytes are prepared from whole blood donations or collected by apheresis. Plasma derivatives such as coagulation factor concentrates, immunoglobulins, and albumin are prepared from large pools of plasma under drug manufacturing conditions.

#### Sources and selection criteria

As well as using our personal reference collections, we searched the Cochrane database (www.cochrane.org), Clinical Evidence (http://clinicalevidence.bmj.com), Best Practice (http://bestpractice.bmj.com), and a library of systematic reviews in transfusion medicine (www.transfusionevidencelibrary.com). The review draws on multiple sources including national guidelines, peer reviewed original research publications including randomised controlled trials, and systematic reviews. Examples include transfusion guidelines from Australia and New Zealand, which were developed from a series of systematic reviews,1 and a special collection of systematic reviews on avoiding unnecessary transfusion in the Cochrane Library.2

The process of getting a unit of …
A Method for Solving the Visibility Problem (1984)

This method for describing the visibility problem is based on the concept of analyzing the problem utilizing connectivity information. The result is a uniform description of visibility algorithms in terms of two basic functions, the test of projective equivalence and the comparison of the distance from the observer, and the use of connectivity information. This result leads to a hierarchy of visibility algorithms, which allows the characterization of the typical advantages and disadvantages of certain strategies independently of the quality of the implementation. The calculation rate of the new algorithm is substantially better than that of existing methods. Study of the distributivity of the visibility problem also shows that the use of connectivity information leads to an algorithmic improvement as well as a better usage of distributed systems.
Studies related to the design and synthesis of a molecular octal counter (2001)

An approach to the storage of multiple bits of information at the molecular level employs molecules with a large number of distinct oxidation states. Europium triple-decker sandwich molecules composed of porphyrins and phthalocyanines afford four cationic states and are very attractive for molecular information-storage applications. A larger number of states can be achieved by combinations of triple deckers that afford interleaved oxidation potentials. In order to identify suitable candidates for effective interleaving of oxidation potentials, a library of 19 new triple-decker complexes was prepared. Electron-donating groups have been attached to the porphyrin and/or phthalocyanine moieties in order to achieve oxidation states in the low potential regime. The triple deckers are of three different types: (Pc)Eu(Pc)Eu(Por), (Pc)Eu(Por)Eu(Pc), and (Por)Eu(Pc)Eu(Por). The solution electrochemistry of each member of the library was examined. These studies revealed suitable pairs of triple deckers that provide effective interleaving of oxidation potentials. Six triple deckers of type (Pc)Eu(Pc)Eu(Por) were derivatized with a thioacetyl or thiocyanate group on the porphyrin unit for attachment to an electroactive surface. Each of the S-(acetylthio)-derivatized triple deckers forms a self-assembled monolayer (SAM) on Au viain situ cleavage of the thiol protecting group. The SAM of each triple decker is electrochemically robust and exhibits four, well-resolved reversible oxidation waves. Upon disconnection from the source of applied potential, the triple-decker SAMs retain charge for tens to hundreds of seconds. The exact value of the charge-retention time depends on the specific porphyrin/phthalocyanine in the triple decker and the particular oxidation state of the molecules in the SAM (e.g., mono- vs. di- vs. tri- vs. tetracation). For all of the triple-decker SAMs, the charge-retention time monotonically increases as the oxidation state of the molecules in the SAM increases. Collectively, the studies suggest that the triple-decker complexes are excellent candidates for multibit molecular information storage elements.
Calculation of Carriers in Depletion Region of Semiconductors with Capacitance-Voltage Measurements (1988)

Abstract : Profiles obtained by the capacitance-voltage (C-V) method cannot give carrier distributions information right from the semiconductor surface. Since the prediction of ultimate device performance depends strongly upon an accurate knowledge of the entire carrier depth profile, it is very important to know this profile for the entire crystal including the surface depletion layer. A method was developed for obtaining the measured C-V data. This method was successfully applied to simulated C-V data created from various known linear, parabolic, and LSS Gaussian distributions, and then finally was demonstrated through experimentally measured C-V profiles obtained from Si-implanted GaAs. In this method, barrier potential was assumed to be 0.8 eV for n-type Si-implanted GaAs. Theses.
Molecular characterization of the murine interferon γ receptor cDNA (1989)

