gebhart/patrepeval huggingface dataset:
Psychrophilic proteases dramatically reduce single cell RNA-seq artifacts: A molecular atlas of kidney development (2017)

Single-cell RNA-seq is a powerful technique. Nevertheless, there are important limitations, including the technical challenges of breaking down an organ or tissue into a single-cell suspension. Invariably, this has required enzymatic incubation at 37°C, which can be expected to result in artifactual changes in gene expression patterns. Here, we describe a dissociation method that uses a protease with high activity in the cold, purified from a psychrophilic microorganism. The entire procedure is carried out at 6°C or colder, at which temperature mammalian transcriptional machinery is largely inactive, thereby effectively 'freezing in' the <i>in vivo</i> gene expression patterns. To test this method, we carried out RNA-seq on 20,424 single cells from postnatal day 1 mouse kidneys, comparing the results of the psychrophilic protease method with procedures using 37°C incubation. We show that the cold protease method provides a great reduction in gene expression artifacts. In addition, the results produce a single-cell resolution gene expression atlas of the newborn mouse kidney, an interesting time in development when mature nephrons are present yet nephrogenesis remains extremely active.
Polymer fiber Bragg gratings tunable dispersion compensation (2005)

We propose a new scheme for tunable dispersion with a large tuning range and a fixed center wavelength using linearly chirped polymer fiber Bragg gratings. Simple tension and uniform heating are employed as the control process.
18Fluorodeoxyglucose Positron Emission Tomography in the Diagnosis and Staging of Lung Cancer: A Systematic Review (2007)

Lung cancer is the leading cause of cancer-related death in industrialized countries. The overall mortality rate for lung cancer is high, and early diagnosis provides the best chance for survival. Diagnostic tests guide lung cancer management decisions, and clinicians increasingly use diagnostic imaging in an effort to improve the management of patients with lung cancer. This systematic review, an expansion of a health technology assessment conducted in 2001 by the Institute for Clinical and Evaluative Sciences, evaluates the accuracy and utility of 18fluorodeoxyglucose positron emission tomography (PET) in the diagnosis and staging of lung cancer. Through a systematic search of the literature, we identified relevant health technology assessments, randomized trials, and meta-analyses published since the earlier review, including 12 evidence summary reports and 15 prospective studies of the diagnostic accuracy of PET. PET appears to have high sensitivity and reasonable specificity for differentiating benign from malignant lesions as small as 1 cm. PET appears superior to computed tomography imaging for mediastinal staging in non-small cell lung cancer (NSCLC). Randomized trials evaluating the utility of PET in potentially resectable NSCLC report conflicting results in terms of the relative reduction in the number of noncurative thoracotomies. PET has not been studied as extensively in patients with small-cell lung cancer, but the available data show that it has good accuracy in staging extensive- versus limited-stage disease. Although the current evidence is conflicting, PET may improve results of early-stage lung cancer by identifying patients who have evidence of metastatic disease that is beyond the scope of surgical resection and that is not evident by standard preoperative staging procedures. Further trials are necessary to establish the clinical utility of PET as part of the standard preoperative assessment of early-stage lung cancer.
Estradiol increases and anti-estrogens antagonize the growth factor-induced activator protein-1 activity in MCF7 breast cancer cells without affecting c-fos and c-jun synthesis (1993)

