Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatio-temporal activation of caspase revealed by indicator that is insensitive to environmental effects

Indicator molecules for caspase-3 activation have been reported that use fluorescence resonance energy transfer (FRET) between an enhanced cyan fluorescent protein (the donor) and enhanced yellow fluorescent protein (EYFP; the acceptor). Because EYFP is highly sensitive to proton (H+) and chloride ion (Cl−) levels, which can change during apoptosis, this indicator's ability to trace the precise dynamics of caspase activation is limited, especially in vivo. Here, we generated an H+- and Cl−-insensitive indicator for caspase activation, SCAT, in which EYFP was replaced with Venus, and monitored the spatio-temporal activation of caspases in living cells. Caspase-3 activation was initiated first in the cytosol and then in the nucleus, and rapidly reached maximum activation in 10 min or less. Furthermore, the nuclear activation of caspase-3 preceded the nuclear apoptotic morphological changes. In contrast, the completion of caspase-9 activation took much longer and its activation was attenuated in the nucleus. However, the time between the initiation of caspase-9 activation and the morphological changes was quite similar to that seen for caspase-3, indicating the activation of both caspases occurred essentially simultaneously during the initiation of apoptosis.
Exploring digital libraries: integrating browsing, searching, and visualization

Exploring services for digital libraries (DLs) include two major paradigms, browsing and searching, as well as other services such as clustering and visualization. In this paper, we formalize and generalize DL exploring services within a DL theory. We develop theorems to indicate that browsing and searching can be converted or mapped to each other under certain conditions. The theorems guide the design and implementation of exploring services for an integrated archaeological DL, ETANA-DL. Its integrated browsing and searching can support users in moving seamlessly between these operations, minimizing context switching, and keeping users focused. It also integrates browsing and searching into a single visual interface for DL exploration. A user study to evaluate ETANA-DL's exploring services helped validate our hypotheses
A BiCMOS Time-to-Digital Converter with Time Stretching Interpolators

A time-to-digital converter (TDC) capable to measure time intervals over a range of several microseconds with an accuracy of 100 - 200 ps has been designed. The TDC has been fabricated in a 1.2 um BiCMOS process and according to preliminary test results the single-shot resolution is better than 200 ps and the nonlinearity is less than 150 ps when input time intervals range from 2.5 to 2500 ns.
STATES OF THE LARYNX IN LAUGHTER

Although laughter can occur in various sequential (horizontal) patterns that have been well described, the voice quality components that can occur in laughter also need to be described in order to constitute a vertical array of possible phonetic contrasts. These components have been referred to as ‘states of the larynx’ and interact with pitch and with the ‘segmental’ components of laughter in predictable ways. Changes in laryngeal state can influence the phonetic shape of the voiceless/voiced parameter. Alternations between sources of periodic vibration also play a role in the description of laughter, where these laryngeal components might not otherwise play a role in the phonetics of the given language. Canonical profiles of the principal states of the larynx during various episodes of laughter are demonstrated.
A TWO-DIMENSIONAL ANALYSIS OF SURFACE ACOUSTIC WAVES IN FINITE ANISOTROPIC SOLIDS WITH ELECTRODES

Analytical solutions of surface acoustic waves in finite solids with electrodes are of great interests in both theoretical study and practical applications, and the two-dimensional theory based on the expansion of the exact solutions from semi-infinite solids offers an excellent two-dimensional theory with complete equations and boundary conditions similar to well-known plate theories for high frequency vibration applications. By considering the electrode layer on a piezoelectric substrate, the effects are evaluated through the integration of displacement fields along the thickness direction, effectively including both mass and stiffness. Extending these solutions to substrates with periodic electrodes, we can study the surface acoustic waves for accurate prediction of the phase velocity and displacement fields, thus enabling detailed analysis for actual resonator devices. We conclude this study with straight-crested wave solutions of surface acoustic waves in a finite solid with electrode to demonstrate the theory, solution technique, and the applications.
Detecting Individual Sites Subject to Episodic Diversifying Selection

The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic: a large proportion of positively selected sites. We present a mixed effects model of evolution (MEME) that is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site. Using empirical and simulated data, we demonstrate the superior performance of MEME over older models under a broad range of scenarios. We find that episodic selection is widespread and conclude that the number of sites experiencing positive selection may have been vastly underestimated.
Urocortin is not a significant regulator of intermittent electrofootshock-induced adrenocorticotropin secretion in the intact male rat.

