Miracle-dz/UniFAR-FTUs huggingface dataset:
Myopalladin, a Novel 145-Kilodalton Sarcomeric Protein with Multiple Roles in Z-Disc and I-Band Protein Assemblies

We describe here a novel sarcomeric 145-kD protein, myopalladin, which tethers together the COOH-terminal Src homology 3 domains of nebulin and nebulette with the EF hand motifs of α-actinin in vertebrate Z-lines. Myopalladin's nebulin/nebulette and α-actinin–binding sites are contained in two distinct regions within its COOH-terminal 90-kD domain. Both sites are highly homologous with those found in palladin, a protein described recently required for actin cytoskeletal assembly (Parast, M.M., and C.A. Otey. 2000. J. Cell Biol. 150:643–656). This suggests that palladin and myopalladin may have conserved roles in stress fiber and Z-line assembly. The NH2-terminal region of myopalladin specifically binds to the cardiac ankyrin repeat protein (CARP), a nuclear protein involved in control of muscle gene expression. Immunofluorescence and immunoelectron microscopy studies revealed that myopalladin also colocalized with CARP in the central I-band of striated muscle sarcomeres. Overexpression of myopalladin's NH2-terminal CARP-binding region in live cardiac myocytes resulted in severe disruption of all sarcomeric components studied, suggesting that the myopalladin–CARP complex in the central I-band may have an important regulatory role in maintaining sarcomeric integrity. Our data also suggest that myopalladin may link regulatory mechanisms involved in Z-line structure (via α-actinin and nebulin/nebulette) to those involved in muscle gene expression (via CARP).
A Tag-Based Hybrid Music Recommendation System Using Semantic Relations and Multi-domain Information

In this paper, we propose a hybrid approach for music recommendation. Firstly, we describe an approach for creating music recommendations based on user-supplied tags that are augmented with a hierarchical structure extracted for top level genres from Dbpedia. In this structure, each genre is represented by its stylistic origins, typical instruments, derivative forms, sub genres and fusion genres. We use this well-organized structure in dimensionality reduction in user and item profiling. We compare two recommenders, one using our method and the other using Latent Semantic Analysis (LSA) in dimensionality reduction. The recommender using our approach outperforms the other. In addition to different dimensionality reduction methods, we evaluate the recommenders with different user profiling methods. Moreover, our approach collects personal interests (favorite movies and television series) from the Face book profiles. These user profiles are then used to find the similarity between users. At the end, items belonging to the most similar users' profiles and having a high score against users' profiles are recommended. Thus, we have focused on a hybrid system using tag-based contextual information of music tracks and user interests acquired from Face book profiles. Initial results are promising such that using similarities of users affects the recommendation positively.
andscape structure and habitat management differentially influence insect atural enemies in an agricultural landscape

Increasing evidence suggests that landscape composition is an important driver of beneficial insect populations and resulting ecosystem services. Additionally, local-scale manipulations such as planting floral strips are used at the field-level to provide resources for beneficial insects to increase their services. It has been proposed that the benefits of local manipulations will depend on the landscape context, with greater benefits in simplified landscapes and smaller benefits in landscapes with an abundance of non-crop resources. To test this, we used soybean aphid, Aphis glycines, and its coccinellid predators as a model system to elucidate the effects of habitat management and landscape on biocontrol services in soybean. We selected pairs of soybean fields in landscapes of varying composition and planted buckwheat, occinellidae Fagopyrum esculentum, strips adjacent to one field in each pair. We measured coccinellid abundance and biocontrol in each field. Coccinellid abundance was higher in buckwheat than in control field margins in all landscapes, and coccinellid abundance in soybean was positively related to amount of semi-natural vegetation in the landscape. We found no evidence of an interaction between landscape and local variables, and biocontrol services were high in all contexts. For soybean aphid suppression, landscape factors dator are the key drivers of pre
UvA-DARE (Digital Academic Repository) Attributes Make Sense on Segmented Objects Attributes make sense on segmented objects