In estrogen receptor positive human breast cancer cells, anti-estrogens inhibit the mitogenic effect of growth factors in the absence of estrogens. As activator protein-1 (AP-1) activity is one of the first nuclear events following growth factor receptor activation, we studied the effects of estrogens and anti-estrogens on growth factor-induced AP-1 activity using transient transfection of the AP-1-responsive gene (AP-1)4-TK-CAT into MCF7 cells. The growth factor-induced AP-1 response was increased by estradiol and inhibited by anti-estrogens in conditions where growth factor-induced c-fos and c-jun mRNA levels were unchanged by hormone and anti-hormone treatments. The same regulations were obtained when the AP-1 response was directly induced by co-transfection of c-fos and c-jun expression vectors. Co-transfection of the wild-type estrogen receptor HEGO amplified both effects. Inhibition of AP-1 activity by anti-estrogens was unlikely to be explained by the presence of residual estrogens in MCF7 cells. (i) anti-estrogens inhibited AP-1 activity in conditions where they had no effect on basal ERE-mediated activity levels, whereas estradiol was as efficient in stimulating both activities. (ii) The relative efficacy of the two anti-estrogens, OH-tamoxifen and ICI 164,384 in inhibiting these two activities was different; OH-tamoxifen was more efficient in inhibiting ERE-mediated activity, whereas ICI 164,384 was more efficient in trans-repressing AP-1-mediated activity. We conclude that in conditions where c-fos and c-jun syntheses were not affected, the estrogen receptor cooperated with growth factors to stimulate the AP-1 response when activated by estrogens but inhibited AP-1-mediated transcription when occupied by anti-estrogens.
"Synthetic Studies on Indoles and Related Compounds." Part XXX. A new general synthetic route for 1-substituted 4-oxygenated .BETA.-carbolines. (1991)

Two naturally occurring 1-substituted 4-methoxy-β-carboline (1b, c) weer synthesized from ethyl indole-2-carboxylate (5b) and its 1-benzyl derivative (5a), respectively. The synthesis routes involved elaboration of the ester group of 5a, b, cyclization of the substituent at the 2-position toward the 3-position of the indole nucleus, and functionalization at the 1-position of the β-carboline nucleus by a modified Reissert reaction. The β-carbolites (1b, c) thus prepared should be mother compounds for the synthesis of their congeners.
Microglial cells in neurodegenerative disorders. (2005)

Microglia are resident immune cells of the CNS. They are involved in the pathogenesis of diverse neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, prion diseases as well as multiple sclerosis, amyotrophic lateral sclerosis and AIDS dementia complex. It is widely accepted that microglia contribute to the neurodegeneration through a release of a variety of proinflammatory substances. In fact, they are not the only cells which contribute to immunological processes inside the nervous system. The CNS is composed of different cell populations that answer to pathological factors and influence each other and modulate their reactions. These complex interactions are responsible for the development of brain pathology. This paper reviews the available information on microglial cells contribution to AD, PD and prion diseases development.
RF Photonic Techniques for Same Frequency Simultaneous Duplex Antenna Operation (2007)

Same frequency, broadband, simultaneous transmit/ receive on the same antenna is facilitated by employing a balanced architecture to cancel that part of the transmit signal that leaks into the receive path. The concurrent detection of the receive signal and the cancellation of the transmitter leakage into the receive path are accomplished in the optical domain with a dual-port optical modulator and a differential photodetector pair.
Analysis of surface dose variation in CT procedures (2001)

An experimental and theoretical study has been made of the variations in air kerma-length product (AKLP) at the surface of a phantom exposed in a CT scanner, using clinical parameters. For the theoretical part, a computer simulation was developed, based on a simple analytical model, requiring information generic to the scanner model. The effects of patient size, position within the gantry plane and beam-shaping filter type were studied using three different elliptical phantoms. A dose reduction technique based on a sinusoidal tube current modulation system was also investigated. The surface AKLP was shown to be independent of phantom size (within experimental error) but decreases as the surface moves vertically away from the isocentre. The major contributor to this variation is the beam-shaping filter. A maximum difference of 19% between the values of surface AKLP was calculated for the two beam-shaping filters available. When the tube current modulation system was used, the maximum surface dose reduction was 18%. A maximum difference of 2% was found between measurements and computer simulations. It is therefore possible to predict the behaviour of AKLP using the analytical model. As the dose measured on the surface of a patient is simply related to AKLP, the model can be applied to data obtained from patient surface dose surveys and can be helpful in interpreting the sources of variation in the latter.
CDC23 regulates cancer cell phenotype and is overexpressed in papillary thyroid cancer (2011)

