gebhart/patrepeval huggingface dataset:
Capillary electrophoresis-mass spectrometry (1995)

As an on-line separation method, capillary electrophoresis (CE)-mass spectrometry (MS) distinguishes analytes by both their differences in electrophoretic mobilities and structural information. CE-MS combines the advantages of CE and MS so that information on both high separation efficiency and molecular masses and/or fragmentation can be obtained in one analysis. During the past few years CE-MS has undergone significant development both in instrumentation and application. Several ionization methods have been used for CE-MS. These include electrospray ionization, ion spray or pneumatically assisted electrospray ionization, and continuous-flow fast atom bombardment. The direct coupling of CE to desorption MS has not yet been reported, although publications have appeared on the off-line coupling of CE with matrix-assisted laser desorption ionization and 252Cf plasma desorption MS using fraction collection. Numerous new applications of CE-MS have been published in the areas of biological sciences, pharmaceutical and drug metabolism, and environmental analysis. The majority of applications of CE-MS have been in the field of biological and biochemical studies. Several limitations associated with CE-MS have precluded the technique being widely accepted for routine analysis. The major limitation is its relatively poor concentration sensitivity. The concentration detection limits of currently available CE-MS instrumentation are too high for most real-world applications. Other drawbacks with CE-MS include the fluctuation in analyte migration time and limitations in electrolyte selections. Approaches to improve the concentration sensitivity of CE-MS include on-line preconcentration either by capillary isotachophoresis or chromatographic methods. Another solution to increasing the sensitivity of CE-MS is the development of alternative types of mass spectrometers which offer the potential for greater sensitivity, such as ion trap, Fourier transform ion cyclotron resonance, and time-of-flight (TOF) mass spectrometers. Coated capillaries are useful in improving separation efficiencies of biomolecules by minimizing their adsorption onto the CE capillary walls. At present, CE-MS is still not generally considered for routine analysis mainly due to its limited concentration sensitivity. As a complementary separation method to LC-MS with extremely high efficiency, CE-MS has the potential for wide acceptance in the future. The popularity of CE-MS will continue to grow, as more sensitive MS instrumentation and CE-MS interface are developed.
TotalReCaller: improved accuracy and performance via integrated alignment and base-calling (2011)

fabian.menges@nyu.edu.
POSSIBLE NEPHROTOXICITY OF THE PROPHYLACTIC USE OF OKT3 MONOCLONAL ANTIBODY AFTER CADAVERIC RENAL TRANSPLANTATION (1989)

TOUSSAINT, CHARLES; PAUW, LUC DE; VEREERSTRAETEN, PIERRE; KINNAERT, PAUL; ABRAMOWICZ, DANIEL; GOLDMAN, MICHEL Author Information
Antioxidants in tears and plasma: Inter-relationships and effect of vitamin C supplementation (2003)

Ascorbate concentration in both plasma and tears increased with vitamin C supplementation, but the total antioxidant capacity of these fluids did not. Furthermore, the increase in tear ascorbate was modest in comparison to that in plasma, and is suggestive of a "ceiling" for tear ascorbate of under 40 micro M. Results support the concept of a control mechanism for an integrated antioxidant defense system, and suggest that the amount of ascorbate in tears is both actively controlled and purposefully limited.
A Unique Population of Extrathymically Derived αβTCR+CD4−CD8− T Cells with Regulatory Functions Dominates the Mouse Female Genital Tract (2003)

