gebhart/patrepeval huggingface dataset:
Diagnosis and management of<i>Pneumocystis jirovecii</i>infection (2017)

Pneumocystis jirovecii is a ubiquitous fungus, which causes pneumonia in humans. Diagnosis was hampered by the inability to culture the organism, and based on microscopic examination of respiratory samples or clinical presentation. New assays can assist in the diagnosis and even aid with the emergence of resistant infections. Areas covered: This manuscript will provide background information on Pneumocystis pneumonia (PcP). Diagnosis, from radiological to non-microbiological (e.g. Lactate dehydrogenase) and microbiological investigations (Microscopy, PCR, β-D-Glucan) will be discussed. Recommendations on prophylactic and therapeutic management will be covered. Expert commentary: PcP diagnosis using microscopy is far from optimal and false negatives will occur. With an incidence of 1% or less, the pre-test probability of not having PcP is 99% and testing is suited to excluding disease. Microscopy provides a high degree of diagnostic confidence but it is not infallible, and its lower sensitivity limits its application. Newer diagnostics (PCR, β-D-Glucan) can aid management and improve performance when testing less invasive specimens, such as upper respiratory samples or blood, alleviating clinical pressure. Combination testing may allow PcP to be both diagnosed and excluded, and molecular testing can assist in the detection of emerging resistant PcP.
Somatic Embryogenesis and Plant Regeneration from Callus Cultures of Nonbulbing Onions (1986)

Abstract Seeds of Allium fistulosum L. ‘Japanese Bunching’ onion and A. fistulosum × A. cepa L. ‘Beltsville Bunching’ onion were germinated on a modified B5 medium containing 4.5 μM 2,4-D and 4.6 μM kinetin. Within 2 weeks after seed germination, prolific callus grew from radicles. Callus was embryogenic and formed shoots when transferred to a similar medium containing 7.0 μM kinetin. Rooting of shoots was induced by transferring to an IBA-fortified medium. Several thousand plants were grown to maturity and selfed and the resulting seeds were grown in the field for further evaluations. Chemical names used: (2,4-dichlorophenoxy)acetic acid (2,4-D); N -(2-fur-anylmethyI)-1 H -purin-6-amine (kinetin); 1 H -indole-3-butanoic acid (IBA).
Detection of cytomegalovirus DNA in CD34+ cells from blood and bone marrow (1995)

Infection of hematopoietic progenitor cells with the human cytomegalovirus (HCMV) has been proposed as an explanation for the cytopenias associated with HCMV-related disease. To test this hypothesis, CD34+ cells, which include the hematopoietic progenitors, as well as mature leukocyte populations were purified on a fluorescence-activated cell sorter and analyzed for HCMV DNA by polymerase chain reaction (PCR). A total of 33 samples from 31 immunosuppressed as well as immunocompetent HCMV-seropositive individuals were studied. CD34+ cells were PCR-positive in four of seven bone marrow aspirates from allogeneic bone marrow transplant recipients, in three of eight aspirates from patients with acquired immunodeficiency syndrome, and in the first of two bone marrow samples from an immunocompetent patient with primary HCMV disease. CD34+ cells purified from peripheral blood for autologous and allogeneic transplantation were also analyzed, and 4 of 13 samples were HCMV DNA-positive. Interestingly, two of the four HCMV-positive samples were from healthy allogeneic donors. Among the mature leukocyte populations, the monocytes were most frequently found to be HCMV DNA-positive. No HCMV DNA was detected in the total bone marrow leukocytes of 13 healthy seropositive bone marrow donors or in the CD34+ cell fraction of three further seropositive donors. In conclusion, the data provide strong evidence that CD34+ hematopoietic progenitor cells can be infected with HCMV in immunosuppressed patients, while this cell population was not identified as a major viral reservoir in healthy HCMV-seropositive individuals.
Enantioselective Synthesis and Photoracemization Studies of (+)-2-Cyclopropyl-7,8-dimethoxy-2<i>H</i>- chromene-5-carboxylic Acid Methyl Ester, an Advanced Intermediate of a Dihydrofolate Reductase Inhibitor (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTEnantioselective Synthesis and Photoracemization Studies of (+)-2-Cyclopropyl-7,8-dimethoxy-2H- chromene-5-carboxylic Acid Methyl Ester, an Advanced Intermediate of a Dihydrofolate Reductase InhibitorPeter Wipf and Warren S. WeinerView Author Information Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 Cite this: J. Org. Chem. 1999, 64, 14, 5321–5324Publication Date (Web):June 19, 1999Publication History Received26 February 1999Published online19 June 1999Published inissue 1 July 1999https://pubs.acs.org/doi/10.1021/jo990352shttps://doi.org/10.1021/jo990352sbrief-reportACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1370Altmetric-Citations65LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Catalysts,Inhibitors,Light,Peptides and proteins Get e-Alerts
Chain Initiation Efficiency in Cobalt- and Nickel-Mediated Polypeptide Synthesis (2000)

