Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphorylation of linker histone is associated with transcriptional activation in a normally silent nucleus

Previous studies have suggested that micronuclear linker histones are phosphorylated by cAMP-dependent protein kinase (PKA) in Tetrahymena (Sweet, M.T., and C.D. Allis. 1993. Chromosoma. 102: 637-647). In this study, we report that a rapid and dramatic phosphorylation of the micronuclear linker histone, delta, occurs early in the sexual pathway, conjugation. Phosphorylated isoforms of delta are detected as early as 30 min after mixing cells of different mating types; blocking pair formation abolishes this induction completely. Phosphorylation of delta is stimulated by the addition of N6-benzoyladenosine 3':5' cyclic monophosphate to starved (nonmating) cells, suggesting that a PKA/cAMP signal transduction pathway is involved. Maximal phosphorylation of delta is observed during meiotic prophase, a period when micronuclei become transcriptionally active. In situ staining, using phospho-delta- specific antibodies combined with [3H]uridine autoradiography, shows that decondensed micronuclear chromatin undergoing active transcription is enriched in phosphorylated delta isoforms. In contrast, condensed inactive micronuclear chromatin is enriched in dephosphorylated delta. These results strongly suggest that phosphorylation of linker histone plays an important and previously unsuspected role in establishing transcriptional competence in micronuclei.
Imaging of a patterned and buried molecular layer by coherent acoustic phonon spectroscopy

A molecular layer of aminopropyltriethoxysilane is patterned with a focused ion beam and subsequently covered by a gold film. The gold-polymer-substrate structures are afterwards imaged by ultrafast coherent acoustic phonon spectroscopy in reflection geometry. We demonstrate that the lateral structure of the covered polymer layer can be detected via the damping time of the vibrational mode of the gold film. Furthermore, we utilize Brillouin oscillations originating from the silicon substrate to map the structures and to estimate the molecular layer thickness.
Sp110 enhances macrophage resistance to Mycobacterium tuberculosis via inducing endoplasmic reticulum stress and inhibiting anti-apoptotic factors

Tuberculosis remains a leading health problem worldwide and still accounts for about 1.3 million deaths annually. Expression of the mouse Sp110 nuclear body protein (Sp110) upregulates the apoptotic pathway, which plays an essential role in enhancing host immunity to Mycobacterium tuberculosis (Mtb). However, the mechanism of this upregulation is unclear. Here, we have identified 253 proteins in mouse macrophages that interact with Sp110, of which 251 proteins were previously uncharacterized. The results showed that Sp110 interacts with heat shock protein 5 (Hspa5) to activate endoplasmic reticulum (ER) stress-induced apoptosis, and that this is essential for Sp110 enhanced macrophage resistance to Mtb. Inhibition of the ER stress pathway abolishing the Sp110-enhanced macrophage apoptosis and resulted in increased intracellular survival of Mtb in macrophages overexpressing Sp110 Further studies revealed that Sp110 also interacts with the RNA binding protein, Ncl to promote its degradation. Consequently, the expression of Bcl2, usually stabilized by Ncl, was downregulated in Sp110 overexpressing macrophages. Moreover, overexpression of Sp110 promotes degradation of ribosomal protein Rps3a, resulting in upregulation of the activity of the pro-apoptotic poly (ADP-ribose) polymerase (PARP). In addition, macrophages from transgenic cattle with increased Sp110 expression confirmed that activation of the ER stress response is the main pathway through which Sp110-enhanced macrophages impart resistance to Mtb. This work has revealed the mechanism of Sp110 enhanced macrophage apoptosis in response to Mtb infection, and provides new insights into the study of host-pathogen interactions.
Representation of curved surfaces in responses of mechanoreceptive afferent fibers innervating the monkey's fingerpad

The aim was to elucidate how the population of digital nerve afferents signals information about the shape of objects in contact with the fingerpads during fine manipulations. Responses were recorded from single mechanoreceptive afferent fibers in median nerves of anesthetized monkeys. Seven spherical surfaces were used, varying from a highly curved surface (radius, 1.44 mm; curvature, 694 m-1) to a flat surface (radius, infinity; curvature, 0 m-1). These were applied to the fibers' receptive fields, which were located on the central portion of a fingerpad. When the objects were located at the centers of the receptive fields, the responses of the slowly adapting fibers (SAIs) increased as the curvature of the surface increased and as the contact force increased. All SAIs behaved in the same way, differing only by a scaling factor (the sensitivity of the individual afferent). Responses of the rapidly adapting afferents were small and did not vary systematically with the stimulus parameters, and most Pacinians did not respond at all. Stimuli were applied at different positions in the receptive fields of SAIs to define the response profiles of the afferents (response as a function of position on the fingerpad). All SAIs had similarly shaped profiles for the same surface curvature and the shape differed for different curvatures. These profiles reflected the shape of the stimulus. An increase in contact force scaled these profiles upward. Thus, the population of digital nerve fibers signals unambiguous information about the shape and contact force of curved surfaces contacting the fingerpad.
Therapeutic In Situ Autovaccination against Solid Cancers with Intratumoral Poly-ICLC: Case Report, Hypothesis, and Clinical Trial

