Miracle-dz/UniFAR-FTUs huggingface dataset:
Red cell glucose phosphate isomerase (GPI): a molecular study of three novel mutations associated with hereditary nonspherocytic hemolytic anemia

Molecular characteristics of red blood cell (RBC) glucose phosphate isomerase (GPI) deficiency are described in two Spanish patients with chronic nonspherocytic hemolytic anemia. One patient, with residual GPI activity in RBCs of around 7% (GPI‐Catalonia), is homozygous for the missense mutation c.1648A>G (p.Lys550Glu) in exon 18. The other patient, with residual activity in RBCs of around 20% (GPI‐Barcelona), was found to be a compound heterozygote for two different missense mutations: c.341A>T (p.Asp113Val) in exon 4 and c.663T>G (p.Asn220Lys) in exon 7. Molecular modeling using the human crystal structure of GPI as a model was performed to determine how these mutations could affect enzyme structure and function. © 2006 Wiley‐Liss, Inc.
Simulated Vehicle-to-Vehicle Message Propagation Efficiency on Atlanta's I-75 Corridor

Exploitation of in-vehicle information technology (e.g., mobile computing and wireless communications) in surface transportation systems is a clear emerging trend. Equipping vehicles with computing, communication, and sensing capabilities presents significant opportunities for a vast array of transportation services. Vehicle-to-vehicle communication may be considered for applications such as incident detection, traveler information dissemination, network operations, etc. In-vehicle computing systems facilitate the customization of information services to the needs and characteristics of individual travelers. In addition, in-vehicle systems allow coverage to extend beyond areas where roadside equipment has been placed. This study provides the initial investigation needed to test the feasibility of these advanced communication networks. Several observations may be drawn from this study. First, vehicle-to-vehicle communication is a feasible way to propagate information along freeways in metro areas, although propagation performance depends critically on factors such as the density of instrumented vehicles along the end-to-end path. Second, the simulation methodology described within this study allows one to estimate the minimum required fleet penetration ratio for effective communication, given the traffic density and application requirements. Third, the message propagation delay is highly variable when instrumented vehicle density is low. A particular delay may be well below or above the average depending on traffic conditions. For applications requiring highly reliable, minimal message propagation it may be necessary to design networks that provide extra support to avoid such variation. Future research is required to examine additional traffic conditions (e.g., congestion due to an incident) and study the effectiveness of this approach for particular applications. TRB 2005 Annual Meeting CD-ROM Paper revised from original submittal. Wu, H. , J. Lee, M. Hunter, R. Fujimoto, R. Guensler, J. Ko 3
Solution of large unsymmetric systems of linear equations

The numerical solution of large systems of linear equations lies at the heart of many scientific computing efforts. Sparse systems with several hundreds of thousands ofunknowns have to be solved today. Ill-conditioned systems with unsymmetric matrices whose irregular sparsity structures reflect irregularly refined discretization grids for partial differential equations are particularly difficult to solve. Dozens or hundreds of such systems occur in a single semiconductor device simulation, and the linear solver is the main timeconsuming operation in this application. Direct sparse solvers, based on classical triangularfactorizations, cannot be used for very large matrices. Their storage requirements increase superlinearly with the problem size, and the growth factor increases with the dimensionality of the discretization grid. Iterative linear solvers are a viable alternative, even if none of the current approaches suits all the requirements alone. All successful iterative methods approximate the solution by stationary points in sequences of Krylov subspaces. GMRES uses the minimum number of matrix-vector products to minimize the residual in a given Krylov subspace, but its storage requirements increase linearly with the iteration number. Truncated or restarted variants are much less effective. BiCG and variants thereof do not have such a minimization property, but are often more successful, and have constant and low storage requirements. In our experience, Bi-CGSTAB is currently the fastest and most robust method in this class. BiCG and its variants have a bad reputation because of breakdown and cancellation problems, but the rare real occurrences of these effects can be fixed through restarting.
Nonlinear acoustic echo cancellation based on Volterra filters