In the presence of certain ligands and solvents, nickel- and cobalt-mediated living polymerizations of α-amino acid-N-carboxyanhydrides (NCAs) produce polymers with molecular weights several times greater than predicted by initial molar ratios of monomer to initiator. Such molecular weight inflation could result either from competitive formation of catalytic intermediates of reduced activity or from incomplete formation of a single catalytically active species. Evidence is presented here supporting the latter possibility. Specifically, evidence is given that the concentration of the key amido−amidate metallacyclic active species is reduced in situ by (1) complexation of metal(0) preinitiator by CO liberated upon addition of an NCA monomer to another molecule of preinitiator, (2) incomplete ring contraction of a six-membered amido−alkylmetallacyclic intermediate due to inefficient proton migration, and (3) dimerization of the amido−amidate active species to give catalytically inactive complexes.
Tuning before feedback (2004)

Both ranking functions and user queries are very important factors affecting a search engine's performance. Prior research has looked at how to improve ad-hoc retrieval performance for existing queries while tuning the ranking function, or modify and expand user queries using a fixed ranking scheme using blind feedback. However, almost no research has looked at how to combine ranking function tuning and blind feedback together to improve ad-hoc retrieval performance. In this paper, we look at the performance improvement for ad-hoc retrieval from a more integrated point of view by combining the merits of both techniques. In particular, we argue that the ranking function should be tuned first, using user-provided queries, before applying the blind feedback technique. The intuition is that highly-tuned ranking offers more high quality documents at the top of the hit list, thus offers a stronger baseline for blind feedback. We verify this integrated model in a large scale heterogeneous collection and the experimental results show that combining ranking function tuning and blind feedback can improve search performance by almost 30% over the baseline Okapi system.
Ovarian cancer (review). Etiology, diagnosis, prognosis, surgery, radiotherapy, chemotherapy and endocrine therapy. (1988)

The increased incidence of ovarian cancer in women whose ovulations were not suppressed by pregnancy or oral contraceptives and the increase in the incidence of the disease with the onset of climacterium support the hypothesis that ovarian cancer is an endocrine-related disease. Animal experimental results further support this contention. However, identification of a population at risk, prevention, and early detection is difficult. At present, tumor markers are useful in monitoring the disease, though cannot be used for screening. Most of the diagnosed cases are of advanced stages. Besides staging, tumor histology, and residual tumor load are of prognostic importance. The need for accurate initial surgical staging with optimal tumor cytoreduction and the importance of second-look surgery to confirm the response to therapy are emphasized. The precise role for radiotherapy in the treatment of ovarian cancer is still to be established. Presently, response rates of 80% are achieved using cisplatin based combination chemotherapy. In spite of this, long term survival has not improved. Endocrine therapy has hitherto been used empirically and mainly as a last resort in the treatment of advanced ovarian cancer. Response rates of about 10% have been reported. Information on tumor predisposition related to hormonal control should be a key parameter in selecting the appropriate therapy. Tumor analysis has shown that androgen receptors predominate in ovarian cancer, compared to estrogen and progestin receptors. A clinical trial based on endocrine parameters is warranted.
Analysis and Compensation of Phase Variations Versus Gain in Amplifiers Verified by SiGe HBT Cascode RFIC (2009)

