Miracle-dz/UniFAR-FTUs huggingface dataset:
G12/13 Signaling Pathways Substitute for Integrin αIIbβ3-Signaling for Thromboxane Generation in Platelets

Background We have previously shown that ADP-induced TXA2 generation requires signaling from αIIbβ3 integrin in platelets. Here we observed that, unlike ADP, protease-activated receptor (PAR)-mediated TXA2 generation occurs independently of αIIbβ3. PAR agonists, but not ADP, activate G12/13 signaling pathways. Hence, we evaluated the role of these pathways in TXA2 generation. Principal Findings Inhibition of ADP-induced thromboxane generation by fibrinogen receptor antagonist SC57101 was rescued by co-stimulation of G12/13 pathways with YFLLRNP. This observation suggested an existence of a common signaling effector downstream of integrins and G12/13 pathways. Hence, we evaluated role of three potential tyrosine kinases; c-Src, Syk and FAK (Focal Adhesion Kinase) that are known to be activated by integrins. c-Src and Syk kinase did not play a role in ADP-induced functional responses in platelets. Selective activation of G12/13 pathways resulted in the activation of FAK, in the absence of integrin signaling. Interestingly, αIIbβ3-mediated FAK activation occurred in a Src family kinase (SFK)-independent manner whereas G12/13 pathway caused FAK activation in a SFK and RhoA-dependent manner. A FAK selective inhibitor TAE-226, blocked TXA2 generation. However, in comparison to WT mice, Pf4-Cre/Fak-Floxed mice did not show any difference in platelet TXA2 generation. Conclusions Therefore, we conclude that differential activation of FAK occurs downstream of Integrins and G12/13 pathways. However, the common effector molecule, possibly a tyrosine kinase downstream of integrins and G12/13 pathways contributing to TXA2 generation in platelets remains elusive.
Deployment-specific lifetime/real-time optimization for wireless ad hoc networks

This paper introduces a method for lifetime/real-time optimization of wireless ad hoc networks. The method utilizes a network simulator to model the network signature for actual deployments and routing paths. Since the transmit power is fixed, many nodes may not save energy from communication. At the same time, all nodes save energy from calculations and the number of hops may be controlled. The network station controls the balance between lifetime and real-time performance. We have developed an ad hoc network simulator, ANTS, and utilized it to verify the method.
Intergenomic Rearrangements after Polyploidization of Kengyilia thoroldiana (Poaceae: Triticeae) Affected by Environmental Factors

Polyploidization is a major evolutionary process. Approximately 70–75% species of Triticeae (Poaceae) are polyploids, involving 23 genomes. To investigate intergenomic rearrangements after polyploidization of Triticeae species and to determine the effects of environmental factors on them, nine populations of a typical polyploid Triticeae species, Kengyilia thoroldiana (Keng) J.L. Yang et al. (2n = 6x = 42, StStPPYY), collected from different environments, were studied using genome in situ hybridization (GISH). We found that intergenomic rearrangements occurred between the relatively large P genome and the small genomes, St (8.15%) and Y (22.22%), in polyploid species via various types of translocations compared to their diploid progenitors. However, no translocation was found between the relatively small St and Y chromosomes. Environmental factors may affect rearrangements among the three genomes. Chromosome translocations were significantly more frequent in populations from cold alpine and grassland environments than in populations from valley and lake-basin habitats (P<0.05). The relationship between types of chromosome translocations and altitude was significant (r = 0.809, P<0.01). Intergenomic rearrangements associated with environmental factors and genetic differentiation of a single basic genome should be considered as equally important genetic processes during species' ecotype evolution.
Human land uses enhance sediment denitrification and N 2 O production in Yangtze lakes primarily by influencing lake water quality

