Miracle-dz/UniFAR-FTUs huggingface dataset:
Tumor necrosis factor α-induced protein 3 (A20) is dysregulated in pediatric Crohn disease

Purpose A significant feature of pediatric inflammatory bowel diseases (IBD), which include Crohn disease (CD), and ulcerative colitis (UC), is failure to suppress inflammation. The inability to regulate inflammation renders a major challenge toward establishing effective treatments in IBD. Nuclear factor kappa-light-chain-enhancer of activated B-cells-induced inflammation is inhibited by A20 through interactions with TAX1BP1 (Tax1-binding protein 1) and A20-binding inhibitor of NF-κβ activation (ABIN)-1 (A20 binding and inhibitor of NF-κβ) and upon phosphorylation by inhibitor of nuclear factor kappa-β kinase subunit beta (IKKβ), which stabilizes it. We hypothesized that dysregulation of A20 is an important factor in uncontrolled inflammation in pediatric IBD. Patients and methods Gene expression of A20, IKKβ, ABIN-1, TAX1BP1, A20 protein, cytokine levels, and A20 phosphorylation was analyzed in the terminal ileum (TI) of 39 patients (14 non-IBD, 15 CD, and 10 UC). A20 expression and protein in T-84 cells and ex vivo biopsies of patients were measured after treatment with Escherichia coli strains or tumor necrosis factor (TNF)-α. Results TNF-α levels and A20 expression were increased in the TI of CD patients. A20 protein levels and ABIN-1 expression were low, TAX1BP1 expression was high, and IKKβ was unchanged. A20 expression positively correlated with biopsy TNF-α levels and inflammatory markers in CD patients. A20 phosphorylation appeared lower in CD patients. A20 expression in TI biopsies from CD patients and T84 cells was triggered with E. coli, strain LF82, while A20 protein levels remained unchanged. Conclusion We describe a potential mechanism related to failure of A20 to suppress inflammation in CD, characterized by high A20 expression and low A20 protein levels. The dysregulation of A20 is potentially due to alterations in ABIN-1, and infection with E. coli strain LF82 could affect the function and stability of A20. Our study signifies an important finding in A20 regulation in IBD, which prevents it from suppressing inflammation.
The Digital Work Environment-a Challenge and an Opportunity for CSCW

In this exploratory paper we will present the emerging concept of the Digital Work Environment. This is concept rooted in Swedish debate on the workplace, information and communication technology (ICT) and well-being. We argue that the concept can be understood as a boundary object uniting different actors (mainly researchers, unions, and policy makers) in a common discourse on what has been labelled as the dark side of information technology. We also argue that the concept needs to embrace an organisational perspective as well as the relational aspects of the psychosocial work environment. Such a move would open the door to a large volume of relevant research that might reinvigorate the concept. More specifically we will show how this would allow the inclusion of the increasingly important aspect of cyberbullying, which at the same time is an example of blurring borders between work and non-work ICT use.
A Four-Arm Circularly Polarized High-Gain High-Tilt Beam Curl Antenna for Beam Steering Applications

A novel circularly polarized (CP) beam-steering four-arm curl antenna with four feed points is presented. The antenna provides steerable high-gain high-tilt right-handed CP (RHCP) beams for satellite communications. The antenna operates over a test frequency band of 1500–1670 MHz and covers the entire L1 band. The four arms are arranged symmetrically with respect to the center of the antenna, and each arm is fed by a coaxial line. When one of the four feed points is excited and the remaining feed points are either open-circuited or terminated to 50 Ω impedance, the antenna generates an RHCP tilted beam of 49° in the elevation plane. At a test frequency of 1575 MHz, the antenna provides a gain of 8.12 dBic. The antenna can switch the tilted beam in the four different space quadrants in the azimuth plane by exciting one feed point at a time. It is found that over the test band, the antenna provides a total efficiency of more than 89% and a gain of greater than 8 dBic.
Search for Narrow Resonances in the b-Tagged Dijet Mass Spectrum in Proton-Proton Collisions at sqrt[s]=8  TeV.