Urocortin (Ucn) is a newly identified mammalian member of the CRF family of peptides. Ucn activates CRF receptors (both CRF-R1 and CRF-R2) with greater potency than CRF itself, suggesting that Ucn may play an endogenous role in eliciting (at least some) CRF receptor-mediated events. Because the most characterized physiological function of CRF receptors is the activation of pituitary ACTH secretion, we have compared the effects and potential endogenous roles of CRF and Ucn in regulating plasma ACTH concentrations in intact male rats. Synthetic rat Ucn injected i.v. (0.09-9.0 nmol/kg) elicited ACTH secretion in a dose-dependent manner, causing greater ACTH secretion than CRF at each dose tested. The increases in plasma ACTH concentrations produced by CRF or Ucn were virtually abolished by pretreatment with the CRF receptor antagonist, astressin (3 mg/kg), and were partially attenuated (by 27-37%) by an antiarginine vasopressin serum. These data indicate that both Ucn and CRF elicit ACTH secretion via CRF receptor-dependent mechanisms, and that the ACTH-releasing activities of both CRF and Ucn are potentiated by endogenous arginine vasopressin. Intravenous administration of rabbit anti-Ucn serum, which inhibited ACTH secretion produced by Ucn, but not CRF, had no statistically significant effect on either resting (midday) plasma ACTH concentrations or the rise in ACTH levels elicited by 30 min of intermittent electrofootshocks. By contrast, treatment with a rabbit anti-CRF serum that specifically inhibited the ACTH response to CRF lowered plasma concentrations in control unstressed rats and largely prevented the plasma ACTH response to electrofootshocks. These data indicate that although Ucn is a more potent ACTH secretagogue than CRF in the intact male rat, it is not a major endogenous regulator of pituitary ACTH secretion under basal (midday) conditions or during acute footshock stress.
OmpSs@Zynq all-programmable SoC ecosystem

OmpSs is an OpenMP-like directive-based programming model that includes heterogeneous execution (MIC, GPU, SMP, etc.) and runtime task dependencies management. Indeed, OmpSs has largely influenced the recently appeared OpenMP 4.0 specification. Zynq All-Programmable SoC combines the features of a SMP and a FPGA and benefits DLP, ILP and TLP parallelisms in order to efficiently exploit the new technology improvements and chip resource capacities. In this paper, we focus on programmability and heterogeneous execution support, presenting a successful combination of the OmpSs programming model and the Zynq All-Programmable SoC platforms.
Multiple Sequence Elements are Involved in the Transcriptional Regulation of the Human Squalene Synthase Gene*

The expression of human squalene synthase (HSS) gene is transcriptionally regulated in HepG-2 cells, up to 10-fold, by variations in cellular cholesterol homeostasis. An earlier deletion analysis of the 5′-flanking region of the HSS gene demonstrated that most of the HSS promoter activity is detected within a 69-base pair sequence located between nucleotides −131 and −200. ADD1/SREBP-1c, a rat homologue of sterol regulatory element-binding protein (SREBP)-1c binds to sterol regulatory element (SRE)-1-like sequence (HSS-SRE-1) present in this region (Guan, G., Jiang, G., Koch, R. L. and Shechter, I. (1995) J. Biol. Chem. 270, 21958-21965). In our present study, we demonstrate that mutation of this HSS-SRE-1 element significantly reduced, but did not abolish, the response of HSS promoter to change in sterol concentration. Mutation scanning indicates that two additional DNA promoter sequences are involved in sterol-mediated regulation. The first sequence contains an inverted SRE-3 element (Inv-SRE-3) and the second contains an inverted Y-box (Inv-Y-box) sequence. A single mutation in any of these sequences reduced, but did not completely remove, the response to sterols. Combination mutation studies showed that the HSS promoter activity was abolished only when all three elements were mutated simultaneously. Co-expression of SRE-1- or SRE-2-binding proteins (SREBP-1 or SREBP-2) with HSS promoter-luciferase reporter resulted in a dramatic increase of HSS promoter activity. Gel mobility shift studies indicate differential binding of the SREBPs to regulatory sequences in the HSS promoter. These results indicate that the transcription of the HSS gene is regulated by multiple regulatory elements in the promoter.
Taking the Skeletons Out of the Closets: A Simple and Efficient Topology Discovery Scheme for Large Ethernet LANs