Abstract. Sediment denitrification in lakes alleviates the effects of eutrophication through the removal of nitrogen to the atmosphere as N2O and N2. However, N2O contributes notably to the greenhouse effect and global warming. Human land uses (e.g. agricultural and urban areas) strongly affect lake water quality and sediment characteristics, which, in turn, may regulate lake sediment denitrification and N2O production. In this study, we investigated sediment denitrification and N2O production and their relationships to within-lake variables and watershed land uses in 20 lakes from the Yangtze River basin in China. The results indicated that both lake water quality and sediment characteristics were significantly influenced by watershed land uses. N2O production rates increased with increasing background denitrification rates. Background denitrification and N2O production rates were positively related to water nitrogen concentrations but were not significantly correlated with sediment characteristics and plant community structure. A significant positive relationship was observed between background denitrification rate and percentage of human-dominated land uses (HDL) in watersheds. Structural equation modelling revealed that the indirect effects of HDL on sediment denitrification and N2O production in Yangtze lakes were mediated primarily through lake water quality. Our findings also suggest that although sediments in Yangtze lakes can remove large quantities of nitrogen through denitrification, they may also be an important source of N2O, especially in lakes with high nitrogen content.
Co-Interactive DNA-Binding between a Novel, Immunophilin-Like Shrimp Protein and VP15 Nucleocapsid Protein of White Spot Syndrome Virus

White spot syndrome virus (WSSV) is one of the most serious pathogens of penaeid shrimp. Although its genome has been completely characterized, the functions of most of its putative proteins are not yet known. It has been suggested that the major nucleocapsid protein VP15 is involved in packaging of the WSSV genome during virion formation. However, little is known in its relationship with shrimp host cells. Using the yeast two-hybrid approach to screen a shrimp lymphoid organ (LO) cDNA library for proteins that might interact with VP15, a protein named PmFKBP46 was identified. It had high sequence similarity to a 46 kDa-immunophilin called FKBP46 from the lepidopteran Spodoptera frugiperda (the fall armyworm). The full length PmFKBP46 consisted of a 1,257-nucleotide open reading frame with a deduced amino acid sequence of 418 residues containing a putative FKBP-PPIase domain in the C-terminal region. Results from a GST pull-down assay and histological co-localization revealed that VP15 physically interacted with PmFKBP46 and that both proteins shared the same subcellular location in the nucleus. An electrophoretic mobility shift assay indicated that PmFKBP46 possessed DNA-binding activity and functionally co-interacted with VP15 in DNA binding. The overall results suggested that host PmFKBP46 might be involved in genome packaging by viral VP15 during virion assembly.
CXCL9 and CXCL10 accelerate acute transplant rejection mediated by alloreactive memory T cells in a mouse retransplantation model

C-X-C motif chemokine ligand (CXCL) 9 and CXCL10 play key roles in the initiation and development of acute transplant rejection. Previously, higher levels of RANTES expression and secretion were demonstrated in retransplantation or T-cell memory-transfer models. In the present study, the effect of the chemokines, CXCL9 and CXCL10, were investigated in a mouse retransplantation model. BALB/c mice were used as donors, while C57BL/6 mice were used as recipients. In the experimental groups, a heterotopic heart transplantation was performed six weeks following skin grafting. In the control groups, a heterotopic heart transplantation was performed without skin grafting. Untreated mice served as blank controls. The mean graft survival time of the heterotopic heart transplantations was 7.7 days in the experimental group (n=6), as compared with 3.25 days in the control group (n=6; P<0.001). On day three following cardiac transplantation, histological evaluation of the grafts revealed a higher International Society for Heart & Lung Transplantation grade in the experimental group as compared with the control group. In addition, gene expression and serum concentrations of CXCL9, CXCL10, interferon-γ, and interleukin-2 were markedly higher in the experimental group when compared with the control group. Differences between the levels of CXCL9 and CXCL10 in the pre- and post-transplant mice indicated that the chemokines may serve as possible biomarkers to predict acute rejection. The results of the present study demonstrated that CXCL9 and CXCL10 play a critical role in transplantation and retransplantation. High levels of these cytokines during the pre-transplant period may lead to extensive acute rejection. Thus, the observations enhance the understanding of the mechanism underlying the increased expression and secretion of CXCL9 and CXCL10 by alloreactive memory T cells.
Adaptive approach for nonlinear sensitivity analysis of reaction kinetics

