Miracle-dz/UniFAR-FTUs huggingface dataset:
c-Jun Can Mediate Androgen Receptor-induced Transactivation*

The proto-oncoprotein c-Jun forms as a heterodimer with c-Fos, the transcription factor AP-1. AP-1 regulates transcription through transactivation, a process requiring DNA binding. Here we report an indirect mechanism by which c-Jun can regulate transcription via the androgen receptor. In this process, c-Jun is able to support androgen receptor-mediated transactivation in the absence of an interaction with c-Fos or any apparent DNA binding. This positive effect of c-Jun was dose-dependent. Both exogenously added and endogenously induced c-Jun are able to act on the androgen receptor. Transactivation by the androgen receptor can undergo self-squelching, and this was relieved by transfected c-Jun. Using a time-course experiment, we provide evidence that the c-Jun effect is primary. c-Fos is able to block human androgen receptor activity in both the absence and presence of transfected c-Jun. Using a modified form of the yeast two-hybrid system, we show in Cos cells that c-Jun can interact with the DNA binding domain/hinge region (CD regions) of the androgen receptor. Therefore, we propose that c-Jun functions as a mediator for androgen receptor-induced transactivation.
Full counting statistics of nano-electromechanical systems

We develop a theory for the full counting statistics (FCS) for a class of nanoelectromechanical systems (NEMS), describable by a Markovian generalized master equation. The theory is applied to two specific examples of current interest: vibrating C60-molecules and quantum shuttles. We report a numerical evaluation of the first three cumulants for the C60 setup; for the quantum shuttle we use the third cumulant to substantiate that the giant enhancement in noise observed at the shuttling transition is due to a slow switching between two competing conduction channels. Especially the last example illustrates the power of the FCS.
The application of knemometry to measure childhood short-term growth among the indigenous Shuar of Ecuador.

OBJECTIVES Knemometry, the precise measurement of lower leg (LL) length, suggests that childhood short-term (e.g., weekly) growth is a dynamic, nonlinear process. However, owing to the large size and complexity of the traditional knemometer device, previous study of short-term growth among children has been restricted predominantly to clinical settings in industrialized Western nations. The aim of the present study is to address this limitation and promote broader understandings of global variation in childhood development by: (1) describing a custom-built portable knemometer and assessing its performance in the field; and (2) demonstrating the potential application of such a device by characterizing childhood short-term LL growth among the indigenous Shuar of Amazonian Ecuador. MATERIALS AND METHODS Mixed-longitudinal LL length data were collected weekly from 336 Shuar children age 5-12 years old using the custom portable knemometer (n = 1,145 total observations). Device performance and Shuar short-term LL growth were explored using linear mixed effects models and descriptive statistics. RESULTS The portable knemometer performed well across a range of participant characteristics and possesses a low technical error of measurement of 0.18 mm. Shuar childhood LL growth averages 0.47 mm/week (SD = 0.75 mm/week), but exhibits large between- and within-individual variation. DISCUSSION Knemometry can be reliably performed in the field, providing a means for evaluating childhood short-term growth among genetically and ecologically diverse populations. Preliminary findings suggest that Shuar weekly LL growth is comparable in mean magnitude but likely more variable than reported for healthy Western children. Future work will further explore these patterns. Am J Phys Anthropol 160:353-357, 2016. © 2016 Wiley Periodicals, Inc.
An Information-Theoretic Measure of Intrusion Detection Capability

