gebhart/patrepeval huggingface dataset:
Rod Packings and Metal−Organic Frameworks Constructed from Rod-Shaped Secondary Building Units (2005)

The principal structure possibilities for packing infinite rod-shaped building blocks are described. Some basic nets derived from linking simple rods (helices and ladders) are then enumerated. We demonstrate the usefulness of the concept of rod secondary building units in the design and synthesis of metal-organic frameworks (MOFs). Accordingly, we present the preparation, characterization, and crystal structures of 14 new MOFs (named MOF-69A-C and MOF-70-80) of 12 different structure types, belonging to rod packing motifs, and show how their structures are related to basic nets. The MOFs reported herein are of polytopic carboxylates and contain one of Zn, Pb, Co, Cd, Mn, or Tb. The inclusion properties of the most open members are presented as evidence that MOF structures with rod building blocks can indeed be designed to have permanent porosity and rigid architectures.
Rapid Detection and Quantification of RNA of Ebola and Marburg Viruses, Lassa Virus, Crimean-Congo Hemorrhagic Fever Virus, Rift Valley Fever Virus, Dengue Virus, and Yellow Fever Virus by Real-Time Reverse Transcription-PCR (2002)

Viral hemorrhagic fevers (VHFs) are acute infections with high case fatality rates. Important VHF agents are Ebola and Marburg viruses (MBGV/EBOV), Lassa virus (LASV), Crimean-Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), dengue virus (DENV), and yellow fever virus (YFV). VHFs are clinically difficult to diagnose and to distinguish; a rapid and reliable laboratory diagnosis is required in suspected cases. We have established six one-step, real-time reverse transcription-PCR assays for these pathogens based on the Superscript reverse transcriptase-Platinum Taq polymerase enzyme mixture. Novel primers and/or 5'-nuclease detection probes were designed for RVFV, DENV, YFV, and CCHFV by using the latest DNA database entries. PCR products were detected in real time on a LightCycler instrument by using 5'-nuclease technology (RVFV, DENV, and YFV) or SybrGreen dye intercalation (MBGV/EBOV, LASV, and CCHFV). The inhibitory effect of SybrGreen on reverse transcription was overcome by initial immobilization of the dye in the reaction capillaries. Universal cycling conditions for SybrGreen and 5'-nuclease probe detection were established. Thus, up to three assays could be performed in parallel, facilitating rapid testing for several pathogens. All assays were thoroughly optimized and validated in terms of analytical sensitivity by using in vitro-transcribed RNA. The >or=95% detection limits as determined by probit regression analysis ranged from 1,545 to 2,835 viral genome equivalents/ml of serum (8.6 to 16 RNA copies per assay). The suitability of the assays was exemplified by detection and quantification of viral RNA in serum samples of VHF patients.
Axl Mediates Acquired Resistance of Head and Neck Cancer Cells to the Epidermal Growth Factor Receptor Inhibitor Erlotinib (2013)

Elevated expression and activity of the epidermal growth factor receptor (EGFR) is associated with development and progression of head and neck cancer (HNC) and a poor prognosis. Clinical trials with EGFR tyrosine kinase inhibitors (e.g., erlotinib) have been disappointing in HNC. To investigate the mechanisms mediating resistance to these agents, we developed an HNC cell line (HN5-ER) with acquired erlotinib resistance. In contrast to parental HN5 HNC cells, HN5-ER cells exhibited an epithelial-mesenchymal (EMT) phenotype with increased migratory potential, reduced E-cadherin and epithelial-associated microRNAs (miRNA), and elevated vimentin expression. Phosphorylated receptor tyrosine kinase profiling identified Axl activation in HN5-ER cells. Growth and migration of HN5-ER cells were blocked with a specific Axl inhibitor, R428, and R428 resensitized HN5-ER cells to erlotinib. Microarray analysis of HN5-ER cells confirmed the EMT phenotype associated with acquired erlotinib resistance, and identified activation of gene expression associated with cell migration and inflammation pathways. Moreover, increased expression and secretion of interleukin (IL)-6 and IL-8 in HN5-ER cells suggested a role for inflammatory cytokine signaling in EMT and erlotinib resistance. Expression of the tumor suppressor miR-34a was reduced in HN5-ER cells and increasing its expression abrogated Axl expression and reversed erlotinib resistance. Finally, analysis of 302 HNC patients revealed that high tumor Axl mRNA expression was associated with poorer survival (HR = 1.66, P = 0.007). In summary, our results identify Axl as a key mediator of acquired erlotinib resistance in HNC and suggest that therapeutic inhibition of Axl by small molecule drugs or specific miRNAs might overcome anti-EGFR therapy resistance.
Flexible, Stretchable, Transparent Carbon Nanotube Thin Film Loudspeakers (2008)