Interferon gamma receptors (IFN-gamma R) exhibit remarkable species specificity. In order to understand the basis for this phenomenon, we have isolated a recombinant cDNA clone corresponding to the mouse (Mu) IFN-gamma R. Microinjection of the mRNA synthesized in vitro corresponding to the cloned cDNA into Xenopus laevis oocytes resulted in the synthesis of a protein that specifically binds Mu-IFN-gamma. Analysis of murine genomic and RNA blots with the cDNA probe indicates the presence of a single gene and a single mRNA species of about 2300 bases. Sequence analysis of the cDNA encoding the Mu-IFN-gamma R and comparison with the corresponding human IFN-gamma R sequence shows about 68% conservation of the extracellular domains and 51% conservation of the cytoplasmic domains at the nucleotide level. The results indicate that, as expected, the sequence of the receptor confers species specificity for the binding of IFN-gamma to the cell surface receptor. Moreover, it was previously shown that a human factor is required in addition to the receptor for the human IFN-gamma to function in hamster or mouse cells (Jung, V., Rashidbaigi, A., Jones, C., Tischfield, J.A., Shows, T.B., and Pestka, S. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4151-4155). These results suggest an explanation for the second species-specific event required for function of the human receptor in mouse or hamster cells in that the intracellular domains are significantly different and thus cannot interact with the corresponding heterologous factor.
Smad5 and DPC4 Are Key Molecules in Mediating BMP-2-induced Osteoblastic Differentiation of the Pluripotent Mesenchymal Precursor Cell Line C2C12 (1998)

Since the bone morphogenetic proteins (BMPs) are members of the transforming growth factor-beta (TGF-beta) superfamily that induce the differentiation of mesenchymal precursor cells into the osteogenic cells, we identified the relevant signaling molecules responsible for mediating BMP-2 effects on mesenchymal precursor cells. BMP-2 induces osteoblastic differentiation of the pluripotent mesenchymal cell line C2C12 by increasing alkaline phosphatase activity and osteocalcin production. As recent studies have demonstrated that cytoplasmic Smad proteins are involved in TGF-beta superfamily signaling, we plan to isolate the relevant Smad family members involved in osteoblastic differentiation. We identified human Smad5, which is highly homologous to Smad1. BMP-2 caused serine phosphorylation of Smad5 as well as Smad1. In contrast, TGF-beta failed to cause serine phosphorylation of Smad1 and Smad5. We found Smad5 is directly activated by BMP type Ia or Ib receptors through physical association with these receptors. Following phosphorylation, Smad5 bound to DPC4, another Smad family member, and the complex was translocated to the nucleus. Overexpression of point-mutated Smad5 (G419S) or a C-terminal deletion mutant DPC4 (DPC4 delta C) blocked the induction of alkaline phosphatase activity, osteocalcin production, and Smad5-DPC4 signaling cascades upon BMP-2 treatment in C2C12 cells. These data suggest that activation of Smad5 and subsequent Smad5-DPC4 complex formation are key steps in the BMP signaling pathway, which mediates BMP-2-induced osteoblastic differentiation of the C2C12 mesenchymal cells.
Adaptive real-time femtosecond pulse shaping (1998)

Experimental results of a practical self-learning pulse-shaping system are presented. Real-time adaptive pulse shaping of uncharacterized pulses is achieved. A cross-correlation feedback measurement of the output pulses is used by a simulated-annealing algorithm to modify the pulses iteratively toward target shapes. This scheme can readily be used for coherent control of quantum dynamics.
Oral administration of CpG-ODNs suppresses antigen-induced asthma in mice (2005)

