Miracle-dz/UniFAR-FTUs huggingface dataset:
Cleavage of the signaling mucin Msb2 by the aspartyl protease Yps1 is required for MAPK activation in yeast

Signaling mucins are cell adhesion molecules that activate RAS/RHO guanosine triphosphatases and their effector mitogen-activated protein kinase (MAPK) pathways. We found that the Saccharomyces cerevisiae mucin Msb2p, which functions at the head of the Cdc42p-dependent MAPK pathway that controls filamentous growth, is processed into secreted and cell-associated forms. Cleavage of the extracellular inhibitory domain of Msb2p by the aspartyl protease Yps1p generated the active form of the protein by a mechanism incorporating cellular nutritional status. Activated Msb2p functioned through the tetraspan protein Sho1p to induce MAPK activation as well as cell polarization, which involved the Cdc42p guanine nucleotide exchange factor Cdc24p. We postulate that cleavage-dependent activation is a general feature of signaling mucins, which brings to light a novel regulatory aspect of this class of signaling adhesion molecule.
Medical Image Registration Using Knowledge of Adjacency of Anatomical Structures

Abstract The combination of multimodality medical images is generating increasing clinical interest, but the absence of robust automatic registration algorithms is an obstacle to these techniques entering routine clinical use. In this paper, we present a new algorithm based on surface fitting that makes use of anatomical knowledge of adjacency of identified anatomical structures to solve the 3D rigid body registration problem. The algorithm has been applied to the registration of MR CT and vascular images of the head, and has achieved accuracies similar to those obtained using interactive location of corresponding landmarks.
TBL 1 XR 1 in physiological and pathological states

Transducin (beta)-like 1X related protein 1 (TBL1XR1/TBLR1) is an integral subunit of the NCoR (nuclear receptor corepressor) and SMRT (silencing mediator of retinoic acid and thyroid hormone receptors) repressor complexes. It is an evolutionally conserved protein that shares high similarity across all species. TBL1XR1 is essential for transcriptional repression mediated by unliganded nuclear receptors (NRs) and othe regulated transcription factors (TFs). However, it can also act as a transcription activator through the recruitment of the ubiquitin-conjugating/19S proteasome complex that mediates the exchange of corepressors for coactivators. TBL1XR1 is required for the activation of multiple intracellular signaling pathways. TBL1XR1 germline mutations and recurrent mutations are linked to intellectual disability. Upregulation of TBL1XR1 is observed in a variety of solid tumors, which is associated with advanced tumor stage, metastasis and poor prognosis. A variety of genomic alterations, such as translocation, deletion and mutation have been identified in many types of neoplasms. Loss of TBL1XR1 in B-lymphoblastic leukemia disrupts glucocorticoid receptor recruitment to chromatin and results in glucocorticoid resistance. However, the mechanisms of other types of genomic changes in tumorogenesis are still not clear. A pre-clinical study has shown that the disruption of the interaction between TBL1X and β-catenin using a small molecule can inhibit the growth of AML stem and blast cells both in vitro and in vivo. These findings shed light on the therapeutic potentials of targeting TBL1XR1 related proteins in cancer treatment.
FrogWild! - Fast PageRank Approximations on Graph Engines

We propose FrogWild, a novel algorithm for fast approximation of high PageRank vertices, geared towards reducing network costs of running traditional PageRank algorithms. Our algorithm can be seen as a quantized version of power iteration that performs multiple parallel random walks over a directed graph. One important innovation is that we introduce a modification to the GraphLab framework that only partially synchronizes mirror vertices. This partial synchronization vastly reduces the network traffic generated by traditional PageRank algorithms, thus greatly reducing the per-iteration cost of PageRank. On the other hand, this partial synchronization also creates dependencies between the random walks used to estimate PageRank. Our main theoretical innovation is the analysis of the correlations introduced by this partial synchronization process and a bound establishing that our approximation is close to the true PageRank vector. We implement our algorithm in GraphLab and compare it against the default PageRank implementation. We show that our algorithm is very fast, performing each iteration in less than one second on the Twitter graph and can be up to 7x faster compared to the standard GraphLab PageRank implementation.
Modeling Propagation in Multifloor Buildings Using the FDTD Method

A three-dimensional parallel implementation of the finite-difference time-domain (FDTD) method has been used to identify and isolate the dominant propagation mechanisms in a multistorey building at 1.0 GHz. A novel method to visualize energy flow by computing streamlines of the Poynting vector has been developed and used to determine the dominant propagation mechanisms within the building. It is found that the propagation mechanisms depend on the level of internal clutter modeled. Including metallic and lossy dielectric clutter in the environment increases attenuation on some propagation paths, thereby altering the dominant mechanisms observed. This causes increases in the sector-averaged path loss and changes the distance-dependency exponents across a floor from 2.2 to 2.7. The clutter also reduces Rician K-factors across the floor. Directly comparing sector-averaged path loss from the FDTD simulations with experimental measurements shows an RMS error of 14.4 dB when clutter is ignored. However, this is reduced to 10.5 dB when the clutter is included, suggesting that the effects of clutter should not be neglected when modeling propagation indoors.
Colitis complicating chronic granulomatous disease. A clinicopathological case report.