A better understanding of the regulatory role of genital tract T cells is much needed. In this study, we have analyzed the phenotype, distribution, and function of T lymphocytes in the female genital tract of naive, pregnant, or Chlamydia trachomatis-infected C57BL/6 mice. Unexpectedly, we found that the dominant lymphocyte population (70-90%) in the genital tract was that of CD3(+)alphabetaTCR(int)CD4(-)CD8(-) T cells. Moreover, these cells were CD90(low) but negative for the classical T cell markers CD2 and CD5. The CD3(+)B220(low) cells were NK1.1 negative and found in nude mice as well as in mice deficient for MHC class II, beta(2)-microglobulin, and CD1, indicating extrathymic origin. They dominated the KJ126(+)Vbeta8.2(+) population in the genital tract of DO11.10 OVA TCR-transgenic mice, further supporting the idea that the CD3(+)B220(low) cells are truly T cells. The function of these T cells appeared not to be associated with immune protection, because only CD4(+) and CD8(+) T cells increased in the genital tract following chlamydial infection. Notwithstanding this, the infected, as well as the uninfected and the pregnant, uterus was dominated by a high level of the CD3(+)CD4(-)CD8(-)B220(low) cells. Following in vitro Ag or polyclonal stimulation of the CD3(+)CD4(-)CD8(-)B220(low) cells, poor proliferative responses were observed. However, these cells strongly impaired splenic T cell proliferation in a cell density-dependent manner. A large fraction of the cells expressed CD25 and produced IFN-gamma upon anti-CD3 plus anti-CD28 stimulation, arguing for a strong regulatory role of this novel T cell population in the mouse female genital tract.
Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry (2007)

A novel method for on-tissue identification of proteins in spatially discrete regions is described using tryptic digestion followed by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with MS/MS analysis. IMS is first used to reveal the protein and peptide spatial distribution in a tissue section and then a serial section is robotically spotted with small volumes of trypsin solution to carry out in situ protease digestion. After hydrolysis, 2,5-Dihydroxybenzoic acid (DHB) matrix solution is applied to the digested spots, with subsequent analysis by IMS to reveal the spatial distribution of the various tryptic fragments. Sequence determination of the tryptic fragments is performed using on-tissue MALDI MS/MS analysis directly from the individual digest spots. This protocol enables protein identification directly from tissue while preserving the spatial integrity of the tissue sample. The procedure is demonstrated with the identification of several proteins in the coronal sections of a rat brain.
Halobacterium denitrificans sp. nov., an Extremely Halophilic Denitrifying Bacterium (1986)

Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5%), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005% yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production. A type culture has been deposited with the American Type Culture Collection, Rockville, Md. (ATCC 35960).
Evolution of a Pathway to Novel Long-Chain Carotenoids (2004)

Using methods of laboratory evolution to force the C(30) carotenoid synthase CrtM to function as a C(40) synthase, followed by further mutagenesis at functionally important amino acid residues, we have discovered that synthase specificity is controlled at the second (rearrangement) step of the two-step reaction. We used this information to engineer CrtM variants that can synthesize previously unknown C(45) and C(50) carotenoid backbones (mono- and diisopentenylphytoenes) from the appropriate isoprenyldiphosphate precursors. With this ability to produce new backbones in Escherichia coli comes the potential to generate whole series of novel carotenoids by using carotenoid-modifying enzymes, including desaturases, cyclases, hydroxylases, and dioxygenases, from naturally occurring pathways.
Improved electroluminescence on nonpolar m ‐plane InGaN/GaN quantum wells LEDs (2007)

Abstract Improved nonpolar m ‐plane $\bar 1$ light emitting diodes (LEDs) with a thick InGaN multi‐quantum‐well (MQW) structure have been fabricated on low extended defect bulk m ‐plane GaN substrates using metal organic chemical vapor deposition (MOCVD). The peak wavelength of the electroluminescence emission from the packaged LEDs was 402 nm, which is in the blue‐violet region. The output power and EQE were 28 mW and 45.4%, respectively, at a pulsed driving current of 20 mA. With increasing current, the output power increased linearly, and fairly flat EQE was observed with increasing drive current. At 200 mA, the power and EQE were 250 mW and 41%, respectively. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Micro-masonry for 3D Additive Micromanufacturing (2014)

