gebhart/patrepeval huggingface dataset:
Action Spectrum for Melatonin Regulation in Humans: Evidence for a Novel Circadian Photoreceptor (2001)

The photopigment in the human eye that transduces light for circadian and neuroendocrine regulation, is unknown. The aim of this study was to establish an action spectrum for light-induced melatonin suppression that could help elucidate the ocular photoreceptor system for regulating the human pineal gland. Subjects (37 females, 35 males, mean age of 24.5 +/- 0.3 years) were healthy and had normal color vision. Full-field, monochromatic light exposures took place between 2:00 and 3:30 A.M. while subjects' pupils were dilated. Blood samples collected before and after light exposures were quantified for melatonin. Each subject was tested with at least seven different irradiances of one wavelength with a minimum of 1 week between each nighttime exposure. Nighttime melatonin suppression tests (n = 627) were completed with wavelengths from 420 to 600 nm. The data were fit to eight univariant, sigmoidal fluence-response curves (R(2) = 0.81-0.95). The action spectrum constructed from these data fit an opsin template (R(2) = 0.91), which identifies 446-477 nm as the most potent wavelength region providing circadian input for regulating melatonin secretion. The results suggest that, in humans, a single photopigment may be primarily responsible for melatonin suppression, and its peak absorbance appears to be distinct from that of rod and cone cell photopigments for vision. The data also suggest that this new photopigment is retinaldehyde based. These findings suggest that there is a novel opsin photopigment in the human eye that mediates circadian photoreception.
Molecular cloning of a human novel type I cytokine receptor related to δ1/TSLPR (2001)

In a search for a human sequence related to a recently identified type I cytokine receptor delta1, which turned out to be a receptor subunit for a cytokine called TSLP, we have now identified a novel human type I cytokine receptor from a human T lymphocyte cDNA library. The deduced amino acid sequence of 371 residues has a typical signal sequence and a membrane-spanning region. The mature protein is predicted to have a molecular mass of 39,698 Da. The N-terminal extracellular region contains two fibronectin type III-like domains, four conserved cysteine residues, and a WSXWS box-like motif. The C-terminal intracellular region contains box 1 and box 2-like motifs. Thus, it has common characteristics of type I cytokine receptor family members, and we tentatively termed this protein CRLF2, which stands for cytokine receptor-like factor 2. Northern blot analysis revealed CRLF2 mRNA in liver, kidney, heart, and skeletal muscle. The fetal liver also expresses CRLF2 transcripts. The gene for CRLF2 was mapped to the pseudoautosomal region, Xp22.3 and Yp11.3 by FISH analysis, a region where genes encoding the IL-3 receptor alpha and the GM-CSF receptor alpha chains are also located. The biological function of this newly identified receptor is now under investigation.
On Strategies for Dynamic Resource Management in Virtualized Server Environments (2007)

Virtualization rapidly gains popularity affecting multiple levels of the computing stack. Since it decouples resources from their users it provides greater flexibility in terms of resource allocation but also brings new challenges for optimal design, provisioning, and runtime management of systems. This paper presents an analytical model of virtual machine migration that provides an estimate of the expected improvement in response time due to a migration decision. The model explicitly accounts for predictability of resource demands and characteristics of the virtualization infrastructure, such as migration time and overhead. It brings new insights into the decision strategies that should be used to improve the overall responsiveness of the system when dynamically managing virtual machines. The model is validated using simulations driven by data center resource utilization traces.
Fungal pneumonias in transplant recipients (2003)

Fungi are ubiquitous in the environment. Opportunistic fungal pneumonias in the immunocompromised host continue to increase most commonly due to Aspergillus sp. Affected patients are usually hematopoietic stem cell and lung transplant recipients. Clinical presentation is protean, and the diagnosis is challenging. Culture of respiratory specimens has limited utility. The detection of circulating fungal antigens and DNA seems promising, but more studies are needed. Value of prophylactic strategies or preemptive therapy remains contentious. New antifungal drugs for managing invasive pulmonary aspergillosis continue to emerge, with better safety, efficacy, and pharmacologic profiles.
Persistent Decreases in Blood Plasmacytoid Dendritic Cell Number and Function Despite Effective Highly Active Antiretroviral Therapy and Increased Blood Myeloid Dendritic Cells in HIV-Infected Individuals (2002)