In this paper we aim for object classiﬁcation and segmentation by attributes. Where existing work considers attributes either for the global image or for the parts of the object, we propose, as our ﬁrst novelty, to learn and extract attributes on segments containing the entire object. Object-level attributes suﬀer less from accidental content around the object and accidental image conditions such as partial occlusions, scale changes and viewpoint changes. As our second novelty, we propose joint learning for simultaneous object classiﬁcation and segment proposal ranking, solely on the basis of attributes. This naturally brings us to our third novelty: object-level attributes for zero-shot, where we use attribute descriptions of unseen classes for localizing their instances in new images and classifying them accordingly. Results on the Caltech UCSD Birds, Leeds Butterﬂies, and an a-Pascal subset demonstrate that i) extracting attributes on oracle object-level brings substantial beneﬁts ii) our joint learning model leads to accurate attribute-based classiﬁcation and segmentation, approaching the oracle results and iii) object-level attributes also allow for zero-shot classiﬁcation and segmentation. We conclude that attributes make sense on segmented objects.
Long-term sequelae of acute kidney injury in the ICU

Purpose of reviewAcute kidney injury (AKI) in the ICU is associated with adverse outcomes. We review the long-term consequences of AKI in ICU patients. Recent findingsObservational studies show associations between AKI and mortality, prolonged length of ICU stay, dependence on mechanical ventilation, the development and progression of chronic kidney disease (CKD), and need for permanent renal replacement therapy. Few studies evaluate ICU AKI outcomes specifically, and data on long-term outcomes of survivors from this population are sparse. Little information exists comparing AKI in ICU and non-ICU settings, and prospective study designs to address such questions are problematic. AKI in the ICU should be distinguished from AKI in other clinical settings, as the underlying pathophysiology, severity of illness, and risk for permanent sequelae may be different. AKI and CKD are not mutually exclusive, but are part of a clinical spectrum in which AKI can potentiate the risk for CKD and pre-existing CKD increases risks of AKI. SummaryFurther research is necessary to delineate the mechanisms by which AKI may lead to CKD, and to understand how CKD enhances the risk for developing AKI. Whereas restrospective observational studies of this population exist, prospective clinical studies and trials evaluating the long-term clinical outcomes of AKI specifically in ICU patients are needed.
Advances in automatic meeting record creation and access

Oral communication is transient, but many important decisions, social contracts and fact findings are first carried out in an oral setup, documented in written form and later retrieved. At Carnegie Mellon University's Interactive Systems Laboratories we have been experimenting with the documentation of meetings. The paper summarizes part of the progress that we have made in this test bed, specifically on the question of automatic transcription using large vocabulary continuous speech recognition, information access using non-keyword based methods, summarization and user interfaces. The system is capable of automatically constructing a searchable and browsable audio-visual database of meetings and provide access to these records.
Effect of Topical Application of Chlorogenic Acid on Excision Wound Healing in Rats

Abstract This study was undertaken to evaluate the therapeutic effects of topical chlorogenic acid on excision wounds in Wistar rats. A 1 % (w/w) chlorogenic acid or silver sulfadiazine ointment was applied topically once a day for 15 days on full-thickness excision wounds created on rats. The 1 % (w/w) chlorogenic acid ointment had potent wound healing capacity as evident from the wound contraction on the 15th post-surgery day, which was similar to that produced by 1 % (w/w) silver sulfadiazine ointment. Increased rates of epithelialization were observed in the treated rats. It also improved cellular proliferation, increased tumor necrosis factor-α levels during the inflammatory phase (12 h, 24 h, 48 h, and 72 h post-wounding) of wound healing, upregulated transforming growth factor-β1 and elevated collagen IV synthesis in the chlorogenic acid-treated group. The results also indicated that chlorogenic acid possesses potent antioxidant activity by increasing superoxide dismutase, catalase, and glutathione, and decreasing lipid peroxidation. In conclusion, these results demonstrate that topical application of chlorogenic acid can accelerate the process of excision wound healing by its ability to increase collagen synthesis through upregulation of key players such as tumor necrosis factor-α and transforming growth factor-β1 in different phases of wound healing as well as by its antioxidant potential.
Circadian clocks, feeding time, and metabolic homeostasis

