Miracle-dz/UniFAR-FTUs huggingface dataset:
Anterior–Posterior Axis Specification in Drosophila Oocytes: Identification of Novel bicoid and oskar mRNA Localization Factors

The Drosophila melanogaster anterior–posterior axis is established during oogenesis by the localization of bicoid and oskar mRNAs to the anterior and posterior poles of the oocyte. Although genetic screens have identified some trans-acting factors required for the localization of these transcripts, other factors may have been missed because they also function at other stages of oogenesis. To circumvent this problem, we performed a screen for revertants and dominant suppressors of the bicaudal phenotype caused by expressing Miranda–GFP in the female germline. Miranda mislocalizes oskar mRNA/Staufen complexes to the oocyte anterior by coupling them to the bicoid localization pathway, resulting in the formation of an anterior abdomen in place of the head. In one class of revertants, Miranda still binds Staufen/oskar mRNA complexes, but does not localize to the anterior, identifying an anterior targeting domain at the N terminus of Miranda. This has an almost identical sequence to the N terminus of vertebrate RHAMM, which is also a large coiled-coil protein, suggesting that it may be a divergent Miranda ortholog. In addition, we recovered 30 dominant suppressors, including multiple alleles of the spectroplakin, short stop, a lethal complementation group that prevents oskar mRNA anchoring, and a female sterile complementation group that disrupts the anterior localization of bicoid mRNA in late oogenesis. One of the single allele suppressors proved to be a mutation in the actin nucleator, Cappuccino, revealing a previously unrecognized function of Cappuccino in pole plasm anchoring and the induction of actin filaments by Long Oskar protein.
Simulation-based estimation of the partition function and the information rate of two-dimensional models

Monte Carlo methods are considered to compute, first, the partition function of graphical models, and second, the information rate of source/channel models, in both cases for factor graphs with cycles. The convergence of two basic Monte Carlo methods is improved by sampling only a cycle breaking subset of the variables and using exact sum-product computations for the remaining variables. The methods are demonstrated by their application to a two-dimensional Ising model and to a two-dimensional intersymbol interference channel.
Frontal eye field, where art thou? Anatomy, function, and non-invasive manipulation of frontal regions involved in eye movements and associated cognitive operations

The planning, control and execution of eye movements in 3D space relies on a distributed system of cortical and subcortical brain regions. Within this network, the Eye Fields have been described in animals as cortical regions in which electrical stimulation is able to trigger eye movements and influence their latency or accuracy. This review focuses on the Frontal Eye Field (FEF) a “hub” region located in Humans in the vicinity of the pre-central sulcus and the dorsal-most portion of the superior frontal sulcus. The straightforward localization of the FEF through electrical stimulation in animals is difficult to translate to the healthy human brain, particularly with non-invasive neuroimaging techniques. Hence, in the first part of this review, we describe attempts made to characterize the anatomical localization of this area in the human brain. The outcome of functional Magnetic Resonance Imaging (fMRI), Magneto-encephalography (MEG) and particularly, non-invasive mapping methods such a Transcranial Magnetic Stimulation (TMS) are described and the variability of FEF localization across individuals and mapping techniques are discussed. In the second part of this review, we will address the role of the FEF. We explore its involvement both in the physiology of fixation, saccade, pursuit, and vergence movements and in associated cognitive processes such as attentional orienting, visual awareness and perceptual modulation. Finally in the third part, we review recent evidence suggesting the high level of malleability and plasticity of these regions and associated networks to non-invasive stimulation. The exploratory, diagnostic, and therapeutic interest of such interventions for the modulation and improvement of perception in 3D space are discussed.
IBIsCO: A molecular dynamics simulation package for coarse‐grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse‐grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe–Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse‐graining. The reverse nonequilibrium molecular dynamics simulation method (Müller‐Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Segment reduction in disyllabic words with tones in standard Chinese

