gebhart/patrepeval huggingface dataset:
JNK Activity Is Essential for <i>Atf4</i> Expression and Late-Stage Osteoblast Differentiation (2008)

Osteoblasts differentiate from mesodermal progenitors and play a pivotal role in bone formation and mineralization. Several transcription factors including runt-related transcription factor 2 (RUNX2), Osterix (OSX), and activating transcription factor4 (ATF4) are known to be crucial for the process, whereas the upstream signal transduction controlling the osteoblast differentiation sequence is largely unknown. Here, we explored the role of c-jun N-terminal kinase (JNK) in osteoblast differentiation using in vitro differentiation models of primary osteoblasts and MC3T3-E1 cells with ascorbic acid/beta-glycerophosphate treatment. Terminal osteoblast differentiation, represented by matrix mineralization, was significantly inhibited by the inactivation of JNK with its specific inhibitor and exogenous overexpression of MKP-M (MAP kinase phosphatase isolated from macrophages), which preferentially inactivates JNK. Conversely, enhanced mineral deposition was observed by inducible overexpression of p54(JNK2), whereas it was not observed by the overexpression of p46(JNK1) or p46(JNK2), indicating a distinct enhancing role of p54(JNK2) in osteoblast differentiation. Inactivation of JNK significantly inhibited late-stage molecular events of osteoblast differentiation, including gene expression of osteocalcin (Ocn) and bone sialoprotein (Bsp). In contrast, earlier differentiation events including alkaline phosphatase (ALP) activation and osteopontin (Opn) expression were not inhibited by JNK inactivation. Although the expression levels of two transcription factor genes, Runx2 and Osx, were not significantly affected by JNK inactivation, induction of Atf4 mRNA during osteoblast differentiation was significantly inhibited. Taken together, these data indicate that JNK activity is specifically required for the late-stage differentiation events of osteoblasts.
Animating wrinkles on clothes (1999)

This paper describes a method to simulate realistic wrinkles on clothes without fine mesh and large computational overheads. Cloth has very little in-plane deformations, as most of the deformations come from buckling. This can be looked at as area conservation property of cloth. The area conservation formulation of the method modulates the user defined wrinkle pattern, based on deformation of individual triangle. The methodology facilitates use of small in-plane deformation stiffnesses and a coarse mesh for the numerical simulation, this makes cloth simulation fast and robust. Moreover, the ability to design wrinkles (even on generalized deformable models) makes this method versatile for synthetic image generation. The method inspired from cloth wrinkling problem, being geometric in nature, can be extended to other wrinkling phenomena.
Research and the Long Tail: A Large-Scale Citation Analysis (2009)

Where sales used to be limited to a few best-selling products as characterized by the Pareto principle, the Internet has transformed the business environment by enabling a long tail market for "non-hit" products. This study views research articles as products of the research community and equates citations with product sales to investigate the long tail effects within research. First, we determine if the long tail phenomenon is present in research. Second, we study changes in citation patterns prior to, during, and after prevalent use of the Internet in research. We gathered and analyzed 90,000+ articles published over 37 years. Results indicate that the long tail is beginning to work in both information behavior and research at large, albeit differently from commerce. Our research reveals convincing evidence that researchers, consciously or not, are starting to cite more "non-hit" articles. These findings signify a constructive and fundamental shift in our research practices.
Widespread expression of an exogenous gene in the eye after intravenous administration. (2002)

Widespread expression of an exogenous gene throughout the retina pigmented epithelium or other structures of the eye is possible with a noninvasive intravenous administration of a nonviral plasmid that is reformulated with gene-targeting technology. The cellular specificity of gene expression in the eye can be regulated with the use of cell-specific gene promoters.
Project Monitoring Methods Exploratory Case Analysis: Industry Responses (2009)