: Today, Ethernet is the dominant local area network (LAN) technology. These networks, typically, comprise large number of elements from different vendors. This raises considerable difﬁculties in performing network management tasks, such as resource management and root cause analysis, which are practically impossible without an up-to-date knowledge of the physical network topology. Given the dynamic nature of today’s LANs, keeping track of topology information manually is a daunting (if not impossible) task. Therefore, it is essential to develop practical schemes for automatic inference of the physical topology of Ethernet networks. In this paper, we propose a simple and efﬁcient algorithmic solution for discovering the physical topology of large, heterogeneous Ethernet LANs that may include multiple subnets as well as uncooperative network elements, like hubs. Our scheme utilizes only generic MIB information and does not required any hardware or software modi-ﬁcation of the underlying network elements. By rigorous analysis, we prove that our method correctly infers the network topology and has low communication and computational overheads. Our simulation results show that the scheme successfully infers the complete topology in the vast majority of the cases, including many instances in which other methods fail. Finally, we implemented the proposed scheme to verify its inference capabilities. These properties conﬁrm the practicality of our scheme for network management.
Isolation, Screening and Characterization of Phosphate Solubilizing Bacteria from Karwar Costal Region

Phosphorus solubilizing bacteria (PSB) play important role by enhancing its availability to plants through release from inorganic and organic soil P by solubilization and mineralization. Phosphorus is vital to seed formation and its content is higher in seeds than in any other part of the plant. It helps plants to survive winter seasons and also contributes to disease resistance in some plants. Also known to improve quality of many fruits, vegetables and grain crops. The ability of some microorganisms to convert insoluble phosphorus to a soluble form, like orthophosphate, is an important trait in a Plant growth promoting bacteria for increasing plant yields. The inoculation of P-solubilizing microorganisms (PSM) is an efficient technique because it can increase P availability in the soil. In the present work we have made efforts to isolate the phosphate solubilizing microorganism form soil followed by its biochemical characterization. In this study, isolation, screening and characterization of 35 isolates of phosphate solubilizing bacteria from different regions of karwar were carried out. Phosphate solubilizing activities of all isolates were tested on National Botanical Research Institute's phosphate growth medium (NBRIP), and Pikovskaya medium (PVK), medium by analyzing the soluble-P content with different incubation temperature and pH. This article incorporates the recent developments and Preliminary results obtained in the manipulation of bacterial strains for improving capacity for phosphate solubilization and application of this knowledge to improving agricultural inoculants is discussed.
Place of Residence and Outcomes of Patients With Heart Failure: Analysis From the Telemonitoring to Improve Heart Failure Outcomes Trial

