Miracle-dz/UniFAR-FTUs huggingface dataset:
Angiogenic Gene Signature Derived from Subtype Specific Cell Models Segregate Proneural and Mesenchymal Glioblastoma

Intertumoral molecular heterogeneity in glioblastoma identifies four major subtypes based on expression of molecular markers. Among them, the two clinically interrelated subtypes, proneural and mesenchymal, are the most aggressive with proneural liable for conversion to mesenchymal upon therapy. Using two patient-derived novel primary cell culture models (MTA10 and KW10), we developed a minimal but unique four-gene signature comprising genes vascular endothelial growth factor A (VEGF-A), vascular endothelial growth factor B (VEGF-B) and angiopoietin 1 (ANG1), angiopoietin 2 (ANG2) that effectively segregated the proneural (MTA10) and mesenchymal (KW10) glioblastoma subtypes. The cell culture preclassified as mesenchymal showed elevated expression of genes VEGF-A, VEGF-B and ANG1, ANG2 as compared to the other cell culture model that mimicked the proneural subtype. The differentially expressed genes in these two cell culture models were confirmed by us using TCGA and Verhaak databases and we refer to it as a minimal multigene signature (MMS). We validated this MMS on human glioblastoma tissue sections with the use of immunohistochemistry on preclassified (YKL-40 high or mesenchymal glioblastoma and OLIG2 high or proneural glioblastoma) tumor samples (n = 30). MMS segregated mesenchymal and proneural subtypes with 83% efficiency using a simple histopathology scoring approach (p = 0.008 for ANG2 and p = 0.01 for ANG1). Furthermore, MMS expression negatively correlated with patient survival. Importantly, MMS staining demonstrated spatiotemporal heterogeneity within each subclass, adding further complexity to subtype identification in glioblastoma. In conclusion, we report a novel and simple sequencing-independent histopathology-based biomarker signature comprising genes VEGF-A, VEGF-B and ANG1, ANG2 for subtyping of proneural and mesenchymal glioblastoma.
Shape Matching for Foliage Database Retrieval

Short overview of the Chapter—Computer-aided foliage image retrieval systems have the potential to dramatically speed up the process of plant species identification. Despite previous research, this problem remains challenging due to the large intra-class variability and inter-class similarity of leaves. This is particularly true when a large number of species are involved. In this chapter, we present a shape-based approach, the inner-distance shape context, as a robust and reliable solution. We show that this approach naturally captures part structures and is appropriate to the shape of leaves. Furthermore, we show that this approach can be easily extended to include texture information arising from the veins of leaves. We also describe a real electronic field guide system that uses our approach. The effectiveness of the proposed method is demonstrated in experiments on two leaf databases involving more than 100 species and 1000 leaves.
Repetitive Supra‐Physiological Shear Stress Impairs Red Blood Cell Deformability and Induces Hemolysis

The supra-physiological shear stress that blood is exposed to while traversing mechanical circulatory assist devices affects the physical properties of red blood cells (RBCs), impairs RBC deformability, and may induce hemolysis. Previous studies exploring RBC damage following exposure to supra-physiological shear stress have employed durations exceeding clinical instrumentation, thus we explored changes in RBC deformability following exposure to shear stress below the reported "hemolytic threshold" using shear exposure durations per minute (i.e., duty-cycles) reflective of that employed by circulatory assist devices. Blood collected from 20 male donors, aged 18-38 years, was suspended in a viscous medium and exposed to an intermittent shear stress protocol of 1 s at 100 Pa, every 60 s for 60 duty-cycles. During the remaining 59 s/min, the cells were left at stasis until the subsequent duty-cycle commenced. At discrete time points (15/30/45/60 duty-cycles), an ektacytometer measured RBC deformability immediately after shear exposure at 100 Pa. Plasma-free hemoglobin, a measurement of hemolysis, was quantified via spectrophotometry. Supra-physiological shear stress impaired RBC properties, as indicated by: (1) decreased maximal elongation of RBCs at infinite shear stress following 15 duty-cycles (P <0.05); (2) increased real-time RBC deformability during application of the supra-physiological shear stress protocol (100 Pa) following exposure to 1 duty-cycle (F (1.891, 32.15) = 12.21, P = 0.0001); and (3) increased plasma-free hemoglobin following 60 duty-cycles (P < 0.01). The present study indicates that exposure of RBCs to short-term, repeated supra-physiological shear stress, impairs RBC deformability, with the extent of impairment exacerbated with each duty-cycle, and ultimately precipitates hemolysis.
In Vivo Transduction of an Stx-Encoding Phage in Ruminants