In project type product production the need for feedback creates the task of collecting field progress measurements. This task may be completed by experienced engineers or assigned to interns and field hands. Whichever the case, the process of field production feedback is inherently inaccurate and may lead to unforeseen project events. It is possible that other industry divisions have similar issues and used solutions applicable to construction. This paper summarizes a case-based analysis of responses from a focus group. The conclusions drawn from the focus group are then further defined through a questionnaire survey. A majority (55% to 75% @95% confidence level (CL)) of construction professionals (i.e., salaried) do not use software tools beyond Microsoft office, which indicates software tools (initial/reorganization/training/support) costs are more than the perceived benefits provided. The Programmable Logic Controller (PLC) system collects measurements from sensors and links these measurements to an activity's programmable recipe formula and monitoring report. While, this system may not be applicable to most construction sites, components and concepts may be.
Ultrawideband Vivaldi Antenna for DVB-T, WLAN, and WiMAX Applications (2014)

Compact Vivaldi patch antenna with a parasitic meander line is presented in this paper. A PIN diode switch is used to connect and disconnect ultrahigh frequency band (UHF) with ultrawide bandwidth (UWB). The operating frequencies can be switched among different services, depending on the switching states (ON/OFF) to add the lower band when required. This antenna is suitable for portable DVB-T which extended from 450 MHz to 850 MHz receiver applications and the WLAN (Wireless Local Area Network) IEEE 802.11b,g (5.1–5.8) GHz frequency bands and WiMAX band (3.3–3.8) GHz. The measured reflection coefficient of the proposed antenna is compared with the simulated one; good agreement is observed. Also, simulated radiation pattern of the antenna is presented. All simulations are carried out using the EM commercial simulator, high frequency structure simulator (HFSS) ver.13.
Prevalence of gallbladder disease in American Indian populations: Findings from the Strong Heart Study (2002)

American Indians are believed to be at high risk of gallbladder disease (GBD), but there has been no systematic evaluation of its prevalence among diverse groups of American Indians. Therefore, we determined the prevalence of GBD and associated risk factors among specified American Indian populations using ultrasonography of the gallbladder and standardized diagnostic criteria. Enrolled members, aged 47 years and older, of 13 American Indian tribes or communities in Arizona, Oklahoma, and South and North Dakota who participated in the Strong Heart Study were analyzed. GBD was the sum of gallstones (determined by ultrasound examination) and cholecystectomy (determined by ultrasound and self-report). The proportion of American Indian heritage was based on the heritage of the grandparents of participants. GBD prevalence was determined among 3,296 participants at the 3 sites. Among women, 17.8% had gallstones, and 46.3% had evidence of a cholecystectomy, for a total of 64.1% with GBD. Among men, 17.4% had gallstones, and 12.1% had evidence of a cholecystectomy, for a total of 29.5% with GBD. When figures were adjusted for age and Indian heritage, there was no significant difference in GBD prevalence across the 3 geographical areas. In multivariate logistic regression analysis, age, American Indian heritage, and waist circumference were associated with GBD among men, and age, American Indian heritage, diabetes, and parity were associated with GBD among women. Body mass index was not independently associated with GBD in either sex. In conclusion, GBD was found in epidemic proportions in diverse American Indian populations.
Visual interestingness in image sequences (2013)

Interestingness is said to be the power of attracting or holding one's attention (because something is unusual or exciting, etc.). We, as humans, have the great capacity to direct our visual attention and judge the interestingness of a scene. Consider for example the image sequence in the figure on the right. The spider in front of the camera or the snow on the lens are examples of events that deviate from the context since they violate the expectations, and therefore are considered interesting. On the other hand, weather changes or a camera shift, do not raise human attention considerably, even though large regions of the image are influenced. In this work we firstly investigate what humans consider as "interesting" in image sequences. Secondly we propose a computer vision algorithm to automatically spot these interesting events. To this end, we integrate multiple cues inspired by cognitive concepts and discuss why and to what extent the automatic discovery of visual interestingness is possible.
ATP Depletion Increases Tyrosine Phosphorylation of β-Catenin and Plakoglobin in Renal Tubular Cells (1999)