Background—Recent studies show an association between neighborhood-level measures of socioeconomic status (SES) and outcomes for patients with heart failure. We do not know whether neighborhood SES has a primary effect or is a marker for individual SES. Methods and Results—We used the data from participants of the Telemonitoring to Improve Heart Failure Outcomes (Tele-HF) trial, recruited from 33 US internal medicine and cardiology practices and examined the association between neighborhood SES and outcomes of patients with heart failure. We used census tracts as proxies for neighborhoods and constructed summary SES scores that included information about wealth and income, education, and occupation. The primary end points were readmission and all-cause mortality at 6 months. We conducted patient interviews and medical chart reviews to obtain demographic information, clinical factors, therapies, and individual SES. We included 1557 patients: 524, 516, and 517 from low, medium, and high SES neighborhoods, respectively (mean age, 61.1±15.2 years; 42.2% women). Overall, 745 patients (47.8%) had ≥1 readmission and 179 patients (11.5%) died. When compared with patients in high SES neighborhoods, those living in low-SES neighborhoods were more likely to be readmitted (odds ratio, 1.35; 95% confidence interval, 1.01–1.82), but the mortality rates were not significantly different (odds ratio, 0.78; 95% confidence interval, 0.50–1.18). The results were consistent after multivariable adjustments for individual demographics, clinical factors, and individual SES. Conclusions—Among patients with heart failure, neighborhood SES was significantly associated with 6-month all-cause readmission even after adjusting for other patient-level factors, including individual SES. Greater number of events and longer follow-up is required to ascertain the potential effect of neighborhood SES on mortality. Clinical Trial Registration—URL: http://clinicaltrials.gov/. Unique identifier: NCT00303212.
Distributed Convolutional-Coded Differential Space-Time Block Coding

A low complexity distributed coding scheme is proposed for communications over Rayleigh fading channels. Convolutional Coding (CC) assisted Differential Phase-Shift Keying (DPSK) modulation is employed at the source node for conveying the source signals to two relay nodes as well as to the destination node during the first transmission period. Iterative detection exchanging extrinsic information between the DPSK demapper and CC decoder is carried out at each relay node in order to recover the source signals. Then, the CC-encoded bits are re-encoded by the two relays to generate Differential Space-Time Block Coding (DSTBC) symbols for transmission to the destination node during the second transmission period. At the destination node, iterative decoding exchanging extrinsic information is invoked between the DPSK demapper and the concatenated CC-DSTBC decoder, where the later is viewed as a single amalgamated decoder. The relay and destination nodes do not have to estimate the channel's fading coefficients due to the employment of DPSK and DSTBC schemes. Our design requires only two decoding iterations between the DPSK and CC decoders at each relay in order to further reduce the complexity of the relay nodes. Our distributed coding scheme assisted by two low-complexity relay nodes outperforms the non-cooperative benchmarker scheme by about 8~dBs, when aiming for a bit error ratio of $10^{-5}$.
Architecture of a network-aware P2P-TV application: the NAPA-WINE approach

Peer to Peer streaming (P2P-TV) applications have recently emerged as cheap and efficient solutions to provide real time streaming services over the Internet. For the sake of simplicity, typical P2P-TV systems are designed and optimized following a pure layered approach, thus ignoring the effect of design choices on the underlying transport network. This simple approach, however, may constitute a threat for the network providers, due to the congestion that P2P-TV traffic can potentially generate. In this article, we present and discuss the architecture of an innovative, network cooperative P2PTV application that is being designed and developed within the STREP Project NAPA WINE1 Our application is explicitly targeted to favor cooperation between the application and the transport network layer.
Liver-function tests.

NUMEROUS attempts have been made for over half a century to measure the function of the liver by one or another test; these procedures have been proposed for several purposes. First, in cases in which the diagnosis is entirely obscure, it has been hoped that the presence of liver disease might be ruled in or out. Second, in the presence of known liver disease function studies have been used to define, if possible, the degree of damage and the type of lesion. Finally, these procedures seem to have a valuable place in appraising the course of hepatic disturbances— whether downhill or toward recovery. The discovery of the glycogenic activity of the liver, in 1857, by Claude Bernard, stimulated extensive studies of carbohydrate metabolism, and by the late decades of the century alert clinicians were attempting to develop carbohydrate tests for liver function. The general idea was that, if one fed
Near-miss modeling: a segment-based approach to speech recognition