This paper describes a nonlinear acoustic echo cancellation algorithm, mainly focused on loudspeaker distortions. The proposed system is composed of two distinct modules organized in a cascaded structure: a nonlinear module based on polynomial Volterra filters models the loudspeaker, and a second module of standard linear filtering identifies the impulse response of the acoustic path. The tracking of the overall system model is achieved by a modified normalized-least mean square algorithm for which equations are derived. Stability conditions are given, and particular attention is placed on the transient behavior of cascaded filters. Finally, results of real data recorded with Alcatel GSM material are presented.
Overexpression of Reg3α increases cell growth and the levels of cyclin D1 and CDK4 in insulinoma cells

Regenerating gene (Reg) family protein Reg3α is normally expressed in pancreatic acinar and endocrine cells. In order to explore its effect on islet β-cell replication, insulinoma MIN6 cells were stably transfected with murine Reg3α cDNA. Determined using real-time PCR and Western blots, the levels of Reg3α mRNA and protein in Reg3α-transfected clones were increased 10- and 6-fold, respectively. Western blots also revealed that the protein was released into the culture medium, consistent with an endocrine effect. In MTT cell proliferation assay, Reg3α-overexpressing cells exhibited a 2-fold increase in the rate of cell growth. In order to investigate the intracellular mechanism, we studied cell cycle regulatory proteins. In Reg3α-expressing cells, we detected 2.2- and 2.5-fold increased levels of cyclin D1 and CDK4, respectively, which paralleled a 1.8-fold increase in the rate of Akt phosphorylation. It is established that β-cell replication is associated with increased cyclin D1 and CDK4 levels; deficiency in CDK4 or cyclin D2 results in reduced β-cell mass and diabetes. Our results suggest that Reg3α stimulates β-cell replication, by activating Akt kinase and increasing the levels of cyclin D1/CDK4.
Activity Pacing in Chronic Pain: Concepts, Evidence, and Future Directions

Background:Activity pacing (AP) is a concept that is central to many chronic pain theories and treatments, yet there remains confusion regarding its definition and effects. Objective:To review the current knowledge concerning AP and integrate this knowledge in a manner that allows for a clear definition and useful directions for future research. Methods:A narrative review of the major theoretical approaches to AP and of the empirical evidence regarding the effects of AP interventions, followed by an integrative discussion. Results:The concept of AP is derived from 2 main traditions: operant and energy conservation. Although there are common elements across these traditions, significant conceptual and practical differences exist, which has led to confusion. Little empirical evidence exists concerning the efficacy of AP as a treatment for chronic pain. Discussion:Future research on AP should be based on a clear theoretical foundation, consider the context in which the AP behavior occurs and the type of pacing problem (“underactivity” vs. “overactivity”), and should examine the impact of AP treatment on multiple clinical outcomes. We provide a provisional definition of AP and specific recommendations that we believe will move the field forward.
Assessment for Android apps permissions a proactive approach toward privacy risk

Mobile devices store users' personal data. When mobile applications have access to this data they may leak it to third parties without users' consent. Google's Android platforms include a permission model that restricts applications' access to users' personal data. However, users are not aware of how their personal data would be used once applications are installed and permissions granted. This raises a potential privacy concern. In this paper we propose a proactive approach towards users' awareness of the privacy risk involved with granting permissions to Android applications. We present a dynamic privacy risk assessment model that assesses the risk to users' privacy associated to an application which requires a set of permissions. The parameters of this model are the severity and the relative importance of permissions and their interactions. Severity is evaluated according to a standard severity assessment method. The relative importance is estimated according to an analytic method. An experimental study to validate our proactive approach has been conducted. The originality of this works lies in that the privacy risk for a given device owned by an individual varies dynamically based on its different uses applications and related permissions.
Persons-In-Places: a Deep Features Based Approach for Searching a Specific Person in a Specific Location