This study examines the hypothesis that the loss of integrity of the junctional complex induced by ATP depletion is related to alterations in tyrosine phosphorylation of the adherens junction proteins beta-catenin and plakoglobin. ATP depletion of cultured mouse proximal tubular (MPT) cells induces a marked increase in tyrosine phosphorylation of both beta-catenin and plakoglobin. The tyrosine phosphatase inhibitor vanadate has the same effect in ATP-replete (control) monolayers, whereas genistein, a tyrosine kinase inhibitor, reduces phosphorylation of both proteins in ATP-replete monolayers and prevents the hyperphosphorylation of these proteins with ATP depletion. This study also demonstrates that the fall in the transepithelial resistance of MPT monolayers induced by ATP depletion can be reproduced by treatment of ATP-replete monolayers with vanadate, whereas genistein substantially ameliorates the fall in transepithelial resistance induced by ATP depletion. Also, using immunofluorescence microscopy it was demonstrated that ATP depletion results in a marked diminution of E-cadherin staining in the basolateral membrane of MPT cells. Vanadate mimics this effect of ATP depletion, whereas genistein ameliorates the reduction in the intensity of E-cadherin staining induced by ATP depletion. Because it is has been well established that hyperphosphorylation of the catenins leads to dissociation of the adherens junction and to dysfunction of the junctional complex, it is proposed that the increase in tyrosine phosphorylation of catenins observed in MPT cells during ATP depletion contributes to the loss of function of the junctional complex associated with sublethal injury.
Well-defined diblock brush polymer–drug conjugates for sustained delivery of paclitaxel (2015)

Using the 3(rd) generation Grubbs' catalyst as the initiator, diblock brush polymer drug conjugates (BPDCs) were synthesized by sequential ring-opening metathesis polymerization (ROMP) of a hydrophilic poly(ethylene glycol) (PEG)-based norbornene (NB)-functionalized macromonomer and a hydrophobic paclitaxel (PTXL)-based NB-functionalized monomer. These amphiphilic diblock BPDCs had well-defined structures, with narrow molecular weight distributions (Mw/Mn = 1.10-1.16). They self-assembled into multi-molecular nanostructures in aqueous solutions. Although the PTXL moieties were connected to the backbone with cycloacetal-based conjugation linkages, the cleavage of these linkages from the assemblies of diblock BPDCs was relatively slow and exhibited limited acid-sensitivity, indicating a significant influence of the macromolecular structure and assembly of BPDCs on their drug release behaviour. The cytotoxicity study not only showed that the diblock BPDCs are therapeutically effective against cancer cells, but also revealed a correlation between cytotoxicity and grafting structures of BPDCs. In summary, the results obtained in this work provide new insight into the structure-dependent properties of brush polymer-based drug delivery systems.
Mlc of <i>Thermus thermophilus</i> : a Glucose-Specific Regulator for a Glucose/Mannose ABC Transporter in the Absence of the Phosphotransferase System (2006)

We report the presence of Mlc in a thermophilic bacterium. Mlc is known as a global regulator of sugar metabolism in gram-negative enteric bacteria that is controlled by sequestration to a glucose-transporting EII(Glc) of the phosphotransferase system (PTS). Since thermophilic bacteria do not possess PTS, Mlc in Thermus thermophilus must be differently controlled. DNA sequence alignments between Mlc from T. thermophilus (Mlc(Tth)) and Mlc from E. coli (Mlc(Eco)) revealed that Mlc(Tth) conserved five residues of the glucose-binding motif of glucokinases. Here we show that Mlc(Tth) is not a glucokinase but is indeed able to bind glucose (K(D) = 20 microM), unlike Mlc(Eco). We found that mlc of T. thermophilus is the first gene within an operon encoding an ABC transporter for glucose and mannose, including a glucose/mannose-binding protein and two permeases. malK1, encoding the cognate ATP-hydrolyzing subunit, is located elsewhere on the chromosome. The system transports glucose at 70 degrees C with a K(m) of 0.15 microM and a V(max) of 4.22 nmol per min per ml at an optical density (OD) of 1. Mlc(Tth) negatively regulates itself and the entire glucose/mannose ABC transport system operon but not malK1, with glucose acting as an inducer. MalK1 is shared with the ABC transporter for trehalose, maltose, sucrose, and palatinose (TMSP). Mutants lacking malK1 do not transport either glucose or maltose. The TMSP transporter is also able to transport glucose with a K(m) of 1.4 microM and a V(max) of 7.6 nmol per min per ml at an OD of 1, but it does not transport mannose.
Altered Intestinal Absorption of L-Thyroxine Caused by Coffee (2008)