ABSTRACT We assessed the ability of a kanamycin-marked Stx phage to move into a commensal, ovine Escherichia coli strain in the ruminant gastrointestinal tract. Transduction was detected in 19/24 sheep tested, resulting in the recovery of 47 transductants. Subtherapeutic doses of the quinolone antibiotic enrofloxacin did not increase the rate of transduction.
Rule Specialization in Networks of Fuzzy Basis Functions

ABSTRACTThe structure identification of adaptive fuzzy logic systems, realized as networks of Fuzzy Basis Functions (FBF's) and trained on numerical data, is studied for a handwritten character recognition problem. An FBF network with fewer rules than classes to be discriminated is unable to recognize some classes, while, when the number of rules is increased up to the number of classes to be discriminated, a sharp increase in the performance is observed. Experimental results point out that the behavior of the FBF network is closer to that of a competitive model showing a strong specialization of the fuzzy rules.
Longitudinal stent deformation: insights on mechanisms, treatments and outcomes from the Food and Drug Administration Manufacturer and User Facility Device Experience database.

AIMS Longitudinal stent deformation (LSD) is a recently described complication of PCI, but mechanisms contributing to its occurrence and associated clinical outcomes remain unclear. The FDA Manufacturer and User Facility Device Experience (MAUDE) database was searched to identify cases of LSD to gain insight into procedural and anatomical factors that predispose to this complication and associated clinical outcomes. METHODS AND RESULTS The MAUDE database is a voluntary international electronic reporting system whose aim is to capture major adverse events involving medical devices. Using defined search terms, we identified 57 unique cases of LSD ranging from 2004-2011. A significant increase in the reporting of LSD in the last two years was observed with most reported cases in stents based on the Element platform (90%). The lesions in which LSD was reported were complex (vessel calcification 26%; tortuosity 25%; long 28%; ostial disease 21%) and most frequently occurred following attempts to pass or withdraw secondary devices through a previously deployed stent (89% cases where mechanism identified). Adverse clinical outcomes including emergent cardiac surgery and acute and sub-acute stent thrombosis occurred in eight cases. CONCLUSIONS LSD can occur secondary to a variety of mechanisms; identification and treatment is important since adverse incidents such as emergent CABG and stent thrombosis may occur. A novel classification system is proposed to facilitate future reporting of this complication.
Arbuscular Mycorrhizal Fungi Elicit a Novel Intracellular Apparatus in Medicago truncatula Root Epidermal Cells before Infection[W]

The penetration of arbuscular mycorrhizal (AM) fungi through the outermost root tissues of the host plant is a critical step in root colonization, ultimately leading to the establishment of this ecologically important endosymbiotic association. To evaluate the role played by the host plant during AM infection, we have studied in vivo cellular dynamics within Medicago truncatula root epidermal cells using green fluorescent protein labeling of both the plant cytoskeleton and the endoplasmic reticulum. Targeting roots with Gigaspora hyphae has revealed that, before infection, the epidermal cell assembles a transient intracellular structure with a novel cytoskeletal organization. Real-time monitoring suggests that this structure, designated the prepenetration apparatus (PPA), plays a central role in the elaboration of the apoplastic interface compartment through which the fungus grows when it penetrates the cell lumen. The importance of the PPA is underlined by the fact that M. truncatula dmi (for doesn't make infections) mutants fail to assemble this structure. Furthermore, PPA formation in the epidermis can be correlated with DMI-dependent transcriptional activation of the Medicago early nodulin gene ENOD11. These findings demonstrate how the host plant prepares and organizes AM infection of the root, and both the plant–fungal signaling mechanisms involved and the mechanistic parallels with Rhizobium infection in legume root hairs are discussed.
The role of ecological feedbacks in the evolution of host defence: what does theory tell us?

