gebhart/patrepeval huggingface dataset:
Sensing cell metabolism by time-resolved autofluorescence (2006)

We built a time-resolved confocal fluorescence spectroscopy system equipped with the multichannel time-correlated single-photon-counting technique. The instrument provides a unique approach to study the fluorescence sensing of cell metabolism via analysis of the wavelength- and time-resolved intracellular autofluorescence. The experiments on monolayered cell cultures show that with UV excitation at 365 nm the time-resolved autofluorescence decays, dominated by free-bound reduced nicotinamide adenine dinucleotide signals, are sensitive indicators for cell metabolism. However, the sensitivity decreases with the increase of excitation wavelength possibly due to the interference from free-bound flavin adenine dinucleotide fluorescence. The results demonstrate that time-resolved autofluorescence can be potentially used as an important contrast mechanism to detect epithelial precancer.
Sunlight and Age-Related Macular Degeneration (1993)

These data suggest that exposure to sunlight may be associated with age-related maculopathy. However, longitudinal studies of these associations are needed.
Ion trap tandem mass spectrometry applied to small multiply charged oligonucleotides with a modified base (1994)

Two isomeric oligodeoxynucleotide hexamers, 5'-d(N-6meATGCAT)-3' and 5'-d(ATGSmeCAT)-3', were subjected to analysis by electrospray and ion trap mass spectrometry. In the case of the isomer with a modified adenine, location of the modified base in the sequence was straightforward and a triple mass spectrometry experiment provided information on the identity of the modification. In contrast, the isomer with the methylated cytosine did not yield definitive information on the location or identity of the modification. Tandem mass spectrometry data in this case could indicate that the modification was present on either the third or fourth nucleoside. The two isomers represent extremes in the facility with which modified bases can be identified and located in a small oligonucleotide via multiple mass spectrometry of multiply charged anions. A preference for loss of particular bases strongly influences which structurally diagnostic ions are formed upon collisional activation. The likelihood for locating and identifying a modified base is dependent, therefore, upon the likelihood that the base is lost directly from the parention.
Fast and simple modeling of non-rectangular transistors (2008)

As CMOS feature size scales down to 65nm and below, challenges for device and circuit manufacturability are emerging. As commonly seen in real designs, devices with distorted gate shapes and rough line-edges are manufactured despite the applications of aggressive resolution enhancement techniques (RET). It has been shown that such irregular gates could introduce significant extra leakage current. Existing tools and device models cannot handle non-rectangular geometries. Therefore, it is critical that a modeling flow capable of handling such irregular devices is developed and smoothly integrated into the post-lithography delay and leakage circuit analysis process. Previously proposed methods either model an irregular transistor as two different rectangular devices, one for on and the other for off state analyses; or they are difficult to be implemented. In this paper, we propose a new modeling approach that serves as a fast and simple solution to this problem and overcomes these drawbacks. We found that by adjusting both gate length and width of the equivalent device, a single equivalent rectangular device can be determined. Through TCAD and SPICE simulation experiments, we demonstrate that our model can accurately capture both on and off currents of the modeled nonrectangular gate device. The average error of our modeling approach is 1.6% for I<sub>on</sub> and 7.5% for I<sub>off</sub>.
Poly‐benzylic Ammonium Chloride Resins as Solid Catalysts for Fructose Dehydration (2014)