Coffee should be added to the list of interferers of T4 intestinal absorption, and T4 to the list of compounds whose absorption is affected by coffee.
Rapid determination of short‐chain fatty acids in colonic contents and faeces of humans and rats by acidified water‐extraction and direct‐injection gas chromatography (2005)

Short-chain fatty acids (SCFAs) have attracted much attention recently because of their positive physiological effects. In this work, a rapid and reliable gas chromatographic method for determination of eight SCFAs, in colonic and faecal samples from rats and humans has been developed and validated. The methodology involves extraction of the SCFAs in water before a direct injection procedure on a FFAP capillary column. A stock standard solution containing acetic acid, propionic acid, n-butyric acid, i-butyric acid, n-valeric acid, i-valeric acid, n-caproic acid and n-heptanoic acid was prepared and used. A high linearity (r2 > 0.9990), low quantification limit (2.38-30.14 microm) and high recovery for most acids were obtained. Acidification of faecal samples was found to be crucial for quantitative determination of the SCFAs, and adjustment of pH to 2-3 was regarded as necessary. Glass wool inserted in the glass liner of the injection port proved effective in preventing the contamination of the column by non-volatiles, and 12% formic acid reduced the ghost peak that appeared gradually after several injections. After validation, the methodology was applied on two faecal samples from rats fed diets containing different amount of dietary fibre and one faecal sample from human fed a normal diet to test the accuracy of the developed method.
Plasma-assisted etching mechanisms: The implications of reaction probability and halogen coverage (1985)

Evidence is presented which indicates that the way in which energetic ion bombardment accelerates the etching of Si in a fluorine environment is by a direct acceleration of the product formation step and not by damage-enhanced chemistry. The use of fluorine coverage to characterize the etching process is discussed in detail and the assumption that the etch rate of Si can be decoupled into a spontaneous and an ion-assisted contribution is questioned. Finally, examples of the influence of ion bombardment on Al(100)–Cl2, Cu(100)–Cl2 at 310 °C, and Nb–XeF2 are used to emphasize that some of the conclusions reached for the Si–XeF2 system are not generally applicable to all gas–solid combinations.
Antimicrobial effect of irrigant combinations within dentinal tubules (1998)

The aim of this study was to investigate sodium hypochlorite (with and without EDTA), chlorhexidine, and hydrogen peroxide in varying concentrations when used in sequence or in combination as endodontic irrigants. Sterile saline served as the control. Six standardized bovine incisor root specimens, which had been infected with Enterococcus faecalis (CG 110), were exposed to each solution. Following exposure to the test agents dentine samples were taken from within the lumina using ISO 023 to 035 burs. The dentine powder samples were incubated and the quantity of bacteria present assessed using spectrophotometry. All irrigant regimens were more effective than saline in killing bacteria. Chlorhexidine and sodium hypochlorite were similarly effective. At specific concentrations a synergistic effect was noted when mixtures of chlorhexidine and hydrogen peroxide were under test.
GaInAsP-InP distributed feedback waveguides for all-optical switching (2000)

All-optical switching characteristics of waveguide devices having a nonlinear distributed feedback structure are reported theoretically and experimentally. These devices were composed of a strip-loaded GaInAsP-InP waveguide and a Bragg reflector, which were suitable for optical integrated circuit. In the experiments, all-optical and gate operation and set-reset operation for two output ports were successfully demonstrated.
Melanin‐concentrating hormone receptor 1 antagonists for the treatment of depression and anxiety (2005)