The transmission phase variations versus gain in common emitter and common base amplifiers are analyzed revealing that these stages can be tuned to yield opposite phase characteristics versus gain. By cascading these two stages, e.g., on the basis of a cascode, and optimizing added feedback elements, it is possible to compensate these phase variations. A universal analysis based on bipolar transistors is derived. However, the insights can be mapped to other transistors such as field-effect transistors. The analysis is verified by implementation of a low-noise cascode amplifier in 0.25-mum silicon germanium heterojunction bipolar transistors. At 50-Omega terminations, 1.6-V supply voltage, 1-mA current consumption, and a gain of 7 dB plusmn 0.25 dB, a noise figure of less than 3.2 dB, and a third-order output intercept point of -3 dBm are measured within a frequency range from 5.2 to 5.9 GHz. For a gain control range of 12 and 20 dB, the transmission phase variations are reduced to 3deg and 6deg, respectively, which is around a factor of 7 better than for a conventional noncompensated cascode topology. The fully integrated circuit is well suited for wireless local area network systems applying adaptive antenna combining and operating in accordance to the 802.11 a/n standards.
Fabrication of gravity-driven microfluidic device (2008)

We have studied the micro total analysis system as a blood test. A microfluidic device with a three-pronged microchannel and artificial capillary vessels was fabricated. The microchannel is to transport blood, focus blood cells, and line them up. The vessels are to observe red blood cell deformation. An excimer laser was used to form grooves and so on. Numbers of thermosetting resin film and fluororesin were piled up on a cover glass. A laser fabricated part of the channel at the each film every lamination, and then a three-dimensional structure microchannel was fabricated. The channel sizes have widths of 50-150 microm and depths of 45 mum. Through holes used as artificial capillary vessels are made in the fluororesin having a minimum diameter of 5 microm and a length of 100 microm. As blood and a physiological saline are injected into the microchannel, the device stands upward facing the channel, and blood cells go into the vessels by the force of gravity and sheath flow of the saline. By gravity various groove patterns were made changing the width and length for measurement of blood focusing. Moreover, the red blood cell deformation was observed in the vessels with a microscope.
Efficient linear text segmentation based on information retrieval techniques (2009)

The task of linear text segmentation is to split a large text document into shorter fragments, usually blocks of consecutive sentences. The algorithms that demonstrated the best performance for this task come at the price of high computational complexity. In our work we present an algorithm that has a computational complexity of O(n) with n being the number of sentences in a document. The performance of our approach is evaluated against algorithms of higher complexity using standard benchmark data sets and we demonstrate that our approach provides comparable accuracy.
<i>Haemophilus Influenzae</i> in Lung Explants of Patients with End-stage Pulmonary Disease (1998)

In order to determine the presence and distribution of Haemophilus influenzae in lung tissue sections, we obtained lung explants from 49 lung transplant recipients with cystic fibrosis (CF) (n = 16), chronic obstructive pulmonary disease (COPD) including emphysema (n = 16), bronchiectasis (n = 5), pulmonary hypertension (n = 9), Langerhans cell histiocytosis (n = 1), and idiopathic pulmonary fibrosis (n = 2). Analysis was done by selective culturing, immunoperoxidase (IP) staining, and by polymerase chain reaction (PCR). H. influenzae was cultured from specimens of the lung explants from one CF and one COPD patient. IP staining of tissue sections was positive in 24 patients (10 CF patients, eight COPD patients, two bronchiectasis patients, and four patients with noninfectious pulmonary diseases). IP-positive tissue sections were PCR-positive, and IP-negative sections were PCR-negative. H. influenzae was more frequently detected in tissue sections of lung explants from CF and COPD patients than from patients with bronchiectasis or noninfectious pulmonary diseases. H. influenzae was diffusely present in the epithelium, the submucosa of the bronchi, the bronchioles, the interstitium, and the alveolar epithelium. H. influenzae was localized extracellularly alone and in bacterial clusters, and was also associated with macrophages in CF patients. The results of this study demonstrate that H. influenzae is often present in the lungs of patients with end-stage pulmonary disease, especially CF and COPD patients. H. influenzae is diffusely present in the respiratory epithelium and subepithelial layers of the lungs of these patients.
Efficacy and Safety/Toxicity Study of Recombinant Vaccinia Virus JX-594 in Two Immunocompetent Animal Models of Glioma (2010)