A fundamental problem in intrusion detection is what metric(s) can be used to objectively evaluate an intrusion detection system (IDS) in terms of its ability to correctly classify events as normal or intrusion. In this paper, we provide an in-depth analysis of existing metrics. We argue that the lack of a single unified metric makes it difficult to fine tune and evaluate an IDS. The intrusion detection process can be examined from an information-theoretic point of view. Intuitively, we should have less uncertainty about the input (event data) given the IDS output (alarm data). We thus propose a new metric called Intrusion Detection Capability, CID, which is simply the ratio of the mutual information between IDS input and output, and the entropy of the input. CID has the desired property that: (1) it takes into account all the important aspects of detection capability naturally, i.e., true positive rate, false positive rate, positive predictive value, negative predictive value, and base rate; (2) it objectively provide an intrinsic measure of intrusion detection capability; (3) it is sensitive to IDS operation parameters. We propose that CID is the appropriate performance measure to maximize when fine tuning an IDS. The thus obtained operation point is the best that can be achieved by the IDS in terms of its intrinsic ability to classify input data. We use numerical examples as well as experiments of actual IDSs on various datasets to show that using CID, we can choose the best (optimal) operating point for an IDS, and can objectively compare different IDSs.
Task Alternation in Parallel Sentence Retrieval for Twitter Translation

We present an approach to mine comparable data for parallel sentences using translation-based cross-lingual information retrieval (CLIR). By iteratively alternating between the tasks of retrieval and translation, an initial general-domain model is allowed to adapt to in-domain data. Adaptation is done by training the translation system on a few thousand sentences retrieved in the step before. Our setup is time- and memory-efficient and of similar quality as CLIR-based adaptation on millions of parallel sentences.
Inactivation of the Sodium Current in Myxicola Giant Axons

Experiments were conducted on Myxicola giant axons to determine if the sodium activation and inactivation processes are coupled or independent. The main experimental approach was to examine the effects of changing test pulses on steady-state inactivation curves. Arguments were presented to show that in the presence of a residual uncompensated series resistance the interpretation of the results depends critically on the manner of conducting the experiment. Analytical and numerical calculations were presented to show that as long as test pulses are confined to an approximately linear negative conductance region of the sodium current-voltage characteristic, unambiguous interpretations can be made. When examined in the manner of Hodgkin and Huxley, inactivation in Myxicola is quantitatively similar to that described by the h variable in squid axons. However, when test pulses were increased along the linear negative region of the sodium current-voltage characteristic, steady-state inactivation curves translate to the right along the voltage axis. The shift in the inactivation curve is a linear function of the ratio of the sodium, conductance of the test pulses, showing a 5.8 mv shift for a twofold increase in conductance. An independent line of evidence indicated that the early rate of development of inactivation is a function of the rise of the sodium conductance.
Stochastic Dependency Parsing Based on A* Admissible Search

Dependency parsing has gained attention in natural language understanding because the representation of dependency tree is simple, compact and direct such that robust partial understanding and task portability can be achieved more easily. However, many dependency parsers make hard decisions with local information while selecting among the next parse states. As a consequence, though the obtained dependency trees are good in some sense, the N-best output is not guaranteed to be globally optimal in general. In this paper, a stochastic dependency parsing scheme based on A* admissible search is formally presented. By well representing the parse state and appropriately designing the cost and heuristic functions, dependency parsing can be modeled as an A* search problem, and solved with a generic algorithm of state space search. When evaluated on the Chinese Tree Bank, this parser can obtain 85.99% dependency accuracy at 68.39% sentence accuracy, and 14.62% node ratio for dynamic heuristic. This parser can output N-best dependency trees, and integrate the semantic processing into the search process easily.
Advanced Automobile Recognition Through the Use of Image Processing Techniques

Many law enforcement agencies have recently shown interest in automated automobile recognition and tracking technologies such as license plate reading or GPS tracking. However, some criminals may drive vehicles that have false license plates or are not equipped with GPS tracking devices, making the pursuit of such vehicles diﬃcult. This project aims to create a computer vision system capable of taking real-time input from a static camera and identifying passing cars by make and model in order to assist law enforcement agencies in the tracking of suspect or stolen vehicles. Vehicle identiﬁcation is accomplished using a combination of old and new algorithmic image processing techniques.
Recent Progress on Metamaterial-inspired Antennas