5-hydroxymethylfurfural (HMF) is one of the most promising platform molecules, and can be converted into a variety of interesting chemicals. The production of HMF is essentially targeted at bulk chemicals downstream, such as chemicals for the fuels and plastics industries. One critical challenge in HMF production processes is the link to further value-adding reactions in a simple and efficient way (e.g., fewer isolation and purification steps). Herein, a novel poly-benzyl ammonium chloride (PBnNH3 Cl) resin is developed as a highly efficient and stable catalyst for dehydration of carbohydrates into HMF. In the isopropanol system, PBnNH3 Cl produces high purity HMF that is suitable as feedstock for oxidation to 2,5-furandicarboxylic acid (FDCA). The excellent catalytic properties together with its easy synthesis, low cost, and nontoxic nature make this poly-ammonium resin a promising catalyst for the development of new and efficient processes for biomass-based chemicals.
Molecular properties of pyruvate formate-lyase activating enzyme (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular properties of pyruvate formate-lyase activating enzymeKenny K. Wong, Brion W. Murray, Sandra A. Lewisch, Michael K. Baxter, Todd W. Ridky, Lucy Ulissi-DeMario, and John W. KozarichCite this: Biochemistry 1993, 32, 51, 14102–14110Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/bi00214a005https://doi.org/10.1021/bi00214a005research-articleACS PublicationsRequest reuse permissionsArticle Views375Altmetric-Citations56LEARN 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
Down-regulation of NKD1 increases the invasive potential of non-small-cell lung cancer and correlates with a poor prognosis (2011)

NKD1 protein is reduced but NKD1 mRNA is elevated in NSCLC. Reduced NKD1 protein expression correlates with a poor prognosis in NSCLC. NKD1 might inhibit the activity of the canonical Wnt pathway through Dishevelled-1.
Overproduction of the Lon protease triggers inhibition of translation in Escherichia coli: involvement of the yefM‐yoeB toxin‐antitoxin system (2004)

In Escherichia coli, the Lon ATP-dependent protease is responsible for degradation of several regulatory proteins and for the elimination of abnormal proteins. Previous studies have shown that the overproduction of Lon is lethal. Here, we showed that Lon overproduction specifically inhibits translation through at least two different pathways. We have identified one of the pathways as being the chromosomal yefM-yoeB toxin-antitoxin system. The existence of a second pathway is demonstrated by the observation that the deletion of the yefM-yoeB system did not completely suppress lethality and translation inhibition. We also showed that the YoeB toxin induces cleavage of translated mRNAs and that Lon overproduction specifically activates YoeB-dependent mRNAs cleavage. Indeed, none of the other identified chromosomal toxin-antitoxin systems (relBE, mazEF, chpB and dinJ-yafQ) was involved in Lon-dependent lethality, translation inhibition and mRNA cleavage even though the RelB and MazE antitoxins are known to be Lon substrates. Based on our results and other studies, translation inhibition appears to be the key element that triggers chromosomal toxin-antitoxin systems. We propose that under Lon overproduction conditions, translation inhibition is mediated by Lon degradation of a component of the YoeB-independent pathway, in turn activating the YoeB toxin by preventing synthesis of its unstable YefM antidote.
Swimming against the Tide: Mobility of the Microtubule-Associated Protein Tau in Neurons (2007)

Long-haul transport along microtubules is crucial for neuronal polarity, and transport defects cause neurodegeneration. Tau protein stabilizes microtubule tracks, but in Alzheimer's disease it aggregates and becomes missorted into the somatodendritic compartment. Tau can inhibit axonal transport by obstructing motors on microtubules, yet tau itself can still move into axons. We therefore investigated tau movement by live-cell fluorescence microscopy, FRAP (fluorescence recovery after photobleaching), and FSM (fluorescence speckle microscopy). Tau is highly dynamic, with diffusion coefficients of ∼3 μm 2 /s and microtubule dwell times of ∼4 s. This facilitates the entry of tau into axons over distances of millimeters and periods of days. For longer distances and times, two mechanisms of tau transport are observed. At low near-physiological levels, tau is cotransported with microtubule fragments from cell bodies into axons, moving at instantaneous velocities ∼1 μm/s. At high concentrations, tau forms local accumulations moving bidirectionally at ∼0.3 μm/s. These clusters first appear at distal endings of axons and may indicate an early stage of neurite degeneration.
Synthesis of new substituted tetrazines: electrochemical and spectroscopic properties (2004)