A search for narrow resonances decaying to bottom quark-antiquark pairs is presented, using a data sample of proton-proton collisions at sqrt[s]=8 TeV corresponding to an integrated luminosity of 19.7 fb^{-1}. The search is extended to masses lower than those reached in typical searches for resonances decaying into jet pairs at the LHC, by taking advantage of triggers that identify jets originating from bottom quarks. No significant excess of events is observed above the background predictions. Limits are set on the product of cross section and branching fraction to bottom quarks for spin 0, 1, and 2 resonances in the mass range of 325-1200 GeV. These results improve on the limits for resonances decaying into jet pairs in the 325-500 GeV mass range.
Altered brain activation and connectivity during anticipation of uncertain threat in trait anxiety

In the research field of anxiety, previous studies generally focus on emotional responses following threat. A recent model of anxiety proposes that altered anticipation prior to uncertain threat is related with the development of anxiety. Behavioral findings have built the relationship between anxiety and distinct anticipatory processes including attention, estimation of threat, and emotional responses. However, few studies have characterized the brain organization underlying anticipation of uncertain threat and its role in anxiety. In the present study, we used an emotional anticipation paradigm with functional magnetic resonance imaging (fMRI) to examine the aforementioned topics by employing brain activation and general psychophysiological interactions (gPPI) analysis. In the activation analysis, we found that high trait anxious individuals showed significantly increased activation in the thalamus, middle temporal gyrus (MTG), and dorsomedial prefrontal cortex (dmPFC), as well as decreased activation in the precuneus, during anticipation of uncertain threat compared to the certain condition. In the gPPI analysis, the key regions including the amygdala, dmPFC, and precuneus showed altered connections with distributed brain areas including the ventromedial prefrontal cortex (vmPFC), dorsolateral prefrontal cortex (dlPFC), inferior parietal sulcus (IPS), insula, para‐hippocampus gyrus (PHA), thalamus, and MTG involved in anticipation of uncertain threat in anxious individuals. Taken together, our findings indicate that during the anticipation of uncertain threat, anxious individuals showed altered activations and functional connectivity in widely distributed brain areas, which may be critical for abnormal perception, estimation, and emotion reactions during the anticipation of uncertain threat.
Addressing personal barriers to advance care planning: Qualitative investigation of a mindfulness-based intervention for adults with cancer and their family caregivers

Abstract Objective Advance care planning (ACP) increases quality of life and satisfaction with care for those with cancer and their families, yet these important conversations often do not occur. Barriers include patients’ and families’ emotional responses to cancer, such as anxiety and sadness, which can lead to avoidance of discussing illness-related topics such as ACP. Interventions that address psychological barriers to ACP are needed. The purpose of this study was to explore the effects of a mindfulness intervention designed to cultivate patient and caregiver emotional and relational capacity to respond to the challenges of cancer with greater ease, potentially decreasing psychological barriers to ACP and enhancing ACP engagement. Method The Mindfully Optimizing Delivery of End-of-Life (MODEL) Care intervention provided 12 hours of experiential training to two cohorts of six to seven adults with advanced-stage cancer and their family caregivers (n = 13 dyads). Training included mindfulness practices, mindful communication skills development, and information about ACP. Patient and caregiver experiences of the MODEL Care program were assessed using semistructured interviews administered immediately postintervention and open-ended survey questions delivered immediately and at 4 weeks postintervention. Responses were analyzed using qualitative methods. Result Four salient themes were identified. Patients and caregivers reported the intervention (1) enhanced adaptive coping practices, (2) lowered emotional reactivity, (3) strengthened relationships, and (4) improved communication, including communication about their disease. Significance of results The MODEL Care intervention enhanced patient and caregiver capacity to respond to the emotional challenges that often accompany advanced cancer and decreased patient and caregiver psychological barriers to ACP.
Risk and Benefit of Different Cooking Methods on Essential Elements and Arsenic in Rice