Dendritic cells (DC) have an instrumental role in the activation and function of both innate and adaptive immune responses. In humans, at least two distinct DC subsets have been characterized based on phenotypic markers: the myeloid DC (MDC) and the plasmacytoid DC (PDC). Both subsets are critical producers of cytokines (IL-12 for MDC and type I/II IFNs for PDC) and are functionally different. We show in this study that HIV(+) individuals have a significant decrease in the number of the Lin(-)HLA-DR(+)CD123(+) and BDCA-2(+) PDC compared with uninfected donors (p = 0.0001). HIV(+) individuals also have a sustained impairment in viral-induced IFN-alpha production (p < 0.0001). The decrease of the PDC subsets did not correlate with CD4 count or viral load and was not reversed in subjects under virally suppressive treatment, suggesting an irreversible change after infection. By contrast, the absolute number and median frequency of MDC in HIV-infected individuals were similar to those observed in uninfected controls, while a significant decrease was present in subjects with >5000 HIV-1 copies/ml. The inverse association with viral load of the MDC number, but not of IFN-alpha secretion or the number of PDC, suggests a role for MDC in viral control. Our data suggest that DC subsets are differentially reconstituted during the immune recovery associated with antiviral therapy. The persistent impairment of certain DC subsets may result in a sustained defect in DC-mediated innate immune functions despite an effective treatment regimen.
Phase retrieval for improved three-dimensional velocimetry of dynamic x-ray blood speckle (2008)

High-resolution synchrotron-based x-ray phase-contrast images of in vitro blood flow have been collected. We demonstrate that the application of a single-image phase retrieval algorithm to the images leads to improved detail in particle image velocimetry correlation peaks. Out-of-plane variation in flow has been extracted from the peaks leading to the three-dimensional reconstruction of velocity across an axially symmetric cylinder.
ChemInform Abstract: MESOIONIC HETEROCYCLES BASED ON 2‐AMINO‐1,2,4‐TRIAZOLO(1.5‐A)PYRIDINE (1982)

Abstract Beispiele für die im Titel genannte Verbindungsklasse sind die im Formelschema mit Syntheseweg angegebenen Verbindungen (IV), (IX) bzw. (XII).
Natural language processing in an operational clinical information system (1995)

Abstract This paper describes a natural language text extraction system, called MEDLEE, that has been applied to the medical domain. The system extracts, structures, and encodes clinical information from textual patient reports. It was integrated with the Clinical Information System (CIS), which was developed at Columbia-Presbyterian Medical Center (CPMC) to help improve patient care. MEDLEE is currently used on a daily basis to routinely process radiological reports of patients at CPMC. In order to describe how the natural language system was made compatible with the existing CIS, this paper will also discuss engineering issues which involve performance, robustness, and accessibility of the data from the end users' viewpoint. Also described are the three evaluations that have been performed on the system. The first evaluation was useful primarily for further refinement of the system. The two other evaluations involved an actual clinical application which consisted of retrieving reports that were associated with specified diseases. Automated queries were written by a medical expert based on the structured output forms generated as a result of text processing. The retrievals obtained by the automated system were compared to the retrievals obtained by independent medical experts who read the reports manually to determine whether they were associated with the specified diseases. MEDLEE was shown to perform comparably to the experts. The technique used to perform the last two evaluations was found to be a realistic evaluation technique for a natural language processor.
A NEW METHOD FOR THE CONVERSION OF NITRILES TO ALDEHYDES1 (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA NEW METHOD FOR THE CONVERSION OF NITRILES TO ALDEHYDES1Carl J. Claus and John L. Morgenthau Jr.Cite this: J. Am. Chem. Soc. 1951, 73, 10, 5005–5006Publication Date (Print):October 1, 1951Publication History Published online1 May 2002Published inissue 1 October 1951https://pubs.acs.org/doi/10.1021/ja01154a547https://doi.org/10.1021/ja01154a547research-articleACS PublicationsRequest reuse permissionsArticle Views123Altmetric-Citations34LEARN 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-Alertsclose Get e-Alerts
Improving JavaScript performance by deconstructing the type system (2014)