Original tetrazines substituted by heterocyclic rings have been prepared. Their syntheses, as well as their electrochemical and spectroscopic features, are described. Calculations have also been made on the cation radicals, anion radicals and neutral compounds and are in correct agreement with the experimental results. All compounds are electroactive, both in oxidation and reduction, and display two absorption bands in the UV and visible regions of the spectrum. Reduction potentials and maximum wavelengths are correlated with the electron-rich character of the heterocyclic substituent on the tetrazine ring. None of these compounds gives good quality polymers upon electro-oxidation, which was unexpected, especially for the bis(2-pyrrolyl) tetrazine. This latter result can be explained by the occurrence of a self-deprotonation equilibrium in the cation radical.
Rbm15 Modulates Notch-Induced Transcriptional Activation and Affects Myeloid Differentiation (2007)

RBM15 is the fusion partner with MKL in the t(1;22) translocation of acute megakaryoblastic leukemia. To understand the role of the RBM15-MKL1 fusion protein in leukemia, we must understand the normal functions of RBM15 and MKL. Here, we show a role for Rbm15 in myelopoiesis. Rbm15 is expressed at highest levels in hematopoietic stem cells and at more moderate levels during myelopoiesis of murine cell lines and primary murine cells. Decreasing Rbm15 levels with RNA interference enhances differentiation of the 32DWT18 myeloid precursor cell line. Conversely, enforced expression of Rbm15 inhibits 32DWT18 differentiation. We show that Rbm15 alters Notch-induced HES1 promoter activity in a cell type-specific manner. Rbm15 inhibits Notch-induced HES1 transcription in nonhematopoietic cells but stimulates this activity in hematopoietic cell lines, including 32DWT18 and human erythroleukemia cells. Moreover, the N terminus of Rbm15 coimmunoprecipitates with RBPJkappa, a critical factor in Notch signaling, and the Rbm15 N terminus has a dominant negative effect, impairing activation of HES1 promoter activity by full-length-Rbm15. Thus, Rbm15 is differentially expressed during hematopoiesis and may act to inhibit myeloid differentiation in hematopoietic cells via a mechanism that is mediated by stimulation of Notch signaling via RBPJkappa.
ATPase inhibitors suppress actinomycin D-induced apoptosis in leukemia cells. (2003)

Since geldanamycin and radicicol are specific inhibitors of the ATPase in HSP90, the present result implies that ATPase activity in HSP90 plays some role in this apoptosis.
Low-Density Lipoprotein Postsecretory Modification, Monocyte Function, and Circulating Adhesion Molecules in Type 2 Diabetic Patients With and Without Macrovascular Complications (2000)

This is the first demonstration of increased IL-1beta secretion and increased adhesion of monocytes to endothelium from normotriglyceridemic diabetic subjects and of decreased monocyte activity and sCAMs with AT therapy in diabetic subjects with and without macrovasculopathy.
Prevalence of Heparin-Associated Antibodies Without Thrombosis in Patients Undergoing Cardiopulmonary Bypass Surgery (1997)

Approximately one fifth of patients undergoing cardiopulmonary bypass surgery have heparin-induced platelet antibodies detectable before the procedure as a result of prior heparin exposure, and many more develop antibodies after surgery. The absence of an association between these antibodies and thromboembolic complications in this study may be, in part, attributable to careful avoidance of heparin after surgery. The high prevalence of heparin-induced antibodies in this setting suggests that these patients may be at risk of developing thrombotic complications with additional heparin exposure.
CD8+ T Cells Are Required for Primary Immunity in C57BL/6 Mice Following Low-Dose, Intradermal Challenge with Leishmania major (2002)

