Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Wnt Activity and Cell Physiology by Butyrate in LT97 Microadenoma Cells

Dietary fiber intake is linked to a reduced risk of colon cancer. This effect may in part be due to butyrate, the fermentation product of fiber in the colon. Butyrate is a short-chain fatty acid that acts as a histone deacetylase inhibitor (HDACi). Butyrate induces apoptosis and represses clonal growth of colorectal cancer (CRC) cells, in a manner dependent upon the hyperactivation of Wnt /beta-catenin signaling. While fiber has been linked to CRC prevention, in vitro studies on the action of butyrate have used CRC cell lines, instead of cells representative of earlier stages of colonic neoplasia, which are the likely target of butyrate-mediated preventive activity. The LT97 cell line is derived from a microadenoma, the earliest stage of colonic neoplasia from which cells can be isolated. We characterized LT97 cells with respect to effects of butyrate on Wnt signaling and apoptosis, and we determined whether modulation of CREB binding protein (CBP)/p300 activity influences the ability of butyrate to induce Wnt activity and apoptosis. We report that in LT97 cells, butyrate induces apoptosis, strongly upregulates Wnt signaling, and the upregulation of Wnt signaling is dependent upon CBP/p300 activity. In addition, findings from overexpression experiments suggest differences between CBP and p300 in their ability to influence Wnt signaling in LT97 cells; p300, but not CBP, stimulates basal Wnt activity. We also evaluated differences in gene expression between early stage LT97 cells and late stage metastatic SW620 CRC cells that exhibit markedly different cellular phenotypes. The comparative gene expression analyses revealed differences that may impact neoplastic progression and the sensitivity to the effects of butyrate. The findings have implications for the prevention of CRC by fiber/butyrate.
Energy-efficient instruction set synthesis for application-specific processors

Several techniques have been proposed to enhance the energy-efficiency of ASIPs (Application-Specific Instruction set Processors). While those techniques can reduce the energy consumption with a minimal change in the instruction set (IS), they fail to exploit the opportunity of designing the entire IS from the energy-efficiency perspective. In this paper, we present an energy-efficient IS synthesis technique that can comprehensively reduce the energy-delay product (EDP) of ASIPs through optimal instruction encoding, considering both the instruction bitwidth and the dynamic instruction count. Experimental results with a typical embedded RISC processor show that our technique can generate application-specific IS's that are up to 40% more energy-efficient over the native IS for several application benchmarks.
Validity of 24-h physical activity recall: physical activity measurement survey.

PURPOSE The primary purpose of this study was to evaluate the validity of an interviewer-administered, 24-h physical activity recall (PAR) compared with that of the SenseWear Armband (SWA) for estimation of energy expenditure (EE) and moderate-to-vigorous physical activity (MVPA) in a representative sample of adults. A secondary goal was to compare measurement errors for various demographic subgroups (gender, age, and weight status). METHODS A sample of 1347 adults (20-71 yr, 786 females) wore an SWA for a single day and then completed a PAR, recalling the previous day's physical activity. The participants each performed two trials on two randomly selected days across a 2-yr time span. The EE and MVPA values for each participant were averaged across the 2 d. Group-level and individual-level agreement were evaluated using 95% equivalence testing and mean absolute percent error, respectively. Results were further examined for subgroups by gender, age, and body mass index. RESULTS The PAR yielded equivalent estimates of EE (compared with those in the SWA) for almost all demographic subgroups, but none of the comparisons for MVPA were equivalent. Smaller mean absolute percent error values were observed for EE (ranges from 10.3% to 15.0%) than those for MVPA (ranges from 68.6% to 269.5%) across all comparisons. The PAR yielded underestimates of MVPA for younger, less obese people but overestimates for older, more obese people. CONCLUSIONS For EE measurement, the PAR demonstrated good agreement relative to the SWA. However, the use of PAR may result in biased estimates of MVPA both at the group and individual level in adults.
Direct Liquid Cooling Method Verified With an Axial-Flux Permanent-Magnet Traction Machine Prototype

