gebhart/patrepeval huggingface dataset:
Gene expression in human brown adipose tissue (2010)

Brown adipose tissue (BAT) has profound effects on body weight and metabolism in rodents. Recent reports show that human adults have significant amounts of BAT. Our aim was to study the gene expression profile of human BAT. Biopsies of adipose tissue with brown-red color and subcutaneous white adipose tissue (WAT) were obtained from 24 patients undergoing surgery in the thyroid region. Intrascapular BAT and epididymal WAT biopsies were obtained from 10 mice. Expression was analyzed by DNA microarray, real-time PCR and immunohistochemistry. Using the expression of the brown adipocyte-specific gene uncoupling protein 1 (UCP1) as a marker, approximately half of the human brown-red adipose tissue biopsies taken in the thyroid region contained BAT, and the presence of cells with brown adipocyte morphology was also verified by histology. Microarray analysis of 9 paired human BAT and WAT samples showed that 17 genes had at least a 4-fold higher expression in BAT compared to WAT and five of them (CKMT1, KCNK3, COBL, HMGCS2, TGM2) were verified using real-time PCR (P<0.05 for all). In addition, immunohistochemistry showed that the UCP1, KCNK3 and CKMT1 proteins are expressed in brown adipocytes. Except for UCP1 and KCNK3, the genes overexpressed in human BAT were not overexpressed in mouse BAT compared to mouse WAT. Our analysis identified genes that are differentially expressed in human BAT compared to WAT. The results also show that there are species-specific differences in BAT gene expression and this emphasizes the need for further molecular characterization of human BAT to clarify the mechanisms involved in regulated heat production in humans.
Detection of Mycobacterium tuberculosis directly from sputum by using a prototype automated Q-beta replicase assay (1997)

We have adapted an assay for the direct detection of Mycobacterium tuberculosis using a prototype automated instrument platform in which probes are amplified with Q-beta replicase. The assay was based on amplification of specific detector probe following four cycles of background reduction (reversible target capture) in a closed disposable pack. The assay signal was the time required for fluorescence to exceed background levels (response time [RT]). RT was inversely related to the number of M. tuberculosis rRNA target molecules in the sample. Equivalent signals and noises were observed in assays containing either sputum or buffer. All mock samples containing > or = 10 CFU of M. tuberculosis responded in the assay (average RT, 13.91 min), while most (83%) samples containing as many as 10(7) CFU of Mycobacterium avium gave no response during a 25-min amplification reaction. The samples containing M. avium which did respond had an average RT of 17.04 min. Seventy-five percent (167 of 223) of samples containing no target gave no responses; the remaining 25% had an average RT of 15.53 min. Eighty-three frozen sputum samples were tested to develop a candidate cutoff RT for the assay prior to more extensive clinical testing. After resolution of discrepant results and with a 14-min RT cutoff, 30 of 38 M. tuberculosis-positive samples were positive by the assay; 1 of 45 negative samples responded within 14 min. Assay sensitivity, specificity, and positive and negatives predictive values in this pilot study were 79, 98, 97, and 85%, respectively.
Ultrahigh-density atomic force microscopy data storage with erase capability (1999)

We report a simple atomic force microscopy-based concept for a hard disk-like data storage technology. Thermomechanical writing by heating a Si cantilever in contact with a spinning polycarbonate disk has already been reported. Here the medium has been replaced with a thin polymer layer on a Si substrate, resulting in significant improvements in storage density. With this new medium, we achieve bit sizes of 10–50 nm, leading to data densities of 500 Gbit/in.2. We also demonstrate a novel high-speed and high-resolution thermal readback method, which uses the same Si cantilevers that are used in the writing process, and the capability to erase and rewrite data features repeatedly.
Singlet Fission in Quinoidal Oligothiophenes (2016)