Cancer gender disparities have been observed for a variety of human malignancies. Thyroid cancer is one such example where there is a dramatic difference in the incidence, aggressiveness, and death rate by gender. The molecular basis for gender disparity is poorly understood. To address this, we performed genome-wide gene expression profiling in matched papillary thyroid cancer (PTC) samples and identified nine candidate genes differentially expressed by gender. One of these genes was CDC23 that was upregulated in PTC in men compared with women. Because the function and expression of CDC23 is unknown in eukaryotic cells, we further characterized the expression of CDC23 in normal, hyperplastic, and PTC tissue samples. We found CDC23 was overexpressed in PTC and absent in normal and hyperplastic thyroid tissue. In thyroid cancer cells, functional knockdown of CDC23 resulted in an increase in the number of cells in both the S and G(2)M phases of the cell cycle, and an inhibition of cellular proliferation, tumor spheroid formation, and anchorage-independent growth. Cellular arrest in both S and G(2)M phases was associated with significant cyclin B1 and securin protein accumulation after CDC23 knockdown. Moreover, the effect of CDC23 on cellular proliferation and cell cycle progression was reversed on triple knockdown studies of CDC23, cyclin B1, and securin. Our data taken together suggests CDC23 has important biologic effects on cell proliferation and cell cycle progression. The effect of CDC23 on cellular proliferation and cell cycle progression is mediated, at least in part, by cyclin B1 and securin protein levels. Therefore, we propose that CDC23 is a critical regulator of cell cycle and cell growth, and may be involved in thyroid cancer initiation and progression, and may explain the different tumor biology observed by gender.
H-DNA and Related Structures (1994)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
A Psychobiological Model of Temperament and Character (1993)

In this study, we describe a psychobiological model of the structure and development of personality that accounts for dimensions of both temperament and character. Previous research has confirmed four dimensions of temperament: novelty seeking, harm avoidance, reward dependence, and persistence, which are independently heritable, manifest early in life, and involve preconceptual biases in perceptual memory and habit formation. For the first time, we describe three dimensions of character that mature in adulthood and influence personal and social effectiveness by insight learning about self-concepts. Self-concepts vary according to the extent to which a person identifies the self as (1) an autonomous individual, (2) an integral part of humanity, and (3) an integral part of the universe as a whole. Each aspect of self-concept corresponds to one of three character dimensions called self-directedness, cooperativeness, and self-transcendence, respectively. We also describe the conceptual background and development of a self-report measure of these dimensions, the Temperament and Character Inventory. Data on 300 individuals from the general population support the reliability and structure of these seven personality dimensions. We discuss the implications for studies of information processing, inheritance, development, diagnosis, and treatment.
Antisense oligonucleotides: a new therapeutic principle (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntisense oligonucleotides: a new therapeutic principleEugen Uhlmann and Anusch PeymanCite this: Chem. Rev. 1990, 90, 4, 543–584Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/cr00102a001https://doi.org/10.1021/cr00102a001research-articleACS PublicationsRequest reuse permissionsArticle Views4204Altmetric-Citations1412LEARN 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
A Comparison of Seven Tests for Serological Diagnosis of Tuberculosis (2000)

