gebhart/patrepeval huggingface dataset:
Robust RT-qPCR Data Normalization: Validation and Selection of Internal Reference Genes during Post-Experimental Data Analysis (2011)

Reverse transcription and real-time PCR (RT-qPCR) has been widely used for rapid quantification of relative gene expression. To offset technical confounding variations, stably-expressed internal reference genes are measured simultaneously along with target genes for data normalization. Statistic methods have been developed for reference validation; however normalization of RT-qPCR data still remains arbitrary due to pre-experimental determination of particular reference genes. To establish a method for determination of the most stable normalizing factor (NF) across samples for robust data normalization, we measured the expression of 20 candidate reference genes and 7 target genes in 15 Drosophila head cDNA samples using RT-qPCR. The 20 reference genes exhibit sample-specific variation in their expression stability. Unexpectedly the NF variation across samples does not exhibit a continuous decrease with pairwise inclusion of more reference genes, suggesting that either too few or too many reference genes may detriment the robustness of data normalization. The optimal number of reference genes predicted by the minimal and most stable NF variation differs greatly from 1 to more than 10 based on particular sample sets. We also found that GstD1, InR and Hsp70 expression exhibits an age-dependent increase in fly heads; however their relative expression levels are significantly affected by NF using different numbers of reference genes. Due to highly dependent on actual data, RT-qPCR reference genes thus have to be validated and selected at post-experimental data analysis stage rather than by pre-experimental determination.
Animal antibiotic use has an early but important impact on the emergence of antibiotic resistance in human commensal bacteria (2002)

Antibiotic use is known to promote the development of antibiotic resistance, but substantial controversy exists about the impact of agricultural antibiotic use (AAU) on the subsequent emergence of antibiotic-resistant bacteria among humans. AAU for animal growth promotion or for treatment or control of animal diseases generates reservoirs of antibiotic-resistant (AR) bacteria that contaminate animal food products. Mathematical models are an important tool for understanding the potential medical consequences of this increased exposure. We have developed a mathematical model to evaluate factors affecting the prevalence of human commensal AR bacteria that cause opportunistic infections (e.g., enterococci). Our analysis suggests that AAU hastens the appearance of AR bacteria in humans. Our model indicates that the greatest impact occurs very early in the emergence of resistance, when AR bacteria are rare, possibly below the detection limits of current surveillance methods.
A ribozyme-mediated, gene “knockdown” strategy for the identification of gene function in zebrafish (1997)

The zebrafish system offers many unique opportunities for the study of molecular biology. To date, only random mutagenesis, and not directed gene knockouts, have been demonstrated in this system. To more fully develop the potential of the zebrafish system, an approach to effectively inhibit the expression of any targeted gene in the developing zebrafish embryo has been developed. This approach uses a transient, cytoplasmic, T7 expression system, injected into the fertilized zebrafish egg to rapidly produce high levels of a ribozyme directed against the mRNA encoded by the targeted gene to inhibit its expression. In a demonstration of this strategy, expression of the recessive dominant zebrafish no tail gene was effectively inhibited by using this strategy to yield a phenotype identical to that resulting from a known defective mutation in this same gene. This, ribozyme-mediated, message deletion strategy may have use in determining the function of genetic coding sequences of unknown function.
Several regions of Antennapedia and thyroid transcription factor 1 homeodomains contribute to DNA binding specificity. (1991)

The DNA binding specificities of the homeodomains contained in thyroid transcription factor 1 and Antennapedia have been compared. The two homeodomains recognize different DNA sequences, despite the similar amino acid sequences of their recognition helix. Mutations that make the recognition helix of thyroid transcription factor 1 identical to the one contained in Antennapedia have no effects on the binding specificity of thyroid transcription factor 1. The exchange of other segments between these two homeodomains allows the identification of the regions responsible for the observed DNA binding specificities. These results indicate that amino acid residues outside of the recognition helix play an important role in the determination of the DNA binding specificities of these two homeodomains.
Identification and Characterization of KLK-L4, a New Kallikrein-like Gene That Appears to be Down-regulated in Breast Cancer Tissues (2000)