Many attributes of metamaterials have led to the consideration of engineering metamaterialinspired structures for a variety of applications. This includes the miniaturization of resonators and their use for improving the performance characteristics of electrically small antennas from the microwave region up through to the optical region. Achieving higher directivity from electrically small antennas by introducing structured ground planes has been considered successfully. Active metamaterial constructs have been introduced to increase the bandwidths at low frequencies and to overcome the losses at high frequencies. They have led to recent non-Foster antenna designs which have some preliminary experimental results. Thus the development of an efficient, high directivity, large bandwidth electrically small antenna is rapidly becoming a possibility.
A G 1-like state allows HIV-1 to bypass SAMHD 1 restriction in macrophages

An unresolved question is how HIV-1 achieves efficient replication in terminally differentiated macrophages despite the restriction factor SAMHD1. We reveal inducible changes in expression of cell cycle-associated proteins including MCM2 and cyclins A, E, D1/D3 in macrophages, without evidence for DNA synthesis or mitosis. These changes are induced by activation of the Raf/MEK/ERK kinase cascade, culminating in upregulation of CDK1 with subsequent SAMHD1 T592 phosphorylation and deactivation of its antiviral activity. HIV infection is limited to these G1-like phase macrophages at the single-cell level. Depletion of SAMHD1 in macrophages decouples the association between infection and expression of cell cycle-associated proteins, with terminally differentiated macrophages becoming highly susceptible to HIV-1. We observe both embryo-derived and monocyte-derived tissueresident macrophages in a G1-like phase at frequencies approaching 20%, suggesting how macrophages sustain HIV-1 replication in vivo. Finally, we reveal a SAMHD1-dependent antiretroviral activity of histone deacetylase inhibitors acting via p53 activation. These data provide a basis for host-directed therapeutic approaches aimed at limiting HIV-1 burden in macrophages that may contribute to curative interventions.
Multiscale modeling of dewetting damage in highly filled particulate composites

Particle debonding or dewetting constitutes one of the key damage processes in highly filled particulate composites such as solid propellant and other energetic materials. To analyze this failure process, we have developed a multiscale finite element framework that combines, at the microscale, a nonlinear description of the binder response with a cohesive model of the damage process taking place in a representative periodic unit cell (PUC). To relate micro‐scale damage to the macroscopic constitutive response of the material, we employ the mathematical theory of homogenization (MTH). After a description of the numerical scheme, we present the results of the damage response of a highly filled particulate composite subjected to a uniaxial macroscopic strain, and show the direct correlation between the complex damage processes taking place in the PUC and the nonlinear macroscopic constitutive response. We also present a detailed study of the PUC size and a comparison between the finite element MTH‐based stud.
Misfolded Proinsulin Affects Bystander Proinsulin in Neonatal Diabetes*

It has previously been shown that misfolded mutant Akita proinsulin in the endoplasmic reticulum engages directly in protein complexes either with nonmutant proinsulin or with “hProCpepGFP” (human proinsulin bearing emerald-GFP within the C-peptide), impairing the trafficking of these “bystander” proinsulin molecules (Liu, M., Hodish, I., Rhodes, C. J., and Arvan, P. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 15841–15846). Herein, we generated transgenic mice, which, in addition to expressing endogenous proinsulin, exhibit β-cell-specific expression of hProCpepGFP via the Ins1 promoter. In these mice, hProCpepGFP protein levels are physiologically regulated, and hProCpepGFP is packaged and processed to CpepGFP that is co-stored in β-secretory granules. Visualization of CpepGFP fluorescence provides a quantifiable measure of pancreatic islet insulin content that can be followed in live animals in states of health and disease. We examined loss of pancreatic insulin in hProCpepGFP transgenic mice mated to Akita mice that develop neonatal diabetes because of the expression of misfolded proinsulin. Loss of bystander insulin in Akita animals is detected initially as a block in CpepGFP/insulin production with intracellular accumulation of the precursor, followed ultimately by loss of pancreatic β-cells. The data support that misfolded proinsulin perturbs bystander proinsulin in the endoplasmic reticulum, leading to β-cell failure.
Image Matting with KL-Divergence Based Sparse Sampling