Seven serological tests, two immunochromatographic tests, ICT Tuberculosis and RAPID TEST TB, and five enzyme-linked immunosorbent assays, TUBERCULOSIS IgA EIA, PATHOZYME-TB complex, PATHOZYME-MYCO IgG, PATHOZYME-MYCO IgA, and PATHOZYME-MYCO IgM, were evaluated simultaneously with 298 serum samples from three groups of individuals: 44 patients with active tuberculosis, 204 controls who had undergone the Mantoux test (89 Mantoux test-positive and 115 Mantoux test-negative controls), and 50 anonymous controls. The sensitivities of the tests with sera from patients with active tuberculosis were poor to modest, ranging from 16 to 57%. All the tests performed equally with sera from subgroups of those with active tuberculosis, those with pulmonary (33 patients) versus extrapulmonary (11 patients) disease, and those who were smear positive (24 patients) versus smear negative (12 patients) (P > 0.05). The specificities of the tests ranged from 80 to 97% with sera from the Mantoux test controls and 62 to 100% with sera from the anonymous controls. The TUBERCULOSIS IgA EIA had the highest sensitivity (57%) with sera from patients with active tuberculosis, with a high specificity of 93% with sera from the Mantoux test controls, but a very poor specificity of 62% with sera from the anonymous controls. Overall, ICT Tuberculosis followed by PATHOZYME-MYCO IgG had the best performance characteristics, with sensitivities of 41 and 55%, respectively, with sera from patients with active tuberculosis and specificities of 96 and 89%, respectively, with sera from the Mantoux test controls and 88 and 90%, respectively, with sera from the anonymous controls. By combining all the test results, a maximum sensitivity of 84% was obtained, with reciprocal drops in specificities to 55 and 42% for the Mantoux test controls and anonymous controls, respectively. The best combination was that of ICT Tuberculosis and PATHOZYME-MYCO IgG, with a sensitivity of 66% and a specificity of 86% for the Mantoux test controls and a sensitivity and specificity of 78% for the anonymous controls. While a negative result by any one of these tests would be useful in helping to exclude disease in a population with a low prevalence of tuberculosis, a positive result may aid in clinical decision making when applied to symptomatic patients being evaluated for active tuberculosis.
The Manganese-containing Ribonucleotide Reductase ofCorynebacterium ammoniagenes Is a Class Ib Enzyme (1998)

Ribonucleotide reductases (RNRs) are key enzymes in living cells that provide the precursors of DNA synthesis. The three characterized classes of RNRs differ by their metal cofactor and their stable organic radical. We have purified to near homogeneity the enzymatically active Mn-containing RNR of Corynebacterium ammoniagenes, previously claimed to represent a fourth RNR class. N-terminal and internal peptide sequence analyses clearly indicate that the C. ammoniagenes RNR is a class Ib enzyme. In parallel, we have cloned a 10-kilobase pair fragment from C. ammoniagenes genomic DNA, using primers specific for the known class Ib RNR. The cloned class Ib locus contains the nrdHIEF genes typical for class Ib RNR operon. The deduced amino acid sequences of the nrdE and nrdF genes matched the peptides from the active enzyme, demonstrating that C. ammoniagenes RNR is composed of R1E and R2F components typical of class Ib. We also show that the Mn-containing RNR has a specificity for the NrdH-redoxin and a response to allosteric effectors that are typical of class Ib RNRs. Electron paramagnetic resonance and atomic absorption analyses confirm the presence of Mn as a cofactor and show, for the first time, insignificant amounts of iron and cobalt found in the other classes of RNR. Our discovery that C. ammoniagenes RNR is a class Ib enzyme and possesses all the highly conserved amino acid side chains that are known to ligate two ferric ions in other class I RNRs evokes new, challenging questions about the control of the metal site specificity in RNR. The cloning of the entire NrdHIEF locus of C. ammoniagenes will facilitate further studies along these lines.
Blue phases and twist grain boundary phases (TGBA and TGBC) in a series of fluoro-substituted chiral tolane derivatives (1997)

A series of fluoro-substituted tolane derivatives: (R)-1-methylheptyl 3-fluoro-4-(3-fluoro-4- n alkoxybenzoyloxy)tolane-4-carboxylates is reported. Some members of this series exhibit the phase sequence: Cr-SmC*-TGBC-TGBA-BPI-BPII-BPIII-I. The blue phases, the TGBA and TGBC phases and the SmC* phase were characterized in detail by microscopic observation, differential scanning calorimetry, helical pitch measurements, X-ray structural analysis and electro-optical study. The blue phases directly next to the TGBA phase were shown to be a new type of blue phase exhibiting smectic ordering. A commensurate TGBC phase with constant number of slabs per pitch was observed.
Characterization of a new IgGλ myeloma plasma cell line (EJM): a further tool in the investigation of the biology of multiple myeloma (1990)