Kallikreins are a subgroup of serine proteases and these proteolytic enzymes have diverse physiological functions in many tissues. Growing evidence suggests that many kallikreins are implicated in carcinogenesis. In rodents, kallikreins constitute a large multigene family, but in humans, only three genes were identified. By using the positional candidate gene approach, we were able to identify a new kallikrein-like gene, tentatively named KLK-L4 (for kallikrein-like gene 4). This new gene maps to chromosome 19q13. 3-q13.4, is formed of five coding exons and four introns, and shows structural similarity to other kallikreins and kallikrein-like genes. KLK-L4 is expressed in a variety of tissues including prostate, salivary gland, breast, and testis. Our preliminary results show that KLK-L4 is down-regulated, at the mRNA level, in breast cancer tissues and breast cancer cell lines. Its expression is regulated by steroid hormones in the breast cancer cell line BT-474. This gene may be involved in the pathogenesis and/or progression of breast cancer and may find applicability as a novel cancer biomarker.
Increased lysis of melanoma by in vivo-elicited human lymphokine-activated killer cells after addition of antiganglioside antibodies in vitro. (1990)

Thirty-nine melanoma patients were treated with cyclophosphamide (350 mg/m2) followed 3 days later by 5 daily doses of interleukin 2 (3.6 million units/m2 i.v.) weekly for 2 weeks. This cycle was repeated at least twice with a 1-week interval between cycles. Natural killer and lymphokine-activated killer (LAK) cell activity in peripheral blood mononuclear cells were measured before treatment and on the last day of each cycle by chromium release assays. Development of LAK activity of greater than 10 lytic units was correlated with a clinical response. There was no correlation between natural killer activity and clinical response. Antibody-dependent cell-mediated cytotoxicity of in vivo-induced LAK cells after the addition of mouse monoclonal antibodies (MAbs) in vitro was measured in 30 cases on the last day of each interleukin 2 cycle. Anti-GD3 MAbs MB3.6, 11C64, 6H4, and R24 increased LAK cell cytotoxicity against GD3-positive GD2 melanoma cells while anti-GD2 MAb 14.18 increased LAK cell cytotoxicity against GD3-negative GD2-positive melanoma cells. MAb 9.2.27 (IgG2a) directed against a chondroitin sulfate proteoglycan and its core protein with a molecular weight of 250,000 (p250) on human melanoma cells did not mediate antibody-dependent cell-mediated cytotoxicity. The effector cells in these antibody-dependent cell-mediated cytotoxicity. The effector cells in these antibody-dependent cell-mediated cytotoxicity reactions were Leu-19 positive. In preincubation experiments the MAbs showed superior binding to the melanoma target cells than to effector cells. Our results show that low dose interleukin 2 preceded by low dose cyclophosphamide effectively induces LAK cells in vivo. The cytotoxicity of these in vivo-activated LAK cells can be augmented in vitro by mouse MAbs against glycolipid antigens on the tumor.
Regulatory T cells interfere with the development of bronchus-associated lymphoid tissue (2007)

Presence and extent of bronchus-associated lymphoid tissue (BALT) is subject to considerable variations between species and is only occasionally observed in lungs of mice. Here we demonstrate that mice deficient for the chemokine receptor CCR7 regularly develop highly organized BALT. These structures were not present at birth but were detectable from day 5 onwards. Analyzing CCR7(-/-)/wild-type bone marrow chimeras, we demonstrate that the development of BALT is caused by alterations of the hematopoietic system in CCR7-deficient mice. These observations together with the finding that CCR7-deficient mice possess dramatically reduced numbers of regulatory T cells (T reg cells) in the lung-draining bronchial lymph node suggest that BALT formation might be caused by disabled in situ function of T reg cells. Indeed, although adoptive transfer of wild-type T reg cells to CCR7-deficient recipients resulted in a profound reduction of BALT formation, neither naive wild-type T cells nor T reg cells from CCR7(-/-) donors impair BALT generation. Furthermore, we provide evidence that CCR7-deficient T reg cells, although strongly impaired in homing to peripheral lymph nodes, are fully effective in vitro. Thus our data reveal a CCR7-dependent homing of T reg cells to peripheral lymph nodes in conjunction with a role for these cells in controlling BALT formation.
SMT-centric power-aware thread placement in chip multiprocessors (2013)

