Miracle-dz/UniFAR-FTUs huggingface dataset:
Value of freedom to choose encoded by the human brain.

Humans and animals value the opportunity to choose by preferring alternatives that offer more rather than fewer choices. This preference for choice may arise not only from an increased probability of obtaining preferred outcomes but also from the freedom it provides. We used human neuroimaging to investigate the neural basis of the preference for choice as well as for the items that could be chosen. In each trial, participants chose between two options, a monetary amount option and a "choice option. " The latter consisted of a number that corresponded to the number of everyday items participants would subsequently be able to choose from. We found that the opportunity to choose from a larger number of items was equivalent to greater amounts of money, indicating that participants valued having more choice; moreover, participants varied in the degree to which they valued having the opportunity to choose, with some valuing it more than the increased probability of obtaining preferred items. Neural activations in the mid striatum increased with the value of the opportunity to choose. The same region also coded the value of the items. Conversely, activation in the dorsolateral striatum was not related to the value of the items but was elevated when participants were offered more choices, particularly in those participants who overvalued the opportunity to choose. These data suggest a functional dissociation of value representations within the striatum, with general representations in mid striatum and specific representations of the value of freedom provided by the opportunity to choose in dorsolateral striatum.
Abstract 1260: Analysis of death receptor 5 and caspase-8 expression in primary and metastatic head and neck squamous cell carcinoma and their prognostic impact

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC Death receptor 5 (DR5) and caspase-8 are major components in the extrinsic apoptotic pathway. The alterations of the expression of these proteins during the metastasis of head and neck squamous cell carcinoma (HNSCC) and their prognostic impact have not been reported. The present study analyzes the expression of DR5 and caspase-8 by immunohistochemistry (IHC) in primary and metastatic HNSCCs and their impact on patient survival. Tumor samples in this study included approximately 90 primary HNSCC with no evidence of metastasis and approximately 90 primary HNSCC and their matching lymph node metastasis. IHC analysis revealed a significant loss or downregulation of DR5 expression in primary tumors with metastasis [weight index (WI) = 221 ± 64.9 (mean ± SD), n = 92] and their matching lymph node metastasis (WI = 224 ± 71.6, n = 85) compared to primary tumors with no evidence of metastasis (WI = 250 ± 43.9, n = 94) (P < 0.01). A similar trend was also observed in caspase-8 expression although it is not statistically significant. Downregulation of caspase-8 and DR5 expression was significantly correlated with poorly differentiated tumors compared to moderately and well differentiated tumors (P < 0.05). Univariate analysis indicates that, in HNSCC with no metastasis, higher expression of caspase-8 significantly correlated with better disease-free survival and overall survival (P < 0.05 or 0.001) if mean value is used as a cutoff. However, in HNSCC with lymph node metastasis, higher caspase-8 expression significantly correlated with poorer disease-free survival and overall survival (< 0.05 or 0.01). Similar results were also generated when we combined both DR5 and caspase-8. Moreover, multivariable analysis indicates that in patients without lymph node metastasis, high caspase-8 is significantly associated with better survival after adjusting age and stage (P < 0.0001). Together, we suggest that both proteins may be involved in regulation of HNSCC metastasis. (G.C., D.M.S., F.R.K. and S-Y.S. are Georgia Cancer Coalition Distinguished Cancer Scholars. This study was supported by funds from the Georgia Cancer Coalition Distinguished Cancer Scholar and NIH Head and Neck SPORE P50 CA128613 awards) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1260.
Quantitative Lateral and Axial Flow Imaging with Optical Coherence Microscopy and Tomography References and Links