Efficient cooling is needed, for example, in traction motors which face regularly high torque peaks and generate high stator Joule losses. This paper studies the feasibility of the direct liquid cooling in the thermal management of a low-power low-voltage permanent-magnet machine. A tooth-coil axial-flux permanent-magnet double-stator-single-rotor test machine was first equipped with indirect liquid cooling using water cooling jackets and then with direct winding cooling. The winding material used is a hybrid conductor comprising a stainless steel coolant conduit tightly wrapped with stranded Litz wire. The performance of the motor is examined at various power levels using oil or water as the cooling fluid. The results confirm that the proposed direct cooling method is practical also in small machines, and furthermore, it offers significant improvements in the machine thermal management, especially, in cases where stator Joule losses dominate.
Document clustering using a graph covering with pseudostable sets

In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organisation. In this paper we present a new graph theoretical approach to document clustering and its application on a real-world data set. We will show that the well-known graph partition to stable sets or cliques can be generalized to pseudostable sets or pseudocliques. This allows to make a soft clustering as well as a hard clustering. We will present an integer linear programming and a greedy approach for this NP-complete problem and discuss some results on random instances and some real world data for different similarity measures.
Ocean fronts drive marine fishery production and biogeochemical cycling

Significance Fronts in the ocean act as oases in a fluid desert that are not fully accounted for in climate or fisheries model projections. Fronts act to increase production by channeling nutrients through multiple trophic levels, including commercially important fishes and marine mammals, and enhance carbon export to the deep ocean. Fronts consequently have immense effects on the ocean, from base of the food chain up through the dinner table and mediation of global climate change. Here we show how fronts can be incorporated into current models, using a technique from fluid dynamics to improve both climate and fisheries models. Long-term changes in nutrient supply and primary production reportedly foreshadow substantial declines in global marine fishery production. These declines combined with current overfishing, habitat degradation, and pollution paint a grim picture for the future of marine fisheries and ecosystems. However, current models forecasting such declines do not account for the effects of ocean fronts as biogeochemical hotspots. Here we apply a fundamental technique from fluid dynamics to an ecosystem model to show how fronts increase total ecosystem biomass, explain fishery production, cause regime shifts, and contribute significantly to global biogeochemical budgets by channeling nutrients through alternate trophic pathways. We then illustrate how ocean fronts affect fishery abundance and yield, using long-term records of anchovy–sardine regimes and salmon abundances in the California Current. These results elucidate the fundamental importance of biophysical coupling as a driver of bottom–up vs. top–down regulation and high productivity in marine ecosystems.
Dynamic common sub-expression elimination during scheduling in high-level synthesis

We introduce a new approach, "Dynamic Common Sub-expression Elimination (CSE)", that dynamically eliminates common sub-expressions based on new opportunities created during scheduling of control-intensive designs. Classical CSE techniques fail to eliminate several common sub-expressions in control-intensive designs due to the presence of a complex mix of control and data-flow. Aggressive speculative code motions employed to schedule control-intensive designs often re-order, speculate and duplicate operations, hence changing the control flow between the operations with common sub-expressions. This leads to new opportunities for applying CSE dynamically. We have implemented dynamic CSE in a high-level synthesis framework called Spark and present results for experiments performed using various combinations of CSE and dynamic CSE. The benchmarks used consist of four functional blocks derived from two moderately complex industrial-strength applications, namely, MPEG-1 and the GIMP image processing tool. Our dynamic CSE techniques result in improvements of up to 22% in the controller size and up to 31% in performance; easily surpassing the improvements obtained by the traditional CSE approach. We also observe an unexpected (and significant) reduction in the number of registers using our approach.
A Novel Efficient Remote Data Possession Checking Protocol in Cloud Storage