Salazar and colleagues describe an ongoing trial of sequential intratumoral and intramuscular poly-ICLC vaccination, partly based on results in a pilot volunteer patient with advanced rhabdomyosarcoma; the authors postulate conversion of tumor into a personalized vaccine, activating innate and adaptive immunity. Pathogen-associated molecular patterns (PAMP) are stand-alone innate and adaptive immunomodulators and critical vaccine components. We present a strategy of sequential intratumoral (i.t.) and intramuscular (i.m.) injections of the stabilized dsRNA viral mimic and PAMP, polyinosinic–polycytidylic acid-polylysine-carboxymethylcellulose (poly-ICLC, Hiltonol; Oncovir). We report the first treated patient, a young man with an exceptionally advanced facial embryonal rhabdomyosarcoma with extension to the brain. After treatment, the patient showed tumor inflammation consistent with immunotherapy, followed by gradual, marked tumor regression, with extended survival. Sequential i.t. and i.m. poly-ICLC injections mimicking a viral infection can induce an effective, in situ, personalized systemic therapeutic “autovaccination” against tumor antigens of a patient. We postulate a three-step immunomodulatory process: (i) innate-immune local tumor killing induced by i.t. poly-ICLC; (ii) activation of dendritic cells with Th1 cell– and CTL–weighted priming against the released tumor antigens; and (iii) i.m. poly-ICLC maintenance of the systemic antitumor immune response via chemokine induction, facilitation of CTL killing through the induction of costimulators such as OX40, inflammasome activation, and increase in the T-effector/Treg ratio. These results support the use of certain simple and inexpensive i.t. PAMPs to favorably stimulate effective immunity against solid cancers. A phase II clinical trial testing the hypothesis presented has begun accrual (clinicaltrials.gov, NCT01984892). Cancer Immunol Res; 2(8); 720–4. ©2014 AACR.
Improving Fiber Alignment in HARDI by Combining Contextual PDE Flow with Constrained Spherical Deconvolution

We propose two strategies to improve the quality of tractography results computed from diffusion weighted magnetic resonance imaging (DW-MRI) data. Both methods are based on the same PDE framework, defined in the coupled space of positions and orientations, associated with a stochastic process describing the enhancement of elongated structures while preserving crossing structures. In the first method we use the enhancement PDE for contextual regularization of a fiber orientation distribution (FOD) that is obtained on individual voxels from high angular resolution diffusion imaging (HARDI) data via constrained spherical deconvolution (CSD). Thereby we improve the FOD as input for subsequent tractography. Secondly, we introduce the fiber to bundle coherence (FBC), a measure for quantification of fiber alignment. The FBC is computed from a tractography result using the same PDE framework and provides a criterion for removing the spurious fibers. We validate the proposed combination of CSD and enhancement on phantom data and on human data, acquired with different scanning protocols. On the phantom data we find that PDE enhancements improve both local metrics and global metrics of tractography results, compared to CSD without enhancements. On the human data we show that the enhancements allow for a better reconstruction of crossing fiber bundles and they reduce the variability of the tractography output with respect to the acquisition parameters. Finally, we show that both the enhancement of the FODs and the use of the FBC measure on the tractography improve the stability with respect to different stochastic realizations of probabilistic tractography. This is shown in a clinical application: the reconstruction of the optic radiation for epilepsy surgery planning.
Bacterial bioluminescence: organization, regulation, and application of the lux genes

Significant advances have been made in the characterization of luciferases and other lux‐specific proteins as well as the lux genes from a number of different species of marine and terrestrial luminescent bacteria. A common lux gene organization (luxCDAB.E) modulated by the presence of specific genes involved in regulation and flavin binding and metabolism (luxF‐I,L,R,Y) has been found with the luciferase genes (luxAB) flanked by the genes involved in synthesis of its fatty aldehyde substrate (luxCDE). For many species, light intensity per cell is highly dependent on cellular growth resulting in a spectacular autoinduction of luminescence at high cell density. Consequently, the bacterial lux system is of particular interest as it can serve as an excellent model for more general signal transduction systems involved in developmental processes, intercellular communication, and even symbioses. Identification of the lux autoinducers and regulatory proteins of Vibrio harveyi and Vibrio fischeri has provided the biochemical and genetic basis for dissection of the luminescent system. Isolation of the lux genes and the ability to transfer these genes into prokaryotic and eukaryotic organisms have greatly expanded the scope and potential uses of bacterial bioluminescence as a safe, rapid, and sensitive sensor for a wide variety of compounds and metabolic processes. —Meighen, E. A. Bacterial bioluminescence: organization, regulation, and application of the lux genes. FASEB J. 7: 1016‐1022; 1993.
"yeah Right": Sarcasm Recognition for Spoken Dialogue Systems