This paper studies the acoustic properties of segments in different syllable positions of words with tones in Standard Chinese. Through the investigation of monophthongs and aspirated stops in disyllabic words in broadcast news speech, gradient reduction is found for both vowels and consonants in the second syllable position-vowels tend to be centralized in the F1/F2 vowel space, and aspirated stops exhibit a continuum of reduction. The differentiation of syllable positions in the phonetic realization of segments is consistent with the prediction of the trochaic metrical structure hypothesis for Standard Chinese.
LaSTUS/TALN @ CLSciSumm-17: Cross-document Sentence Matching and Scientific Text Summarization Systems

Comunicacio presentada a: CL-SciSumm 2017, organitzat com a part de The 2nd Joint Workshop on Bibliometric-enhanced Information Retrieval and Natural Language Processing for Digital Libraries (BIRNDL 2017) i conjuntament amb The 40th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2017)
Searching for a Single Community in a Graph

In standard graph clustering/community detection, one is interested in partitioning the graph into more densely connected subsets of nodes. In contrast, the search problem of this article aims to only find the nodes in a single such community, the target, out of the many communities that may exist. To do so, we are given suitable side information about the target; for example, a very small number of nodes from the target are labeled as such. We consider a general yet simple notion of side information: all nodes are assumed to have random weights, with nodes in the target having higher weights on average. Given these weights and the graph, we develop a variant of the method of moments that identifies nodes in the target more reliably, and with lower computation, than generic community detection methods that do not use side information and partition the entire graph. Our empirical results show significant gains in runtime, and also gains in accuracy over other graph clustering algorithms.
Hedging Barrier Options: Current Methods and Alternatives

This paper applies to the static hedge of barrier options a technique, mean-square hedging, designed to minimize the size of the hedging error when perfect replication is not possible. It introduces an extension of this technique which preserves the computational efficiency of mean-square hedging while being consistent with any prior pricing model or with any linear constraint on the hedging residual. This improves on current static hedging methods, which aim at exactly replicating barrier options and rely on strong assumptions on the availability of traded options with certain strikes or maturities, or on the distribution of the underlying asset.
Comparative Gene Prediction using Conditional Random Fields

Computational gene prediction using generative models has reached a plateau, with several groups converging to a generalized hidden Markov model (GHMM) incorporating phylogenetic models of nucleotide sequence evolution. Further improvements in gene calling accuracy are likely to come through new methods that incorporate additional data, both comparative and species specific. Conditional Random Fields (CRFs), which directly model the conditional probability P(y|x) of a vector of hidden states conditioned on a set of observations, provide a unified framework for combining probabilistic and non-probabilistic information and have been shown to outperform HMMs on sequence labeling tasks in natural language processing. We describe the use of CRFs for comparative gene prediction. We implement a model that encapsulates both a phylogenetic-GHMM (our baseline comparative model) and additional non-probabilistic features. We tested our model on the genome sequence of the fungal human pathogen Cryptococcus neoformans. Our baseline comparative model displays accuracy comparable to the the best available gene prediction tool for this organism. Moreover, we show that discriminative training and the incorporation of non-probabilistic evidence significantly improve performance. Our software implementation, Conrad, is freely available with an open source license at http://www.broad. mit.edu/annotation/conrad/.
Muscular activity when walking in a non-anthropomorphic wearable robot

Wearable robots should be designed not to alter human physiological motion. Perturbations introduced by a robot can be quantified by measuring EMG activity. This paper presents tests on the LENAR, an intrinsically back-drivable non-anthropomorphic lower limb wearable robot designed to provide hip and knee flexion/extension assistance. In previous works the robot was demonstrated to exhibit low mechanical impedance and to introduce minor alterations to human kinematic patterns during walking. In this paper muscular activity is assessed, demonstrating small alterations in the EMG patterns during the interaction with the robot, in both unpowered and assistive mode.
Distributed Optimal Frequency Control Considering a Nonlinear Network-Preserving Model