We present a unified approach for linear and nonlinear sensitivity analysis for models of reaction kinetics that are stated in terms of systems of ordinary differential equations (ODEs). The approach is based on the reformulation of the ODE problem as a density transport problem described by a Fokker–Planck equation. The resulting multidimensional partial differential equation is herein solved by extending the TRAIL algorithm originally introduced by Horenko and Weiser in the context of molecular dynamics (J. Comp. Chem. 2003, 24, 1921) and discussed it in comparison with Monte Carlo techniques. The extended TRAIL approach is fully adaptive and easily allows to study the influence of nonlinear dynamical effects. We illustrate the scheme in application to an enzyme‐substrate model problem for sensitivity analysis w.r. t. to initial concentrations and parameter values. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 941–948, 2005
Dissecting the genetics of major depressive disorder

Purpose of Review We will describe the success of recent genome-wide association studies that identify genetic variants associated with depression and outline the strategies used to reduce heterogeneity and increase sample size. Recent Findings The CONVERGE consortium identified two genetic associations by focusing on a sample of Chinese women with recurrent severe depression. Three other loci have been found in Europeans by combining cohorts with clinical diagnosis and measures of depressive symptoms to increase sample size. 23andMe identified 15 loci associated with depression using self-report of clinical diagnosis in a study of over 300,000 individuals. Summary The first genetic associations with depression have been identified, and this number is now expected to increase linearly with sample size, as seen in other polygenic disorders. These loci provide invaluable insights into the biology of depression and exciting opportunities to develop new biomarkers and therapeutic targets.
Active learning approaches for learning regular expressions with genetic programming

We consider the long-standing problem of the automatic generation of regular expressions for text extraction, based solely on examples of the desired behavior. We investigate several active learning approaches in which the user annotates only one desired extraction and then merely answers extraction queries generated by the system. The resulting framework is attractive because it is the system, not the user, which digs out the data in search of the samples most suitable to the specific learning task. We tailor our proposals to a state-of-the-art learner based on Genetic Programming and we assess them experimentally on a number of challenging tasks of realistic complexity. The results indicate that active learning is indeed a viable framework in this application domain and may thus significantly decrease the amount of costly annotation effort required.
An Introduction to Rclusterpp

The Rclusterpp package provides alternative implementations for common geometric hierarchical clustering algorithms, e.g., average link clustering, that are optimized for large numbers of observations and efficient execution on modern multicore processors. Rclusterpp can be used directly from R as a replacement for stats::hclust, or as a linkable C++ library.
Large-Eddy Simulation of Mesoscale Dynamics and Entrainment Around A Pocket of Open Cells Observed in VOCALS RF 06

Large-eddy simulations of a pocket of open cells (POC) based on VOCALS Regional Experiment (REx) Research Flight 06 are analyzed and compared with aircraft observations. A doubly-periodic domain 192 km×24 km with 125 m horizontal resolution and 5 m vertical resolution near the capping inversion is used. The POC is realized in the model as a fixed 96 km wide region of reduced cloud droplet number concentration (Nc) based on observed values; initialization and forcing are otherwise uniform across the domain. The model reproduces aircraft-observed differences in boundary-layer structure and precipitation organization between a well-mixed overcast region and a decoupled POC with open-cell precipitating cumuli, although the simulated cloud cover is too large in the POC. A sensitivity study in which Nc is allowed to advect following the turbulent flow gives nearly identical results over the 16 hour length of the simulation (which starts at night and goes into the next afternoon). The simulated entrainment rate is nearly a factor of two smaller in the less turbulent POC than in the more turbulent overcast region. However, the inversion rises at a nearly uniform rate across the domain because powerful buoyancy restoring forces counteract horizontal inversion height gradients. A secondary circulation sets up that diverts subsiding free-tropospheric air away from the POC into the surrounding overcast region, counterbalancing the weaker entrainment in the POC with locally weaker
Flexible Setup for the Measurement of CMOS Time-Dependent Variability With Array-Based Integrated Circuits