Use of excess water in cooking of rice is a well-studied short-term arsenic removal technique. However, the outcome on the nutritional content of rice is not well addressed. We determined the benefit of different cooking techniques on arsenic removal and the associated risk of losing the essential elements in rice. Overall, we found 4.5%, 30%, and 44% decrease in the arsenic content of rice when cooked with rice-to-water ratios of 1:3, 1:6 (p = 0.004), and 1:10 (parboiling; p < 0.0001), respectively. All the essential elements (except iron, selenium, and copper) incurred a significant loss when rice was cooked using the 1:6 technique: potassium (50%), nickel (44.6%), molybdenum (38.5%), magnesium (22.4%), cobalt (21.2%), manganese (16.5%), calcium (14.5%), selenium (12%), iron (8.2%), zinc (7.7%), and copper (0.2%) and further reduction was observed on parboiling, except for iron. For the same cooking method (1:6), percentage contribution to the recommended daily intake (RDI) of essential elements was highest for molybdenum (154.7%), followed by manganese (34.5%), copper (33.4%), selenium (13.1%), nickel (12.4%), zinc (10%), magnesium (8%), iron (6.3%), potassium (1.8%), and calcium (0.5%). Hence, cooked rice as a staple is a poor source for essential elements and thus micronutrients.
The Citrulline Recycling Pathway Sustains Cardiovascular Function in Arginine-Depleted Healthy Mice, but Cannot Sustain Nitric Oxide Production during Endotoxin Challenge.

Background The recycling of citrulline by argininosuccinate synthase 1 (ASS1) and argininosuccinate lyase (ASL) is crucial to maintain arginine availability and nitric oxide (NO) production. Pegylated arginine deiminase (ADI-PEG20) is a bacterial enzyme used to deplete circulating arginine. Objective The goal of this research was to test the hypothesis that citrulline is able to sustain intracellular arginine availability for NO production in ADI-PEG20 arginine-depleted mice. Methods Six- to 8-wk-old male C57BL/6J mice injected with ADI-PEG20 (5 IU) or saline (control) were used in 4 different studies. Arginine, citrulline, and NO kinetics were determined by using stable isotopes in unchallenged (study 1) and endotoxin-challenged (study 2) mice. Blood pressure was determined by telemetry for 6 d after ADI-PEG20 administration (study 3), and vasomotor activity and ASS1 and ASL gene expression were determined in mesenteric arteries collected from additional mice (study 4). Results ADI-PEG20 administration resulted in arginine depletion (<1 compared with 111 ± 37 µmol/L) but in greater plasma citrulline concentrations (900 ± 123 compared with 76 ± 8 µmol/L; P < 0.001) and fluxes (402 ± 17 compared with 126 ± 4 µmol ⋅ kg-1 ⋅ h-1; P < 0.001) compared with controls. Endotoxin-challenged ADI-PEG20-treated mice produced less NO than controls (13 ± 1 compared with 27 ± 2 µmol ⋅ kg-1 ⋅ h-1; P < 0.001). No differences (P > 0.50) were observed for cardiovascular variables (heart rate, blood pressure) between ADI-PEG20-treated and control mice. Furthermore, no ex vivo vasomotor differences were observed between the 2 treatments. ADI-PEG20 administration resulted in greater gene expression of ASS1 (∼3-fold) but lower expression of ASL (-30%). Conclusion ADI-PEG20 successfully depleted circulating arginine without any effect on cardiovascular endpoints in healthy mice but limited NO production after endotoxin challenge. Therefore, the citrulline recycling pathway can sustain local arginine availability independently from circulating arginine, satisfying the demand of arginine for endothelial NO production; however, it is unable to do so when a high demand for arginine is elicited by endotoxin.
PerfBound: Conserving Energy with Bounded Overheads in On/Off-Based HPC Interconnects