This paper addresses the distributed optimal frequency control of power systems considering a network-preserving model with nonlinear power flows and excitation voltage dynamics. Salient features of the proposed distributed control strategy are fourfold, first, nonlinearity is considered to cope with large disturbances, second, only a part of generators are controllable, third, no load measurement is required, fourth, communication connectivity is required only for the controllable generators. To this end, benefiting from the concept of “virtual load demand,” we first design the distributed controller for the controllable generators by leveraging the primal-dual decomposition technique. We then propose a method to estimate the virtual load demand of each controllable generator based on local frequencies. We derive incremental passivity conditions for the uncontrollable generators. Finally, we prove that the closed-loop system is asymptotically stable and its equilibrium attains the optimal solution to the associated economic dispatch problem. Simulations, including small and large-disturbance scenarios, are carried on the New England system, demonstrating the effectiveness of our design.
Effects of Subinhibitory Concentrations of Ceftaroline on Methicillin-Resistant Staphylococcus aureus (MRSA) Biofilms

Ceftaroline (CPT) is a novel cephalosporin with in vitro activity against Staphylococcus aureus. Ceftaroline exhibits a level of binding affinity for PBPs in S. aureus including PBP2a of methicillin-resistant S. aureus (MRSA). The aims of this study were to investigate the morphological, physiological and molecular responses of MRSA clinical strains and MRSA biofilms to sub-MICs (1/4 and 1/16 MIC) of ceftaroline by using transmission, scanning and confocal microscopy. We have also used quantitative Real-Time PCR to study the effect of sub-MICs of ceftaroline on the expression of the staphylococcal icaA, agrA, sarA and sasF genes in MRSA biofilms. In one set of experiments, ceftaroline was able to inhibit biofilm formation in all strains tested at MIC, however, a strain dependent behavior in presence of sub-MICs of ceftaroline was shown. In a second set of experiments, destruction of preformed biofilms by addition of ceftaroline was evaluated. Ceftaroline was able to inhibit biofilm formation at MIC in all strains tested but not at the sub-MICs. Destruction of preformed biofilms was strain dependent because the biofilm formed by a matrix-producing strain was resistant to a challenge with ceftaroline at MIC, whereas in other strains the biofilm was sensitive. At sub-MICs, the impact of ceftaroline on expression of virulence genes was strain-dependent at 1/4 MIC and no correlation between ceftaroline-enhanced biofilm formation and gene regulation was established at 1/16 MIC. Our findings suggest that sub-MICs of ceftaroline enhance bacterial attachment and biofilm formation by some, but not all, MRSA strains and, therefore, stress the importance of maintaining effective bactericidal concentrations of ceftaroline to fight biofilm-MRSA related infections.
Instantaneous microwave frequency measurement using a microfiber ring resonator (MRR) based photonic differentiator

A novel photonic approach for the instantaneous microwave frequencies measurement (IFM) using microfiber ring resonator (MRR)-based photonic differentiator is proposed and experimentally demonstrated. A square and monotonic relationship between the amplitude comparison function (ACF) and the frequency of the incoming microwave signal is established and used for the microwave frequency estimation, with a capability of wide measurement range. Since the MRR can be fabricated flexibly and only one light source, one modulator and one photodetector are needed, the complexity and cost of the proposed IFM system is considerably reduced. A proof-of-concept experiment has been performed with a measurement error less than ±0.4 GHz over the frequency range 0.5–12 GHz.
Leveraging Giant Text Corpora to Enhance the Coverage of Pattern-based Information Extraction Systems

Pattern-based approaches for Information Extraction typically apply a pattern learner to a set of domain-specific documents to generate extraction patterns that comprise the IE system. This limits the coverage of the system to the expressions and language constructs used within the training data. This research exploits the vast quantities of text readily available in large corpora, such as The Gigaword Corpus, to expand the coverage of existing pattern-based Information Extraction systems.
Online algorithm for third-order minimum time discrete tracking differentiator