A new IgG lambda myeloma plasma cell line known as EJM was established from a peritoneal effusion from a patient with extramedullary myeloma. The EJM cells have a plasmablastic morphology with abundant rough endoplasmic reticulum and grow in liquid culture with a doubling time of 72 h and a labelling index of 36%. In addition to cytoplasmic IgG lambda, the cells are positive for CD9, 20, 32, 38, 44, 54, 71, 78, MHC Class II DR, DP and DQ. Studies on the control of the cell line proliferation by cytokines have demonstrated stimulation with interleukin 6. In contrast interferon alpha produces marked inhibition of proliferation in doses of greater than 100 units/ml. The culture conditions and the importance of accessory cells and cytokines in supporting myeloma plasma cell growth in vitro are discussed.
Role of CXCR4 in the Pathogenesis of Acute Myeloid Leukemia (2013)

The Chemokine receptor CXCR4 and its ligand stromal derived factor-1 (SDF-1/CXCL12) are important players involved in cross-talk between leukemia cells and the bone marrow (BM) microenvironment. CXCR4 expression is associated with poor prognosis in AML patients with and without the mutated FLT3 gene.CXCL12 which is constrictively secreted from the BM stroma and AML cells is critical for the survival and retention of AML cells within the BM. In vitro, CXCR4 antagonists were shown to inhibit the migration of AML cells in response to CXCL12. In addition, such antagonists were shown to inhibit the survival and colony forming potential of AML cells and abrogate the protective effects of stromal cells on chemotherapy-induced apoptosis in AML cells. In vivo, using immune deficient mouse models, CXCR4 antagonists were found to induce the mobilization of AML cells and progenitor cells into the circulation and enhance anti leukemic effects of chemotherapy. The hypothesis that CXCL12/CXCR4 interactions contribute to the resistance of AML cells to signal transduction inhibitor- and chemotherapy-induced apoptosis is currently being tested in a series of Phase I/II studies in humans.
Synthesis of unitaries with Clifford+T circuits (2013)

We describe a new method for approximating an arbitrary $n$ qubit unitary with precision $\varepsilon$ using a Clifford and T circuit with $O(4^{n}n(\log(1/\varepsilon)+n))$ gates. The method is based on rounding off a unitary to a unitary over the ring $\mathbb{Z}[i,1/\sqrt{2}]$ and employing exact synthesis. We also show that any $n$ qubit unitary over the ring $\mathbb{Z}[i,1/\sqrt{2}]$ with entries of the form $(a+b\sqrt{2}+ic+id\sqrt{2})/2^{k}$ can be exactly synthesized using $O(4^{n}nk)$ Clifford and T gates using two ancillary qubits. This new exact synthesis algorithm is an improvement over the best known exact synthesis method by B. Giles and P. Selinger requiring $O(3^{2^{n}}nk)$ elementary gates.
Dose-rate effects in mammalian cells in culture III. Comparison of cell killing and cell proliferation during continuous irradiation for six different cell lines. (1979)

The effects of continuous irradiation over a wide range of dose rates were studied for six different mammalian cell lines in regard to cell survival and proliferation. Cell lines were chosen in which such characteristics as population doubling time, chromosome number, DNA content, acute dose-survival curve parameters, and division delay were as diverse as possible. There was no correlation between the minimum dose rate necessary to stop cell population growth and any of the above listed characteristics, with the exception of division delay following acute doses. In general, the longer the division delay (min/rad), the lower the dose rate required to stop cell population growth. The effects of cell-cycle redistribution during continuous irradiation in regard to cell survival was dramatic. In some cases a reduction in dose rate resulted in an increase in cell killing for a given total dose. This occurred only when dose rates were sufficient to stop cell population growth and after exposure times sufficient ...