Previous sampling-based image matting methods typically rely on certain heuristics in collecting representative samples from known regions, and thus their performance deteriorates if the underlying assumptions are not satisfied. To alleviate this, in this paper we take an entirely new approach and formulate sampling as a sparse subset selection problem where we propose to pick a small set of candidate samples that best explains the unknown pixels. Moreover, we describe a new distance measure for comparing two samples which is based on KL-divergence between the distributions of features extracted in the vicinity of the samples. Using a standard benchmark dataset for image matting, we demonstrate that our approach provides more accurate results compared with the state-of-the-art methods.
Parsimonious Path Openings and Closings

Path openings and closings are morphological tools used to preserve long, thin, and tortuous structures in gray level images. They explore all paths from a defined class, and filter them with a length criterion. However, most paths are redundant, making the process generally slow. Parsimonious path openings and closings are introduced in this paper to solve this problem. These operators only consider a subset of the paths considered by classical path openings, thus achieving a substantial speed-up, while obtaining similar results. In addition, a recently introduced 1D opening algorithm is applied along each selected path. Its complexity is linear with respect to the number of pixels, independent of the size of the opening. Furthermore, it is fast for any input data accuracy (integer or floating point) and works in stream. Parsimonious path openings are also extended to incomplete paths, i.e., paths containing gaps. Noise-corrupted paths can thus be processed with the same approach and complexity. These parsimonious operators achieve a several orders of magnitude speed-up. Examples are shown for incomplete path openings, where computing times are brought from minutes to tens of milliseconds, while obtaining similar results.
The application of the fibroblast activation protein α-targeted immunotherapy strategy

Cancer immunotherapy has primarily been focused on attacking tumor cells. However, given the close interaction between tumor cells and cancer-associated fibroblasts (CAFs) in the tumor microenvironment (TME), CAF-targeted strategies could also contribute to an integrated cancer immunotherapy. Fibroblast activation protein α (FAP α) is not detectible in normal tissues, but is overexpressed by CAFs and is the predominant component of the stroma in most types of cancer. FAP α has both dipeptidyl peptidase and endopeptidase activities, cleaving substrates at a post-proline bond. When all FAP α-expressing cells (stromal and cancerous) are destroyed, tumors rapidly die. Furthermore, a FAP α antibody, FAP α vaccine, and modified vaccine all inhibit tumor growth and prolong survival in mouse models, suggesting FAP α is an adaptive tumor-associated antigen. This review highlights the role of FAP α in tumor development, explores the relationship between FAP α and immune suppression in the TME, and discusses FAP α as a potential immunotherapeutic target.
Isotonic Hawkes Processes

Hawkes processes are powerful tools for modeling the mutual-excitation phenomena commonly observed in event data from a variety of domains, such as social networks, quantitative finance and healthcare records. The intensity function of a Hawkes process is typically assumed to be linear in the sum of triggering kernels, rendering it inadequate to capture nonlinear effects present in real-world data. To address this shortcoming, we propose an Isotonic-Hawkes process whose intensity function is modulated by an additional nonlinear link function. We also developed a novel iterative algorithm which learns both the nonlinear link function and other parameters provably. We showed that Isotonic-Hawkes processes can fit a variety of nonlinear patterns which cannot be captured by conventional Hawkes processes, and achieve superior empirical performance in real world applications.
XSPECT, estimation of the angular power spectrum by computing cross-power spectra with analytical error bars

We present Xspect, a method to obtain estimates of the angular power spectrum of the cosmic microwave background (CMB) temperature anisotropies including analytical error bars developed for the Archeops experiment. Cross-power spectra are computed from a set of maps and each of them is in itself an unbiased estimate of the power spectrum as long as the detector noises are uncorrelated. Then, the cross-power spectra are combined into a final temperature power spectrum with error bars analytically derived from the cross-correlation matrix. This method presents three main useful properties: (1) no estimation of the noise power spectrum is needed; (2) complex weighting schemes including sky covering and map noise properties can be easily taken into account, and corrected for, for each input map; and (3) error bars are quickly computed analytically from the data themselves with no Monte Carlo simulations involved. Xspect also permits the study of common fluctuations between maps from different sky surveys such as CMB, Sunyaev–Zel'dovich effect or mass fluctuations from weak lensing observations.
An Online Cascaded Approach to Biomedical Named Entity Recognition