The robust understanding of sarcasm in a spoken dialogue system requires a reformulation of the dialogue manager’s basic assumptions behind, for example, user behavior and grounding strategies. But automatically detecting a sarcastic tone of voice is not a simple matter. This paper presents some experiments toward sarcasm recognition using prosodic, spectral, and contextual cues. Our results demonstrate that spectral and contextual features can be used to detect sarcasm as well as a human annotator would, and confirm a long-held claim in the field of psychology – that prosody alone is not sufficient to discern whether a speaker is being sarcastic. Index Terms: dialogue, user modeling, sarcasm, speech acts
IMU and magnetometer modeling for smartphone-based PDR

In this paper, IMU and magnetometer models that enable pedestrian dead-reckoning without step detection or zero velocity updates on hand-held devices such as smartphones are proposed. The models are suitable for usage with any standard Bayesian filtering or smoothing technique and thus, do not require customized estimators. The method is evaluated in a real scenario using a dataset of approximately three minutes with a trajectory length of 302m. It is found that the overall shape of the estimated trajectory matches well with the GPS reference trajectory with an estimated trajectory length of 293m. Some problems in the heading estimation are observed.
Language-shifting objects from Java to Smalltalk: an exploration using JavaConnect

Foreign-function interfaces enable programs in a host language to interoperate with programs written in another language and vice-versa. Two languages that feature such an interface to a common language can even interoperate by means of this common intermediate language. Smalltalk and Java, for example, both offer an interface to C and can therefore interoperate through a connection of these interfaces. However, the resulting interactions will need to occur at the level of abstraction offered by the (low-level) C interfaces, although both Java and Smalltalk are object-oriented languages. In this paper, we describe how the dynamic and reflective facilities of the Smalltalk language permits us to raise the level of abstraction of these inter-language interactions to seamless message passing between objects. In addition, we introduce and explore the concept of language shifting objects where Java objects are not only represented in Smalltalk but can partially or completely migrate from Java to Smalltalk. Language-shifting effectively migrates Java methods to Smalltalk methods such that original Java objects can end up "living" in the Smalltalk environment without needing a connection to their originating Java environment.
Measuring The Role Of Inhibition In Auditory Discrimination In Mice

Understanding how inhibitory neurons affect sensory information processing in the cerebral cortex is an ongoing goal of both neuroscience and statistical physics research. In this master’s thesis research project, an experimental system has been designed and built for studying how auditory dynamic range depends on inhibitory neurons, based on observations of mouse behavior. In this thesis, firstly, the topic of inhibition and information processing has been introduced. Then two papers related to inhibition and dynamic range has been reviewed in detail. One of the papers is an experimental work that analyzes the affect of inhibition on dynamic range. The other paper provides a statistical model to infer that dynamic range is maximized at criticality. Finally, the design and assembly of the experimental setup is described in details along with some preliminary data to test the design and future directions for this research.
Adaptive Hypermedia and Adaptive Web

Adaptive Systems use explicit user models representing user knowledge, goals, interests, etc. that enable them to tailor interaction to different users. Adaptive hypermedia and Adaptive Web have used this paradigm to allow personalization in hypertext systems and the WWW, with diverse applications ranging from museum guides to web-based education. The goal of this chapter is to present the history of adaptive hypermedia, introduce a number of classic but popular techniques, and discuss emerging research directions in the context of the Adaptive and Semantic Web, that challenge the adaptive hypermedia researchers in the new Millennium.
Sampled-data output feedback tracking of magnetic levitation system

In this paper, we present a solution to sampled-data output feedback tracking problem for the cases of known and unknown plant models of magnetic levitation system. For known plant model, magnetic disc of the plant tracks reference signal using Extended Kalman Filter (EKF) and Unscented Kalman filter (UKF). However, when plant model is unknown, EKF and UKF cannot perform. In such a case, state-space recursive least-squares (SSRLS) with constant velocity model is employed to track the reference signal. The controller is designed using feedback linearization. The simulation results show good tracking performance given by EKF and UKF estimator. Moreover, the plant output reasonably tracks the reference signal when SSRLS estimator is used for unknown model case.
DECOMPOSITION OF AIRBORNE LASER SCANNING WAVEFORM DATA BASED ON EM ALGORITHM