The electronic properties of quinoidal oligithiophenes make them interesting for applications in semiconductor technology. Because of their very large singlet–triplet splitting, they are promising candidates for singlet fission (SF), a process in which an initially excited singlet state is converted into two triplet excitons. Thus, the efficiency of solar cells could be increased to overcome the Shockley-Queisser limit. Here, we investigate the ability of a quinoidal bithiophene to undergo SF in solution. We calculated the ground state and low-lying excited states using a combined density functional theory and multireference configuration interaction approach including dispersion corrections. Potential energy curves along normal mode displacements were computed to detect avoided crossings between the initially excited bright singlet state and a dark doubly excited state which can be interpreted as a triplet pair overall coupled to a singlet 1(TT). The studied quinoidal bithiophene meets the energetic requirement for SF. A path enabling intramolecular SF could not be found. In contrast, we were able to identify two vibrational modes relevant for an intermolecular SF process in the slip-stacked dimer: A promoting coordinate that couples a bright singlet state with the 1(TT) state and a separating coordinate that localizes the triplet states on the respective monomers. These results elucidate the mechanism underlying the formation of a triplet pair and the separation of the triplet excitons after initial photoexcitation of the bright singlet state.
Deterioration of red blood cell mechanical properties is reduced in anaerobic storage. (2016)

The perfusion measurements suggest that anaerobically stored RBC retain a greater ability to perfuse networks of artificial capillaries compared to conventionally (aerobically) stored RBC. It is likely that anaerobic storage confers this positive effect on the bulk mechanical properties of stored RBC by significantly reducing the number of non-deformable cells present in the overall population of relatively well-preserved RBC.
The Effect of Steric Hindrance on Radical and Ionic Substitution Reactions of Nucleophiles with Some α-Alkyl- p -Nitrobenzyl Chlorides (1979)

The reactions of the a -alkyl p -nitrobenzyl chlorides, p -NO2C6H4CH(CI)R(R = Me, Pr1, But), with nucleophiles, e.g, nitrite, nitroethanide, benzenethiolate and p -toluenesulfinate ions and the anion derived from diethyl 2-methylmalonate, in dimethyl sulfoxide have been studied. When R = But, SRNl reactions take place and give, in the reaction with p -toluenesulfinate and the anion from diethyl 2-methylmalonate, extremely sterically crowded molecules, which, as a result of bond formation between the more hindered atom in the ambident nucleophile and the benzylic carbon, display dynamic 1H N.M.R. effects. The derivatives where R = Me or Pri undergo radical and/or ionic processes depending on the nucleophile being used. Pathways accounting for some of the unusual compounds produced, e.g. 5-methyl-3,5-bis( p -nitropheny1)-2-isoxazoline N-oxide and (E)- and (Z)- p -nitroiso-butyrophenone O -( p -nitrobenzoyl) oximes from reaction of nitrite ion with the a -methyl and a - isopropyl compounds respectively, are proposed.
ID1 Promotes Breast Cancer Metastasis by S100A9 Regulation (2014)

Novel pathways by Id1 regulation in metastasis.
Compiler-directed selective data protection against soft errors (2005)

Soft errors in electronic devices are a growing concern for many embedded systems from diverse domains. Chip vendors are already working with system customers on ways to guard against the effects of soft errors. While error code based protection mechanisms for memories such as ECC are important, indiscriminately applying them to all data can have serious memory space and energy overheads. This paper demonstrates how an optimizing compiler can be useful in deciding which data elements need to be protected based on user-specified annotations. The proposed idea makes use of a variant of forward slicing.
TEPOXALIN, A NOVEL IMMUNOMODULATORY COMPOUND, SYNERGIZES WITH CSA IN SUPPRESSION OF GRAFT-VERSUS-HOST REACTION AND ALLOGENEIC SKIN GRAFT REJECTION (1995)