Standard murine models of cutaneous leishmaniasis, involving s.c. inoculation of large numbers of Leishmania major promastigotes, have not supported an essential role for CD8(+) T cells in the control of primary infection. Recently, a L. major model combining two main features of natural transmission, low parasite dose and inoculation into a dermal site, has been established in resistant C57BL/6 mice. In the present studies, C57BL/6 mice with CD8(+) T cell deficiencies, including CD8(-/-) and CD8-depleted mice, failed to control the growth of L. major following inoculation of 100 metacyclic promastigotes into the ear dermis. The resulting dermal pathology was minor and delayed. Lesion formation in wild-type mice was coincident with the killing of parasites in the inoculation site. Both events were associated with the accumulation of CD8(+) T lymphocytes in the skin and with the capacity of CD8(+) T cells recovered from draining lymph nodes or infected dermis to release IFN-gamma following coculture with infected dendritic cells. Reconstitution of resistance to L. major in RAG(-/-) mice using T cells from naive donors was optimal when both CD4(+) and CD8(+) T cells were transferred. Primed CD8(+) T lymphocytes obtained from C57BL/6 mice during the acute stage of infection were able to mediate both pathology and immunity when transferred alone. The low dose, intradermal challenge model reveals that CD8(+) T cells play an essential role in both pathogenesis of and immunity to primary infection with L. major in the skin.
Adult Bone Marrow Transplantation after Stroke in Adult Rats (2001)

We transplanted adult whole bone marrow prelabeled with bromodeoxyuridine (BrdU) into the ischemic boundary zone of the adult rat brain at 1 day after 2 h of middle cerebral artery occlusion (MCAo). Approximately 3.3% of 10(6) transplanted bone marrow cells were BrdU reactive at 14 days after MCAo. BrdU-reactive cells expressed neuronal and astrocytic proteins, neuronal nuclei protein (NeuN, 1%), and glial fibrillary acidic protein (GFAP, 5%) immunoreactivities, respectively. In addition, bone marrow transplantation promoted proliferation of ependymal and subependymal cells, identified by nestin (a neuroepithelial stem cell marker), within the ventricular zone and subventricular zone (VZ/SVZ). These data suggest that intracerebral transplantation of bone marrow could potentially be used to induce plasticity in ischemic brain.
Dialogical Models of Explanation. (2007)

This paper takes on the task of providing a formal system of dialogue CE in which the speech acts of requesting and pro-viding an explanation are represented as dialogue moves in the system. CE has opening rules, locution rules, dialogue rules, success rules and closing rules. The system is meant to be simple and basic, to provide a platform for develop-ing more specialized formal dialogue systems of explanation used for specific purposes. The dialogical theory of explana-tion postulates that an explanation is a dialogue between two parties, one of whom asks a question requesting understand-ing of something which he or she claims not to understand, while the other offers a response that claims to convey the requested understanding to the party asking the question. In the last half of the twentieth century, the dominant model of explanation was the covering law (deductive-nomological) model associated with Hempel (1965), its chief advocate. This model took an explanation to be a de-ductive inference from a set of facts called initial conditions and a set of general rules to a proposition to be explained. It would have been anathema to the analytical philosophers who accepted this model to suggest that an explanation should be thought of as a dialogue between two parties. Times have changed. Much recent work in AI has been based the dialogue model of explanation. Cawsey’s work (1992) on computational generation of explanatory dia-logue used an interactive or dialogue approach, and Moore’s dialogue-based analysis of explanation for advice-giving in expert systems (1995) can also be cited. According to Moore (1995, p. 1) explanation is “an inherently incremental and interactive process ” that requires a dialogue between an ex-planation presenter who is trying to explain something and a questioner who has asked for an explanation. The dialog-ical model of explanation has also been advocated and de-veloped by Schank and his colleagues in cognitive science
Darwin Oval: Field of Dreams, Battleground for Rights. Australian Rules Football in Darwin, 1916-1942 (2007)

While the role of sport in developing and sustaining a sense of community is often acknowledged, it has a central role in the social history presented in this article. More than just a sports ground, the Darwin town oval serves as a stage to observe the evolution of Darwin society. Australian Rules football became the battleground for the struggle for greater rights for Darwin's non-European community which was, until 1916, largely excluded from the town's sport. In the period 1926-1939 Australian rules was continually disrupted by issues pertaining to 'colour'. Much of this hitherto poorly-documented history is retained in the 'social memory' of the community and in personal records. The oral history project discussed here provides a window to this contentious period of Darwin's social history lying at the heart of Darwin's reputation as a multi-racial city.
Expression and significance of Hsp70,Fas and FasL in breast cancer (2005)