The purpose of this study was to investigate the oncolytic potential of the recombinant, granulocyte macrophage colony-stimulating factor (GM-CSF)-expressing vaccinia virus (VV) JX-594 in experimental malignant glioma (MGs) in vitro and in immunocompetent rodent models. We have found that JX-594 killed all MG cell lines tested in vitro. Intratumoral (i.t.) administration of JX-594 significantly inhibited tumor growth and prolonged survival in rats-bearing RG2 intracranial (i.c.) tumors and mice-bearing GL261 brain tumors. Combination therapy with JX-594 and rapamycin significantly increased viral replication and further prolonged survival in both immunocompetent i.c. MG models with several animals considered "cured" (three out of seven rats >120 days, terminated experiment). JX-594 infected and killed brain tumor-initiating cells (BTICs) from patient samples grown ex vivo, and did so more efficiently than other oncolytic viruses MYXV, Reovirus type-3, and VSV(ΔM51). Additional safety/toxicity studies in nontumor-bearing rodents treated with a supratherapeutic dose of JX-594 demonstrated GM-CSF-dependent inflammation and necrosis. These results suggest that i.c. administered JX-594 triggers a predictable GM-CSF-mediated inflammation in murine models. Before proceeding to clinical trials, JX-594 should be evaluated in the brains of nonhuman primates and optimized for the viral doses, delivery routes as well as the combination agents (e.g., mTOR inhibitors).
Interaction between poly(ethylene glycol) and water as studied by differential scanning calorimetry (2001)

The interaction between poly(ethylene glycol) (PEG) and water was studied by differential scanning calorimetry (DSC). The DSC curves of PEG–water systems were classified into three groups according to the difference in molecular weight. The melting peaks of eutectic mixture appeared for PEG with molecular weight higher than 1000. The eutectic point temperature shifted to higher temperatures and the eutectic point composition shifted to lower concentrations of PEG with increasing molecular weight. The maximum hydration number per ethylene glycol (EG) unit was estimated as 1.6, 2.4, and 3.3 for samples with molecular weights 400, 1540, and 70,000, respectively. No thermal change was found in PEG1540-water system for a narrow weight fraction range of 0.585–0.605 for overall measuring temperatures due to perfect supercooling. The glass transition temperature shifted to higher temperatures with increasing molecular weight of PEG. A modified Flory–Huggins equation was used to fit curves for experimental liquidus data in phase diagrams. © 2001 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 39: 496–506, 2001
All-fibre gyroscope using depolarised superluminescent diode (1986)

An all-fibre gyroscope using a depolarised superluminescent diode which has a coherence length of 8 μm and a degree of polarisation of 0.03 is constructed. Although the configuration is very simple and the fibre length is as short as 200 m, the drift and detection limits are less than 14 deg/h and 1.5 deg/h, respectively.
Recent Developments in the use of Acoustic Sensors and Signal Processing Tools to Target Early Infestations of Red Palm Weevil in Agricultural Environments<sup>1</sup> (2011)