BACKGROUND--This report concerns a female patient now aged 24 years, diagnosed at the age of 7 years as suffering from chronic granulomatous disease. At age 20 she developed diarrhoea accompanied by rectal bleeding. Endoscopy showed extensive colitis. She failed to respond to medical treatment and underwent total colectomy two years later. AIMS--To discuss the histological changes in the colon in chronic granulomatous disease. RESULTS--There was extensive mucosal inflammation throughout colon and rectum resembling ulcerative colitis. In addition characteristic large pigmented macrophages were distributed in the basal mucosa and superficial submucosa. Similar cells accompanied by granulomata were present in mesenteric lymph nodes. CONCLUSIONS--Colitis is an unusual clinical manifestation of chronic granulomatous disease but the presence and characteristic distribution of such pigmented macrophages in colonic biopsy in children and young adults may suggest the diagnosis.
Cluster based massive MIMO channel model for indoor environment using ray tracing technique

This paper proposes a novel stationary channel model for massive multiple input multiple output (MIMO) communication systems. The model is based on the clusters formed by grouping the scatterers and is applied in an indoor environments. A linear array antenna with adequate number of elements is considered at the base station (BS) to form a massive MIMO system. By using ray tracing technique, interaction between the electromagnetic rays and the clusters are computed in 2-dimensional (2D) environments. By applying Snell's law, single and double reflections from all environment boundaries are computed. Three states of direct cluster, wall-cluster and double-cluster reflections are taken into accounts to extract different channel parameters such as power delay profile (PDP), angle of arrivals (AoAs) and time delays. This proposed model can accelerate characterization of the massive MIMO channels.
Individualized care, quality of life and satisfaction with nursing care.

AIMS This paper reports a study of the maintenance of individualized care from surgical patients' point of view and examines associations between individualized care, patient satisfaction with nursing care, and health-related quality of life. Rationale. There is preliminary evidence that individualized care is effective from patients' point of view, and is associated with improved patient outcomes, such as patient satisfaction and quality of life. However, individualized care has mainly been studied from the vantage-point of nurses' experiences. METHODS In this cross-sectional, descriptive, correlational study the data were collected with surgical adult patients (n = 279, response rate 93%) in surgical wards in Finland using self-administered questionnaires including the Individualized Care Scales, Patient-Satisfaction Scale, and Finnish versions of the Nottingham Health Profile and EuroQol 5D. Associations between individualized care, satisfaction with care and health-related quality of life were examined. Cronbach's alpha values and item analysis were used to evaluate the psychometric properties of the instruments, especially the Individualized Care Scales. RESULTS The more often patients felt they received support for individuality through specific nursing interventions, the higher the individuality of care received. Secondly, the more individualized patients regarded their care, the higher the level of reported patient satisfaction with nursing care. However, the correlation between individualized care and health-related quality of life was fairly low, albeit statistically significant. CONCLUSION Individualized care may produce positive outcomes, such as patient satisfaction. Further research is needed to explore individualized care in relation to health-related quality of life.
Sequential Isotopic Signature Along Gladius Highlights Contrasted Individual Foraging Strategies of Jumbo Squid (Dosidicus gigas)

Background Cephalopods play a major role in marine ecosystems, but knowledge of their feeding ecology is limited. In particular, intra- and inter-individual variations in their use of resources has not been adequatly explored, although there is growing evidence that individual organisms can vary considerably in the way they use their habitats and resources. Methodology/Principal Findings Using δ13C and δ15N values of serially sampled gladius (an archival tissue), we examined high resolution variations in the trophic niche of five large (>60 cm mantle length) jumbo squids (Dosidicus gigas) that were collected off the coast of Peru. We report the first evidence of large inter-individual differences in jumbo squid foraging strategies with no systematic increase of trophic level with size. Overall, gladius δ13C values indicated one or several migrations through the squid's lifetime (∼8–9 months), during which δ15N values also fluctuated (range: 1 to 5‰). One individual showed an unexpected terminal 4.6‰ δ15N decrease (more than one trophic level), thus indicating a shift from higher- to lower-trophic level prey at that time. The data illustrate the high diversity of prey types and foraging histories of this species at the individual level. Conclusions/Significance The isotopic signature of gladii proved to be a powerful tool to depict high resolution and ontogenic variations in individual foraging strategies of squids, thus complementing traditional information offered by stomach content analysis and stable isotopes on metabolically active tissues. The observed differences in life history strategies highlight the high degree of plasticity of the jumbo squid and its high potential to adapt to environmental changes.
What Is the Longest River in the USA? Semantic Parsing for Aggregation Questions