Hosts have evolved a diverse range of defence mechanisms in response to challenge by infectious organisms (parasites and pathogens). Whether defence is through avoidance of infection, control of the growth of the parasite once infected, clearance of the infection, tolerance to the disease caused by infection or innate and/or acquired immunity, it will have important implications for the population ecology (epidemiology) of the host–parasite interaction. As a consequence, it is important to understand the evolutionary dynamics of defence in the light of the ecological feedbacks that are intrinsic to the interaction. Here, we review the theoretical models that examine how these feedbacks influence the nature and extent of the defence that will evolve. We begin by briefly comparing different evolutionary modelling approaches and discuss in detail the modern game theoretical approach (adaptive dynamics) that allows ecological feedbacks to be taken into account. Next, we discuss a number of models of host defence in detail and, in particular, make a distinction between ‘resistance’ and ‘tolerance’. Finally, we discuss coevolutionary models and the potential use of models that include genetic and game theoretical approaches. Our aim is to review theoretical approaches that investigate the evolution of defence and to explain how the type of defence and the costs associated with its acquisition are important in determining the level of defence that evolves.
Dynamic Control of Interference Limited Underlay D2D Network

Device-to-Device (D2D) communication appears as a key communication paradigm to realizing the vision of Internet of Things (IoT) into reality by supporting heterogeneous objects interconnection in a large scale network. These devices may be many types of objects with embedded intelligence and communication capabilities, e.g., smart phones, cars, or home appliances. The issue in in this type of communication is the interference to cellular communication caused by D2D communication. Thus, proper power control and resource allocation should be coordinated in D2D network to prevent excessive interference and drastic decrease in the throughput of the cellular system. In this paper, we consider the problem of cross-layer resource allocation in time-varying cellular wireless networks with D2D communication and incorporate average interference to cellular system as a quality-of-service constraint. Specifically, each D2D pair in the network injects packets to its queue, at rates chosen in order to maximize a global utility function, subject to network stability and interference constraints. The interference constraint enforces an arbitrarily low interference to the cellular system caused by D2D communication. We first obtain the stability region for the multiuser systems assuming that the nodes have full channel state information (CSI) of their neighbors. Then, we provide a joint flow control and scheduling scheme, which is proven to achieve a utility arbitrarily close to the maximum achievable utility. Finally, we address the consequences of practical implementation issue such as distributed scheduling by a designing algorithm, which is capable of taking advantage of diversity gain introduced by fading channels. We demonstrate the efficacy of our policies by numerical studies under various network conditions.
Protein Structure and Function Prediction Using I‐TASSER

I‐TASSER is a hierarchical protocol for automated protein structure prediction and structure‐based function annotation. Starting from the amino acid sequence of target proteins, I‐TASSER first generates full‐length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic‐level structure refinement. The biological functions of the protein, including ligand‐binding sites, enzyme commission number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I‐TASSER is freely available as both an on‐line server and a stand‐alone package. This unit describes how to use the I‐TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I‐TASSER modeling quality for distant‐homologous and multi‐domain protein targets. © 2015 by John Wiley & Sons, Inc.
Fingerprints, Pharmaceutical and Radical Scavenging Activity Evaluation of an Alzheimer-Targeted Herbal Preparation

