Miracle-dz/UniFAR-FTUs huggingface dataset:
LDLR and PCSK9 Are Associated with the Presence of Antiphospholipid Antibodies and the Development of Thrombosis in aPLA Carriers

Introduction The identification of the genetic risk factors that could discriminate non- thrombotic from thrombotic antiphospholipid antibodies (aPLA) carriers will improve prognosis of these patients. Several human studies have shown the presence of aPLAs associated with atherosclerotic plaque, which is a known risk factor for thrombosis. Hence, in order to determine the implication of atherosclerosis in the risk of developing thrombosis in aPLA positive patients, we performed a genetic association study with 3 candidate genes, APOH, LDLR and PCSK9. Material & Methods For genetic association study we analyzed 190 aPLA carriers -100 with non-thrombotic events and 90 with thrombotic events- and 557 healthy controls. Analyses were performed by χ2 test and were corrected by false discovery rate. To evaluate the functional implication of the newly established susceptibility loci, we performed expression analyses in 86 aPLA carrier individuals (43 with thrombotic manifestations and 43 without it) and in 45 healthy controls. Results Our results revealed significant associations after correction in SNPs located in LDLR gene with aPLA carriers and thrombotic aPLA carriers, when compared with healthy controls. The most significant association in LDLR gene was found between SNP rs129083082 and aPLA carriers in recessive model (adjusted P-value = 2.55 x 10−3; OR = 2.18; 95%CI = 1.49–3.21). Furthermore, our work detected significant allelic association after correction between thrombotic aPLA carriers and healthy controls in SNP rs562556 located in PCSK9 gene (adjusted P-value = 1.03 x 10−2; OR = 1.60; 95%CI = 1.24–2.06). Expression level study showed significantly decreased expression level of LDLR gene in aPLA carriers (P-value <0.0001; 95%CI 0.16–2.10; SE 0.38–1.27) in comparison to the control group. Discussion Our work has identified LDLR gene as a new susceptibility gene associated with the development of thrombosis in aPLA carriers, describing for the first time the deregulation of LDLR expression in individuals with aPLAs. Besides, thrombotic aPLA carriers also showed significant association with PCSK9 gene, a regulator of LDLR plasma levels. These results highlight the importance of atherosclerotic processes in the development of thrombosis in patients with aPLA.
Modeling Oncogenic Signaling in Colon Tumors by Multidirectional Analyses of Microarray Data Directed for Maximization of Analytical Reliability

Background Clinical progression of colorectal cancers (CRC) may occur in parallel with distinctive signaling alterations. We designed multidirectional analyses integrating microarray-based data with biostatistics and bioinformatics to elucidate the signaling and metabolic alterations underlying CRC development in the adenoma-carcinoma sequence. Methodology/Principal Findings Studies were performed on normal mucosa, adenoma, and carcinoma samples obtained during surgery or colonoscopy. Collections of cryostat sections prepared from the tissue samples were evaluated by a pathologist to control the relative cell type content. The measurements were done using Affymetrix GeneChip HG-U133plus2, and probe set data was generated using two normalization algorithms: MAS5.0 and GCRMA with least-variant set (LVS). The data was evaluated using pair-wise comparisons and data decomposition into singular value decomposition (SVD) modes. The method selected for the functional analysis used the Kolmogorov-Smirnov test. Expressional profiles obtained in 105 samples of whole tissue sections were used to establish oncogenic signaling alterations in progression of CRC, while those representing 40 microdissected specimens were used to select differences in KEGG pathways between epithelium and mucosa. Based on a consensus of the results obtained by two normalization algorithms, and two probe set sorting criteria, we identified 14 and 17 KEGG signaling and metabolic pathways that are significantly altered between normal and tumor samples and between benign and malignant tumors, respectively. Several of them were also selected from the raw microarray data of 2 recently published studies (GSE4183 and GSE8671). Conclusion/Significance Although the proposed strategy is computationally complex and labor–intensive, it may reduce the number of false results.
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In vitro cultivation of Wolbachia in insect and mammalian cell lines

SummaryWolbachia infecting the small brown planthopper, Laodelphax striatellus, were successfully maintained and cultivated in two insect and one mammalial cell lines. The bacteria with the planthopper ovary were introduced into the flasks with the cultures of the cell lines. The Wolbachia proliferated in mosquito (Aedes albopictus) and lepidopteran (Heliothis zea) cell lines and in the mouse cell line, L929. Proliferation of Wolbachia was confirmed by electron microscopy and quantitative polymerase chain reaction. This simple method for the cultivation of Wolbachia was applicable to other strains of Wolbachia, such as the one found in the lepidopteran eggs, and should facilitate fundamental and applied studies of this important group of microorganisms.
Comparison of seismic processing and interpretation tradeoffs between Kirchoff and finite-difference migrations, using poststack migrated data in the west Niger Delta, Nigeria