Optical coherence tomography (OCT) and optical coherence microscopy (OCM) allow the acquisition of quantitative three-dimensional axial flow by estimating the Doppler shift caused by moving scatter-ers. Measuring the velocity of red blood cells is currently the principal application of these methods. In many biological tissues, blood flow is often perpendicular to the optical axis, creating the need for a quantitative measurement of lateral flow. Previous work has shown that lateral flow can be measured from the Doppler bandwidth, albeit only for simplified optical systems. In this work, we present a generalized model to analyze the influence of relevant OCT/OCM system parameters such as light source spectrum, numerical aperture and beam geometry on the Doppler spectrum. Our analysis results in a general framework relating the mean and variance of the Doppler frequency to the axial and lateral flow velocity components. Based on this model, we present an optimized acquisition protocol and algorithm to reconstruct quantitative measurements of lateral and axial flow from the Doppler spectrum for any given OCT/OCM system. To validate this approach, Doppler spectrum analysis is employed to quantitatively measure flow in a capillary with both extended focus OCM and OCT. Optical coherence tomography-principles and applications, " Rep. Mobility and transverse flow visualization using phase variance contrast with spectral domain optical coherence tomography, " Opt. Speckle variance detection of microvasculature using swept-source optical coherence tomography, " Opt. In vivo volumetric imaging of vascular perfusion within human retina and choroids with optical micro-angiography, " Opt.ric angiography of cortical microvasculature with optical coherence tomography, " Opt. Extended focus high-speed swept source OCT with self-reconstructive illumination, " Opt. In vivo bidirectional color Doppler flow imaging of picoliter blood volumes using optical coherence tomography, " Opt. Optical Doppler tomographic imaging of fluid flow velocity in highly scattering media, " Opt. " Real-time measurement of in vitro flow by Fourier-domain color Doppler optical coherence tomography, " Opt. Resonant Doppler flow imaging and optical vivisection of retinal blood vessels, " Opt. Flow velocity estimation using joint spectral and time-domain optical coherence tomography, " Opt. Doppler optical micro-angiography for volumetric imaging of vascular perfusion in vivo, " Opt. Quantitative cerebral blood flow with optical coherence tomography, " Opt. retinal blood flow measurement with ultrahigh speed swept source/Fourier domain OCT, " Biomed. of microvasculature by dual-beam phase-resolved Doppler optical coherence tomography, " Opt. Three-dimensional quantitative imaging of retinal and choroidal blood flow velocity using joint spectral and …
Inductive charging of an EDLC powered wristband device for medical measurements

Electronic devices for measuring body parameters in healthcare environments generally exhibit hygienic problems. Furthermore, they require regular battery replacement or recharging. This paper presents an electronic wristband for medical measurements that can be charged wirelessly. Its power supply is equipped with a Qi compatible inductive power receiver, an Electrochemical Double-Layer Capacitor (EDLC) energy buffer and a series of voltage regulators that can be disconnected from the energy buffer by a microcontroller. Because the wireless power receiver was placed behind a display, a study was performed of the effects of the display on receiver coil characteristics and system performance. For the selection of the EDLC, a selection process is presented, making a tradeoff between device autonomy and charging time. The result is a completely sealable and thus sterilizable device that can be charged in less than 5 seconds while being worn on the wrist.
Co‐word maps and topic modeling: A comparison using small and medium‐sized corpora (N < 1,000)

Induced by “big data,” “topic modeling” has become an attractive alternative to mapping co‐words in terms of co‐occurrences and co‐absences using network techniques. Does topic modeling provide an alternative for co‐word mapping in research practices using moderately sized document collections? We return to the word/document matrix using first a single text with a strong argument (“The Leiden Manifesto”) and then upscale to a sample of moderate size (n = 687) to study the pros and cons of the two approaches in terms of the resulting possibilities for making semantic maps that can serve an argument. The results from co‐word mapping (using two different routines) versus topic modeling are significantly uncorrelated. Whereas components in the co‐word maps can easily be designated, the topic models provide sets of words that are very differently organized. In these samples, the topic models seem to reveal similarities other than semantic ones (e.g., linguistic ones). In other words, topic modeling does not replace co‐word mapping in small and medium‐sized sets; but the paper leaves open the possibility that topic modeling would work well for the semantic mapping of large sets.
MicroRNA characterize genetic diversity and drug resistance in pediatric acute lymphoblastic leukemia

Background MicroRNA regulate the activity of protein-coding genes including those involved in hematopoietic cancers. The aim of the current study was to explore which microRNA are unique for seven different subtypes of pediatric acute lymphoblastic leukemia. Design and Methods Expression levels of 397 microRNA (including novel microRNA) were measured by quantitative real-time polymerase chain reaction in 81 cases of pediatric leukemia and 17 normal hematopoietic control cases. Results All major subtypes of acute lymphoblastic leukemia, i.e. T-cell, MLL-rearranged, TEL-AML1-positive, E2A-PBX1-positive and hyperdiploid acute lymphoblastic leukemia, with the exception of BCR-ABL-positive and ‘B-other’ acute lymphoblastic leukemias (defined as precursor B-cell acute lymphoblastic leukemia not carrying the foregoing cytogenetic aberrations), were found to have unique microRNA-signatures that differed from each other and from those of healthy hematopoietic cells. Strikingly, the microRNA signature of TEL-AML1-positive and hyperdiploid cases partly overlapped, which may suggest a common underlying biology. Moreover, aberrant down-regulation of let-7b (~70-fold) in MLL-rearranged acute lymphoblastic leukemia was linked to up-regulation of oncoprotein c-Myc (PFDR<0.0001). Resistance to vincristine and daunorubicin was characterized by an approximately 20-fold up-regulation of miR-125b, miR-99a and miR-100 (PFDR≤0.002). No discriminative microRNA were found for prednisolone response and only one microRNA was linked to resistance to L-asparaginase. A combined expression profile based on 14 microRNA that were individually associated with prognosis, was highly predictive of clinical outcome in pediatric acute lymphoblastic leukemia (5-year disease-free survival of 89.4%±7% versus 60.8±12%, P=0.001). Conclusions Genetic subtypes and drug-resistant leukemic cells display characteristic microRNA signatures in pediatric acute lymphoblastic leukemia. Functional studies of discriminative and prognostically important microRNA may provide new insights into the biology of pediatric acute lymphoblastic leukemia.
Research of the changeability of the vessels traffic intensity of inland waterways – case study for Lower Vistula