Data storage capacity and high processing speed available today has made it possible to digitally sample and store the entire reflected waveform of Small-Footprint Airborne Lidar (light detection and ranging), instead of only extracting the discrete coordinates which form the so-called point clouds. One of the most important advantages from waveforms data is that it gives the user the chance to extract three-dimensional coordinates by himself in the post-processing. Decomposition return waveform is a key step during analyzing waveform data. Conventional algorithm to decompose is maximum and centre of gravity, or simply by using the thresholding method provided by equipment vendor. Both show lack of high accuracy. In this paper, an improved Expectation Maximum (EM) algorithm is adopted to extract peak location and pulse width from raw waveform data, proving it is a reliable and high accurate decomposition algorithm. Moreover, the high-quality point-cloud data could be obtained which provides high-quality resources for DSM(Digital Surface Model) and DTM(Digital Terrain Model) production. Derived forest biophysical parameters, such as vegetation height and crown volume are able to describe the horizontal and vertical forest canopy structure. ∗ Email:qli_rs@yahoo.com. cn
Catalysts for Re-Examining Pedagogical Assumptions: A Phenomenological Inquiry into Higher Education Faculty Designing and Teaching Online Courses.

This research concerns the potential of online teaching to prompt university faculty members to reflect on the essence of good teaching, and as a result enhance their pedagogy in both online and face-to-face courses. Ideas of developmental psychologists melded with related concepts from online-learning theorists were used as a theoretical framework for identifying key cognitive steps in the process of rethinking what it means to teach well. In particular, catalysts that can help motivate faculty to rethink teaching were suggested by the views of developmental psychologists Vygotsky, Piaget and Bruner about the social context within which learning takes place, the advantages of learning from and with peers, and the value of cognitive dissonance as an impetus to learning; additional catalysts were suggested by the views of online-learning theorists Dede, Ally, Mayes, Moore and Swann about the ways that innovative technologies and web-based learning affect how people interact. To investigate how, and the degree to which, these potential catalysts actually come into play in online teaching, a phenomenological research study was carried out based on interviews with six experienced university faculty members concerning their experiences designing and teaching online courses, with special emphasis on how their views of good teaching may have changed during that process. The study highlighted catalysts that in most but not all cases helped to bring about the faculty members’ re-examination of pedagogical assumptions as they planned and taught online courses and reflected on the experience. The catalysts included the novel online-learning environment, new roles and relationships the participants encountered during the process of teaching online, the unfamiliar course-design process, and new forms of interaction they encountered. As more students take courses online and more faculty members are called upon to teach such courses, institutions of higher education have an opportunity to improve pedagogy both by tapping into teachers’ passion for teaching and by making the most of the catalysts illuminated in this study.
WL under-driving scheme with decremental step voltage and incremental step time for high-capacity NAND flash memory

In this work, we compared the WL driving schemes in 512 Gb planar NAND with 32 KB page size. In the conventional WL driving scheme, the rising time of the selected WL voltage is very large because of the large coupling capacitance between the selected and unselected WLs. The WL under-driving scheme (WLUDS) reduces the effect of coupling capacitance by using the 2-phase control of unselected WL voltage. However, when WLUDS is used, the relationship between the rising time and overshoot of the selected WL voltage should be considered in order to achieve the small rising time Therefore, we proposes a novel implementation method for WLUDS that controls the under-driving voltage and under-driving timing by using the decremental step voltage and incremental step time (DSVIST) to enhance the rising time considering the overshoot constraint. The HSPICE simulation using the 0.25-μm PTM model with the parasitic RC in 32 KB page size shows that the rising time in the proposed WLUDS with DSVIST is improved to 988 μs compared to 1206 μs in the conventional WL driving scheme.
Time and Space Efficient Implementation of Robust Biclustering Algorithm ( ROBA )

A biclustering algorithm named Robust Biclustering Algorithm (ROBA) [2] has been used in a number of recent research works. The existing implementation of ROBA is not that time and space efficient. In this work, we develop a time and space efficient implementation of ROBA. We elicit some subtle properties of the base principle of ROBA to achieve these efficiencies. We reduce both time and space requirements by a factor of L where L is the number of distinct values present in the N x M input data matrix. The comparison of time and space requirement between the existing implementation and our implementation is summarized in table 1.
Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

Abstract DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome.
Credit Cycles, Credit Risk, and Prudential Regulation

This paper finds strong empirical support of a positive, although quite lagged, relationship between rapid credit growth and loan losses. Moreover, it contains empirical evidence of more lenient credit standards during boom periods, both in terms of screening of borrowers and in collateral requirements. We find robust evidence that during upturns, riskier borrowers get bank loans, while collateralized loans decrease. We develop a regulatory prudential tool, based on a countercyclical, or forward-looking, loan loss provision that takes into account the credit risk profile of banks’ loan portfolios along the business cycle. Such a provision might contribute to reinforce the soundness and the stability of banking systems.