Video retrieval is a challenging task in computer vision, especially with complex queries. In this paper, we consider a new type of complex query which simultaneously covers person and location information. The aim to search a specific person in a specific location. Bag-Of-Visual-Words (BOW) is widely known as an effective model for presenting rich-textured objects and scenes of places. Meanwhile, deep features are powerful for faces. Based on such state-of-the-art approaches, we introduce a framework to leverage BOW model and deep features for person-place video retrieval. First, we propose to use a linear kernel classifier instead of using $L_2$ distance to estimate the similarity of faces, given faces are represented by deep features. Second, scene tracking is employed to deal with the cases face of the query person is not detected. Third, we evaluate several strategies for fusing individual person search and location search results. Experiments were conducted on standard benchmark dataset (TRECVID Instance Search 2016) with more than 300 GB in storage and 464 hours in duration.
Intramolecular cyclization of the antimicrobial peptide Polybia‐MPI with triazole stapling: influence on stability and bioactivity

Cationic antimicrobial peptides have attracted increasing attention as a novel class of antibiotics to treat infectious diseases caused by pathogenic bacteria. However, susceptibility to protease is a shortcoming in their development. Cyclization is one approach to increase the proteolytic resistance of peptides. Therefore, to improve the proteolytic resistance of Polybia‐MPI, we have synthesized the MPI cyclic analogs C‐MPI‐1 (i‐to‐i+4) and C‐MPI‐2 (i‐to‐i+6) by copper(I)‐catalyzed azide–alkyne cycloaddition. Compared with MPI, C‐MPI‐1 displayed sustained antimicrobial activity and had enhanced anti‐trypsin resistance, while C‐MPI‐2 displayed no antimicrobial activity. The relationship between peptide structure and bioactivity was further investigated by probing the secondary structure of the peptides by circular dichroism. This showed that C‐MPI‐1 adopted an α‐helical structure in aqueous solution and, interestingly, had increased α‐helical conformation in 30 mM sodium dodecyl sulfate and 50% trifluoroethyl alcohol compared with MPI. C‐MPI‐2 that was not α‐helical in structure, suggesting that the propensity for α‐helix conformation may play an important role in cyclic peptide design. In addition, scanning electron microscopy, propidium iodide uptake, and membrane permeabilization assays indicated that MPI and the optimized analog C‐MPI‐1 had membrane‐active action modes, indicating that the peptides would not be susceptible to conventional resistance mechanisms. Our study provides additional insight into the influence of intramolecular cyclization at various positions on peptide structure and biological activity. In conclusion, the design and synthesis of cyclic analogs via click chemistry offer a new strategy for the development of stable antimicrobial agents. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
SEARCHES FOR TIME-DEPENDENT NEUTRINO SOURCES WITH ICECUBE DATA FROM 2008 TO 2012

In this paper searches for flaring astrophysical neutrino sources and sources with periodic emission with the IceCube neutrino telescope are presented. In contrast to time-integrated searches, where steady emission is assumed, the analyses presented here look for a time-dependent signal of neutrinos using the information from the neutrino arrival times to enhance the discovery potential. A search was performed for correlations between neutrino arrival times and directions, as well as neutrino emission following time-dependent light curves, sporadic emission, or periodicities of candidate sources. These include active galactic nuclei, soft γ-ray repeaters, supernova remnants hosting pulsars, microquasars, and X-ray binaries. The work presented here updates and extends previously published results to a longer period that covers 4 years of data from 2008 April 5 to 2012 May 16, including the first year of operation of the completed 86 string detector. The analyses did not find any significant time-dependent point sources of neutrinos, and the results were used to set upper limits on the neutrino flux from source candidates.
Cytotoxic Properties of Lyophilized Beers in a Malignant Cell Line