Metabolic processes exhibit diurnal variation from cyanobacteria to humans. The circadian clock is thought to have evolved as a time keeping system for the cell to optimize the timing of metabolic events according to physiological needs and environmental conditions. Circadian rhythms temporally separate incompatible cellular processes and optimize cellular and organismal fitness. A modern 24 h lifestyle can run at odds with the circadian rhythm dictated by our molecular clocks and create desynchrony between internal and external timing. It has been suggested that this desynchrony compromises metabolic homeostasis and may promote the development of obesity (Morris et al., 2012). Here we review the evidence supporting the association between circadian misalignment and metabolic homeostasis and discuss the role of feeding time.
Safety Improvements at Highway-Railroad Crossing for Pedestrians and Bicyclists and the Assessment of Long-Term Effects of Centerline Curbing

“This report was funded in part through grant[s] from the Federal Highway Administration [and Federal Transit Administration], U.S. Department of Transportation. The views and opinions of the authors [or agency] expressed herein do not necessarily state or reflect those of the U. S. Department of Transportation. ” Nebraska Transportation Center 262 WHIT 2200 Vine Street Lincoln, NE 68583-0851 (402) 472-1975 Zheng Luo Researcher 26-1121-0004-001
Comparative Analysis of the Mucosal Adjuvanticity of the Type II Heat-Labile Enterotoxins LT-IIa and LT-IIb

ABSTRACT Cholera toxin (CT) and the heat-labile enterotoxin ofEscherichia coli (LT-I) are members of the serogroup I heat-labile enterotoxins (HLT) and can serve as systemic and mucosal adjuvants. However, information is lacking with respect to the structurally related but antigenically distinct serogroup II HLT, LT-IIa and LT-IIb, which have different binding specificities for ganglioside receptors. The purpose of this study was to assess the effectiveness of LT-IIa and LT-IIb as mucosal adjuvants in comparison to the prototypical type I HLT, CT. BALB/c mice were immunized by the intranasal (i.n.) route with the surface protein adhesin AgI/II ofStreptococcus mutans alone or supplemented with an adjuvant amount of CT, LT-IIa, or LT-IIb. Antigen-specific antibody responses in saliva, vaginal wash, and plasma were assayed by enzyme-linked immunosorbent assay. Mice given AgI/II with LT-IIa or LT-IIb by the i.n. route had significantly higher mucosal and systemic antibody responses than mice immunized with AgI/II alone. Anti-AgI/II immunoglobulin A (IgA) antibody activity in saliva and vaginal secretions of mice given AgI/II with LT-IIa or LT-IIb was statistically similar in magnitude to that seen in mice given AgI/II and CT. LT-IIb significantly enhanced the number of AgI/II-specific antibody-secreting cells in the draining superficial cervical lymph nodes compared to LT-IIa and CT. LT-IIb and CT induced significantly higher plasma anti-AgI/II IgG titers compared to LT-IIa. When LT-IIb was used as adjuvant, the proportion of plasma IgG2a relative to IgG1 anti-AgI/II antibody was elevated in contrast to the predominance of IgG1 antibodies promoted by AgI/II alone or when CT or LT-IIa was used. In vitro stimulation of AgI/II-specific cells from the superficial lymph nodes and spleen revealed that LT-IIa and LT-IIb induced secretion of interleukin-4 and significantly higher levels of gamma interferon compared to CT. These results demonstrate that the type II HLT LT-IIa and LT-IIb exhibit potent and distinct adjuvant properties for stimulating immune responses to a noncoupled protein immunogen after mucosal immunization.
A Protege Plug-in for Defeasible Reasoning

We discuss two approaches for defeasible reasoning in Description Logics that allow for the statement of defeasible subsumptions of the form “α subsumed by β usually holds”. These approaches are known as prototypical reasoning and presumptive reasoning and are both rooted in the notion of Rational Closure developed by Lehmann and Magidor for the propositional case. Here we recast their definitions in a defeasible DL context and define algorithms for prototypical and presumptive reasoning in defeasible DL knowledge bases. In particular, we present a plug-in for the Protege ontology editor which implements these algorithms for OWL ontologies. The plug-in is called RaMP and allows the modeller to indicate defeasible information in OWL ontologies and check entailment of defeasible subsumptions from defeasible knowledge bases.
Towards an error free plagarism detection process