This paper presents the third-order minimum time discrete tracking differentiator, which is to generate transient profiles of setpoint reference signal as well as the first and second derivatives, corresponding to transients of the position, velocity and acceleration. These signals contain useful information of dynamics that can improve the tracking performance of control systems. In order to accomplish the derivation of the minimum time tracking differentiator, a general algorithm is derived for solving minimum time control of discrete time systems. Then we focus on the third-order differentiator and make the implementation algorithm online applicable. The computation complexity is also evaluated by a simple formula, which judges whether the computation can be accomplished before the next time instant. Numerical examples are provided to illustrate the effectiveness of the proposed methods.
Curcuminoids Inhibit the Angiogenic Response Stimulated by Fibroblast Growth Factor-2, Including Expression of Matrix Metalloproteinase Gelatinase B*

We have studied mechanisms controlling activation of the gelatinase B gene (matrix metalloproteinase-9) by fibroblast growth factor-2 (FGF-2) during angiogenesis, and the effects of the natural product curcuminoids on this process. Using a transgenic mouse (line 3445) harboring a gelatinase B promoter/lacZ fusion gene, we demonstrate FGF-2 stimulation of reporter gene expression in endothelial cells of invading neocapillaries in the corneal micropocket assay. Using cultured corneal cells, we show that FGF-2 stimulates DNA binding activity of transcription factor AP-1 but not NF-κB and that AP-1 stimulation is inhibited by curcuminoids. We further show that induction of gelatinase B transcriptional promoter activity in response to FGF-2 is dependent on AP-1 but not NF-κB response elements and that promoter activity is also inhibited by curcuminoids. In rabbit corneas, the angiogenic response induced by implantation of an FGF-2 pellet is inhibited by the co-implantation of a curcuminoid pellet, and this correlates with inhibition of endogenous gelatinase B expression induced by FGF-2. Angiostatic efficacy in the cornea is also observed when curcuminoids are provided to mice in the diet. Our findings provide evidence that curcuminoids target the FGF-2 angiogenic signaling pathway and inhibit expression of gelatinase B in the angiogenic process.
Genetic Polymorphisms of SULT1A1 and SULT1E1 and the Risk and Survival of Breast Cancer

We examined whether common single nucleotide polymorphisms (SNP) in SULT1A1 (c.779G>A, *14A>G, and *85C>T) and SULT1E1 (IVS1-447C>A, IVS4-1653T>C, and *959G>A) genes influenced the risk and survival of breast cancer. Our study population consisted of 989 histologically confirmed sporadic breast cancer patients and 1,054 controls without history of cancer recruited from three teaching hospitals in Seoul. Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated by logistic regression model. In the survival analysis for 529 breast cancer patients with completed treatments, the hazard ratios (HR) were calculated with Cox proportional hazard model. Women with the SULT1E1 *959 GA/AA genotype had a moderately decreased breast cancer risk compared with those with the GG genotypes (OR, 0.8; 95% CI, 0.70-1.00). When the haplotypes were considered, the homozygous *959 AA genotype together with the IVS4-1653 T>C base change (CTA-CCA haplotype) was associated with halved breast cancer risk (OR, 0.5; 95% CI, 0.24-0.88) compared with the wild type CTG-CTG haplotype. No other significant overall association was observed between the SULT1A1 and SULT1E1 SNPs nor haplotypes and breast cancer risk. When stratified by survival, patients with the SULT1E1 IVS4-1653 TC/CC genotypes showed a >3-fold risk of recurrence (HR, 3.2; 95% CI, 1.39-7.48) compared with those with the TT genotype. Moreover, when the haplotypes were considered, the SULT1E1 *959 G>A base change together with the IVS4-1653 T>C base change (CTG-CCA haplotype) was associated with a >4-fold risk of breast cancer (OR, 4.2; 95% CI, 1.15-15.15). These findings suggest that genetic polymorphisms of SULT1E1 are associated with increased risk and a disease free survival of breast cancer in Korean women.
Mobile D-loops are a preferred substrate for the Bloom's syndrome helicase