Tepoxalin, a dual 5-lipoxygenase and cyclooxygenase inhibitor with nonsteroidal antiinflammatory effects, has recently been shown to suppress NF kappa B transactivation and inhibit T cell proliferation via a mechanism very different from cyclosporine (CsA). In this report, we demonstrate that this novel immunosuppressive effect of tepoxalin is manifested in in vivo transplantation models. Tepoxalin suppressed murine spleen cell proliferation in a mixed lymphocyte reaction (MLR) with an IC50 of 1.3 microM. Coadministration of tepoxalin and CsA in MLR cultures showed an additive inhibitory effect. Oral administration of tepoxalin at 12 mg/kg/day to mice suppressed local graft-versus-host (GVH) responses by about 40% (n = 10). Combination of tepoxalin and CsA at suboptimal doses synergized their immunosuppressive effects on GVH responses (n = 20). In skin transplantation, the median survival time of allogeneic BALB/cByJ (H-2d) mouse skin grafted onto C3H/HeJ (H-2 kappa) mice was 10.5 days (n = 8), and was prolonged to 15.0 days (n = 9) for recipient mice administered tepoxalin at 50 mg/kg/day. Coadministration of suboptimal doses of tepoxalin (12.5 mg/kg/day) and CsA (50 mg/kg/day) prolonged skin graft rejections dramatically (55% of the grafts survived for more than 40 days, n = 9). Taken together, these results demonstrate that tepoxalin is a potent immunomodulatory compound that, when combined with CsA, provides synergistic immunosuppressive activity. The fact that tepoxalin and CsA act on different transcription factors, NF kappa B and NFAT respectively, might explain the synergistic suppressive effects when both compounds were used. Tepoxalin could be an important addition to the cohort of immunosuppressive therapies currently used in solid organ and bone marrow transplantations.
Millimeter-scale positioning of a nerve-growth-factor source and biological activity in the brain (1999)

Toxicity prevents the systemic administration of many therapeutic proteins, and attempts at protein targeting via the circulatory system (i.e., "magic bullets") have failed in all but a few special cases. Direct administration at the target site is a logical alternative, particularly in the central nervous system, but the limits of direct administration have not been defined clearly. Nerve growth factor (NGF) enhances survival of cholinergic neurons and, therefore, has generated considerable interest for the treatment of Alzheimer's disease. We tested the effectiveness of local delivery by implanting small polymer pellets that slowly released NGF into the central nervous system of adult rats at controlled distances from a target site containing transplanted fetal cholinergic cells. NGF-releasing implants placed within 1-2 mm of the treatment site enhanced the biological function of cellular targets, whereas identical implants placed approximately 3 mm from the target site of treatment produced no beneficial effect. Effective NGF therapy required millimeter-scale positioning of the NGF source, and efficacy correlated with the spatial distribution of NGF concentration in the tissue; this result suggests that NGF must be delivered within several millimeters of the target to be effective in treating Alzheimer's disease. Because the human brain is divided into functional regions that are typically several centimeters in diameter and often irregular in shape, new methods for sculpting larger-scale drug fields are needed. We illustrate a concept, called pharmacotectonics, in which drug-delivery systems are arranged spatially in tissues to shape concentration fields for potent agents.
고등학교 수준 미술전자교과서 개발 연구 (2007)

정보화시대의 도래와 함께 미술교육에 대한 패러다임 또한 변화되었다. 시각정보의 비판적 수용능력과 새로운 문화를 창조해 내는 창의력을 기르는데 있어 미술이해와 감상교육에 대한 요구는 확대되고 있으나 수업시수의 부족과 교과서의 한정된 정보제공 등으로 인하여 교육현장에서의 적용은 미흡한 것이 현실이다. 이러한 문제의 대안으로써 다양한 자료를 담을수 있고 영상 미술 등의 감상을 지원할 수 있는 미술전자교과서의 도입이 요구된다. 전자교과서는 단순히 인쇄교과서를 전자화 한 것을 의미하는 것이 아니라 다양한 가능성을 지닌 교육자료의 총체적 변화로 이해할 수 있으며 학습효과를 높이기 위해서는 미술교과의 특수한 성격과 학년별 특수성을 고려한 다양한 사례연구가 필요하다. 본 연구에서는 고학년 미술교육은 저학년 미술교육과 달리 비교감상과 맥락적 분석적 감상이 이루어져야 한다는 점에 기초하여 이러한 학습을 가능하게 해주는 미술전자교과서의 설계모형에 대해 연구하였다. 먼저 항해유형(Navigation)이 학습효과에 영향을 미치는가에 대한 연구문제를 제기하고 인지적 융통성 이론에 기반한 연계적 항해유형과, 위계적 항해유형의 두가지 유형의 비술전자교과서를 개발하고 실제 교육현장에서 고등학교1학년을 대상으로 시험학습을 실시하였다. 그 결과 연계적 항해유형의 미술전자교과서는 위계적 유형의 전자교과서에 비하여 학습자의 이해수준의 차이를 극복할 수 있고 다중맥락적 이해를 지원하는 데 유리하다는 연구결과를 얻을 수 있었다.
Organic synthesis toward small-molecule probes and drugs (2011)