As an important application in cloud computing, cloud storage offers user scalable, flexible, and high-quality data storage and computation services. A growing number of data owners choose to outsource data files to the cloud. Because cloud storage servers are not fully trustworthy, data owners need dependable means to check the possession for their files outsourced to remote cloud servers. To address this crucial problem, some remote data possession checking (RDPC) protocols have been presented. But many existing schemes have vulnerabilities in efficiency or data dynamics. In this paper, we provide a new efficient RDPC protocol based on homomorphic hash function. The new scheme is provably secure against forgery attack, replace attack, and replay attack based on a typical security model. To support data dynamics, an operation record table (ORT) is introduced to track operations on file blocks. We further give a new optimized implementation for the ORT, which makes the cost of accessing ORT nearly constant. Moreover, we make the comprehensive performance analysis, which shows that our scheme has advantages in computation and communication costs. Prototype implementation and experiments exhibit that the scheme is feasible for real applications.
Endothelial progenitor cells and mesenchymal stem cells seeded onto beta-TCP granules enhance early vascularization and bone healing in a critical-sized bone defect in rats.

UNLABELLED QUESTION/AIM: Lack of vessels indicates an insufficient nutritional supply of a bone graft and may limit the recruitment of bone-forming cells. Our aim was to evaluate the influence of endothelial progenitor cells (EPCs) alone or in combination with mesenchymal stem cells (MSCs) on early vascularization and bone healing in critical-sized defect (CSD) in vivo. METHODS MSCs from human bone marrow and EPCs from buffy coat were used. A femoral CSD in adult athymic rats was created and stabilized by an external fixateur. The remaining defects were filled with fibronectin-coated beta-tricalcium phosphate (beta-TCP) granules, EPCs seeded on beta-TCP, MSCs seeded on beta-TCP, coculture of EPCs/MSCs seeded on beta-TCP, or autologous bone. Vascularization and bone formation were determined by immunohistology, microCT analysis, and biomechanical testing after 1, 4, and 8 weeks. RESULTS Early vascularization was significantly improved in EPC/MSC group or EPC group, respectively. At 4 weeks bone formation increased significantly when the CSD was treated with coculture of MSCs/EPCs. Eight weeks after transplantation CSD showed significantly more bony bridgings and significantly increased ultimate load in the EPC/MSC group compared to the other groups. DISCUSSION This cell approach suggests that there is a synergistic effect and that the initial stage of neovascularization by EPCs is considered to be crucial for complete bone regeneration in the late phase.
ISOLATION, IDENTIFICATION AND RESISTANT CHARACTERIZATION OF DYE-ADAPTED BACTERIA FROM TIRUPUR TEXTILE EFFLUENT

The textile Industries in Tirupur releases million litres of untreated effluents into the Noyyal River. The discharge of coloured compound into water bodies affect photosynthesis of aquatic plants and these dyes are carcinogenic in nature which is dangerous to human being. This study confirms that Noyyal River Textile effluents are a major source of aquatic pollution in Tirupur with high amount of chemical oxygen demand (COD), biological oxygen demand (BOD) and low amount of DO. These Textile effluents provide an environment for growth of various kinds of microorganisms with capability to adapt and degrade the dyes along with multiple resistant activities. Hence in the present study, the bacterial strains were isolated from textile effluent of Tirupur Noyyal River and it predominately contains Pseudomonas sp. For species identification, Pseudomonas like organisms creates lot of problems when identified with the help of morphological and biochemical characters. So, sequencing of 16S rRNA region is a suitable technique for species identification. Therefore Nucleotide sequences of Pseudomonas isolates were confirmed by 16S rRNA sequencing with universal bacterial primers (16S-UP-F, UP-R) and the sequences showed 100% similarity with the already established species P.aeruginosa which was deposited in GENBANK. The deposited 16S r DNA sequence of P.aeruginosa was given the accession number KU041528. The phylogenetic tree was constructed based on 16S r DNA sequence of P.aeruginosa. Multiple resistant activities of P. aeruginosa was detected through protease and Phospholipase test and WORLD JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES SJIF Impact Factor 6.647 Volume 6, Issue 9, 1111-1125 Research Article ISSN 2278 – 4357 Article Received on 01 July 2017, Revised on 21 July 2017, Accepted on 11 August 2017 DOI: 10.20959/wjpps20179-9973 *Corresponding Author
Isoform specificity of progesterone receptor antibodies