Transfer printing is a method to transfer solid micro/nanoscale materials (herein called 'inks') from a substrate where they are generated to a different substrate by utilizing elastomeric stamps. Transfer printing enables the integration of heterogeneous materials to fabricate unexampled structures or functional systems that are found in recent advanced devices such as flexible and stretchable solar cells and LED arrays. While transfer printing exhibits unique features in material assembly capability, the use of adhesive layers or the surface modification such as deposition of self-assembled monolayer (SAM) on substrates for enhancing printing processes hinders its wide adaptation in microassembly of microelectromechanical system (MEMS) structures and devices. To overcome this shortcoming, we developed an advanced mode of transfer printing which deterministically assembles individual microscale objects solely through controlling surface contact area without any surface alteration. The absence of an adhesive layer or other modification and the subsequent material bonding processes ensure not only mechanical bonding, but also thermal and electrical connection between assembled materials, which further opens various applications in adaptation in building unusual MEMS devices.
IL-1ra alleviates inflammatory hyperalgesia through preventing phosphorylation of NMDA receptor NR-1 subunit in rats (2007)

Although it has been shown that pro-inflammatory cytokines such as interleukin-1beta (IL-1beta) facilitate perception of noxious inputs at the spinal level, the mechanisms have not been understood. This study determined the cell type that produces IL-1beta, the co-localization of IL-1 receptor type I (IL-1RI) and Fos and NR1 in the spinal cord, and the effects of IL-1 receptor antagonist (IL-1ra) on NR1 phosphorylation and hyperalgesia in a rat model of inflammatory pain. Phosphorylation of NR1, an essential subunit of the NMDA receptor (NMDAR), is known to modulate NMDAR activity and facilitate pain. Hyperalgesia was induced by injecting complete Freund's adjuvant (CFA, 0.08ml, 40microg Mycobacterium tuberculosis) into one hind paw of each rat. Paw withdrawal latency (PWL) was tested before CFA (-48h) for baseline and 2 and 24h after CFA to assess hyperalgesia. IL-1ra was given (i.t.) 24h before CFA to block the action of basal IL-1beta and 2h prior to each of two PWL tests to block CFA-induced IL-1beta. Spinal cords were removed for double immunostaining of IL-1beta/neuronal marker and IL-1beta/glial cell markers, IL-1RI/Fos and IL-1RI/NR1, and for Western blot to measure NR1 phosphorylation. The data showed that: (1) astrocytes produce IL-1beta, (2) IL-1RI is localized in Fos- and NR1-immunoreactive neurons within the spinal dorsal horn, and (3) IL-1ra at 0.01mg/rat significantly increased PWL (P<0.05) and inhibited NR1 phosphorylation compared to saline control. The results suggest that spinal IL-1beta is produced by astrocytes and enhances NR1 phosphorylation to facilitate inflammatory pain.
Deoxyribonucleotide Triphosphate Metabolism in Cancer and Metabolic Disease (2018)

The maintenance of a healthy deoxyribonucleotide triphosphate (dNTP) pool is critical for the proper replication and repair of both nuclear and mitochondrial DNA. Temporal, spatial, and ratio imbalances of the four dNTPs have been shown to have a mutagenic and cytotoxic effect. It is, therefore, essential for cell homeostasis to maintain the balance between the processes of dNTP biosynthesis and degradation. Multiple oncogenic signaling pathways, such as c-Myc, p53, and mTORC1 feed into dNTP metabolism, and there is a clear role for dNTP imbalances in cancer initiation and progression. Additionally, multiple chemotherapeutics target these pathways to inhibit nucleotide synthesis. Less is understood about the role for dNTP levels in metabolic disorders and syndromes and whether alterations in dNTP levels change cancer incidence in these patients. For instance, while deficiencies in some metabolic pathways known to play a role in nucleotide synthesis are pro-tumorigenic (e.g., p53 mutations), others confer an advantage against the onset of cancer (G6PD). More recent evidence indicates that there are changes in nucleotide metabolism in diabetes, obesity, and insulin resistance; however, whether these changes play a mechanistic role is unclear. In this review, we will address the complex network of metabolic pathways, whereby cells can fuel dNTP biosynthesis and catabolism in cancer, and we will discuss the potential role for this pathway in metabolic disease.
Integrin αvβ3 expression confers on tumor cells a greater propensity to metastasize to bone (2002)