Answering natural language questions against structured knowledge bases (KB) has been attracting increasing attention in both IR and NLP communities. The task involves two main challenges: recognizing the questions' meanings, which are then grounded to a given KB. Targeting simple factoid questions, many existing open domain semantic parsers jointly solve these two subtasks, but are usually expensive in complexity and resources.In this paper, we propose a simple pipeline framework to efficiently answer more complicated questions, especially those implying aggregation operations, e.g., argmax, argmin.We first develop a transition-based parsing model to recognize the KB-independent meaning representation of the user's intention inherent in the question. Secondly, we apply a probabilistic model to map the meaning representation, including those aggregation functions, to a structured query.The experimental results showed that our method can better understand aggregation questions, outperforming the state-of-the-art methods on the Free917 dataset while still maintaining promising performance on a more challenging dataset, WebQuestions, without extra training.
The Influence of Narrative Voice of a Story on Judgments of Past Injustice and Present Day Discrimination

ii Acknowledgments. iv Vita . v List of Tables . vii List of Figures . viii Chapter 1: Introduction . 1 Chapter 2: Study 1 . 6 Chapter 3: Study 2 . 37 Chapter 4: General Discussion. 50 References . 58 Appendix A: First-person Narrative Story . 61 Appendix B: Third-person Narrative Story . 64
A The Rotten Tomatoes Paradox , and Uncertainty

Frequent visitors to the website, Rotten Tomatoes, may be surprised to discover that a movie with a 15% positive rating is not necessarily better reviewed than than one which gets, say, 45% positive. This is because dichotomizing reviews as either just good or bad, period, discards lots of information. A strong consensus that a film is not great (say, mostly C-) will result in a low percentage of positives. On the other hand, a movie with a lot of terrible reviews but a strong lukewarm contingent (say, 55% Fs and Ds, 45% C+) can have a much higher “positive” percentage. While the subject-matter is much less important, this example has exactly the structure of voters located on a one-dimensional latent political space being forced to chose between two candidates. More generally, this points to the importance of uncertainty assessments. Even if one were to accept all of Groseclose’s modeling assumptions, the reader of Left Turn has no idea of what the views of the hypothetical unbiased American voter are. The reader knows Groseclose’s point estimate (≈ 25, as we said), but this estimate, like every other, is uncertain and surrounded by some margin of error. Since it is a function of earlier estimates, themselves imprecise7, the obvious and correct thing to do is to propagate the uncertainty. But Left Turn gives no sense of how much uncertainty attaches to its claims, even of a purely statistical sort. Equally seriously, Nyhan [2005] and Gasper [2011] have shown that estimates from Groseclose’s first, ideal-point model are highly sensitive to details of which data are included in the analysis, adding systematic to statistical uncertainty. We do not know how big the margin of error for Groseclose’s estimate of the location of Unbiased America should be, but it surely matters if a good confidence interval is [22, 28] or [10, 90], or indeed [0, 100].
Nitration of surfactant protein A (SP-A) tyrosine residues results in decreased mannose binding ability.

Nitric oxide (.NO) is a signal transducing free radical which can modify oxidant stress by limiting superoxide (O2.-)-mediated injury. However, the product of . NO reaction with O2. -, peroxynitrite (ONOO-), is a potent oxidizing and nitrating agent. Exposure of a mixture containing phosphatidylcholine liposomes and surfactant apoprotein A (SP-A; 10% by weight) to increasing concentrations of . NO, generated by spermine NONOate, and constant O2. - levels, produced by the action of xanthine oxidase on lumazine, suppressed O2. (-)-induced lipid peroxidation in the presence of Fe3(+)- EDTA. On the other hand, an increase in the . NO/O2. - value resulted in nitration of SP-A tyrosine residues, located in the carbohydrate recognition domain (CRD), and decreased the ability of SP-A to aggregate lipids and bind mannose, two functions that require an intact CRD. SP-A was also nitrated to a large extent following exposure to 3-morpholinosydnonimine (SIN-1) or tetranitromethane at pH 8. In each case, increased nitrotyrosine content correlated in a monotonic fashion with inhibition of lipid aggregation and mannose binding, correlated with the extent of functional inhibition. Superoxide dismutase (2400 U/ml) and urate (100 microM; nonspecific scavenger of both ONOO- and hydroxyl radical), but not mannitol (50 mM; hydroxyl radical scavenger), prevented the SIN-1-induced injury to SP-A. In contrast, spermine NON-Oate or xanthine oxidase plus lumazine alone neither inhibited SP-A function nor nitrated the protein. These results indicate that at high concentrations, . NO inhibit O2. -induced lipid peroxidation. However, ONOO. , formed by the reaction of . NO and O2. -, nitrates SP-A leading to decreased ability to aggregate lipids and bind mannose.
1, 000 Tables Inside the From