The article presents an analysis of the changeability of traffic intensity of inland waterway vessels in the Vistula Delta. The concept of traffic intensity was defined, traffic flows and disturbances were identified in the studied area. The characteristics of the inland waterway traffic model are presented. The results of the analysis indicate the need to carry out modernization of inland waterways for the needs of inland waterway transport: introduction of a traffic control system, unification of the navigational marking system and strict correlation of renovation/modernization works of hydrotechnical structures with a navigation period.
Extending WordNet with compound nouns for semi-automatic annotation in data integration systems

The focus of data integration systems is on producing a comprehensive global schema successfully integrating data from heterogeneous data sources (heterogeneous in format and in structure). Starting from the “meanings” associated to schema elements (i.e. class/attribute labels) and exploiting the structural knowledge of sources, it is possible to discover relationships among the elements of different schemata. Lexical annotation is the explicit inclusion of the “meaning” of a data source element according to a lexical resource. Accuracy of semi-automatic lexical annotator tools is poor on real-world schemata due to the abundance of non-dictionary compound nouns. It follows that a large set of relationships among different schemata is discovered, including a great amount of false positive relationships. In this paper we propose a new method for the annotation of non-dictionary compound nouns, which draws its inspiration from works in the natural language disambiguation area. The method extends the lexical annotation module of the MOMIS data integration system.
ON/OFF and Beyond - A Boolean Model of Apoptosis

Apoptosis is regulated by several signaling pathways which are extensively linked by crosstalks. Boolean or logical modeling has become a promising approach to capture the qualitative behavior of such complex networks. Here we built a large-scale literature-based Boolean model of the central intrinsic and extrinsic apoptosis pathways as well as pathways connected with them. The model responds to several external stimuli such as Fas ligand, TNF-α, UV-B irradiation, interleukin-1β and insulin. Timescales and multi-value node logic were used and turned out to be indispensable to reproduce the behavior of the apoptotic network. The coherence of the model was experimentally validated. Thereby an UV-B dose-effect is shown for the first time in mouse hepatocytes. Analysis of the model revealed a tight regulation emerging from high connectivity and spanning crosstalks and a particular importance of feedback loops. An unexpected feedback from Smac release to RIP could further increase complex II formation. The introduced Boolean model provides a comprehensive and coherent description of the apoptosis network behavior. It gives new insights into the complex interplay of pro- and antiapoptotic factors and can be easily expanded to other signaling pathways.
Learning to Reoptimize Consumption at New Income Levels: A Rationale for Prospect Theory

This paper provides a theoretical rationale for three experimental results of Prospect Theory: risk preferences are over gains and losses, loss aversion, and diminishing sensitivity. We consider a (boundedly rational) decision maker who does not find her new optimal consump-tion bundle with certainty when she is faced with a new income level. This alters her indirect utility function and makes her more risk averse at her current reference income level and less risk averse for a range of incomes below her reference income level. (JEL: D11) Copyright (c) 2004 by the European Economic Association.
V for Vicissitude: The Challenge of Scaling Complex Big Data Workflows

In this paper we present the scaling of BTWorld, our MapReduce-based approach to observing and analyzing the global BitTorrent network which we have been monitoring for the past 4 years. BTWorld currently provides a comprehensive and complex set of queries implemented in Pig Latin, with data dependencies between them, which translate to several MapReduce jobs that have a heavy-tailed distribution with respect to both execution time and input size characteristics. Processing BitTorrent data in excess of 1 TB with our BTWorld workflow required an in-depth analysis of the entire software stack and the design of a complete optimization cycle. We analyze our system from both theoretical and experimental perspectives and we show how we attained a 15 times larger scale of data processing than our previous results.
The Formation of an Oxygen Wave by Magnetic Reconnection