The Kirchoff and Finite-Difference migrations were carried out on seismic data from the western part of the Niger Delta of Nigeria. The survey for the acquisition of the data was oriented southwest-north-east, at an angle of 45.4490 o . The KIRCH and FXMIG seismic migration programs were used to process and display the seismic sections. The sections were interpreted for diffractions, faults, and structures. It was observed that the dipping structures were incorrectly positioned downdip from the true reflection point. Prior to migration, the dipping structures were steeper and longer. For both Kirchoff and Finite-Difference migrations, there was proper imaging of the dipping structures. The structures were accurately moved updip and diffractions collapsed. The faulting pattern is a growth fault system as is generally the case in the Niger Delta basin. The reflectors became shorter, anticlines more clearly defined, and reflection events terminating at fault planes. Finite-Difference migration is preferred because it is faster, handles velocity variation and noise better, and events appearance is sufficiently distinctive for the interpreter to find traps, seals and reservoirs.
Dear Shit-Shovellers: Humour, Censure and the Discourse of Complaint

In this article we analyse letters of complaint about instances of comic discourse where the humour is regarded as overstepping the mark and causing offence. We are particularly interested in how this sense of offence is registered and how complainants articulate the offence for which they seek some form of redress. In pursuing this interest, we seek to bring together two distinctive modes of analysis: linguistic discourse analysis and symbolic cultural analysis. This is methodologically appropriate to the discourse involved because of the ways in which epistolary complaints use forms of linguistic framing for offsetting potential objections to what they want to say, and because of the highly figurative language which is employed in voicing the substantive complaint and the censure of the humour that is entailed in this. Our focus overall is on the underlying ambivalence involved in negotiations between ethical and comic discourse.
Simulation of magnetic particles in blood flow to improve failsafe particle detection of microspheres based detoxification system

In acute liver dysfunction therapy a microspheres based detoxification system is used for high specific toxin removal [1]. A hollow fiber membrane filter separates blood plasma from an extracorporeal blood circuit, which is led to a secondary circuit with immersed specific adsorbent microparticles. In case of filter rupture, the particles can contaminate the patient. Fluorescent magnetic particles are added to the secondary circuit in order to magnetically trap and optically detect the contaminant as a failsafe system before re-entering the patient (Fig. 1a). In preliminary work a theoretical analysis of magnetic particle accumulations at certain magnetic gradient fields from neodymium iron boron magnets was performed using a continuous Lagrangian approach [2]. The blood was represented by its viscosity, density and a given flow rate. Individual blood cell collisions with the magnetic particle compound could not be analyzed. In order to analyze interactions of individual blood cells with agglomerating magnetic particles a newly developed simulation tool is used. Magnetic particles and blood cells are treated as individual subjects, similar to to the idea of molecular dynamics or discrete element simulations [3]. The simple Stokes drag is a good approximation for laminar flow. Here we combine magnetic particle dynamics and complex hydrodynamics computed with the lattice Boltzmann method. We extended the softmatter simulation environment ESPResSo [4] with an immersed boundary model of individual red blood cells and magnetic particles (Fig. 1b). The objects are represented by a boundary mesh of interacting immersed boundary nodes. Magnetic interactions are calculated in the center of mass whereas the hydrodynamics and the objects elasticity are computed at the boundary nodes. The goal of this work is a very small agglomeration plug for highly sensitive optical measurement of the fluorescent intensity. The intensity is proportional to the amount of collected particles and hence an indicator for a ruptured filter membrane (Fig. 1c). Using the developed simulation tool, the magnetic gradient field can be optimized such, that magnetic particles are collected at a small spatial region with respect to colliding blood cells and passing blood plasma (Fig. 1d). Figure 1: a) Microspheres based detoxification system. b) Interacting immersed boundary models of elastic red blood cell and rigid magnetic particles. c) Drastic increase in particle count after rupture of filter membrane. d) Agglomeration of magnetic particles at high field gradients of permanent magnets.
Structure and Change of the IIP-D Pre- and Postpsychotherapy