Moderate beer consumption can be considered as part of a healthy diet since it may protect against heart disease, cancer and osteoporosis. The protective effects of beer reside in its polyphenol content whose chemical composition appears extremely complex. In the present study, five commercial beers with different polyphenol content (ranging between 690 - 2400 μM equivalents of quercetin) were employed to investigate their cytotoxic effect in vitro on HL-60 cells derived from a human promyelocytic leukemia cell line. A significant reduction in cell viability was measured after 48 hours treatment. Lyophilized beers with higher polyphenol content showed the highest cytotoxicity compared to those with lower concentrations. However, when the assay was performed applying equal amounts of total polyphenols from different lyophilized beers, the sample possessing lowest amount of polyphenols (690 μM equivalents of quercetin) resulted the most effective in reducing cell viability. These data suggest that the biological activities of polyphenols present in beer are not simply dependent upon their total concentration, but qualitative profile and relative concentrations are even more important in determining their antiproliferative effects on cancer cells.
HELP or HELP to: What Do Corpora Have to Say?

In this paper, we will examine a range of factors that may potentially influence a language user's choice of a full or bare infinitive following HELP. The factors include language variety, language change, spoken/written distinction, semantic distinction, and syntactic conditions, namely, an intervening noun phrase or adverbial, the number of intervening words, to preceding HELP, the passive construction, inflections of HELP, and it as the subject. Six corpora are used in this paper, four written corpora (LOB, Brown, FLOB and Frown) and two spoken corpora (the speech section of the BNC and the Corpus of Professional Spoken American English, CPSA).
Vanin-1 Is a Key Activator for Hepatic Gluconeogenesis

Vanin-1 (VNN1) is a liver-enriched oxidative stress sensor that has been implicated in the regulation of multiple metabolic pathways. Clinical investigations indicated that the levels of VNN1 were increased in the urine and blood of diabetic patients, but the physiological significance of this phenomenon remains unknown. In this study, we demonstrated that the hepatic expression of VNN1 was induced in fasted mice or mice with insulin resistance. Gain- and loss-of-function studies indicated that VNN1 increased the expression of gluconeogenic genes and hepatic glucose output, which led to hyperglycemia. These effects of VNN1 on gluconeogenesis were mediated by the regulation of the Akt signaling pathway. Mechanistically, vnn1 transcription was activated by the synergistic interaction of peroxisome proliferator–activated receptor γ coactivator 1α (PGC-1α) and hepatocyte nuclear factor-4α (HNF-4α). A chromatin immunoprecipitation analysis indicated that PGC-1α was present near the HNF-4α binding site on the proximal vnn1 promoter and activated the chromatin structure. Taken together, our results suggest an important role for VNN1 in regulating hepatic gluconeogenesis. Therefore, VNN1 may serve as a potential therapeutic target for the treatment of metabolic diseases caused by overactivated gluconeogenesis.
NIEHS Funds New Centers in Texas and California

Purified CenH3 IP material was electrophoretically separated on a 18-20% SDSPAGE gel, individual proteins were either visualized by Coomassie Brilliant Blue stain excised and subjected to an in-gel tryptic digest (digests were performed as described (Shevchenko et al, 1996), or the eluted CenH3 particles were precipitated with 10% trichloroacetic acid, washed once with acetone, dried, re-dissolved in de-ionized water, and digested in solution with Arg-C protease. For CenH3 identification, we could not detect peptides from the protein directly in the gel slice containing the tetramer (confirmed by Western blot analysis). Therefore, we used eluted CenH3 protein from extensively washed CenH3IP-beads.
Trust: Different Views, One Goal

A thorough review of trust models is carried out in this paper to reveal the key capabilities of existing trust models and compare how they differ among disciplines. Trust decisions are risky due to uncertainties and the loss of control. On the other hand, not trusting might mean giving up some potential benefits. Advances in electronic transactions, mutliagent systems, and decision support systems create a necessity to develop trust and reputation models. The development of such models will allow for trust reasoning and decisions to be made in situations with high risk and uncertainty. In recent years, several attempts have been made to model reputation and trust. However, perceiving trust differently and the lack of having a unified trust definition are among the main causes of the proliferation of many trust models across different disciplines.
Monte carlo bayesian hierarchical reinforcement learning