Abstract Melanin‐concentrating hormone (MCH) is a cyclic, 19‐amino‐acid neuropeptide produced in the lateral hypothalamus. MCH is implicated in a number of physiological processes including feeding behavior, energy balance, reproductive function, memory, sleep‐wake regulation, and emotional states. Since the discoveries in the mid‐1990 s that MCH is an appetite stimulant in rodents and that KO mice lacking MCH become lean, together with the findings that MCH receptor 1 (MCH1R) is responsible for these functions, most research has been focused on the roles of the MCH system in feeding and energy homeostasis. It is now established that MCH plays a key role in controlling feeding and energy homeostasis via MCH1R, and some pharmaceutical companies have reported nonpeptidic MCH1R antagonists with diverse structural features in the treatment of obesity. Recently, emerging lines of evidence have indicated that MCH1R plays important roles not only in feeding and energy balance but also in regulation of emotion. Indeed, MCH1R is widely distributed in the regions associated with emotion, and MCH1R antagonists have been demonstrated to exhibit antidepressant and anxiolytic effects in various rodent models. This review describes recent advances in research to clarify the involvement of MCH in depression and anxiety. The paper will also discuss the potential value of MCH1R antagonists in the treatment of depressive and anxiety disorders. Drug Dev. Res. 65:278–290, 2005. © 2005 Wiley‐Liss, Inc.
ARTIMIS: natural dialogue meets rational agency (1997)

We present an effective generic communicating rational agent, ARTIMIS, and its application to cooperative spoken dialogue. ARTIMIS &apos; kernel is the implementation of a formal theory of interaction. This theory involves a set of generic axioms which models, in a homogeneous logical framework, principles of rational behaviour, communication, and cooperation. The theory is interpreted by a specifically designed reasoning engine. When applied to the context of natural dialogue, ARTIMIS includes specialised components for speech and natural language processing. 1
MiRNAs in cancer: Non-coding RNAs as appealing biomarkers for malignancy (2012)

It is estimated that up to 50% of all human proteincoding genes are regulated by miRNAs. This family of non-coding RNAs, with ∼1500 members reported up-to-date, can impact a variety of cellular processes including cellular proliferation, differentiation and apoptosis. It is not surprising that deregulated expression of selected miRNAs can thus promote cancer initiation and progression. Several miRNAs with oncogenic properties, termed oncomirs, as well as miRNAs with tumor suppressive capabilities have been identified in different malignancies and this list is growing at a rapid pace. MiRNA-based therapies are attractive partly due to the fact that these molecules can target multiple genes in different signaling pathways simultaneously. In addition to their therapeutic potential, miRNAs are released into the circulation and measurement of such species in plasma and serum samples highlights the possibility of leveraging these molecules as potential biomarkers for early cancer detection, prognostic assessment and evaluation of therapeutic response in cancer patients. In this issue of Cancer Biomarkers, Lodewijk et al. discuss differentially expressed miRNAs in subtypes of thyroid cancer: papillary, follicular, anaplastic and medullary thyroid carcinomas. A special interest is placed on the diagnostic potential of miRNAs in this malignancy. The current method utilized to characterize thyroid nodules consisting of fine needle aspiration biopsies is described. Unfortunately, 30% of such biopsies are inconclusive and a hemithyroidectomy is required. Their article thus delves into the potential usefulness of identifying amiRNA signature that would help avoid such a procedure and assist clinicians in discriminating between tumor and benign tissues as well as between tumor types. Similarly, Hogan et al. describe in this issue a need for the identification of novel biomarkers in the early detection of colorectal cancer (CRC). 5-year patient survival is over 90% when detected at an early stage compared with less than 10% survival for stage IV patients. While advantages exist with the currentmethods employed for CRC detection, sensitivity and specificity challenges are discussed and the diagnostic potential of miRNAs is assessed. MiRNA stability and their presence in body fluids including feces make them attractive molecules for the development of noninvasive detection methods for this malignancy. Much effort is also directed towards the identification of a circulating miRNA signature in glioblastoma multiforme (GBM), an aggressive type of brain tumor with dismal prognosis. In this issue, Odjele et al. review the progress made in recent years on identifying miRNAs that would assist clinicians in diagnosing this malignancy. MiRNA levels of miR-128 and miR342-3p vary significantly in blood samples of GBM patients when compared with healthy subjects and are thus emerging as early favorites in the search for a GBM-associated miRNA signature. The article also looks at studies recently undertaken in GBM cell and rodent models that showed promising results on the use