We found that very thin carbon nanotube films, once fed by sound frequency electric currents, could emit loud sounds. This phenomenon could be attributed to a thermoacoustic effect. The ultra small heat capacity per unit area of carbon nanotube thin films leads to a wide frequency response range and a high sound pressure level. On the basis of this finding, we made practical carbon nanotube thin film loudspeakers, which possess the merits of nanometer thickness and are transparent, flexible, stretchable, and magnet-free. Such a single-element thin film loudspeaker can be tailored into any shape and size, freestanding or on any insulating surfaces, which could open up new applications of and approaches to manufacturing loudspeakers and other acoustic devices.
Safety and Immunogenicity of Boosting BCG Vaccinated Subjects with BCG: Comparison with Boosting with a New TB Vaccine, MVA85A (2009)

ClinicalTrials.gov NCT00654316 NCT00427830.
Nosocomial Infection by Gentamicin-Resistant Streptococcus faecalis (1987)

Enterococci with high-level resistance to gentamicin account for 55% of clinical isolates of enterococci found in patients at the Ann Arbor Veterans Administration Medical Center. We prospectively studied cultures obtained from all 100 patients hospitalized from 1 December 1985 through 23 January 1986 on the surgical and thoracic intensive care units and a general medical floor. Ten patients' cultures grew colonies of gentamicin-resistant enterococci--six after admission to the intensive care units and four after hospitalization on the medical ward. The initial sites of colonization were the rectal and perineal areas in seven patients, sternal wound in one, urine in one, and the rectal and perineal areas as well as urine after Foley catheter insertion in one. Nine patients died and three of the deaths were associated with enterococcal infection. The acquisition of resistant strains was associated with previous and more frequent exposure to antimicrobial agents, and with geographic clustering of patients. Resistant enterococci were isolated from the hands of hospital personnel and were frequently isolated from environmental surfaces. Nosocomial acquisition and interhospital spread of gentamicin-resistant enterococci was shown to have occurred when plasmid content was used as an epidemiologic marker.
Statistical Shape Analysis, with Applications in R (2016)

A thoroughly revised and updated edition of this introduction to modern statistical methods for shape analysis Shape analysis is an important tool in the many disciplines where objects are compared using geometrical features. Examples include comparing brain shape in schizophrenia; investigating protein molecules in bioinformatics; and describing growth of organisms in biology. This book is a significant update of the highly-regarded `Statistical Shape Analysis’ by the same authors. The new edition lays the foundations of landmark shape analysis, including geometrical concepts and statistical techniques, and extends to include analysis of curves, surfaces, images and other types of object data. Key definitions and concepts are discussed throughout, and the relative merits of different approaches are presented. The authors have included substantial new material on recent statistical developments and offer numerous examples throughout the text. Concepts are introduced in an accessible manner, while retaining sufficient detail for more specialist statisticians to appreciate the challenges and opportunities of this new field. Computer code has been included for instructional use, along with exercises to enable readers to implement the applications themselves in R and to follow the key ideas by hands-on analysis. Statistical Shape Analysis: with Applications in R will offer a valuable introduction to this fast-moving research area for statisticians and other applied scientists working in diverse areas, including archaeology, bioinformatics, biology, chemistry, computer science, medicine, morphometics and image analysis.
Role of interferon α in promoting T helper cell type 1 responses in the small intestine in coeliac disease (2001)