This paper presents an innovative and automated measurement setup for the characterization of variability effects in CMOS transistors using array-based integrated circuits (ICs), through which a better understanding of CMOS reliability could be attained. This setup addresses the issues that come with the need for a trustworthy statistical characterization of these effects: testing a very large number of devices accurately but, also, in a timely manner. The setup consists of software and hardware components that provide a user-friendly interface to perform the statistical characterization of CMOS transistors. Five different electrical tests, comprehending time-zero and time-dependent variability effects, can be carried out. Test preparation is, with the described setup, reduced to a few seconds. Moreover, smart parallelization techniques allow reducing the typically time-consuming aging characterization from months to days or even hours. The scope of this paper thus encompasses the methodology and practice of measurement of CMOS time-dependent variability, as well as the development of appropriate measurement systems and components used in efficiently generating and acquiring the necessary electrical signals.
Teachers’ diagnosis of students’ research skills during the mentoring of the undergraduate thesis

ABSTRACT In higher education, students often write an undergraduate thesis and receive one-to-one or small group support. During mentoring, 10 teachers ideally diagnose students’ research skills, to be able to adapt their support to students’ needs. In this study, we aimed to answer the question of how mentors apply the diagnostic phases of a diagnostic question, a diagnosis, a diagnostic check and an intervention, during mentoring meetings about 15 students’ research skills. Four mentors participated in this multiple case study. Qualitative data were gathered and sixteen videotaped mentoring meetings were coded on the four diagnostic phases. The results were compared within and between mentors, showing that mentors asked several diagnostic questions, seldom articulated and shared their diagnoses explicitly with students, and mainly used interventions. We concluded that more support is needed for mentors who do not automatically use their diagnostic questions to formulate explicit diagnoses about students’ research skills.
Genre Classification Using Harmony Rules Induced from Automatic Chord Transcriptions

Wepresentanautomaticgenreclassificationtechniquemaking use of frequent chord sequences that can be applied on symbolic as well as audio data. We adopt a first-order logic representation of harmony and musical genres: pieces of music are represented as lists of chords and musical genres are seen as context-free definite clause grammars using subsequences of these chord lists. To induce the contextfree definite clause grammars characterising the genres we use a first-order logic decision tree induction algorithm. We report on the adaptation of this classification framework to audio data using an automatic chord transcription algorithm. We also introduce a high-level harmony representation scheme which describes the chords in term of both their degrees and chord categories. When compared to another high-level harmony representation scheme used in a previous study, it obtains better classification accuracies and shorter run times. We test this framework on 856 audio files synthesized from Band in a Box files and covering 3 main genres, and 9 subgenres. We perform 3-way and 2-way classification tasks on these audio files and obtain good classification results: between 67% and 79% accuracy for the 2-way classification tasks and between 58% and 72% accuracy for the 3-way classification tasks.
A map of brain neuropils and fiber systems in the ant Cardiocondyla obscurior

A wide spectrum of occupied ecological niches and spectacular morphological adaptations make social insects a prime object for comparative neuroanatomical studies. Eusocial insects have evolved complex societies based on caste polyphenism. A diverse behavioral repertoire of morphologically distinct castes of the same species requires a high degree of plasticity in the central nervous system. We have analyzed the central brain neuropils and fiber tract systems of the worker of the ant Cardiocondyla obscurior, a model for the study of social traits. Our analysis is based on whole mount preparations of adult brains labeled with an antibody against Drosophila-Synapsin, which cross-reacts strongly with synapses in Cardiocondyla. Neuropil compartments stand out as domains with a certain texture and intensity of the anti-Synapsin signal. By contrast, fiber tracts, which are composed of bundles of axons accompanied by glia and are devoid of synapses, appear as channels or sheaths with low anti-Synapsin signal. We have generated a digital 3D atlas of the Cardiocondyla brain neuropil. The atlas provides a reference for future studies of brain polymorphisms in distinct castes, brain development or localization of neurotransmitter systems.
Configuration and Optimization in Self-Managing Networks : a Tutorial