Progesterone receptors (PR) are prognostic and predictive biomarkers in hormone‐dependent cancers. Two main PR isoforms have been described, PRB and PRA, that differ only in that PRB has 164 extra N‐terminal amino acids. It has been reported that several antibodies empirically exclusively recognize PRA in formalin‐fixed paraffin‐embedded (FFPE) tissues. To confirm these findings, we used human breast cancer xenograft models, T47D‐YA and ‐YB cells expressing PRA or PRB, respectively, MDA‐MB‐231 cells modified to synthesize PRB, and MDA‐MB‐231/iPRAB cells which can bi‐inducibly express either PRA or PRB. Cells were injected into immunocompromised mice to generate tumours exclusively expressing PRA or PRB. PR isoform expression was verified using immunoblots. FFPE samples from the same tumours were studied by immunohistochemistry using H‐190, clone 636, clone 16, and Ab‐6 anti‐PR antibodies, the latter exclusively recognizing PRB. Except for Ab‐6, all antibodies displayed a similar staining pattern. Our results indicate that clones 16, 636, and the H‐190 antibody recognize both PR isoforms. They point to the need for more stringency in evaluating the true specificity of purported PRA‐specific antibodies as the PRA/PRB ratio may have prognostic and predictive value in breast cancer.
Antigen depot is not required for alum adjuvanticity

Alum adjuvants have been in continuous clinical use for more than 80 yr. While the prevailing theory has been that depot formation and the associated slow release of antigen and/or inflammation are responsible for alum enhancement of antigen presentation and subsequent T‐ and B‐cell responses, this has never been formally proven. To examine antigen persistence, we used the chimeric fluorescent protein EαGFP, which allows assessment of antigen presentation in situ, using the Y‐Ae antibody. We demonstrate that alum and/or CpG adjuvants induced similar uptake of antigen, and in all cases, GFP signal did not persist beyond 24 h in draining lymph node antigen‐presenting cells. Antigen presentation was first detectable on B cells within 6‐12 h of antigen administration, followed by conventional dendritic cells (DCs) at 12‐24 h, then finally plasmacytoid DCs at 48 h or later. Again, alum and/or CpG adjuvants did not have an effect on the magnitude or sequence of this response; furthermore, they induced similar antigen‐specific T‐cell activation in vivo. Notably, removal of the injection site and associated alum depot, as early as 2 h after administration, had no appreciable effect on antigen‐specific T‐and B‐cell responses. This study clearly rules out a role for depot formation in alum adjuvant activity. —Hutchison, S. , Benson, R. A. , Gibson, V. B. , Pollock, A. H. , Garside, P., Brewer, J. M. Antigen depot is not required for alum adjuvanticity. FASEB J. 26, 1272‐1279 (2012). www.fasebj. org
Convergent evolution of neural systems in ctenophores