The goal of operational Business Intelligence (BI) is to help organizations improve the efficiency of their business by giving every "operational worker" insights needed to make better operational decisions, and aligning day-to-day operations with strategic goals. Operational BI reporting contributes to this goal by embedding analytics and reporting information into workflow applications so that the business user has all required information (contextual and business data) in order to make good decisions. EII systems facilitate the construction of operational BI reports by enabling the creation and querying of customized virtual database schemas over a set of distributed and heterogeneous data sources with a low TCO. Queries over these virtual databases feed the operational BI reports. We describe the characteristics of operational BI reporting applications and show that they increase the complexity of the source to target mapping defined between source data and virtual databases. We show that this complexity yields the execution of "mega queries", i.e., queries with possible a 1,000 tables in their FROM clause. We present some key optimization methods that have been successfully implemented in SAP Business Objects Data Federator system to deal with mega queries.
Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11

The ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X‐ray crystallography has been a powerful approach to understand protein‐protein interactions; however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article, we describe an application of hydrogen deuterium exchange mass spectrometry (HDX‐MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIβ) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly, we also used HDX‐MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIβ in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPγS and GDP loaded Rab11 were determined. This hybrid HDX‐MS/crystallographic strategy revealed novel aspects of the PI4KIIIβ‐Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein‐protein complexes, and is an excellent strategy to optimize constructs for high‐resolution structural approaches.
CHOLINE ACETYLTRANSFERASE IN INDIVIDUAL NEURONS OF APLYSIA CALIFORNICA 1

The activities of choline acetyltransferase in the various ganglia of the nervous system of Aplysia californica and in some of the individually identifiable neurons in these ganglia were measured. At least four of the neurons were characterized by an apparent absence of the enzyme. The neurons containing measurable amounts of the enzyme had reproducible levels from animal to animal. Individual neurons from the same animal were generally characterized by different levels of activity whether expressed on a cell or a protein basis. However, those pairs of neurons previously classified as ‘homologous’ because of their similar appearance, location and/or electrophysiological function, also contained the same total amounts of enzyme activity.
A Wideband Circularly Polarized Patch Antenna for 60 GHz Wireless Communications

This paper presents the design of a fully packaged 60 GHz wideband patch antenna incorporating an air cavity and a fused silica superstrate. Circular polarization (CP) is realized by introducing a diagonal slot at the center of the square patch. By optimizing the patch and the slot dimensions, a high efficiency (>90%) microstrip fed CP antenna with an impedance bandwidth of 24% and a 6 dB axial ratio bandwidth of 21.5% is designed. A coplanar waveguide (CPW) to microstrip transition with λ/4-open-ended stubs are then designed to match the antenna to the CPW packaging interface. The experimental results of the final packaged antenna agree reasonably with the simulation results, demonstrating an impedance bandwidth of more than 26% and a 6 dB axial ratio bandwidth of 22.7%.
Correlation of serum HIV antigen and antibody with clinical status in HIV‐I infected patients

An enzyme immunoassay (EIA) has been developed which detects antigen(s) (Ag) of the human immunodeficiency virus (HIV) in the serum of patients with the acquired immunodeficiency syndrome (AIDS), AIDS‐related complex (ARC), and patients at high risk for HIV infection. The test has a sensitivity of approximately 50 pg/ml of HIV protein. The specificity of the assay was determined with various virus infected cell lines, normal human sera/plasma, and serum from patients not known to be at risk for HIV infection. No false‐positive HIV‐Ag results were seen. Sera from 69% of patients with AIDS were positive for HIV‐Ag as were 46% of patients with ARC and 19% of asymptomatic, HIV‐antibody‐positive individuals. There were significant associations between the stage of HIV infection–ie, AIDS vs ARC vs asymptomatic‐and the detection of HIV‐Ag in serum (p < 0.0001) and the lack of detection of antibody to HIV core Ag (p < 0.0001). HIV‐Ag was also found in the serum of two asymptomatic antibody‐negative individuals who were at high risk for AIDS and who later developed HIV antibody. The presence of HIV‐Ag in sera was confirmed by an inhibition procedure. Thus. HIV‐Ag can be detected in the serum of infected individuals prior to antibody production and correlates with the clinical stage of HIV infection.
Kramers-map approach for stabilization of a hydrogen atom in a monochromatic field.

The phenomenon of stabilization of highly excited states of a hydrogen atom in a strong monochromatic field is discussed. An approximate description of the dynamics from the introduction of the Kramers map allows one to understand the main properties of this phenomenon through analogy with the Kepler map. The analogy between the stabilization and the channneling of particles in a crystal is also discussed.