In Simultaneous Multi-Threading (SMT) chip multiprocessors (CMPs), thread placement is performed today in a largely power-unaware manner. For example, consolidation of active threads into fewer cores exposes opportunities for power savings that have not been addressed in prior work. The savings opportunity is especially high in the emerging context where per-core power gating (PCPG) is becoming viable. The use of the optimum combination of core-wise SMT level and number of active cores to achieve a desired power-performance efficiency is a knob which has not been explored in prior work nor implemented as part of the operating system task scheduler. This work investigates the opportunities for such efficiency improvement in the context of the IBM POWER7 processor chip. We present a thread consolidation heuristic (TCH) capable of finding power-performance efficient thread placements at runtime, based on power-performance measurements.In the context of the PARSEC benchmark suite, chip power consumption is reduced by up to 21% (averaged across applications) when TCH is adopted instead of the default Linux thread scheduling policy, with minimal performance impact. TCH can create favorable conditions that enable aggressive actuation of PCPG, when that is available. In conjunction with PCPG, TCH can improve power-performance efficiency by a factor of up to 2.1 with respect to the default scheduler. We also evaluate TCH in the context of the SPECpower benchmark. In this case, TCH reduces system power up to 15% without PCPG and up to 22% with PCPG, with no performance degradation.
Synthesis and anti-HIV activities of low molecular weight aurintricarboxylic acid fragments and related compounds (1991)

Several compounds corresponding to fragments of the schematic representation of the polymeric structure of aurintricarboxylic acid (ATA) have been prepared and tested for prevention of the cytopathic effect of HIV-1 and HIV-2 in MT-4 cell culture and HIV-1 in CEM cell culture. Both the triphenylcarbinol 3 as well as the triphenylmethane 5 were found to afford protection against the cytopathogenicity of HIV-2 in MT-4 cells and HIV-1 in CEM cells, but they were inactive against HIV-1 in MT-4 cells. Both substances were also found to inhibit syncytium formation when MOLT-4 cells were cocultured with HIV-2-infected HUT-78 cells, but were inactive in this assay against HIV-1-infected cells. When observed, the activity is generally moderate in degree of protection and requires concentrations in the 10(-4) molar range. In contrast to ATA, both of these substances were inactive when tested for prevention of the binding of the OKT4A monoclonal antibody to the CD4 receptor and also for inhibition of HIV-1 reverse transcriptase. These substances therefore appear act by a mechanism that is distinct from that of polymeric ATA. Several active and inactive structural analogues of 3 and 5 were also synthesized. The anti-HIV activity in this series seems to depend on the presence of anionic carboxylate groups, since the methyl esters 4, 6, and 12 were uniformly inactive. The diphenylmethanes 8, 14, 18, and 19 also reproducibly inhibited the cytopathic effect of HIV-1 in CEM cell culture.
Preclinical Efficacy and Mechanisms of Mesenchymal Stem Cells in Animal Models of Autoimmune Diseases (2014)

Mesenchymal stem cells (MSCs) are present in diverse tissues and organs, including bone marrow, umbilical cord, adipose tissue, and placenta. MSCs can expand easily in vitro and have regenerative stem cell properties and potent immunoregulatory activity. They inhibit the functions of dendritic cells, B cells, and T cells, but enhance those of regulatory T cells by producing immunoregulatory molecules such as transforming growth factor-β, hepatic growth factors, prostaglandin E2, interleukin-10, indolamine 2,3-dioxygenase, nitric oxide, heme oxygenase-1, and human leukocyte antigen-G. These properties make MSCs promising therapeutic candidates for the treatment of autoimmune diseases. Here, we review the preclinical studies of MSCs in animal models for systemic lupus erythematosus, rheumatoid arthritis, Crohn's disease, and experimental autoimmune encephalomyelitis, and summarize the underlying immunoregulatory mechanisms.
Prospective Isolation of Cortical Interneuron Precursors from Mouse Embryonic Stem Cells (2010)

Despite their therapeutic potential, progress in generating fully differentiated forebrain neurons from embryonic stem cells (ESCs) has lagged behind that from more caudal regions of the neuraxis. GABAergic interneuron precursors have the remarkable ability to migrate extensively and survive after transplantation into postnatal cortex, making them an attractive candidate for use in cell-based therapy for seizures or other neuropsychiatric disorders. We have modified a mouse ESC line with an Lhx6-GFP reporter construct that allows for the isolation of newly generated cortical interneuron precursors. When transplanted into postnatal cortex, these cells can migrate into the cortical parenchyma, survive for months, and display morphological, neurochemical, and electrophysiological properties characteristic of mature interneurons. This work demonstrates that forebrain neuronal subtypes with complex traits can be generated from embryonic stem cells, and provides a novel approach to the study of cortical interneuron development and to the establishment of cell-based therapies for neurological disease.
Fundamentals and improvements for directional relays (2010)