Energy and power are key challenges in high-performance computing. System energy efficiency must be significantly improved, and this requires greater efficiency in all subcomponents. An important target of optimization is the interconnect, since network links are always on, consuming power even during idle periods. A large number of HPC machines have a primary interconnect based on Ethernet (about 40 percent of TOP500 machines), which, since 2010, has included support for saving power via Energy Efficient Ethernet (EEE). Nevertheless, it is unlikely that HPC interconnects would use these energy saving modes unless the performance overhead is known and small. This paper presents PerfBound, a self-contained technique to manage on/off-based networks such as EEE, minimizing interconnect link energy consumption subject to a bound on the performance degradation. PerfBound does not require changes to the applications and it uses only local information already available at switches and NICs without introducing additional communication messages, and is also compatible with multi-hop networks. PerfBound is evaluated using traces from a production supercomputer. For twelve out of fourteen applications, PerfBound has high energy savings, up to 70 percent for only 1 percent performance degradation. This paper also presents DynamicFastwake, which extends PerfBound to exploit multiple low-power states. DynamicFastwake achieves an energy–delay product 10 percent lower than the original PerfBound technique.
Using intelligent agents to combine heterogeneous distributed data

Effective interaction with distributed databases means providing the user with location transparency, i.e. it should appear as if the data is located at a single site. One major challenge in obtaining location transparency is the integration and presentation of heterogeneous, distributed data in near-real time with a user-friendly Web-based interface. This paper describes two projects that apply intelligent agents to the problem of integrating and presenting heterogeneous distributed data. The first project is a Web-based, simulation scenario-generating application that integrates data from distributed sources to build a simulation scenario for an interactive wargaming simulation called Janus. This scenario-generating application is called the Dynamic Scenario Builder (DSB) and will ultimately integrate data from the US Army's Functional Description of the Battlespace (FDB) with Janus or other simulation databases to generate simulation scenarios. The second project involves the development of a system to enable logistics planners to access distributed databases from remote locations and autonomously update data sources such that modifications are dynamically mirrored and displayed to all users of the distributed system. A key feature of this research is the visual presentation of the summarized information in a meaningful manner such that "drilling down" to more detailed information is evident. This project applies a platform for mediators called HERMES (Heterogeneous Reasoning and Mediator System) as a means of data integration from several heterogeneous distributed databases.
The homotopy method revisited: Computing solution paths of ℓ1-regularized problems

$ \ell_1 $-regularized linear inverse problems are frequently used in signal processing, image analysis, and statistics. The correct choice of the regularization parameter $ t \in \mathbb{R}_{\geq 0} $ is a delicate issue. Instead of solving the variational problem for a fixed parameter, the idea of the homotopy method is to compute a complete solution path $ u(t) $ as a function of $ t $. In a celebrated paper by Osborne, Presnell, and Turlach, it has been shown that the computational cost of this approach is often comparable to the cost of solving the corresponding least squares problem. Their analysis relies on the one-at-a-time condition, which requires that different indices enter or leave the support of the solution at distinct regularization parameters. In this paper, we introduce a generalized homotopy algorithm based on a nonnegative least squares problem, which does not require such a condition, and prove its termination after finitely many steps. At every point of the path, we give a full characterization of all possible directions. To illustrate our results, we discuss examples in which the standard homotopy method either fails or becomes infeasible. To the best of our knowledge, our algorithm is the first to provably compute a full solution path for an arbitrary combination of an input matrix and a data vector.
Title Histone Methyltransferases MES-4 and MET-1 Promote Meiotic Checkpoint Activation in Caenorhabditis elegans Permalink