Much of the damage caused by red palm weevil larvae to date palms, ornamental palms, and palm offshoots could be mitigated by early detection and treatment of infestations. Acoustic technology has potential to enable early detection, but the short, high-frequency sound impulses produced by red palm weevil larvae can be difficult to distinguish from certain similar sounds produced by other insects or small animals, or by wind-induced tapping noises. Considerable research has been conducted to develop instruments and signal processing software that selectively amplify insect-produced sounds and identify signal features that distinguish sounds produced by a particular target insect from those produced by other causes. Progress has been made in identifying unique spectral and temporal patterns in the sounds produced by larvae during movement and feeding activities. This report describes some of the new instrumentation and signal analyses available for early, reliable detection of red palm weevil larvae in groves and greenhouses.
Ag(I)/PPh3-Catalyzed Diastereoselective Syntheses of the Spiro[indole-3,4'-piperidine] Scaffold and Its Derivatives via Chelation-Controlled Cycloisomerizations of Tryptamine-Ynamides (2021)

A Ag(I)/PPh3-catalyzed chelation-controlled cycloisomerization of tryptamine-ynamide was developed to access the spiro[indole-3,4'-piperidine] scaffold. The asymmetric products with this scaffold were obtained through a diastereoselective synthesis via a chiral pool approach. Such a synthesis could be realized on a gram scale and derivatization of this scaffold afforded various derivatives. DFT calculations indicated that strong non-covalent effects between the substrate and catalyst/ligand complex stabilized the spiroindoleninium intermediate via cation-π-π interactions, leading to the diastereoselective syntheses of spiro[indole-3,4'-piperidine derivatives.
Evolution of the Channelrhodopsin Photocycle Model (2010)

Many processes in green algae are under control of rhodopsin-type photoreceptors, but only a few have been studied at least in some detail in the past. Up to now, functionally and biochemically only the channelrhodpsins ChR1 and ChR2 are characterized. Thus, this short review reports on channelrhodopsin properties with a strong focus on the knowledge about the photoreaction cycle(s).
Comparison of the reinforcing and anxiogenic effects of intravenous cocaine and cocaethylene. (2000)

People report that ethanol improves the experience produced by cocaine. This effect may be attributable to cocaethylene (CE), a cocaine metabolite formed only in the presence of ethanol. To test this, rats were trained to run an alley for a single intravenous dose of either cocaine (0.5-2.0 mg/kg) or an equimolar dose of CE (0.75-2.88 mg/kg). The rats' start latency and running speed measured the reinforcing effects of the drugs and the number of times rats approached but failed to enter the goal box (i.e., approach-avoidance retreats) indexed anxiety. Rats reinforced with CE had shorter start latencies and faster running speeds and exhibited fewer "retreats" than cocaine-reinforced rats. These results suggest that CE is more reinforcing and less anxiogenic than cocaine and hence may account for the combined effects of cocaine and ethanol in humans.
Interleukin 27R regulates CD4+ T cell phenotype and impacts protective immunity during <i>Mycobacterium tuberculosis</i> infection (2015)

CD4+ T cells mediate protection against Mycobacterium tuberculosis (Mtb); however, the phenotype of protective T cells is undefined, thereby confounding vaccination efforts. IL-27 is highly expressed during human tuberculosis (TB), and absence of IL-27R (Il27ra) specifically on T cells results in increased protection. IL-27R deficiency during chronic Mtb infection does not impact antigen-specific CD4+ T cell number but maintains programmed death-1 (PD-1), CD69, and CD127 expression while reducing T-bet and killer cell lectin-like receptor G1 (KLRG1) expression. Furthermore, T-bet haploinsufficiency results in failure to generate KLRG1+, antigen-specific CD4+ T cells, and in improved protection. T cells in Il27ra(-/-) mice accumulate preferentially in the lung parenchyma within close proximity to Mtb, and antigen-specific CD4+ T cells lacking IL-27R are intrinsically more fit than intact T cells and maintain IL-2 production. Improved fitness of IL-27R-deficient T cells is not associated with increased proliferation but with decreased expression of cell death-associated markers. Therefore, during Mtb infection, IL-27R acts intrinsically on T cells to limit protection and reduce fitness, whereas the IL-27R-deficient environment alters the phenotype and location of T cells. The significant expression of IL-27 in TB and the negative influence of IL-27R on T cell function demonstrate the pathway by which this cytokine/receptor pair is detrimental in TB.