The structure and change of the Inventory of Interpersonal Problems in the German Circumplex version (IIP-D; Horowitz, Strauss, & Kordy, 2000) were examined in a study of 393 Swiss psychotherapy outpatients. Replicating results by Vittengl, Clark, and Jarret (2003), interpersonal problems showed a three-factor structure (Interpersonal Distress, Love, and Dominance), with the latter two factors approximating a circumplex, both before and after therapy. Interpersonal Distress, Love, and Dominance changed with therapy. Structural stability, patterns of change, as well as intercultural generalizability of IIP assessments are discussed.
omparison of Safety and Efficacy of ivalirudin Versus Unfractionated Heparin n Percutaneous Peripheral Intervention Single-Center Experience

ethods Consecutive patients who underwent PPI at our institution were treated with either bivairudin or low-dose UFH. Patients were assessed prospectively during index hospital stay for proceural success and bleeding complications. Of 236 patients, 111 were dosed with UFH at 50 U/kg goal activated clotting time of 180 to 240 s), and 125 were dosed with bivalirudin at 0.75-mg/kg/h olus followed by a 1.75-mg/kg infusion. Procedural success was defined as 20% post-procedure esidual stenosis with no flow-limiting dissections or intravascular thrombus formation and major leeding as intracranial or retroperitoneal hemorrhage or a fall in hemoglobin 5 g/dl. Anticoagulaion cost analysis was conducted.
Exercise and diastolic function after myocardial infarction.

PURPOSE The purpose of this study was to determine the effects of exercise training on LV geometry and LV diastolic function in a rat model of MI. METHODS One month after MI induced by ligation of the left anterior descending artery (N = 45) or sham operation (N = 26), rats were randomized to either a sedentary or exercise group. Exercise consisted of treadmill running at 24 m.min-1, 1 h.d-1, 5 d.wk-1, for 3 wk. Passive LV pressure volume relationships were established with an isolated, red-cell-perfused Langendorff preparation. Infarct size was determined histologically and categorized as small (<30% of LV) or large (> or =30% of LV). RESULTS LV end-diastolic pressure-volume relationships were shifted rightward with increasing infarct size (P < 0.05). Exercise training further shifted the LV end-diastolic pressure-volume relationships rightward in sham, small MI and large MI (P < 0.05). Peak LV developed pressure was comparable in sedentary and exercised-trained hearts in sham, small MI, and large MI. LV diameter and septal wall thickness were greatest in large MI (P < 0.05). Exercise-trained hearts showed a tendency for a greater LV diameter and septal wall thickness in sham, small MI, and large MI. Scar thinning was most notable in large MI (P < 0.05). CONCLUSION Moderate-intensity treadmill running induces myocardial remodeling and a rightward shift in the LV end-diastolic pressure-volume relationship after MI, an adaptation similar to what is observed with exercise training in sham hearts without MI.
Classrooms and the Design of Pedagogic Discourse: A Multimodal Approach

This paper offers a social semiotic analysis of the school classroom, in this case the subject English classroom, as a material instantiation of pedagogic discourse. The classroom is looked at as a multimodal sign: the semiotic ‘residue’ or ‘sediment’ of discursive practices over time. In particular it discusses how visual displays and spatial design in the English classroom can be thought of as signs of school English. From this perspective a teacher’s classroom can be understood as a sign of how she or he mediates ‘official’ government and school discourse. Drawing on three illustrative examples of English classrooms from three different schools, the paper argues that the variation between these classrooms can be understood in part as a consequence of the complex web of social relations that mediate and institutionally frame pedagogy.
Influence of Anti-Patterns on Software Maintenance: A Review

Anti-patters are the defects which affects the system quality negatively. An indication of the existence of anti-patterns, in the software is known as ―Code Smell‖ which leads to the refactoring of system. Thus the maintenance becomes difficult to manage. More the number of smells more refactoring is needed. Different approaches have been identified for the detection of anti-patterns in the system. The paper aimed at investigating the impact of anti-patterns on classes and what are the certain kinds of anti-patterns that have a higher impact than others Finally the results have been concluded for the future studies in open source systems. The paper is divided in to four sections in which the introduction is followed by the types of anti-patterns. Furthermore the related work have been examined carefully with a brief conclusion. Thus the paper reveals different approaches for the identification code smells in the software system. Hence the detection of smells will be helpful in providing more reliability during testing and maintenance phases by predicting anti-patterns and faults before the delivery of the product. Moreover the identification of anti-patterns will be of usage to the community of software engineers and managers for improving the software development maintenance activities.
Fair Network Bandwidth Allocation in IaaS Datacenters via a Cooperative Game Approach