For decades many computing departments have deployed systems for the detection of plagiarised student source code submissions. Automated systems to detect free-text student plagiarism are just becoming available and the experience of computing educators is valuable for their successful deployment.This paper describes a Four-Stage Plagiarism Detection Process that attempts to ensure no suspicious similarity is missed and that no student is unfairly accused of plagiarism. Required characteristics of an effective similarity detection engine are proposed and an investigation of a simple engine is described. An innovative prototype tool designed to decrease the workload of tutors investigating undue similarity is also presented.
P6B-11 How Fat Layers Affect the Clinical Diagnosis from Doppler Data

Ultrasound Doppler data are routinely used in the clinical diagnosis of degree of stenosis in the renal artery. In this study the effect of fat layers on maximum velocity estimations was determined using both a Doppler string and flow phantom. Using an ATL HDI 3000 with two broadband transducers (C4-2 and L12-5), the maximum velocity was estimated for a range of velocities with and without the presence of a fat layer. The results indicate that the introduction of a fat layer has a significant effect on the overestimation of the maximum velocity when the string phantom is used. However, in the case of the flow phantom which is more physiologically representative of in vivo conditions, underestimation of the maximum velocity was observed; this may cause patients to be diagnosed as having a smaller stenosis than is actually present.
Data Mining of Medical Data : Opportunities and Challenges in Mining Association Rules

Association rules represent knowledge embedded in data sets as probabilistic implications and are intimately related to computation of frequent item sets. We survey applications of frequent item sets and association rules in medical practice in such areas as nosocomial infections, adverse drug reactions, and the interplay between co-morbidities and the lack of transitivity of association rules. To make this survey as self-content as possible we present in an appendix the Fisher exact test and the χ-test, enumeration of subsets, frequent item sets and the Apriori algorithm, and combinatorial properties of association rules.
Pose Estimation using a Hierarchical 3D Representation of Contours and Surfaces

We present a system for detecting the pose of rigid objects using texture and contour information. From a stereo image view of a scene, a sparse hierarchical scene representation is reconstructed using an early cognitive vision system. We define an object model in terms of a simple context descriptor of the contour and texture features to provide a sparse, yet descriptive object representation. Using our descriptors, we do a search in the correspondence space to perform outlier removal and compute the object pose. We perform an extensive evaluation of our approach with stereo images of a variety of real-world objects rendered in a controlled virtual environment. Our experiments show the complementary role of 3D texture and contour information allowing for pose estimation with high robustness and accuracy.
Genetic and Epigenetic Mechanisms That Maintain Hematopoietic Stem Cell Function

All hematopoiesis cells develop from multipotent progenitor cells. Hematopoietic stem cells (HSC) have the ability to develop into all blood lineages but also maintain their stemness. Different molecular mechanisms have been identified that are crucial for regulating quiescence and self-renewal to maintain the stem cell pool and for inducing proliferation and lineage differentiation. The stem cell niche provides the microenvironment to keep HSC in a quiescent state. Furthermore, several transcription factors and epigenetic modifiers are involved in this process. These create modifications that regulate the cell fate in a more or less reversible and dynamic way and contribute to HSC homeostasis. In addition, HSC respond in a unique way to DNA damage. These mechanisms also contribute to the regulation of HSC function and are essential to ensure viability after DNA damage. How HSC maintain their quiescent stage during the entire life is still matter of ongoing research. Here we will focus on the molecular mechanisms that regulate HSC function.
The t-SNAREs syntaxin 1 and SNAP-25 are present on organelles that participate in synaptic vesicle recycling