The reasons why tumor cells metastasize to bone remain obscure. There is some evidence to support the theory that integrins (acting as cell surface adhesion receptors) play a role in mediating metastasis in certain organs. Here, we report that overexpression of a functionally active integrin alpha(v)b3 in Chinese hamster ovary (CHO) tumor cells drastically increased the incidence, number, and area of bone metastases in nude mice compared with those observed in mock-transfected CHO cells (CHO dhfr+) or in CHO cells expressing a functionally inactive integrin alpha(v)b3 (CHO beta3Delta744). Moreover, a breast cancer cell line (B02) established from bone metastases caused by MDA-MB-231 cells constitutively overexpressed integrin alpha(v)b3, whereas the cell surface expression level of other integrins remained unchanged. In vivo, the extent of bone metastases in B02-bearing mice was significantly increased compared with that of MDA-MB-231-bearing mice. In vitro, B02 cells and CHO cells expressing a functionally active integrin alpha(v)b3 exhibited substantially increased invasion of and adhesion to mineralized bone, bone sialoprotein, and collagen compared with those found with MDA-MB-231, CHO dhfr+, and CHO beta3Delta744 cells, respectively. Overall, our findings suggest that integrin alpha(v)b3 expression in tumor cells accelerates the development of osteolytic lesions, presumably through increased invasion of and adhesion to bone.
Carbanion photochemistry. 11. 1,3-Diphenylisoindenylidene (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbanion photochemistry. 11. 1,3-DiphenylisoindenylideneLaren M. Tolbert and Shahabuddin SiddiquiCite this: J. Am. Chem. Soc. 1984, 106, 19, 5538–5543Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/ja00331a023https://doi.org/10.1021/ja00331a023research-articleACS PublicationsRequest reuse permissionsArticle Views133Altmetric-Citations10LEARN 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
The american college of rheumatology 1991 revised criteria for the classification of global functional status in rheumatoid arthritis (1992)

Although there are limitations inherent in the use of global ordinal scales, the American College of Rheumatology revised criteria will be useful in describing the functional consequences of RA. A more detailed quantitative measure of physical disability should be used, however, for optimal monitoring of patients' clinical status in office practice and clinical research.
Contextual guidance of eye movements and attention in real-world scenes: The role of global features in object search. (2006)

Many experiments have shown that the human visual system makes extensive use of contextual information for facilitating object search in natural scenes. However, the question of how to formally model contextual influences is still open. On the basis of a Bayesian framework, the authors present an original approach of attentional guidance by global scene context. The model comprises 2 parallel pathways; one pathway computes local features (saliency) and the other computes global (scene-centered) features. The contextual guidance model of attention combines bottom-up saliency, scene context, and top-down mechanisms at an early stage of visual processing and predicts the image regions likely to be fixated by human observers performing natural search tasks in real-world scenes.
Use of the growth regulator paclobutrazol in the management of dollar spot of creeping bentgrass in Minnesota (2005)

The control of dollar spot by paclobutrazol applied as a growth regulator on a creeping bentgrass ( Agrostis palustris ) and annual bluegrass ( Poa annua ) fairway turf was compared with two standard fungicide treatments in Minnesota during two growing seasons. Paclobutrazol was applied every 3 weeks, staggered by about 10 days with fungicide treatments (chlorothalonil or propiconazole), also applied every 3 weeks. Paclobutrazol alone significantly reduced the number of dollar spot infection centers during both summers, often by as much as 80%. Chlorothalonil or propiconazole were usually more effective in controlling dollar spot than paclobutrazol. Paclobutrazol improved disease control by fungicides when tested in combination with various rates of chlorothalonil or propiconazole. Paclobutrazol applied as a growth regulator could thus be used to reduce the base line severity of dollar spot of turf.
Roles for two RecA homologs in promoting meiotic chromosome synapsis. (1995)