Increased focus on JavaScript performance has resulted in vast performance improvements for many benchmarks. However, for actual code used in websites, the attained improvements often lag far behind those for popular benchmarks.
A Structural Motif of Acetylcholinesterase That Promotes Amyloid β-Peptide Fibril Formation (2001)

Acetylcholinesterase (AChE) has been found to be associated with the core of senile plaques. We have shown that AChE interacts with the amyloid beta-peptide (Abeta) and promotes amyloid fibril formation by a hydrophobic environment close to the peripheral anionic binding site (PAS) of the enzyme. Here we present evidence for the structural motif of AChE involved in this interaction. First, we modeled the docking of Abeta onto the structure of Torpedo californica AChE, and identified four potential sites for AChE-Abeta complex formation. One of these, Site I, spans a major hydrophobic sequence exposed on the surface of AChE, which had been previously shown to interact with liposomes [Shin et al. (1996) Protein Sci. 5, 42-51]. Second, we examined several AChE-derived peptides and found that a synthetic 35-residue peptide corresponding to the above hydrophobic sequence was able to promote amyloid formation. We also studied the ability to promote amyloid formation of two synthetic 24-residue peptides derived from the sequence of a Omega-loop, which has been suggested as an AChE-Abeta interacting motif. Kinetic analyses indicate that only the 35-residue hydrophobic peptide mimics the effect of intact AChE on amyloid formation. Moreover, RP-HPLC analysis revealed that the 35-residue peptide was incorporated into the growing Abeta-fibrils. Finally, fluorescence binding studies showed that this peptide binds Abeta with a K(d) = 184 microM, independent of salt concentration, indicating that the interaction is primarily hydrophobic. Our results indicate that the homologous human AChE motif is capable of accelerating Abeta fibrillogenesis.
Situation of hantavirus infections and haemorrhagic fever with renal syndrome in European countries as of December 2006 (2008)

Hantavirus infections are widely distributed in Europe with the exception of the far north and the Mediterranean regions. The underlying causes of varying epidemiological patterns differ among regions: in western and central Europe epidemics of haemorrhagic fever with renal syndrome (HFRS) caused by hantavirus infections follow mast years with increased seed production by oak and beech trees followed by increased rodent reproduction. In the northern regions, hantavirus infections and HFRS epidemics occur in three to four year cycles and are thought to be driven by prey - predator interactions. Hantavirus infections and HFRS seem to be on the increase in Europe, partly because of better diagnostics, partly perhaps due to environmental changes. Unfortunately, hantavirus infections are still heavily under-diagnosed in many European countries. Here we report the results of a survey conducted in 2007 amongst the member laboratories of the European Network for diagnostics of Imported Viral Diseases (ENIVD).
Molecular Characterization of Aegyptianella pullorum ( Rickettsiales , Anaplasmataceae ) (2003)

We sequenced the 16S rRNA and groEL genes of Aegyptianella pullorum, a small bacterium that infects and replicates only in avian red blood cells. A specific PCR test was developed to analyze A. pullorum DNA. Phylogenic analysis revealed A. pullorum is most closely related to Anaplasma spp.
Identification of multiple cell adhesion receptors for collagen and fibronectin in human fibrosarcoma cells possessing unique alpha and common beta subunits. (1987)