Currently, most approaches to speech recognition are frame-based in that they represent speech as a temporal sequence of feature vectors. Although these approaches have been successful, they cannot easily incorporate complex modeling strategies that may further improve speech recognition performance. In contrast, segment-based approaches represent speech as a temporal graph of feature vectors and facilitate the incorporation of a wide range of modeling strategies. However, difficulties in segmentbased recognition have impeded the realization of potential advantages in modeling. This thesis describes an approach called near-miss modeling that addresses the major difficulties in segment-based recognition. Probabilistically, each path should account for the entire graph including the segments that are off the path as well as the segments that are on the path. Near-miss modeling is based on the idea that an off-path segment can be modeled as a "near-miss" of an on-path segment. Each segment is associated with a near-miss subset of segments that contains the on-path segment as well as zero or more off-path segments such that the near-miss subsets that are associated with any path account for the entire graph. Computationally, the graph should contain only a small number of segments without introducing a large number of segmentation errors. Near-miss modeling runs a recognizer and produces a graph that contains only the segments on paths that score within a threshold of the best scoring path. A near-miss recognizer using context-independent segment-based acoustic models, diphone context-dependent frame-based models, and a phone bigram language model achieves a 25.5% error rate on the TIMIT core test set over 39 classes. This is a 16% reduction in error rate from our best previously reported result and, to our knowledge, is the lowest error rate that has been reported under comparable conditions. Additional experiments using the ATIS corpus verify that these improvements generalize to word recognition. Thesis Supervisor: James R. Glass Title: Principal Research Scientist
Toward Software-Defined Cellular Networks

Existing cellular networks suffer from inflexible and expensive equipment, complex control-plane protocols, and vendor-specific configuration interfaces. In this position paper, we argue that software defined networking (SDN) can simplify the design and management of cellular data networks, while enabling new services. However, supporting many subscribers, frequent mobility, fine-grained measurement and control, and real-time adaptation introduces new scalability challenges that future SDN architectures should address. As a first step, we propose extensions to controller platforms, switches, and base stations to enable controller applications to (i) express high-level policies based on subscriber attributes, rather than addresses and locations, (ii) apply real-time, fine-grained control through local agents on the switches, (iii)perform deep packet inspection and header compression on packets, and (iv)remotely manage shares of base-station resources.
Theory and Algorithm for Learning with Dissimilarity Functions

We study the problem of classification when only a dissimilarity function between objects is accessible. That is, data samples are represented not by feature vectors but in terms of their pairwise dissimilarities. We establish sufficient conditions for dissimilarity functions to allow building accurate classifiers. The theory immediately suggests a learning paradigm: construct an ensemble of simple classifiers, each depending on a pair of examples; then find a convex combination of them to achieve a large margin. We next develop a practical algorithm referred to as dissimilarity-based boosting (DBoost) for learning with dissimilarity functions under theoretical guidance. Experiments on a variety of databases demonstrate that the DBoost algorithm is promising for several dissimilarity measures widely used in practice.
Parallel MLFMA Performance Analysis Using Performance Analysis Toolsets

The Fast Multipole Method (FMM) and Multi- Level Fast Multipole Algorithm (MLFMA) have been used to solve electromagnetic scattering problems for many years. Parallel implementations of MLFMA is currently a hot topic because it is capable of solving scattering problems with tens of millions of unknowns, with complexity O(NlogN), where N is the number of unknowns. In this paper, we discuss a new perfectly parallel implementation of MLFMA. With the increasing of unknowns and the complexity of computing objects, the program behaviors especially the communication behaviors become chaotic. Thus, it is necessary to discover the bottleneck and the inefficient regions using existing parallel implementation performance analysis toolsets. The main focus of the present paper is to discuss how we use Scalasca (an open source professional analysis toolset) and other analysis tools to analyze our parallel MLFMA implementation, find the bottlenecks and inefficient parts of the implementation and accordingly optimize and modify the code. The paper highlights some necessary tricks that we employed and without which the use of Scalasca to analyze the program would have been impossible.