Coeliac disease (CD) is caused by a CD4 T helper cell type 1 (Th1) response in the small intestinal mucosa to dietary gluten. As the major Th1 inducing cytokine, interleukin 12, is undetectable in CD gut mucosa, the mechanism by which Th1 effector cells are generated remains unknown. Interferon (IFN) alpha, a cytokine capable of promoting IFN-gamma synthesis, has been implicated in the development of Th1 mediated immune diseases. Here we report a case of CD-like enteropathy in a patient receiving IFN-alpha for chronic myeloid leukaemia. Morphological assessment of duodenal biopsies taken from the patient showed total villous atrophy, crypt cell hyperplasia, and a high number of CD3+ intraepithelial lymphocytes. Both antigliadin antibodies and antiendomysial antibodies were positive. RNA analysis revealed pronounced expression of IFN-gamma. Withdrawal of gluten from the diet resulted in a patchy improvement in intestinal morphology, normalisation of laboratory parameters, and resolution of clinical symptoms. By western blot analysis, IFN-alpha protein was seen in the duodenal mucosa from untreated CD patients but not in controls. This was associated with marked expression of IFN-gamma protein in CD mucosa. Collectively, these results suggest a role for IFN-alpha in promoting Th1 responses to gluten.
Residues 10–18 within the C5a Receptor N Terminus Compose a Binding Domain for Chemotaxis Inhibitory Protein of Staphylococcus aureus (2004)

Chemotaxis inhibitory protein of Staphylococcus aureus (CHIPS) is excreted by the majority of S. aureus strains and is a potent inhibitor of C5a- and formylated peptide-mediated chemotaxis of neutrophils and monocytes. Recently, we reported that CHIPS binds to the C5a receptor (C5aR) and the formylated peptide receptor, thereby blocking activation by C5a and formylated peptides, respectively. The anaphylatoxin C5a plays an important role in host immunity and pathological inflammatory processes. For C5a a two-site binding model is proposed in which C5a initially binds the C5aR N terminus, followed by interaction of the C5a C-terminal tail with an effector domain on the receptor. We have shown here that CHIPS does not affect activation of the C5aR by a peptide mimic of the C5a C terminus. Moreover, CHIPS was found to bind human embryonic kidney 293 cells expressing only the C5aR N terminus. Deletion and mutation experiments within this C5aR N-terminal expression system revealed that the binding site of CHIPS is contained in a short stretch of 9 amino acids (amino acids 10-18), of which the aspartic acid residues at positions 10, 15, and 18 plus the glycine at position 12 are crucial. Binding studies with C5aR/C3aR and C5aR/IL8RA chimeras confirmed that CHIPS binds only to the C5aR N terminus without involvement of its extracellular loops. CHIPS may provide new strategies to block the C5aR, which may lead to the development of new C5aR antagonists.
CT artifact reduction via U-net CNN (2018)

Purpose: Our preliminary study showed us the capability of a deep learning neural network (DLNN) based method to eliminate a specific type of artifact in CT images. This work is to comprehensively study the applicability of a U-net CNN architecture in improving the image quality of CT reconstructions by respectively testing its performance in various artifact removal tasks. Methods: A U-net architecture is trained by a big dataset of contaminated and expected image pairs. The expected images known as reference images are acquired from groundtruths or using superior imaging system. A proper initialization of network parameters, a careful normalization of original data and a residual learning objective are incoorprated into the framework to boost training convergence. Both numerical and real data studies are conducted to validate this method. Results: In numerical studies, we found that the DLNN-based artifact reduction is powerful and can work well in reducing nearly all type artifacts and recover detailed structrual information in low-quliaty images (e.g. plain FBP reconstructions) if the network is trained with groundtruths provided. In real situations where groundtruth is not available, the proposed method can characterize the discrepancy between contaminated data and higher-quality reference labels produced by other techniques, mimicking their capability of reducing artifacts. Generalization to disjointed data is also examined using testing data. All results show that the DLNN framework can be applied to various artifact reduction tasks and outperforms conventional methods with shorter runtime. Conclusion: This work gained promising results of the U-net network architecture successfully characterizing both global and local artifact patterns. By forward propagating contaminated images through the trained network, undesired artifacts can be greatly reduced while structrual information maintained for an input of CT image. It should be noted that the proposed deep network should be trained independently for each specific case.
A B-cell-specific DNA Recombination Complex (1998)