Using monoclonal antibody technology and affinity chromatography we have identified four distinct classes of cell surface receptors for native collagen on a cultured human fibrosarcoma cell line, HT-1080. Two classes of monoclonal antibodies prepared against HT-1080 cells inhibited adhesion to extracellular matrix components. Class I antibodies inhibited cell adhesion to collagen, fibronectin, and laminin. These antibodies immunoprecipitated two noncovalently linked proteins (subunits) with molecular masses of 147 and 125 kD, termed alpha and beta, respectively. Class II antibodies inhibited cell adhesion to native collagen only and not fibronectin or laminin. Class II antibodies immunoprecipitated a single cell surface protein containing two noncovalently linked subunits with molecular masses of 145 and 125 kD, termed alpha and beta, respectively. The two classes of antibodies did not cross-react with the same cell surface protein and recognized epitopes present on the alpha subunits. Pulse-chase labeling studies with [35S]methionine indicated that neither class I nor II antigen was a metabolic precursor of the other. Comparison of the alpha and beta subunits of the class I and II antigens by peptide mapping indicated that the beta subunits were identical while the alpha subunits were distinct. In affinity chromatography experiments HT-1080 cells were extracted with Triton X-100 or octylglucoside detergents and chromatographed on insoluble fibronectin or native type I or VI collagens. A single membrane protein with the biochemical characteristics of the class I antigen was isolated on fibronectin-Sepharose and could be immunoprecipitated with the class I monoclonal antibody. The class I antigen also specifically bound to type I and VI collagens, consistent with the observation that the class I antibodies inhibit cell adhesion to types VI and I collagen and fibronectin. The class II antigen, however, did not bind to collagen (or fibronectin) even though class II monoclonal antibodies completely inhibited adhesion of HT-1080 cells to types I and III-VI collagen. The class I beta and II beta subunits were structurally related to the beta subunit of the fibronectin receptor described by others. However, none of these receptors shared the same alpha subunits. Additional membrane glycoprotein(s) with molecular mass ranges of 80-90 and 35-45 kD, termed the class III and IV receptors, respectively, bound to types I and VI collagen but not to fibronectin. Monoclonal antibodies prepared against the class III receptor had no consistent effect on cell attachment or spreading, suggesting that it is not directly involved in adhesion to collagen-coated substrates.(ABSTRACT TRUNCATED AT 400 WORDS)
68Ga-Labeled Inhibitors of Prostate-Specific Membrane Antigen (PSMA) for Imaging Prostate Cancer (2010)

Gallium-68 is a generator-produced radionuclide for positron emission tomography (PET) that is being increasingly used for radiolabeling of tumor-targeting peptides. Compounds [(68)Ga]3 and [(68)Ga]6 are high-affinity urea-based inhibitors of the prostate-specific membrane antigen (PSMA) that were synthesized in decay-uncorrected yields ranging from 60% to 70% and radiochemical purities of more than 99%. Compound [(68)Ga]3 demonstrated 3.78 +/- 0.90% injected dose per gram of tissue (%ID/g) within PSMA+ PIP tumor at 30 min postinjection, while [(68)Ga]6 showed a 2 h PSMA+ PIP tumor uptake value of 3.29 +/- 0.77 %ID/g. Target (PSMA+ PIP) to nontarget (PSMA- flu) ratios were 4.6 and 18.3, respectively, at those time points. Both compounds delineated tumor clearly by small animal PET. The urea series of imaging agents for PSMA can be radiolabeled with (68)Ga, a cyclotron-free isotope useful for clinical PET studies, with maintenance of target specificity.
Preparation and magnetotransport properties of MgO-barrier-based magnetic double tunnel junctions including nonmagnetic nanoparticles (2007)

MgO-barrier-based magnetic double tunnel junctions including Au or Cr nanoparticles were prepared by molecular beam epitaxy, and their magnetotransport properties were investigated. A double junction sample including Au nanoparticles showed the Coulomb blockade effect and clear magnetoresistive hysteresis loops. The observed bias voltage dependence of the resistance and magnetoresistance (MR) suggested that the MR effects of 1–2% at high bias voltages were caused by spin accumulation in the Au nanoparticles. In the case of Cr nanoparticles, a double junction with relatively low sample resistance was obtained, showing a clear Coulomb threshold.
Hepatocyte nuclear factor‐1 beta mutations cause neonatal diabetes and intrauterine growth retardation: support for a critical role of HNF‐1β in human pancreatic development (2006)

HNF-1beta mutations are a rare cause of neonatal diabetes as well as pancreatic exocrine and endocrine dysfunction. Low birth weight is a common feature of patients with HNF-1beta mutations and is consistent with reduced insulin secretion in utero. These findings support a key role for HNF-1beta in early pancreatic progenitor cells in man.
The Jargon of Pedal Movements (2007)