Background: As the most common form of dementia, Alzheimer disease is characterized by progressive loss of memory and deterioration of cognitive functions. It is predicted that about 75.63 million people would suffer from dementia by 2030. Apart from conventional remedies, the application of herbal medicines is on the rise. There are numerous natural medicaments reported in the traditional manuscript of Persian medicine. Accordingly, in the present study, the intended remedy was selected and an appropriate pharmacognostical and pharmaceutical evaluations were performed. Methods: By searching through the traditional pharmaceutical manuscripts such as Qarabadeen-e-Salehi, Qarabadeen-e-Azam, Qarabadeen-e-Ghaderi and Canon of Medicine, a simple but proven compound remedy (frankincense and black pepper) was selected. A floating tablet was designed and formulated from those herbal components. Related pharmaceutical assessments such as weight variation, hardness, friability, and disintegration tests as well as pharmacognostical evaluations such as microscopic characterization, TLC, GC/MS, FT/IR fingerprints, and radical scavenging activity assessment (DPPH) were performed. Results: The resulting formulation, as a floating tablet, included 60% of frankincense gum and 15% of black pepper along with appropriate pharmaceutical ingredients (weight variation: 0.219±0.004 g, hardness: 6.50±0.67, friability: 0.45%, disintegration time >30 min). Microscopic characterization demonstrated stone cells, calcium oxalate crystals, sclereids of endocarp and pitted cells of mesocarp of pepper fruits as well as oil drops of frankincense gum. TLC fingerprinting showed classes of secondary metabolites related to both components. GC/MS analysis revealed Acetyl acetate and trans-Caryophyllene as the main constituent. Moderate radical scavenging activity (IC50 >100 µg/ml) was calculated for the methanol extract of tablets. Conclusion: Carrying out and validating a GC method for standardization of the formulated tablet, and having the structure for the effectiveness of these medicinal herbs in Alzheimer may be the horizon for a new Alzheimer-targeted medicine.
Take Care: Guidelines for Patients with Chronic Hepatitis C

Alcohol consumption has significant impact on the condition of the liver, by itself, and even more in conjunction with other liver diseases such as chronic hepatitis C. Drinking habits might be delicate issues to address and could harm otherwise satisfying communication. Therefore, we intended to outline guidelines for advising hepatitis C patients concerning alcohol consumption. Analysis of a relatively limited knowledge base revealed the complexity of the disease rather than statistically significant findings regarding consumption. Thus, we instead chose to suggest a set of patient educational guidelines, which could be implemented on the Internet, hypothesizing that a better informed patient will be more able to comply with restrictions concerning alcohol consumption. A brief ad hoc evaluation pointed out Internet as a favourable media to present the information. We also suggest a tentative algorithm for further development of clinical decision support systems addressing monitoring of chronic hepatitis C patients.
Enumerating the Junction Trees of a Decomposable Graph

We derive methods for enumerating the distinct junction tree representations for any given decomposable graph. We discuss the relevance of the method to estimating conditional independence graphs of graphical models and give an algorithm that, given a junction tree, will generate uniformly at random a tree from the set of those that represent the same graph. Programs implementing these methods are included as supplemental material.
Evaluación de la comprensión de las preguntas en lectura-orientada-a-tareas

El objetivo del estudio fue analizar una metodologia de evaluacion del modelo mental de tarea, en lectura-orientada-a-tareas. 66 estudiantes universitarios leyeron dos textos y contestaron preguntas. Para cada pregunta elaboramos un item sobre las demandas de la pregunta. Las alternativas de respuesta combinaban versiones correctas o erroneas de los componentes del modelo de pregunta; nucleo y proceso. Analizamos el formato de aplicacion, relacion con rendimiento, capacidad para discriminar entre niveles de comprension y funcionamiento psicometrico de los items. Cuando la evaluacion se aplico antes de responder, las puntuaciones mejoraron y se relacionaron con rendimiento. Esta aplicacion previa discrimino entre niveles de comprension y sugirio que el componente clave en esta distincion es la identificacion del nucleo de la pregunta. Los indices psicometricos resultaron adecuados. Estos resultados sugieren que la evaluacion del modelo mental de pregunta, previamente al proceso de contestacion, resulta efectiva para captar este proceso fundamental en de lectura-orientada-a-tareas.
Correlation of ratio of serum pepsinogen I and II with prevalence of gastric cancer and adenoma in Japanese subjects