We have purified and biochemically characterized a multiprotein complex designated SWAP. In a DNA transfer assay, SWAP preferentially recombines ("swaps") sequences derived from Ig heavy chain switch regions. We identified four of the proteins in the SWAP complex: B23 (nucleophosmin), C23 (nucleolin), poly(ADP-ribose) polymerase (PARP), and SWAP-70. The first three are proteins known to be present in most cells. B23 promotes single-strand DNA reannealing and the formation of joint molecules in a D-loop assay between homologous, but also between Smu and Sgamma sequences. SWAP-70 is a novel protein of 70 kDa. Its cDNA was cloned and sequenced, and the protein was overexpressed in Escherichia coli. SWAP-70 protein expression was found only in B lymphocytes that had been induced to switch to various Ig isotypes and in switching B-cell lines. SWAP-70 is a nuclear protein, has a weak affinity for DNA, binds ATP, and forms specific, high affinity complexes with B23, C23, and poly(ADP-ribose) polymerase. These findings are consistent with SWAP being the long elusive "switch recombinase" and with SWAP-70 being the specific recruiting element that assembles the switch recombinase from universal components.
Magnetic Relaxation Switch Immunosensors Detect Enantiomeric Impurities (2004)

Purity check: The self-assembly of magnetic nanoparticle sensors in the presence of stereoselective antibodies causes a decrease in the T2 relaxation time of surrounding protons. The introduction of enantiomeric impurities disrupts the antibody/magnetic-sensor binding and increases the T2 relaxation time, which can be monitored by magnetic resonance imaging (see picture).
Speech-based retrieval using semantic co-occurrence filtering (1994)

In this paper we demonstrate that speech recognition can be effectively applied to information retrieval (IR) applications. Our system exploits the fact that the intended words of a spoken query tend to co-occur in text documents in close proximity whereas word combinations that are the result of recognition errors are usually not semantically correlated and thus do not appear together. Termed "Semantic Co-occurrence Filtering" this enables the system to simultaneously disambiguate word hypotheses and find relevant text for retrieval. The system is built by integrating standard IR and speech recognition techniques. An evaluation of the system is presented and we discuss several refinements to the functionality.
An Inhibitor of Serine Proteases, Neuroserpin, Acts as a Neuroprotective Agent in a Mouse Model of Neurodegenerative Disease (2006)

Various studies suggest that proteolytic activity may be involved in a number of neurodegenerative disorders, including stroke and seizure. In this report, we examined the role of tryptic serine proteases, plasminogen activators (PAs), in the evolution of a neurodegenerative disease. Transgenic mice overexpressing an axonally secreted inhibitor of serine proteases (neuroserpin) were crossed with mice characterized by a "dying-back" motor neuron disease [progressive motor neuronopathy (pmn/pmn)]. Compared with pmn/pmn mice that showed an increase in PA activity, double mutant mice had decreased PA activity in sciatic nerves and spinal cord; their lifespan was increased by 50%, their motor behavior was stabilized, and histological analysis revealed increased numbers of myelinated axons and rescue of motoneuron number and size. This is the first report showing that a class of serine proteases (PAs) may be involved in the pathogenesis of a motor neuron disease and more specifically in axonal degeneration. Inhibiting serine proteases could offer a new strategy for delaying these disorders.
Stabilization of rinderpest vaccine by modification of the lyophilization process. (1996)