Neurons are defined as polarized secretory cells specializing in directional propagation of electrical signals leading to the release of extracellular messengers – features that enable them to transmit information, primarily chemical in nature, beyond their immediate neighbors without affecting all intervening cells en route. Multiple origins of neurons and synapses from different classes of ancestral secretory cells might have occurred more than once during ~600 million years of animal evolution with independent events of nervous system centralization from a common bilaterian/cnidarian ancestor without the bona fide central nervous system. Ctenophores, or comb jellies, represent an example of extensive parallel evolution in neural systems. First, recent genome analyses place ctenophores as a sister group to other animals. Second, ctenophores have a smaller complement of pan-animal genes controlling canonical neurogenic, synaptic, muscle and immune systems, and developmental pathways than most other metazoans. However, comb jellies are carnivorous marine animals with a complex neuromuscular organization and sophisticated patterns of behavior. To sustain these functions, they have evolved a number of unique molecular innovations supporting the hypothesis of massive homoplasies in the organization of integrative and locomotory systems. Third, many bilaterian/cnidarian neuron-specific genes and ‘classical’ neurotransmitter pathways are either absent or, if present, not expressed in ctenophore neurons (e.g. the bilaterian/cnidarian neurotransmitter, γ-amino butyric acid or GABA, is localized in muscles and presumed bilaterian neuron-specific RNA-binding protein Elav is found in non-neuronal cells). Finally, metabolomic and pharmacological data failed to detect either the presence or any physiological action of serotonin, dopamine, noradrenaline, adrenaline, octopamine, acetylcholine or histamine – consistent with the hypothesis that ctenophore neural systems evolved independently from those in other animals. Glutamate and a diverse range of secretory peptides are first candidates for ctenophore neurotransmitters. Nevertheless, it is expected that other classes of signal and neurogenic molecules would be discovered in ctenophores as the next step to decipher one of the most distinct types of neural organization in the animal kingdom.
Toward Policy-Based Dynamic Context-Aware Adaptation Architecture for Web Service Composition

Dynamic service composition techniques are beneficial for better design, implementation, and deployment of distributed applications. These techniques address the complexity that comes with the significant growth of the number of web services on the Internet and their constantly changing adaptation requirements. However, the previous approaches do not provide a mechanism for a flexible adaptation or re-composition when availability is not the only requirement. There are other business-level or service-level requirement specifications that can be introduced at any time by business or system administrators. These requirements could be business or quality rules, which may adversely affect web service composition (WSC) without changing the definitions of the Web Services' specification (i.e., WSDL, SAWSDL) nor their availability. In this paper we define a new context-oriented graph planning policy-based architecture for dynamic web service composition, and a prototype implementation.
Modulation of the heteromeric Kir4.1–Kir5.1 channel by multiple neurotransmitters via Gαq‐coupled receptors

The heteromeric Kir4.1–Kir5.1 channel is a candidate sensing molecule for central CO2 chemoreception. Since central CO2 chemoreception is subject to neural modulations, we performed studies to test the hypothesis that the Kir4.1–Kir5.1 channel is modulated by the neurotransmitters critical for respiratory control, including serotonin (5‐HT), substance‐P (SP), and thyrotropin releasing hormone (TRH). The heteromeric Kir4.1–Kir5.1 channel was strongly inhibited by SP, TRH, and 5‐HT when expressed in Xenopus oocytes, whereas these neurotransmitters had no effect on the homomeric Kir4.1 channel. Such an inhibition was dose‐dependent and relied on specific Gαq‐protein‐coupled receptors and protein kinase C (PKC). No direct interaction of the channel with G‐proteins was found. Channel sensitivity to CO2/pH was not compromised with the inhibition by these neurotransmitters, as the channel remained to be inhibited by acidic pH following an exposure to the neurotransmitters. The firing rate of CO2‐sensitive brainstem neurons cultured in microelectrode arrays was augmented by SP or a 5‐HT2A receptor agonist, which was blocked by PKC inhibitors suggesting that PKC underscores the inhibitory effect of SP and 5‐HT in cultured brainstem neurons as well. Immunostaining showed that both Kir4.1 and Kir5.1 proteins were co‐localized in the cultured brainstem neurons. These results therefore indicate that the heteromeric Kir4.1–Kir5.1 channel is modulated by the neurotransmitters critical for respiratory control, suggesting a novel neuromodulatory mechanism for the chemosensitivity of brainstem neurons to elevated PCO2 and acidic pH. J. Cell. Physiol. 214:84–95, 2008. © 2007 Wiley‐Liss, Inc.