Oligodeoxynucleotides containing CpG motifs (CpG-ODNs) can protect against eosinophilic airway inflammation in asthma. Previously we have found that parenteral or mucosal administration of CpG-ODNs is effective in preventing (as well as reversing established) disease. In this study, we examined the effect of oral CpG-ODNs on the development of immune tolerance. Using an ovalbumin (OVA)-induced murine model of asthma, we found that CpG-ODNs, administered orally around the time of sensitization, prevented eosinophilic airway inflammation in a dose-dependent manner. Although oral co-administration of CpG-ODNs with OVA (known to induce tolerance) did not significantly change the inhibition of OVA-induced airway eosinophilia, it did modulate OVA-specific immunoglobulin responses: oral administration of OVA alone suppressed OVA-specific IgG1 production, but only mice that received CpG-ODNs demonstrated enhanced levels of OVA-specific IgG2c. Finally, we examined whether oral administration of CpG-ODNs, alone or with OVA, could reverse established eosinophilic airway inflammation. Again, neither OVA nor CpG-ODNs alone modulated established eosinophilic airway inflammation, but a combination of the OVA and CpG-ODNs successfully desensitized the mice. This desensitization was associated with suppression of OVA-specific IgE and enhancement of OVA-specific IgG2c production. These findings provide the first indication that oral administration of CpG-ODNs is effective in preventing and reversing antigen-induced eosinophilic airway inflammation. CpG-ODNs may be useful as a component of oral immunotherapy to promote tolerance in established asthma.
Electrospinning of Polymeric and Ceramic Nanofibers as Uniaxially Aligned Arrays (2003)

Electrospinning has been applied to prepare uniaxially aligned nanofibers made of organic polymers, ceramics, and polymer/ceramic composites. The key to the success of this method was the use of a collector consisting of two pieces of electrically conductive substrates separated by a gap whose width could be varied from hundreds of micrometers to several centimeters. As driven by electrostatic interactions, the charged nanofibers were stretched to span across the gap and thus to become uniaxially aligned arrays over large areas. Because the nanofibers were suspended over the gap, they could be conveniently transferred onto the surfaces of other substrates for subsequent treatments and various applications. Materials that have been successfully incorporated into this procedure include conventional organic polymers, graphite carbon, and metal oxides. By controlling the parameters for electrospinning, we have also fabricated a number of simple device structures, for example, an individual nanofiber spanning across two electrodes, 2D arrays of crossbar junctions, and optical polarizers.
Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli (1988)

A new mutation, parC, causing abnormal chromosome segregation was identified in two thermosensitive mutants of Escherichia coli. The thermosensitive growth of the mutants was corrected by pLC4-14 in the Clarke-Carbon collection. This plasmid carries a putative gene which can suppress the cell division defect due to ftsI (pbpB) and has hence been termed sufI (sui). The nearness of parC to metC was confirmed, and cotransduction frequency of parC was 59% with metC and 20% with glc. The parC-sufI region was analyzed by subcloning the chromosome region of pLC4-14. The parC and the sufI gene products were electrophoretically identified as proteins of 75 and 55 kilodaltons (kDa), respectively. The allelism of parC+ on pLC4-14 to parC1215 was confirmed by cloning parC1215. The sufI gene appeared to be dispensable for cell viability, and overproduction of its product caused suppression of ftsI. An essential gene coding for a 25-kDa protein was found between the parC and the sufI gene. These three genes were transcribed in the same direction and may be organized into an operon, with parC to the proximal side and with internal promoters at least for the distal genes. The localization of the gene products was examined in maxicells. The sufI protein was synthesized as a precursor which could be chased into a mature form. The major part of the mature form was found in the soluble fraction. The 25-kDa protein was found almost exclusively in the membrane fraction. The parC protein was associated with the membrane fraction in the presence of Mg2+ but found in the soluble fraction when Mg2+ was sequestered with EDTA.
Automatic scientific text classification using local patterns (2002)

In this paper, we describe our approach for addressing Task 1 in the KDD CUP 2002 competition. The approach is based on developing and using an improved automatic feature selection method in conjunction with traditional classifiers. The feature selection method used is based on capturing frequently occurring keyword combinations (or motifs) within short segments of the text of a document and has proved to produce more accurate classification results than approaches relying solely on using keyword-based features.
Liquid–Liquid Extraction of Butanol from Dilute Aqueous Solutions Using Soybean‐Derived Biodiesel (2009)