Objective:Gastric cancer (GC) and adenoma (GA) are reported to be related to atrophic gastritis, in which the serum pepsinogen (PG) I level and the PGI/PGII ratio (I/II ratio) are reduced. To verify that the finding of a low PG level increases the risk for GC and GA, we investigated the correlation between low PG levels and the prevalence of GC and GA in individuals.Methods:The 2,039 subjects (734 Japanese men, mean age 68.5 yr, and 1,305 women, mean age 66.7 yr), selected from among 10,996 local residents who underwent health check-ups based on reductions in their serum PG levels, underwent upper gastrointestinal endoscopy.Results:Gastrointestinal endoscopy detected 21 GCs and 15 GAs. The prevalence of GC was higher than that in the residents without low serum PG. The percentage of early stage of GC (90%) was significantly higher than that of GC detected in unscreened residents (56.9%). The prevalence of GC in men was closely and significantly correlated with the I/II ratio (r = 0.935, p= 0.0063), whereas there was less correlation with age (r = 0.842, p= 0.0734). The prevalence of GA was also closely and significantly correlated with the I/II ratio in men (r = 0.881, p= 0.0203), but not with age (r = 0.163, p= 0.7928). In women the prevalence of GC (r 5 0.744, p= 0.090) and GA (r = 0.678, p= 0.1392) did not correlate as strongly with the I/II ratio, although the highest prevalence was seen in the group with the lowest I/II ratio.Conclusion:Our study verified that a low I/II ratio signifies a high risk for GC and GA and that measuring serum PG levels can be used as a screening method for GC and GA.
Lunar interior properties from the GRAIL mission

The Gravity Recovery and Interior Laboratory (GRAIL) mission has sampled lunar gravity with unprecedented accuracy and resolution. The lunar GM, the product of the gravitational constant G and the mass M, is very well determined. However, uncertainties in the mass and mean density, 3345.56 ± 0.40 kg/m3, are limited by the accuracy of G. Values of the spherical harmonic degree‐2 gravity coefficients J2 and C22, as well as the Love number k2 describing lunar degree‐2 elastic response to tidal forces, come from two independent analyses of the 3 month GRAIL Primary Mission data at the Jet Propulsion Laboratory and the Goddard Space Flight Center. The two k2 determinations, with uncertainties of ~1%, differ by 1%; the average value is 0.02416 ± 0.00022 at a 1 month period with reference radius R = 1738 km. Lunar laser ranging (LLR) data analysis determines (C − A)/B and (B − A)/C, where A < B < C are the principal moments of inertia; the flattening of the fluid outer core; the dissipation at its solid boundaries; and the monthly tidal dissipation Q = 37.5 ± 4. The moment of inertia computation combines the GRAIL‐determined J2 and C22 with LLR‐derived (C − A)/B and (B − A)/C. The normalized mean moment of inertia of the solid Moon is Is/MR2 = 0.392728 ± 0.000012. Matching the density, moment, and Love number, calculated models have a fluid outer core with radius of 200–380 km, a solid inner core with radius of 0–280 km and mass fraction of 0–1%, and a deep mantle zone of low seismic shear velocity. The mass fraction of the combined inner and outer core is ≤1.5%.
Reliability and Validity of Query Intent Assessments

In most intent recognition studies, annotations of query intent are created post hoc by external assessors who are not the searchers themselves. It is important for the field to get a better understanding of the quality of this process as an approximation for determining the searcher's actual intent. Some studies have investigated the reliability of the query intent annotation process by measuring the interassessor agreement. However, these studies did not measure the validity of the judgments, that is, to what extent the annotations match the searcher's actual intent. In this study, we asked both the searchers themselves and external assessors to classify queries using the same intent classification scheme. We show that of the seven dimensions in our intent classification scheme, four can reliably be used for query annotation. Of these four, only the annotations on the topic and spatial sensitivity dimension are valid when compared with the searcher's annotations. The difference between the interassessor agreement and the assessor-searcher agreement was significant on all dimensions, showing that the agreement between external assessors is not a good estimator of the validity of the intent classifications. Therefore, we encourage the research community to consider using query intent classifications by the searchers themselves as test data. © 2013 ASIS&T.