Rinderpest (RP), a lethal disease of cattle, was almost eradicated from the African continent under Joint Project 15 (JP15), using an excellent modified live virus vaccine. Due to marked instability of the vaccine, a cold chain was required to ensure that the vaccine was potent at the time of application. Rinderpest re-emerged in the early 1980s. The Pan African Rinderpest Campaign (PARC) was developed to combat the new epidemic. For PARC to be efficacious and affordable, there was a clear need to have a vaccine that was thermostable. The need for a stable vaccine was underscored in politically unstable areas such as the Sudan, where the veterinary infrastructure has diminished and vaccination has been left in the hands of personnel who must act expeditiously. This paper reviews studies on various stabilizers and a modified lyophilization cycle that resulted in a highly thermostable RP vaccine. The useful shelf life of the vaccine, under African field conditions, was increased from less than one week to at least 100 days. For practical reasons, PARC recommends that the vaccine be used within 30 days of leaving refrigeration (the cold chain).
Encapsulated HRh(CO)(PPh3)3 in Microporous and Mesoporous Supports:  Novel Heterogeneous Catalysts for Hydroformylation (2003)

Novel heterogeneous catalysts for hydroformylation of olefins to aldehydes using encapsulation and anchoring methodologies for HRh(CO)(PPh3)3 in zeolite Na−Y and MCM-41 and MCM-48 mesoporous materials have been reported. The heterogeneous catalysts were characterized and used for hydroformylation of linear and branched olefins to show high activity and recyclability without leaching of the Rh metal during the course of reactions. Using CP-MAS NMR, FT-IR, TEM, XPS, and powder XRD studies, characterization of the Rh complex inside the porous structures of the heterogeneous catalysts has been investigated. 31P CP-MAS NMR spectra of the encapsulated Rh complex catalyst inside zeolite Na−Y and mesoporous MCM-41 and MCM-48 supports showed a possible encapsulation of the Rh complex in the pores. TEM images and the diffraction patterns of the heterogenized Rh complex in mesoporous and zeolitic supports further supported a possible entrapment of the complex inside the porous frameworks. Rhodium is present as Rh(I) in the encapsulated catalysts before and after the experiments, as envisaged by XPS spectra. In contrast to other heterogeneous catalytic systems for hydroformylation, the catalysts reported here are highly stable, easily separable, and recyclable. The TON/TOF values of these catalysts were also found to be significantly higher than those of the previously reported heterogeneous catalysts.
Eosinophilic Granulomatosis with Polyangiitis: An Overview (2014)

Eosinophilic granulomatosis with polyangiitis (EGPA) is a multisystemic disorder, belonging to the small vessel anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, defined as an eosinophil-rich and necrotizing granulomatous inflammation often involving the respiratory tract, and necrotizing vasculitis predominantly affecting small to medium-sized vessels, associated with asthma and eosinophilia. EGPA pathogenesis is not well known: HLA-DRB1*04 and *07, HLA-DRB4 and IL10.2 haplotype of the IL-10 promoter gene are the most studied genetic determinants. Among the acquired pathogenetic factors, the exposure to different allergens, infections, vaccinations, drugs, and silica exposure have been involved. Eosinophils are the most characteristic cells in EGPA and different studies have demonstrated their role as effector and immunoregulatory cells. EGPA is considered as a disease with a prevalent activation of the Th-2 cellular-mediated inflammatory response and also humoral immunity plays an important role. A link between B and T inflammatory responses may explain different disease features. EGPA typically develops into three sequential phases: the allergic phase, distinguished by the occurrence of asthma, allergic rhinitis, and sinusitis, the eosinophilic phase, in which the main pathological finding is the eosinophilic organ infiltrations (e.g., lungs, heart, and gastrointestinal system), and the vasculitic phase, characterized by purpura, peripheral neuropathy, and constitutional symptoms. ANCA (especially pANCA anti-myeloperoxidase) are present in 40-60% of the patients. An elevation of IgG4 is frequently found. Corticosteroids and cyclophosphamide are classically used for remission induction, while azathioprine and methotrexate are the therapeutic options for remission maintenance. B-cell depletion with rituximab has shown promising results for remission induction.