Abstract Liquid–liquid extraction (LLE) of mixtures of butanol, 1,3‐propanediol (PDO), and ethanol was performed using soybean‐derived biodiesel as the extractant. The composition of the mixtures simulated the product of the anaerobic fermentation of biodiesel‐derived crude glycerol, which has recently been reported for the first time by the authors. Using a biodiesel: with an aqueous phase volume ratio of 1:1, butanol recovery ranged from 45 to 51% at initial butanol concentrations of 150 and 225 mM, respectively. Less than 10% of the ethanol was extracted, and essentially no PDO was extracted. The partition coefficient for butanol in biodiesel was determined to be 0.91 ± 0.097. This partition coefficient is less than that of oleyl alcohol, which is considered the standard for LLE. However, butanol is suitable for blending with biodiesel, which would eliminate the need for separating the butanol after extraction. Additionally, biodiesel is much less costly than oleyl alcohol. If biodiesel‐derived glycerol is used as the feedstock for butanol production, and biodiesel is used as the extractant to recover butanol from the fermentation broth, production of a biodiesel/butanol fuel blend could be a fully integrated process within a biodiesel facility. This process could ultimately help reduce the cost of butanol separation and ultimately help improve the overall economics of butanol fermentation using renewable feedstocks.
Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger (2013)

Twenty-five years have passed since the discovery of cyclic dimeric (3'→5') GMP (cyclic di-GMP or c-di-GMP). From the relative obscurity of an allosteric activator of a bacterial cellulose synthase, c-di-GMP has emerged as one of the most common and important bacterial second messengers. Cyclic di-GMP has been shown to regulate biofilm formation, motility, virulence, the cell cycle, differentiation, and other processes. Most c-di-GMP-dependent signaling pathways control the ability of bacteria to interact with abiotic surfaces or with other bacterial and eukaryotic cells. Cyclic di-GMP plays key roles in lifestyle changes of many bacteria, including transition from the motile to the sessile state, which aids in the establishment of multicellular biofilm communities, and from the virulent state in acute infections to the less virulent but more resilient state characteristic of chronic infectious diseases. From a practical standpoint, modulating c-di-GMP signaling pathways in bacteria could represent a new way of controlling formation and dispersal of biofilms in medical and industrial settings. Cyclic di-GMP participates in interkingdom signaling. It is recognized by mammalian immune systems as a uniquely bacterial molecule and therefore is considered a promising vaccine adjuvant. The purpose of this review is not to overview the whole body of data in the burgeoning field of c-di-GMP-dependent signaling. Instead, we provide a historic perspective on the development of the field, emphasize common trends, and illustrate them with the best available examples. We also identify unresolved questions and highlight new directions in c-di-GMP research that will give us a deeper understanding of this truly universal bacterial second messenger.
Oxidative stress in endothelial cell dysfunction and thrombosis (2002)

Endothelial dysfunction (ECD) is the earliest phenotypic change in the vasculature following exposure to atherothrombotic risk factors. ECD is associated with decreased synthesis and increased oxidative inactivation of nitric oxide (NO). Critical antioxidant enzymes essential for eliminating reactive oxygen species that can inactivate NO include the superoxide dismutases, the glutathione peroxidases, catalase, and glucose-6-phosphate dehydrogenase. Deficiencies of these enzymes increase oxidative stress and NO inactivation and, as such, can either lead to ECD or account for the underlying mechanism of ECD associated with a given atherothrombotic risk factor. Selected antioxidants improve intracellular redox state and reverse ECD by improving the bioavailability of NO. These observations provide mechanistic insights into the molecular basis of ECD in vascular disease and its treatment.
A PII-like protein in Arabidopsis : Putative role in nitrogen sensing (1998)