Chromosomes that fail to synapse during meiosis become enriched for chromatin marks associated with heterochromatin assembly. This response, called meiotic silencing of unsynapsed or unpaired chromatin (MSUC), is conserved from fungi to mammals. In Caenorhabditis elegans, unsynapsed chromosomes also activate a meiotic checkpoint that monitors synapsis. The synapsis checkpoint signal is dependent on cis-acting loci called Pairing Centers (PCs). How PCs signal to activate the synapsis checkpoint is currently unknown. We show that a chromosomal duplication with PC activity is sufficient to activate the synapsis checkpoint and that it undergoes heterochromatin assembly less readily than a duplication of a non-PC region, suggesting that the chromatin state of these loci is important for checkpoint function. Consistent with this hypothesis, MES4 and MET-1, chromatin-modifying enzymes associated with transcriptional activity, are required for the synapsis checkpoint. In addition, a duplication with PC activity undergoes heterochromatin assembly when mes-4 activity is reduced. MES-4 function is required specifically for the X chromosome, while MES-4 and MET-1 act redundantly to monitor autosomal synapsis. We propose that MES-4 and MET-1 antagonize heterochromatin assembly at PCs of unsynapsed chromosomes by promoting a transcriptionally permissive chromatin environment that is required for meiotic checkpoint function. Moreover, we suggest that different genetic requirements to monitor the behavior of sex chromosomes and autosomes allow for the lone unsynapsed X present in male germlines to be shielded from inappropriate checkpoint activation. Citation: Lamelza P, Bhalla N (2012) Histone Methyltransferases MES-4 and MET-1 Promote Meiotic Checkpoint Activation in Caenorhabditis elegans. PLoS Genet 8(11): e1003089. doi:10.1371/journal.pgen. 1003089 Editor: JoAnne Engebrecht, University of California Davis, United States of America Received May 21, 2012; Accepted September 28, 2012; Published November 15, 2012 Copyright: 2012 Lamelza, Bhalla. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This research was supported by the National Center for Research Resources (NCRR) and the Office of Research Infrastructure Programs (ORIP) (grant number R00RR024110) and by the National Institutes of General Medical Sciences (NIGMS) (grant number 1R01GM097144), both of the National Institutes of Health (NIH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: nbhalla@ucsc.edu ¤ Current address: Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
RelaxedIK: Real-time Synthesis of Accurate and Feasible Robot Arm Motion

—We present a real-time motion-synthesis method for robot manipulators, called RelaxedIK , that is able to not only accurately match end-effector pose goals as done by traditional IK solvers, but also create smooth, feasible motions that avoid joint-space discontinuities, self-collisions, and kinematic singularities. To achieve these objectives on-the-ﬂy, we cast the standard IK formulation as a weighted-sum non-linear optimization problem, such that motion goals in addition to end-effector pose matching can be encoded as terms in the sum. We present a normalization procedure such that our method is able to effectively make trade-offs to simultaneously reconcile many, and potentially competing, objectives. Using these trade-offs, our formulation allows features to be relaxed when in conﬂict with other features deemed more important at a given time. We compare performance against a state-of-the-art IK solver and a real-time motion-planning approach in several geometric and real-world tasks on seven robot platforms ranging from 5-DOF to 8-DOF. We show that our method achieves motions that effectively follow position and orientation end-effector goals without sacriﬁcing motion feasibility, resulting in more successful execution of tasks compared to the baseline approaches.
The stable actin core of mechanosensory stereocilia features continuous turnover of actin cross-linkers

Stereocilia are mechanosensitive protrusions on the surfaces of sensory hair cells in the inner ear that detect sound, gravity, and head movement. Their cores are composed of parallel actin filaments that are cross-linked and stabilized by several actin-binding proteins, including fascin-2, plastin-1, espin, and XIRP2. The actin filaments are the most stable known, with actin turnover primarily occurring at the stereocilia tips. While stereocilia actin dynamics has been well studied, little is known about the behavior of the actin cross-linking proteins, which are the most abundant type of protein in stereocilia after actin and are critical for stereocilia morphogenesis and maintenance. Here, we developed a novel transgenic mouse to monitor EGFP-fascin-2 incorporation. In contrast to actin, EGFP-fascin-2 readily enters the stereocilia core. We also compared the effect of EGFP-fascin-2 expression on developing and mature stereocilia. When it was induced during hair cell development, we observed increases in both stereocilia length and width. Interestingly, stereocilia size was not affected when EGFP-fascin-2 was induced in adult stereocilia. Regardless of the time of induction, EGFP-fascin-2 displaced both espin and plastin-1 from stereocilia. Altering the actin cross-linker composition, even as the actin filaments exhibit little to no turnover, provides a mechanism for ongoing remodeling and repair important for stereocilia homeostasis.