Phase and ground directional elements are relied on for fast and secure protection throughout the power system. Although directional relays have been applied successfully for many years, several new and unique applications and power system disturbances present challenges. Using field and laboratory data, this paper reviews fundamentals, discusses the limits to sensitivity, and shows how and why directional element designs have progressed. The paper also describes how directional elements are applied during loss of voltage conditions. In addition to design basics, we show several practical field examples that illustrate problems and solutions, while providing guidance on applying and setting modern directional relays.
BOUNDARY TENSION BY PENDANT DROPS1 (1938)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBOUNDARY TENSION BY PENDANT DROPS1J. M. ANDREASJ. M. ANDREASMore by J. M. ANDREAS, E. A. HAUSERE. A. HAUSERMore by E. A. HAUSER, and W. B. TUCKERW. B. TUCKERMore by W. B. TUCKERCite this: J. Phys. Chem. 1938, 42, 8, 1001–1019Publication Date (Print):August 1, 1938Publication History Published online1 May 2002Published inissue 1 August 1938https://doi.org/10.1021/j100903a002Request reuse permissionsArticle Views2032Altmetric-Citations503LEARN 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 InReddit PDF (1 MB) Get e-Alerts
Microbial production of next-generation stevia sweeteners (2016)

Screening of the mutant library identified mutations with positive impact on the accumulation of Reb D and Reb M. The effect of the introduced mutations on other reactions in the metabolic grid was characterized. This screen made it possible to identify variants, such as UGT76G1<sub>Thr146Gly</sub> and UGT76G1<sub>His155Leu</sub>, which diminished accumulation of unwanted side-products and gave increased specific accumulation of the desired Reb D or Reb M sweeteners. This improvement in a key enzyme of the Stevia sweetener biosynthesis pathway represents a significant step towards the commercial production of next-generation stevia sweeteners.
[The expression of arrhythmic related genes on Xenopus oocytes for evaluation of class III antiarrhythmic drugs from ocean active material]. (2000)

By techniques of gene clone, microinjection and patch-clamp, human arrhythmic related gene Kv1.5 and Kv4.2 are translated mRNA, and injected into Xenopus Oocytes, respectively. A pure and single K+ current of ultrarapid delayed rectifier K+ current (Ikur) or transient outward K+ current (Ito) is respectively expressed on Xenopus Oocytes. This is a modern pharmacological model for evaluation class III antiarrhythmic drugs, overcomes many defects such as lacking human fresh cardiac muscle cells as material and co-expression of many currents on cell membrane. A new compound A1998 from Ocean material is evaluated in this model for class III antiarrhythmic functions.
A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling (2017)

The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3' end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.
Color Doppler Ultrasonography of Lumbar Artery Blood Flow in Patients With Low Back Pain (2012)

3.
Nitrofurantoin Is Active against Vancomycin-Resistant Enterococci (2001)

The activity of nitrofurantoin was tested against 300 isolates of Enterococcus faecium, Enterococcus faecalis, and Enterococcus gallinarum. No isolates tested were resistant to nitrofurantoin (MIC, >/=128 microg/ml), including vancomycin-resistant E. faecium isolates with vanA- and vanB-positive genotypes and vancomycin-resistant E. gallinarum isolates. We conclude that nitrofurantoin may provide effective treatment of urinary tract infections caused by vancomycin-resistant enterococci.
CCR5-Deficient Mice Control Mycobacterium tuberculosis Infection despite Increased Pulmonary Lymphocytic Infiltration (2004)

The control of Mycobacterium tuberculosis infection is dependent on the development of an adaptive immune response, which is mediated by granulomas. The granuloma is a dynamic structure that forms in the lung and consists primarily of macrophages and lymphocytes. For this structure to be effective in containment of the bacillus, it must develop in an organized and timely manner. The formation of the granuloma is dependent on recruitment of activated cells through adhesion molecules and chemokines. M. tuberculosis infection causes an increase in the expression of beta-chemokines CCL3, CCL4, and CCL5, and their receptor CCR5, in the lungs. In this study, we demonstrate that CCR5-transgenic knockout mice were capable of recruiting immune cells to the lung to form granulomas. CCR5(-/-) mice successfully induced a Th1 response and controlled infection. Unexpectedly, M. tuberculosis infection in these mice resulted in greater numbers of lymphocytes migrating to the lung and higher levels of many inflammatory cytokines, compared with wild-type mice, without apparent long-term detrimental effects. In the absence of CCR5, there were more dendritic cells in the lung-draining lymph nodes and more primed T lymphocytes in these mice. Bacterial numbers in the lymph nodes were also higher in CCR5(-/-) mice. Therefore, CCR5 may play a role in the migration of dendritic cells to and from the lymph nodes during M. tuberculosis infection.