In this paper, we propose to use hierarchical action decomposition to make Bayesian model-based reinforcement learning more efficient and feasible in practice. We formulate Bayesian hierarchical reinforcement learning as a partially observable semi-Markov decision process (POSMDP). The main POSMDP task is partitioned into a hierarchy of POSMDP subtasks; lower-level subtasks get solved first, then higher-level ones. We sample from a prior belief to build an approximate model for each POSMDP, then solve using Monte Carlo Value Iteration with Macro-Actions solver. Experimental results show that our algorithm performs significantly better than that of flat BRL in terms of both reward, and especially solving time, in at least one order of magnitude.
Improving Transparent Visualization of Large-Scale Laser-Scanned Point Clouds by Using Poisson Disk Sampling

In recent years, due to the development of laser-measurement technology, 3D laser-scanned point clouds for cultural assets are often used as the recording format of digital archiving. The acquired point clouds are large-scale and precisely record complex 3D internal structures of the scanned objects. Visualization quality of such point clouds highly depends on density distributional uniformity, that is, the uniformity of the inter-point distances. The visualization quality can be improved by making point distances uniform. In addition, the visibility further improves by emphasizing edges. In this study, first the uniformity and flexible tuning of the point density based on Poisson disk sampling are examined. The resultant high-quality point clouds are then applied to transparent visualization. Moreover, edge emphasis visualization is realized by combining the principal component analysis calculating feature amount and Poisson disk sampling.
Evaluating and improving semistructured merge

While unstructured merge tools rely only on textual analysis to detect and resolve conflicts, semistructured merge tools go further by partially exploiting the syntactic structure and semantics of the involved artifacts. Previous studies compare these merge approaches with respect to the number of reported conflicts, showing, for most projects and merge situations, reduction in favor of semistructured merge. However, these studies do not investigate whether this reduction actually leads to integration effort reduction (productivity) without negative impact on the correctness of the merging process (quality). To analyze that, and better understand how merge tools could be improved, in this paper we reproduce more than 30,000 merges from 50 open source projects, identifying conflicts incorrectly reported by one approach but not by the other (false positives), and conflicts correctly reported by one approach but missed by the other (false negatives). Our results and complementary analysis indicate that, in the studied sample, the number of false positives is significantly reduced when using semistructured merge. We also find evidence that its false positives are easier to analyze and resolve than those reported by unstructured merge. However, we find no evidence that semistructured merge leads to fewer false negatives, and we argue that they are harder to detect and resolve than unstructured merge false negatives. Driven by these findings, we implement an improved semistructured merge tool that further combines both approaches to reduce the false positives and false negatives of semistructured merge. We find evidence that the improved tool, when compared to unstructured merge in our sample, reduces the number of reported conflicts by half, has no additional false positives, has at least 8% fewer false negatives, and is not prohibitively slower.
On Minimum-Latency Broadcast in Multichannel Duty-Cycled Wireless Sensor Networks

Broadcast has critical significance for wide application of wireless sensor networks (WSNs). Minimum-latency broadcast (MLB) studies how to devise a broadcast schedule, which can achieve minimum broadcast latency with no signal interference. In multichannel duty-cycled WSNs, nodes can exploit multiple channels to communicate and periodically fall asleep after working for some time. Nevertheless, most solutions to the MLB problem either focus on nonsleeping scenarios or only exploit one single channel. Therefore, we investigate the MLB problem in multichannel duty-cycled WSNs in this paper and call this problem as MLBCD problem. We prove that MLBCD problem is NP-hard. We propose a new concept of active interference graph (AIG). Based on AIG, we present one novel approximation broadcast algorithm called NAB to solve the MLBCD problem. We prove that our proposed NAB algorithm achieves provable performance guarantee. The results of our extensive evaluations show that NAB algorithm can significantly improve the broadcast latency.