One of the key goals of network administration is configuring a network that is always operating at an optimal state. However, this goal is increasingly time-consuming and expensive as networks increase in size and complexity. One path to offsetting the increasing cost is in the implementation of a network that manages itself – known as a cognitive network. This paper will introduce the concepts of self-configuration and self-optimization as they relate specifically to cognitive networks and more generally to the discipline of artificial intelligence from a nonimplementation specific view. A possible model for the structure of a cognitive network will be presented as a result of these concepts. A minimal knowledge of network architecture is required to understand the following material. This paper is intended in part to be an introduction to the newly formed concept of cognitive networks.
J an 2 00 8 A Self-Consistent NLTE-Spectra Synthesis Model of FeLoBAL

We present detailed radiative transfer spectral synthesis models for the Iron Low Ionization Broad Absorption Line (FeLoBAL) active galactic nuclei (AGN) FIRST J121442.3+280329 and ISO J005645.1-273816. Detailed NLTE spectral synthesis with a spherically symmetric outflow reproduces the observed spectra very well across a large wavelength range. While exact spherical symmetry is probably not required, our model fits are of high quality and thus very large covering fractions are strongly implied by our results. We constrain the kinetic energy and mass in the ejecta and discuss their implications on the accretion rate. Our results support the idea that FeLoBALs may be an evolutionary stage in the development of more “ordinary” QSOs. Subject headings: AGN: FIRST J121442.3+280329, ISO J005645.1−273816
"MY EXERCISE IN LIFE IS TO PRODUCE A REPORT THAT NOBODY READS:" PERCEPTIONS OF CLERY ACT USE, COMPLIANCE, AND EFFECTIVENESS

This qualitative policy study used key informant interviews to determine the perceptions of systems administrators and Title IX coordinators who work at 12 different Colorado state institutions of higher education (IHE) regarding the compliance, use, and effectiveness of the 1990 Jeanne Clery Disclosure of Campus Security Policy and Campus Crime Statistics Act (Clery Act) and its subsequent guidance and amendments on campus safety. Document analysis was used to determine compliance of 2015 Annual Security Reports (ASRs) with changes required by the 2013 Violence Against Women Reauthorization Act (effective October 1, 2015). Additionally, discourse analysis was used as a qualitative methodology to examine discourses that are used in Colorado IHE ASRs and how these discourses shape Colorado IHE expectations and understandings regarding student behavior in relation to Clery Act issues. Finally, general systems theory was applied in understanding results of the document and discourse analyses, as well as the responses of participants.
School Teasing and Bullying After the Presidential Election

In response to media reports of increased teasing and bullying in schools following the 2016 U.S. presidential election, we investigated its prevalence with a Virginia school climate survey completed by approximately 155,000 seventh- and eighth-grade students in 2013, 2015, and 2017. Survey results were mapped onto presidential election results for each school division’s locality. In localities favoring the Republican candidate, there were higher adjusted rates of students reporting that (a) they had experienced some form of bullying in the past year (18% higher) and (b) “students in this school are teased or put down because of their race or ethnicity” (9% higher). For these two outcomes, there were no meaningful differences prior to the election. These results provide modest support for educator concerns about increased teasing and bullying since the 2016 presidential election in some schools and warrant further investigation.
Parameter selection in fuzzy joint points clustering algorithms

Applying fuzzy logic to clustering techniques leads to more robust and autonomous methods like the fuzzy joint points (FJP) which is a density based fuzzy clustering algorithm that requires no parameters to be set. However, a straightforward implementation of the method is rather slow. Recently, a faster but parameter dependent version of the algorithm was proposed and a theoretical bound on the parameter was given so that the algorithm produces the exact same results with the original FJP method. In this work, we investigate the tightness of the bound in practice and analyze the effect of the data distribution on the parameter selection problem of the fuzzy joint points clustering.