Oxygen of ionospheric origin is a ubiquitous particle species in magnetospheric dynamics. We investigate how an oxygen population influences magnetic reconnection and how it is energized, using particle‐in‐cell simulations. The oxygen population is inserted initially in the inflow region, at two equal distances above and below the current sheet, and as time evolves it is captured by the reconnection process. Three simulations with different initial oxygen temperature are investigated. As the oxygen gets involved, layers of high‐oxygen density forms in a region bounded by the Hall electric field. These density striations consist of a quasi‐steady horizontal layer and a dynamic, inclined, wavefront‐like layer. The acceleration of the oxygen population is dominated by electric forces, as the oxygen remains approximately demagnetized for the relevant timescales of the simulation. We describe two mechanisms of oxygen acceleration that lead to these two different structures.
Nuclear magnetic resonance assignment and secondary structure of an ankyrin‐like repeat‐bearing protein: Myotrophin

Multidimensional heteronuclear NMR has been applied to the structural analysis of myotrophin, a novel protein identified from spontaneously hypertensive rat hearts and hypertrophic human hearts. Myotrophin has been shown to stimulate protein synthesis in myocytes and likely plays an important role in the initiation of cardiac hypertrophy, a major cause of mortality in humans. Recent cDNA cloning revealed that myotrophin has 118 amino acids containing 2.5 contiguous ANK repeats, a motif known to be involved in a wide range of macromolecular recognition. A series of two‐ and three‐dimensional heteronuclear bond correlation NMR experiments have been performed on uniformly 15N‐labeled or uniformly 15N/13C‐labeled protein to obtain the 1H, 15N, and 13C chemical shift assignments. The secondary structure of myotrophin has been determined by a combination of NOEs, NH exchange data, 3JHNα coupling constants, and chemical shifts of 1Hα, 13Cα, and 13Cβ. The protein has been found to consist of seven helices, all connected by turns or loops. Six of the seven helices (all but the C‐terminal helix) form three separate helix‐turn‐helix motifs. The two full ANK repeats in myotrophin are characteristic of multiple turns followed by a helix‐turn‐helix motif. A hairpin‐like turn involving L32‐R36 in ANK repeat #1 exhibits slow conformational averaging on the NMR time scale and appears dynamically different from the corresponding region (D65‐I69) of ANK repeat #2.
Expression pattern analysis of SGF‐3/POU‐M1 in relation to sericin‐1 gene expression in the silk gland

Embryonic and larval expression patterns of the sericin‐1 gene and its presumed transcription factor, SGF‐3/POU‐M1, in the silk gland were analyzed by in situ hybridization and immunohistochemistry. The sericin‐1 transcripts were first detected at embryonic stage 26 in an increasing gradient pattern in the middle and posterior part of the middle silk gland (MSG), while at the same stage the SGF‐3/POU‐M1 was already present in the entire anterior silk gland (ASG) and in the MSG but with a decreasing gradient pattern. The latter expression pattern was consistently maintained through all larval stages, while the sericin‐1 expression was detected during the feeding stages but disappeared at the molting stages. These observations suggest that, although the SGF‐3/POU‐M1 was proposed to be a positive transcription factor for the sericin‐1 gene, the protein might function in a negative manner on sericin‐1 gene transcription. Alternatively, it is also possible that the sericin‐1 gene might require another unidentified factor or mediator for in vivo transcription.
Interactive Broadcasting System for VBR Encoded Videos

Video broadcasting has been proved to be an efficient technique to increase the scalability of a video-on-demand (VoD) system. In this paper, we address the problems in providing interactive functions for VBR encoded videos in a broadcast VoD system. A traffic smoothing scheme is proposed to support the VCR functions in delivering VBR videos over CBR channels by the staggered broadcasting protocol. By introducing a small buffering delay, the customers are able to join back to the broadcasting groups after the interactive functions. A system model is then developed to determine the optimal parameters such that the system can meet the delay requirement as well as provide the expected quality of service to the customers. The results show that the proposed system framework is very efficient in terms of bandwidth requirement and buttering delay to provide interactive VoD services.
CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

A complex cell envelope, composed of a mixture of lipid types including lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM‐GUI Martini Maker for coarse‐grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user‐friendly manner. © 2017 Wiley Periodicals, Inc.
Toolkits for multimedia awareness

Informal communication and awareness of coworkers is an important factor in the effectiveness of work in office environments. This dissertation focuses on an architecture for the creation of prototype tools which allow distributed work-groups to collaborate more effectively by communicating informally. This architecture supports the investigation of the area of informal communication and awareness by allowing researchers to quickly develop new application prototypes from reusable components.