Syntaxin 1 and synaptosome-associated protein of 25 kD (SNAP-25) are neuronal plasmalemma proteins that appear to be essential for exocytosis of synaptic vesicles (SVs). Both proteins form a complex with synaptobrevin, an intrinsic membrane protein of SVs. This binding is thought to be responsible for vesicle docking and apparently precedes membrane fusion. According to the current concept, syntaxin 1 and SNAP-25 are members of larger protein families, collectively designated as target-SNAP receptors (t-SNAREs), whose specific localization to subcellular membranes define where transport vesicles bind and fuse. Here we demonstrate that major pools of syntaxin 1 and SNAP-25 recycle with SVs. Both proteins cofractionate with SVs and clathrin-coated vesicles upon subcellular fractionation. Using recombinant proteins as standards for quantitation, we found that syntaxin 1 and SNAP-25 each comprise approximately 3% of the total protein in highly purified SVs. Thus, both proteins are significant components of SVs although less abundant than synaptobrevin (8.7% of the total protein). Immunoisolation of vesicles using synaptophysin and syntaxin specific antibodies revealed that most SVs contain syntaxin 1. The widespread distribution of both syntaxin 1 and SNAP-25 on SVs was further confirmed by immunogold electron microscopy. Botulinum neurotoxin C1, a toxin that blocks exocytosis by proteolyzing syntaxin 1, preferentially cleaves vesicular syntaxin 1. We conclude that t- SNAREs participate in SV recycling in what may be functionally distinct forms.
Notch signalling is off and is uncoupled from HES1 expression in Ewing's sarcoma

Notch can act as an oncogene or as a tumour suppressor and thus can either promote or inhibit tumour cell growth. To establish Notch status in Ewing's sarcoma family of tumours (ESFT), we investigated the Notch pathway by gene expression profiling meta‐analysis or immunohistochemistry in samples obtained from 96 and 24 ESFT patients, respectively. We found that although Notch receptors were highly expressed, Notch did not appear to be active, as evidenced by the absence of Notch receptors in cell nuclei. In contrast, we show that Notch receptors known to be active in colon adenocarcinoma, hepatocarcinoma, and pancreatic carcinoma stain cell nuclei in these tumours. High expression of the Notch effector HES1 transcription factor, usually used as a surrogate marker for active Notch, was also restricted to outside of the nucleus in the majority of ESFT, and analysis of HES1 gene targets indicated HES1 to be transcriptionally inactive. Neither forced activation nor pharmacological or genetic blocking of Notch affected HES1 expression in ESFT cells, indicating HES1 expression to be uncoupled from the Notch pathway. Additional functional studies in ESFT cell lines confirmed Notch to be switched off. Finally, unlike experiments in which HES1 expression was modulated, experimental activation of Notch in ESFT cell lines via several means blocked cell proliferation and reduced their clonogenic potential in soft agar. These indicate that HES1 is uncoupled from Notch in ESFT, that EWS–FLI1‐mediated inhibition of Notch contributes to ESFT aggressive cell growth, and support a role for Notch in ESFT tumour suppression, at least partly through the Notch effector HEY1. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Immune microenvironments differ in immune characteristics and outcome of glioblastoma multiforme

Understanding the interactions between tumors and the host immune system holds great promise to uncover biomarkers for targeted therapies, predict the prognosis of patients and guide clinical treatment. However, the immune signatures of glioblastoma multiforme (GBM) remain largely unstudied in terms of systematic analyses. We aimed to classify GBM samples according to immune‐related genes and complement the existing immunotherapy system knowledge. In this study, we designed a strategy to identify 3 immune subtypes representing 3 different immune microenvironments (M1‐M3) and associated with prognosis. The 3 subtypes were significantly different in terms of specific immune characteristics (immune cell subpopulations, immune responses, immune cells, and checkpoint gene interactions). In additional, copy number variations and methylation changes were identified that correlated with genes related to a worse prognosis subtype in the microenvironment. More importantly, in M3 (worst prognosis subtype) and M2 (best prognosis subtype), the interaction between immune cells and checkpoint genes was different, which had an important effect on the prognosis. Finally, we used risk scores of immune cells and checkpoint genes to evaluate the prognosis of GBM patients and validated the results with 3 independent datasets. Disordered interactions between immune cells and checkpoint genes result in a change in the immune microenvironment and affects the prognosis of patients. We propose that a better understanding of the immune microenvironment of advanced cancers may provide new insights into immunotherapy.