"Organic synthesis" is a compound-creating activity often focused on biologically active small molecules. This special issue of PNAS explores innovations and trends in the field that are enabling the synthesis of new types of small-molecule probes and drugs. This perspective article frames the research described in the special issue but also explores how these modern capabilities can both foster a new and more extensive view of basic research in the academy and promote the linkage of life-science research to the discovery of novel types of small-molecule therapeutics [Schreiber SL (2009) Chem Bio Chem 10:26-29]. This new view of basic research aims to bridge the chasm between basic scientific discoveries in life sciences and new drugs that treat the root cause of human disease--recently referred to as the "valley of death" for drug discovery. This perspective article describes new roles that modern organic chemistry will need to play in overcoming this challenge.
Small-Scale Manufacture of Process Cheese Using a Rapid Visco Analyzer (2005)

Numerous formulation and processing parameters influence the functional properties of process cheese. Recently, a small-scale (25 g) manufacturing and analysis method was developed using a rapid visco analyzer (RVA), which was designed to evaluate the functional properties of process cheese when subjected to various formulations and processing conditions. Although this method successfully manufactured process cheese, there was a significant difference in the functional properties of the process cheese compared with process cheese manufactured on a pilot scale. In the present study, adjustments in the RVA methodology involving the RVA processing conditions, preblend preparation, and texture profile analysis (TPA) techniques for the final process cheese were investigated. Fourteen samples of pasteurized processed cheese food (PCF) were manufactured from 14 different preblends. Each pre-blend was prepared using 1 of the 14 different natural cheeses and was balanced for moisture, fat, and salt. Each of these 14 preblends was split into 3 portions and each portion was subjected to 3 different manufacturing treatments. The first treatment was manufactured in a pilot-scale Blentech twin screw (BTS) cooker, and the remaining 2 treatments were manufactured in an RVA with different processing profiles. The RVA treatments were produced in triplicate. The resulting process cheeses were analyzed for moisture and functional properties. Texture profile analysis and RVA melt analyses were performed on all PCF treatments. Additionally, for the RVA treatments, the data for time of emulsification and end apparent viscosity during RVA manufacture were collected and recorded. The functional properties of the PCF manufactured using the RVA treatments showed good correlation with the functional properties of the PCF produced on the pilot scale. Additionally, the end apparent viscosity during RVA manufacture was correlated with the functional properties of the process cheese. Consequently, the RVA can be used as a small-scale manufacturing and analysis tool for predicting the functional properties of process cheese, and for evaluating how various formulations and processing parameters affect these functional properties. Moreover, the adjustments in the RVA methodology produced process cheese with functionality similar to process cheese produced in the BTS.
Unsupervised learning of semantic relations between concepts of a molecular biology ontology (2005)

In this paper we present an unsupervised model for learning arbitrary relations between concepts of a molecular biology ontology for the purpose of supporting text mining and manual ontology building. Relations between named-entities are learned from the GENIA corpus by means of several standard natural language processing techniques. An in-depth analysis of the output of the system shows that the model is accurate and has good potentials for text mining and ontology building applications.
Sudomotor testing predicts the presence of neutralizing botulinum A toxin antibodies (2002)