The Bloom's syndrome helicase, BLM, is a member of the highly conserved RecQ family, and possesses both DNA unwinding and DNA strand annealing activities. BLM also promotes branch migration of Holliday junctions. One role for BLM is to act in conjunction with topoisomerase IIIα to process homologous recombination (HR) intermediates containing a double Holliday junction by a process termed dissolution. However, several lines of evidence suggest that BLM may also act early in one or more of the recombination pathways to eliminate illegitimate or aberrantly paired DNA joint molecules. We have investigated whether BLM can disrupt DNA displacement loops (D-loops), which represent the initial strand invasion step of HR. We show that mobile D-loops created by the RecA recombinase are a highly preferred substrate for BLM with the invading strand being displaced from the duplex. We have identified structural features of the D-loop that determine the efficiency with which BLM promotes D-loop dissociation. We discuss these results in the context of models for the role of BLM as an ‘anti-recombinase’.
Simultaneous Treatment of Renal Cysts and Stones with Single-Session Retroperitoneoscopic Renal Cyst Decortication and Retroperitoneoscopy-Assisted Percutaneous Nephrolithotomy

Introduction: To determine the safety and efficacy of single-session retroperitoneoscopic renal cyst decortication in conjunction with retroperitoneoscopy-assisted percutaneous nephrolithotomy (PCNL) for simultaneous treatment of renal cysts and stones. Patients and Methods: We enrolled 15 patients (10 men and 5 women, mean age 41 years), who underwent one-stage retroperitoneoscopic renal cyst decortication and retroperitoneoscopy-assisted PCNL between January 2008 and May 2009 for symptomatic renal cysts and concomitant large kidney stones (mean stone area 6.6 cm2). Intraoperative blood loss, duration of operation, and postoperative complications were evaluated. Median follow-up time was 22 months (range 12–26). Results: Average total operative time was 83 ± 12 min and mean duration of PCNL was 45 ± 5 min. Mean estimated blood loss was 80 ± 21 ml. A plain abdominal radiograph revealed an absence of residual stones in all cases. No cyst recurrence occurred within the follow-up period. The mean pre- and postoperative pain score was 7.3 ± 0.8 and 2.8 ± 0.6, respectively. All patients resumed ambulatory activities on the first postoperative day. No severe complications related to the procedure were encountered. Conclusion: The combined laparoscopic approach for simultaneous treatment of renal cysts and stones is safe and feasible. These results encourage further studies to determine long-term outcomes of this combined surgery.
Perception of Human-Derived Risk Influences Choice at Top of the Food Chain

On human-used landscapes, animal behavior is a trade-off between maximizing fitness and minimizing human-derived risk. Understanding risk perception in wildlife can allow mitigation of anthropogenic risk, with benefits to long-term animal fitness. Areas where animals choose to rest should minimize risk from predators, which for large carnivores typically equate to humans. We hypothesize that high human activity leads to selection for habitat security, whereas low activity enables trading security for forage. We investigated selection of resting (bedding) sites by GPS radiocollared adult grizzly bears (n = 10) in a low density population on a multiple-use landscape in Canada. We compared security and foods at resting and random locations while accounting for land use, season, and time of day. On reclaimed mines with low human access, bears selected high horizontal cover far from trails, but did not avoid open (herbaceous) areas, resting primarily at night. In protected areas bears also bedded at night, in areas with berry shrubs and Hedysarum spp. , with horizontal cover selected in the summer, during high human access. On public lands with substantial human recreation, bears bedded at day, selected resting sites with high horizontal cover in the summer and habitat edges, with bedding associated with herbaceous foods. These spatial and temporal patterns of selection suggest that bears perceive human-related risk differentially in relation to human activity level, season and time of day, and employ a security-food trade-off strategy. Although grizzly bears are presently not hunted in Alberta, their perceived risks associated with humans influence resting-site selection.