PII is a protein allosteric effector in Escherichia coli and other bacteria that indirectly regulates glutamine synthetase at the transcriptional and post-translational levels in response to nitrogen availability. Data supporting the notion that plants have a nitrogen regulatory system(s) includes previous studies showing that the levels of mRNA for plant nitrogen assimilatory genes such as glutamine synthetase (GLN) and asparagine synthetase (ASN) are modulated by carbon and organic nitrogen metabolites. Here, we have characterized a PII homolog (GLB1) in two higher plants, Arabidopsis thaliana and Ricinus communis (Castor bean). Each plant PII-like protein has high overall identity to E. coli PII (50%). Western blot analyses reveal that the plant PII-like protein is a nuclear-encoded chloroplast protein. The PII-like protein of plants appears to be regulated at the transcriptional level in that levels of GLB1 mRNA are affected by light and metabolites. To initiate studies of the in vivo function of the Arabidopsis PII-like protein, we have constructed transgenic lines in which PII expression is uncoupled from its native regulation. Analyses of these transgenic plants support the notion that the plant PII-like protein may serve as part of a complex signal transduction network involved in perceiving the status of carbon and organic nitrogen. Thus, the PII protein found in archaea, bacteria, and now in higher eukaryotes (plants) is one of the most widespread regulatory proteins known, providing evidence for an ancestral metabolic regulatory mechanism that may have existed before the divergence of these three domains of life.
Surrogate markers of insulin resistance: A review (2010)

Insulin resistance is a hallmark of obesity, diabetes, and cardiovascular diseases, and leads to many of the abnormalities associated with metabolic syndrome. Our understanding of insulin resistance has improved tremendously over the years, but certain aspects of its estimation still remain elusive to researchers and clinicians. The quantitative assessment of insulin sensitivity is not routinely used during biochemical investigations for diagnostic purposes, but the emerging importance of insulin resistance has led to its wider application research studies. Evaluation of a number of clinical states where insulin sensitivity is compromised calls for assessment of insulin resistance. Insulin resistance is increasingly being assessed in various disease conditions where it aids in examining their pathogenesis, etiology and consequences. The hyperinsulinemic euglycemic glucose clamp is the gold standard method for the determination of insulin sensitivity, but is impractical as it is labor- and time-intensive. A number of surrogate indices have therefore been employed to simplify and improve the determination of insulin resistance. The object of this review is to highlight various aspects and methodologies for current and upcoming measures of insulin sensitivity/resistance. In-depth knowledge of these markers will help in better understanding and exploitation of the condition.
Comparative Analysis of Measures of Viral Reservoirs in HIV-1 Eradication Studies (2013)

HIV-1 reservoirs preclude virus eradication in patients receiving highly active antiretroviral therapy (HAART). The best characterized reservoir is a small, difficult-to-quantify pool of resting memory CD4(+) T cells carrying latent but replication-competent viral genomes. Because strategies targeting this latent reservoir are now being tested in clinical trials, well-validated high-throughput assays that quantify this reservoir are urgently needed. Here we compare eleven different approaches for quantitating persistent HIV-1 in 30 patients on HAART, using the original viral outgrowth assay for resting CD4(+) T cells carrying inducible, replication-competent viral genomes as a standard for comparison. PCR-based assays for cells containing HIV-1 DNA gave infected cell frequencies at least 2 logs higher than the viral outgrowth assay, even in subjects who started HAART during acute/early infection. This difference may reflect defective viral genomes. The ratio of infected cell frequencies determined by viral outgrowth and PCR-based assays varied dramatically between patients. Although strong correlations with the viral outgrowth assay could not be formally excluded for most assays, correlations achieved statistical significance only for integrated HIV-1 DNA in peripheral blood mononuclear cells and HIV-1 RNA/DNA ratio in rectal CD4(+) T cells. Residual viremia was below the limit of detection in many subjects and did not correlate with the viral outgrowth assays. The dramatic differences in infected cell frequencies and the lack of a precise correlation between culture and PCR-based assays raise the possibility that the successful clearance of latently infected cells may be masked by a larger and variable pool of cells with defective proviruses. These defective proviruses are detected by PCR but may not be affected by reactivation strategies and may not require eradication to accomplish an effective cure. A molecular understanding of the discrepancy between infected cell frequencies measured by viral outgrowth versus PCR assays is an urgent priority in HIV-1 cure research.