The increasing number of patients being treated with botulinum toxin A complex (BoNT/A) has led to a higher incidence of neutralizing anti-BoNT/A antibodies (ABAs). Because BoNT/A is known to inhibit sweating, here we report sudometry as a possibility for predicting the presence of ABA. Sixteen patients suffering from spasmodic torticollis were selected: in 2 patients, BoNT/A treatment continued to be effective, in 9 patients, the treatment effect was impaired, and in 5 patients, secondary treatment failure developed. BoNT/A (100 mouse units, Dysport; Ipsen Pharma, Berkshire, United Kingdom) was injected subcutaneously into the lateral calves. Sweating was visualized with iodine starch staining. In addition, quantitative sudomotor axon reflex testing was performed at the injection site. Individual ABA titers were determined with a mouse bioassay. Results of sudometry significantly correlated with the BoNT/A treatment success. The quantitative sudomotor axon reflex testing was 0.58 +/- 0.63 fraction of the normal mean in patients with treatment failure, 0.18 +/- 0.13 fraction of the normal mean in those who responded partially, and 0 in responders (p < 0.01). Accordingly, the areas of the anhidrotic skin after subcutaneous injections were 4.5 +/- 10.3 cm(2), 32.7 +/- 16.5 cm(2), and 62 cm(2) (p < 0.01). Discrimination analysis indicated that the presence of ABA (6 ABA-positive and 10 ABA-negative) could be predicted correctly in all patients from the results of sudometry. Therefore, sudometry is a useful tool for identifying patients with neutralizing ABAs and might be helpful for identifying reasons for BoNT/A treatment failure.
Intramolecular kinetic isotope effects in alkane hydroxylations catalyzed by manganese and iron porphyrin complexes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntramolecular kinetic isotope effects in alkane hydroxylations catalyzed by manganese and iron porphyrin complexesAlexander Sorokin, Anne Robert, and Bernard MeunierCite this: J. Am. Chem. Soc. 1993, 115, 16, 7293–7299Publication Date (Print):August 1, 1993Publication History Published online1 May 2002Published inissue 1 August 1993https://pubs.acs.org/doi/10.1021/ja00069a031https://doi.org/10.1021/ja00069a031research-articleACS PublicationsRequest reuse permissionsArticle Views827Altmetric-Citations121LEARN 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
Rapid prenatal diagnosis of beta thalassemia using DNA amplification and nonradioactive probes (1989)

We used in vitro DNA amplification by the polymerase chain reaction and nonradioactive probes for prenatal diagnosis of beta thalassemia in Chinese from the Guangdong province. Exact molecular diagnoses were made in all 20 fetuses studied over a 6-month period. We conclude that this method of prenatal diagnosis for beta thalassemia is a viable approach in many parts of the world where this disease is common.
Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma (2010)

Ovarian clear cell carcinoma (OCCC) is an aggressive human cancer that is generally resistant to therapy. To explore the genetic origin of OCCC, we determined the exomic sequences of eight tumors after immunoaffinity purification of cancer cells. Through comparative analyses of normal cells from the same patients, we identified four genes that were mutated in at least two tumors. PIK3CA, which encodes a subunit of phosphatidylinositol-3 kinase, and KRAS, which encodes a well-known oncoprotein, had previously been implicated in OCCC. The other two mutated genes were previously unknown to be involved in OCCC: PPP2R1A encodes a regulatory subunit of serine/threonine phosphatase 2, and ARID1A encodes adenine-thymine (AT)-rich interactive domain-containing protein 1A, which participates in chromatin remodeling. The nature and pattern of the mutations suggest that PPP2R1A functions as an oncogene and ARID1A as a tumor-suppressor gene. In a total of 42 OCCCs, 7% had mutations in PPP2R1A and 57% had mutations in ARID1A. These results suggest that aberrant chromatin remodeling contributes to the pathogenesis of OCCC.
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. (1998)

Abstract MOTIVATION: The discovery of motifs in biological sequences is an important problem. RESULTS: This paper presents a new algorithm for the discovery of rigid patterns (motifs) in biological sequences. Our method is combinatorial in nature and able to produce all patterns that appear in at least a (user-defined) minimum number of sequences, yet it manages to be very efficient by avoiding the enumeration of the entire pattern space. Furthermore, the reported patterns are maximal: any reported pattern cannot be made more specific and still keep on appearing at the exact same positions within the input sequences. The effectiveness of the proposed approach is showcased on a number of test cases which aim to: (i) validate the approach through the discovery of previously reported patterns; (ii) demonstrate the capability to identify automatically highly selective patterns particular to the sequences under consideration. Finally, experimental analysis indicates that the algorithm is output sensitive, i.e. its running time is quasi-linear to the size of the generated output.