With wide application of virtualization technology, tenants are able to access isolated cloud services by renting the shared resources in Infrastructure-as-a-Service (IaaS) datacenters. Unlike resources such as CPU and memory, datacenter network, which relies on traditional transport-layer protocols, suffers unfairness due to a lack of virtual machine (VM)-level bandwidth guarantees. In this paper, we model the datacenter bandwidth allocation as a cooperative game, toward VM-based fairness across the datacenter with two main objectives: 1) guarantee bandwidth for VMs based on their base bandwidth requirements, and 2) share residual bandwidth in proportion to the weights of VMs. Through a bargaining game approach, we propose a bandwidth allocation algorithm, Falloc, to achieve the asymmetric Nash bargaining solution (NBS) in datacenter networks, which exactly meets our objectives. The cooperative structure of the algorithm is exploited to develop an online algorithm for practical real-world implementation. We validate Falloc with experiments under diverse scenarios and show that by adapting to different network requirements of VMs, Falloc can achieve fairness among VMs and balance the tradeoff between bandwidth guarantee and proportional bandwidth sharing. Our large-scale trace-driven simulations verify that Falloc achieves high utilization while maintaining fairness among VMs in datacenters.
An Evaluation of Dyadic Peer Support for Caregiving Parents of Children with Chronic Lung Disease Requiring Technology Assistance

Abstract This study evaluated a dyadic peer support pilot intervention for parents of technology-assisted children with chronic lung disease. These medically-fragile children, living at home in the primary care of their parents, require continuous or intermittent assistance from technological support such as home oxygen, respiratory or cardiac monitors and/or mechanical ventilators. The intervention consisted of matching parents with similar caregiving responsibilities, in order to reciprocally engage in parent-to-parent support. Results identified mixed outcomes based on quantitative and qualitative methods. Participants conveyed benefits and limitations of this modality of peer-based support. They generally favoured peer support as a clinical resource for caregiving parents as the intervention offered a valued opportunity for mutual sharing with another parent who could understand the unique realities particular to caring for a medically-fragile child. Sharing daily experiences was reported to reduce isolation, increase knowledge, and provide an important sense of feeling understood. Challenges associated with peer support included scheduling difficulties and personality incompatibility. Recommendations for program development in clinical settings are described.
Multilevel analysis of primary students' perception and deployment of self‐learning strategies

This study focuses on primary students' self‐learning strategies, using a sample of 1253 students from 20 Year 3 and 20 Year 5 classes from 10 primary schools in Hong Kong. Students were asked to name sources from which they could learn. They were then asked to rate 10 self‐learning strategies on perceived usefulness and personal deployment. Students named an average of 2.5 learning sources, with print exposure (reading) being the most commonly nominated source. Multilevel analysis revealed substantial differences (27% of attributable variance) between classes on student ability to name learning sources. In general, the students indicated that all 10 suggested learning strategies were useful. The two most commonly deployed strategies were help‐seeking and locating a quiet study environment. Gender differences were not found on naming learning resources, but girls indicated relatively higher levels of strategy awareness and deployment.
The limiting Temperature of hot nuclei from microscopic Equation of State

The limiting temperature T lim of a series of nuclei is calculated employing a set of microscopic nuclear equation of state (EoS). It is shown that the value of T lim is sensitive to the nuclear matter Equation of State used. Comparison with the values extracted in recent phenomenological analysis appears to favour a definite selection of EoS's. On the basis of this phenomenological analysis, it seems therefore possible to check the microscopic calculations of the nuclear EoS at finite temperature, which is hardly accessible through other experimental informations.
LPDA: A lightweight privacy-preserving data aggregation scheme for smart grid

Security and privacy are challenging issues in smart grid. Failure to address them will hinder the flourish of smart grid. In this paper, aiming at resolving the electricity consumption data security and residential user privacy, we proposed an efficient lightweight privacy-preserving aggregation scheme, called LPDA, for smart grid. The proposed LPDA is characterized by employing one-time masking technique to protect user's privacy while achieving lightweight data aggregation. Detailed security analysis has shown that the proposed LPDA scheme is robust against many security and privacy threats in smart grid. Furthermore, performance evaluation via extensive simulations demonstrates its efficiency in terms of low average aggregation delay.
JiffyNet: a web-based instant protein network modeler for newly sequenced species

Revolutionary DNA sequencing technology has enabled affordable genome sequencing for numerous species. Thousands of species already have completely decoded genomes, and tens of thousands more are in progress. Naturally, parallel expansion of the functional parts list library is anticipated, yet genome-level understanding of function also requires maps of functional relationships, such as functional protein networks. Such networks have been constructed for many sequenced species including common model organisms. Nevertheless, the majority of species with sequenced genomes still have no protein network models available. Moreover, biologists might want to obtain protein networks for their species of interest on completion of the genome projects. Therefore, there is high demand for accessible means to automatically construct genome-scale protein networks based on sequence information from genome projects only. Here, we present a public web server, JiffyNet, specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided. Assessment of the networks by JiffyNet demonstrated generally high predictive ability for pathway annotations. Furthermore, JiffyNet provides network visualization and analysis pages for wide variety of molecular concepts to facilitate network-guided hypothesis generation. JiffyNet is freely accessible at http://www.jiffynet. org.