We present an online cascaded approach to biomedical named entity recognition. This approach uses an online training method to substantially reduce the training time required and a cascaded framework to relax the memory requirement. We conduct detailed experiments on the BioNLP dataset from the JNLPBA shared task and compare the results with other systems and published works. Our experimental results show that our approach achieves comparable performance with great reductions in time and space requirements.
Tautomycetin is a novel and specific inhibitor of serine/threonine protein phosphatase type 1, PP1.

Here we isolated tautomycetin, TC, and examined its phosphatase inhibitory activity. Recently we have reported that the left-hand moiety of tautomycin, TM, and the right one containing the spiroketal are essentially required for inhibition of protein phosphatase, PP, and induction of apoptosis, respectively. TC is structurally almost identical to TM except that TC is lacking the spiroketal, which has the potential apoptosis-inducing activity. TC specifically inhibited PP1 activity, IC50 values for purified PP1 and PP2A enzymes being 1.6 and 62 nM, respectively, whereas the IC50 values of TM were 0.21 and 0.94 nM, respectively. These results demonstrate that TC is the most specific PP1 inhibitor out of over 40 species of natural phosphatase inhibitors reported, strongly suggesting that TC is a novel powerful tool to elucidate the physiological roles of PP1 in various biological events.
Cough assistance device for patients with glottis dysfunction and/or tracheostomy.

OBJECTIVE To estimate the efficiency of a cough assistance device, the Cough Aid, in patients with weak respiratory muscles with bulbar palsy and/or tracheostomy. The Cough Aid is a device that has been developed to substitute for glottis function. DESIGN Before-after trial. SUBJECTS/PATIENTS A total of 74 patients with bulbar palsy and/or tracheostomy, as well as respiratory muscle weakness, were recruited. METHODS Forced vital capacity, unassisted cough peak flow, lung insufflation capacity, and assisted cough peak flow were measured via tracheostomy or oronasal interface. Lung insufflation capacity and assisted cough peak flow were measured using the Cough Aid. RESULTS AND CONCLUSION In all 74 subjects, lung insufflation capacities measured with the device were significantly higher than forced vital capacities (p < 0.01). Assisted cough peak flows measured using the device were also significantly higher than unassisted cough peak flows (p < 0.01). The Cough Aid is effective in helping to increase cough flow and assisting in the air stacking exercise by substituting the function of the glottis in patients who have glottis dysfunction or a tracheostomy tube.
In vivo induction of postsynaptic molecular assembly by the cell adhesion molecule Fasciclin2

Cell adhesion molecules (CAMs) are thought to mediate interactions between innervating axons and their targets. However, such interactions have not been directly observed in vivo. In this paper, we study the function and dynamics of Fasciclin2 (Fas2), a homophilic CAM expressed both pre- and postsynaptically during neuromuscular synapse formation in Drosophila melanogaster. We apply live imaging of functional fluorescent fusion proteins expressed in muscles and find that Fas2 and Discs-Large (Dlg; a scaffolding protein known to bind Fas2) accumulate at the synaptic contact site soon after the arrival of the nerve. Genetic, deletion, and photobleaching analyses suggest that Fas2-mediated trans-synaptic adhesion is important for the postsynaptic accumulation of both Fas2 itself and Dlg. In fas2 mutants, many aspects of synapse formation appear normal; however, we see a reduction in the synaptic accumulation of Scribble (another scaffolding protein) and glutamate receptor subunits GluRIIA and GluRIIB. We propose that Fas2 mediates trans-synaptic adhesion, which contributes to postsynaptic molecular assembly at the onset of synaptogenesis.