Objective To evaluate the altered expression of Hsp70,Fas and FasL in breast cancer and their role in the occurrence and progression of breast cancer.Methods The expression of Hsp70,Fas and FasL was analyzed by immunohistochemistry (IHC) and Western blot in 30 cases of breast cancer.The DNA index (DI) and apoptosis index (AI) of breast cancer cells were analyzed by the flow cytometry (FCM).Results The rates of expression of Hsp70,Fas and FasL in the breast carcinoma tissue and the surrounding non-cancerous tissue were 93.3%,60.0%;53.3%,96.7%;93.3%,63.3% respectively. The difference between the breast carcinoma tissue and the surrounding non-cancerous tissue was significant. The level of expression of Fas was low in breast carcinoma tissue, nevertheless,it was very high in the surrounding non-cancerous tissue.The levels of expression of Hsp70 and FasL were high in breast carcinoma tissue,while they were low in the surrounding non-cancerous tissue.The DI of breast carcinoma tissue and the surrounding non-cancerous tissue was 1.29±0.16 and 0.99±0.44 respectively(t=9.974,P=0.000);the AI was 7.23±0.55 and 9.99±0.52 respectively(t=11.56,P=~0.000 );the differences were statistically significant.Conclusion The level of expression of Fas is low in breast cancer,while that of Hsp70 and FasL is high.The degree of apoptosis in breast cancer is significantly lower than that in the surrounding non-cancerous tissue. The down-regulation of Fas and the up-regulation of Hsp70 and FasL may facilitate the progression of breast cancer.
Gold-nanoparticle/organic linker films: self-assembly, electronic and structural characterisation, composition and vapour sensitivity (2003)

Gold-nanoparticle/organic films were prepared via layer-by-layer self-assembly using dodecylamine-stabilised Au-nanoparticles and poly(propyleneimine) (PPI) dendrimers of generation one to five (G1-G5) or hexadecanedithiol (HDT) as linker compounds. TEM and FE-SEM images revealed that the bulk of the films consisted of nanoparticles with diameters of about 4 nm. XPS was used to study the chemical composition of the films. The C 1s and N 1s signals of an AuPPI-G4 film were interpreted qualitatively according to the dendrimer structure. The absence of the nitrogen signal in case of an AuHDT film indicated that the dodecylamine ligands were quantitatively exchanged during film assembly. About 76% of the sulfur atoms were bound to the nanoparticles. the remainder being present as free thiol (S H) groups. All films displayed linear current voltage characteristics and Arrhenius-type activation of charge transport. The conductivities of the AuPPI films decreased exponentially over approximately two orders of magnitude (6.8 x 10(-2) to 1.0 x 10(-3) ohms(-1) cm(-1)) with a five-fold increase of the dendrimer generation number. Dosing the films with solvent vapours caused their resistances to increase. Using different solvent vapours demonstrated that the sensitivity of this response was determined by the solubility properties of the linker compounds. Microgravimetric measurements showed that absorption of analyte was consistent with a Langmuir adsorption model. These measurements also revealed a linear correlation between the electrical response (deltaR/Rini) and the concentration of absorbed analyte. The absorption of d4-methanol from a saturated vapour atmosphere was studied by neutron reflectometry with an AuPPI-G4 film. This measurement indicated condensation of methanol on top of the film and a uniform distribution of the analyte across the film thickness.
Prediction and explanation in social systems (2017)

Historically, social scientists have sought out explanations of human and social phenomena that provide interpretable causal mechanisms, while often ignoring their predictive accuracy. We argue that the increasingly computational nature of social science is beginning to reverse this traditional bias against prediction; however, it has also highlighted three important issues that require resolution. First, current practices for evaluating predictions must be better standardized. Second, theoretical limits to predictive accuracy in complex social systems must be better characterized, thereby setting expectations for what can be predicted or explained. Third, predictive accuracy and interpretability must be recognized as complements, not substitutes, when evaluating explanations. Resolving these three issues will lead to better, more replicable, and more useful social science.