Previous studies have shown that the RAD51 and DMC1 genes of Saccharomyces cerevisiae encode homologs of the Escherichia coli RecA strand exchange enzyme. Results presented here demonstrate that the dmc1 and rad51 mutants undergo nearly complete chromosome synapsis, but synaptonemal complex formation is delayed substantially compared with wild type. In the zip1 mutant, chromosomes are paired homologously, but not synapsed, and the protein backbones (axial elements) of each pair of chromosomes are connected intimately to each other at a few sites referred to herein as axial associations. dmc1 zip1 and rad51 zip1 double mutants assemble axial elements that are not obviously associated, demonstrating that the Dmc1 and Rad51 proteins are required to establish or stabilize axial associations. We propose that axial associations serve to promote meiotic chromosome synapsis and that the absence of these associations accounts for the delayed and inefficient synapsis observed in dmc1 and rad51 strains. During meiosis in haploid yeast, chromosome synapsis takes place between nonhomologous chromosome segments. In a zip1 haploid, axial associations are not apparent, suggesting that these associations depend on interactions between homologous sequences.
A Novel Mouse Model of Campylobacter jejuni Gastroenteritis Reveals Key Pro-inflammatory and Tissue Protective Roles for Toll-like Receptor Signaling during Infection (2014)

Campylobacter jejuni is a major source of foodborne illness in the developed world, and a common cause of clinical gastroenteritis. Exactly how C. jejuni colonizes its host's intestines and causes disease is poorly understood. Although it causes severe diarrhea and gastroenteritis in humans, C. jejuni typically dwells as a commensal microbe within the intestines of most animals, including birds, where its colonization is asymptomatic. Pretreatment of C57BL/6 mice with the antibiotic vancomycin facilitated intestinal C. jejuni colonization, albeit with minimal pathology. In contrast, vancomycin pretreatment of mice deficient in SIGIRR (Sigirr 2/2 ), a negative regulator of MyD88-dependent signaling led to heavy and widespread C. jejuni colonization, accompanied by severe gastroenteritis involving strongly elevated transcription of Th1/Th17 cytokines. C. jejuni heavily colonized the cecal and colonic crypts of Sigirr 2/2 mice, adhering to, as well as invading intestinal epithelial cells. This infectivity was dependent on established C. jejuni pathogenicity factors, capsular polysaccharides (kpsM) and motility/flagella (flaA). We also explored the basis for the inflammatory response elicited by C. jejuni in Sigirr 2/2 mice, focusing on the roles played by Toll-like receptors (TLR) 2 and 4, as these innate receptors were strongly stimulated by C. jejuni. Despite heavy colonization, Tlr4 2/2 /Sigirr 2/2 mice were largely unresponsive to infection by C. jejuni, whereas Tlr2 2/2 /Sigirr 2/2 mice developed exaggerated inflammation and pathology. This indicates that TLR4 signaling underlies the majority of the enteritis seen in this model, whereas TLR2 signaling had a protective role, acting to promote mucosal integrity. Furthermore, we found that loss of the C. jejuni capsule led to increased TLR4 activation and exaggerated inflammation and gastroenteritis. Together, these results validate the use of Sigirr 2/2 mice as an exciting and relevant animal model for studying the pathogenesis and innate immune responses to C. jejuni.
A survey of remote optical photoplethysmographic imaging methods (2015)

In recent years researchers have presented a number of new methods for recovering physiological parameters using just low-cost digital cameras and image processing. The ubiquity of digital cameras presents the possibility for many new, low-cost applications of vital sign monitoring. In this paper we present a review of the work on remote photoplethysmographic (PPG) imaging using digital cameras. This review specifically focuses on the state-of-the-art in PPG imaging where: 1) measures beyond pulse rate are evaluated, 2) non-ideal conditions (e.g., the presence of motion artifacts) are explored, and 3) use cases in relevant environments are demonstrated. We discuss gaps within the literature and future challenges for the research community. To aid in the continuing advancement of PPG imaging research, we are making available a website with the references collected for this review as well as information on available code and datasets of interest. It is our hope that this website will become a valuable resource for the PPG imaging community. The site can be found at: http://web.mit.edu/~djmcduff/www/ remote-physiology.html.