The lack of unambiguous descriptions in the research literature may mean that clinicians are not always applying treatment options in an appropriate manner. Greater clarity of meaning is required for both basic research and clinical applications.
Prognostic value of CD44 variant expression in primary breast cancer (1999)

CD44 is a family of cell surface transmembrane glycoproteins members which differ in the extracellular part by sequences derived by alternative splicing of 10 variant exons (v1– v10). CD44 proteins containing such variant sequences have been implicated in tumor metastasis formation. Here, we have evaluated the expression of CD44 variants by immuno-histochemistry in primary breast cancer samples of 237 node-negative and 230 node-positive patients. For the analysis of samples derived from node-negative patients, the exon-specific antibodies used were DIII, vff7 and vff18 (v6), vff17 (v7/v8), fw11.24 (v9) and vff16 (v10). With the different antibodies which recognize v6 epitopes, the majority of tumors were positively stained (≥65% of the tumors) with varying intensities. Thirty-nine percent of the tumors were positively stained with the antibody vff16, and approximately half of the tumors with the antibodies vff17 and fw11.24. The expression of CD44 v6 epitopes in tumors from node-negative patients was associated with a favorable prognosis, both upon univariate and multivariate analysis. The expression of CD44 v7/8, v9 or v10 epitopes was not significantly related with relapse-free survival. Samples from node-positive patients were only examined with the antibodies vff7, vff17 and vff18. The staining with none of these antibodies was correlated with the length of relapse-free survival of the patients. Our data suggest that, generally, the usefulness of knowledge of CD44 variant expression is of limited value for assessing the risk of relapse in patients with primary breast cancer. However, the expression of exon v6 of CD44 may be a marker to identify patients with a relatively favorable prognosis in node-negative patients. Int. J. Cancer (Pred. Oncol.) 84:209–215, 1999. © 1999 Wiley-Liss, Inc.
AAV8-Mediated Hepatic Expression of Acid Sphingomyelinase Corrects the Metabolic Defect in the Visceral Organs of a Mouse Model of Niemann–Pick Disease (2005)

Acid sphingomyelinase deficiency is a lysosomal storage disorder in which the defective lysosomal hydrolase fails to degrade sphingomyelin. The resulting accumulation of substrate in the lysosomes of histiocytic cells leads to hepatosplenomegaly and severe pulmonary inflammation. Administration of a recombinant AAV1 vector encoding human acid sphingomyelinase to acid sphingomyelinase knockout (ASMKO) mice effectively reduced the accumulated substrate in all of the affected visceral organs. However, more complete and rapid clearance of sphingomyelin was observed when an AAV8-based serotype vector was used in lieu of AAV1. Importantly, AAV8-mediated hepatic expression of higher and sustained levels of the enzyme also corrected the abnormal cellularity, cell differentials, and levels of the chemokine MIP-1alpha in the bronchoalveolar lavage fluids of the ASMKO mice. Treatment also reversed the morphological aberrations associated with the alveolar macrophages of ASMKO mice and restored their phagocytic activity. No antibodies to the expressed enzyme were detected when the viral vectors were used in conjunction with a transcription cassette harboring a liver-restricted enhancer/promoter. Together, these data support the continued development of AAV8-mediated hepatic gene transfer as an approach to treat the visceral manifestations observed in individuals with acid sphingomyelinase deficiency.
LT TTT - A Flexible Tokenisation Tool (2000)

We describe LT TTT, a recently developed software system which provides tools to perform text tokenisation and mark-up. The system includes ready-made components to segment text into paragraphs, sentences, words and other kinds of token but, crucially, it also allows users to tailor rule-sets to produce mark-up appropriate for particular applications. We present three case studies of our use of LT TTT: named-entity recognition (MUC-7), citation recognition and mark-up and the preparation of a corpus in the medical domain. We conclude with a discussion of the use of browsers to visualise marked-up text. 1. Introduction The LTG&amp;apos;s Text Tokenisation Toolkit (LT TTT, Grover et al., 1999) was developed within an XML processing paradigm whereby tools are combined together in a pipeline allowing each to add, modify or remove some piece of mark-up. The tools are compatible with the LT XML toolset (Thompson et al., 1997) and use the LT XML API to manipulate attribute values and character data ...