Miracle-dz/UniFAR-FTUs huggingface dataset:
Force-Directed Parallel Coordinates

Parallel coordinates are a well-known and valuable technique for the analysis and visualization of high dimensional data sets. However, while Inselberg emphasizes that the strength of parallel coordinates as a methodology is rooted in exploration and interactivity, the set of interaction techniques is currently limited. Axes can be re-ordered and brushing (simple, angular or multi-dimensional) can be performed. In this paper, we propose a force-directed algorithm and related interaction techniques to support the exploration of parallel coordinate plots through a physical metaphor. Our parallel-coordinates visualization offers novel user interaction beyond the standard techniques by allowing the user to rotate the axis according to forcedirected polylines. The new interaction provides the user with a more immersive experience for data exploration that results in greater intuition of the data, especially in cases where many polylines overlap. We demonstrate our approach, then present the results of a qualitative evaluation of the system.
Rapid Synaptic Vesicle Endocytosis in Cone Photoreceptors of Salamander Retina

Following synaptic vesicle exocytosis, neurons retrieve the fused membrane by a process of endocytosis to provide a supply of vesicles for subsequent release and maintain the presynaptic active zone. Rod and cone photoreceptors use a specialized structure called the synaptic ribbon that enables them to sustain high rates of neurotransmitter release. They must also employ mechanisms of synaptic vesicle endocytosis capable of keeping up with release. While much is known about endocytosis at another retinal ribbon synapse, that of the goldfish Mb1 bipolar cell, less is known about endocytosis in photoreceptors. We used capacitance recording techniques to measure vesicle membrane fusion and retrieval in photoreceptors from salamander retinal slices. We found that application of brief depolarizing steps (<100 ms) to cones evoked exocytosis followed by rapid endocytosis with a time constant ∼250 ms. In some cases, the capacitance trace overshot the baseline, indicating excess endocytosis. Calcium had no effect on the time constant, but enhanced excess endocytosis resulting in a faster rate of membrane retrieval. Surprisingly, endocytosis was unaffected by blockers of dynamin, suggesting that cone endocytosis is dynamin independent. This contrasts with synaptic vesicle endocytosis in rods, which was inhibited by the dynamin inhibitor dynasore and GTPγS introduced through the patch pipette, suggesting that the two photoreceptor types employ distinct pathways for vesicle retrieval. The fast kinetics of synaptic vesicle endocytosis in photoreceptors likely enables these cells to maintain a high rate of transmitter release, allowing them to faithfully signal changes in illumination to second-order neurons.
Asset Prices with Heterogeneity in Preferences and Beliefs

In this paper, we study asset prices in a dynamic, continuous-time, general-equilibrium endowment economy where agents have “catching up with the Joneses” utility functions and differ with respect to their beliefs (because of differences in priors) and their preference parameters for time discount, risk aversion, and sensitivity to habit. A key contribution of our paper is to demonstrate how one can obtain a closed-form solution to the consumption-sharing rule for agents who have both heterogeneous priors and heterogeneous preferences without restricting the risk aversion of the two agents to special values. We solve in closed form also for the the state-price density, the riskless interest rate and market price of risk; the stock price, equity risk premium, and volatility of stock returns; the term structure of interest rates; and the conditions necessary to obtain a stationary equilibrium in which both agents survive in the long run. The methodology we develop is sufficiently general that, as long as markets are complete, it can be used to obtain the sharing rule and state prices for models set in discrete or continuous time and for arbitrary endowment and belief updating processes.
Phenotypic variation of erythrocyte linker histone H1.c in a pheasant (Phasianus colchicus L.) population

Our goal was to characterize a phenotypic variation of the pheasant erythrocyte linker histone subtype H1.c. By using two-dimensional polyacrylamide gel electrophoresis three histone H1.c phenotypes were identified. The differently migrating allelic variants H1.c1 and H1.c2 formed either two homozygous phenotypes, c1 and c2, or a single heterozygous phenotype, c1c2. In the pheasant population screened, birds with phenotype c2 were the most common (frequency 0.761) while individuals with phenotype c1 were rare (frequency 0.043).
Hybrid Copula Bayesian Networks

This paper introduces the hybrid copula Bayesian network (HCBN) model, a generalization of the copula Bayesian network (CBN) model developed by Elidan (2010) for continuous random variables to multivariate mixed probability distributions of discrete and continuous random variables. To this end, we extend the theorems proved by Nešlehová (2007) from bivariate to multivariate copulas with discrete and continuous marginal distributions. Using the multivariate copula with discrete and continuous marginal distributions as a theoretical basis, we construct an HCBN that can model all possible permutations of discrete and continuous random variables for parent and child nodes, unlike the popular conditional linear Gaussian network model. Finally, we demonstrate on a numerous synthetic datasets and a real life dataset that our HCBN compares favorably, from a modeling and flexibility viewpoint, to other hybrid models including the conditional linear Gaussian and the mixture of truncated exponentials models.
Perioperative management of patients with severe pulmonary hypertension in major orthopedic surgery: experience-based recommendations

Introduction: It is known that pulmonary hypertension is associated with worse outcome in both cardiac and non-cardiac surgery. The aims of our retrospective analysis were to evaluate the outcomes of our patients with pulmonary hypertension undergoing major orthopedic surgery and to give experience-based recommendations for the perioperative management. Material and methods: From 92 patients with pulmonary hypertension undergoing different kinds of surgical procedures from 2011–2014 in a tertiary academic hospital we evaluated 16 patients with major orthopedic surgery for perioperative morbidity and mortality. Results: Regarding the in-hospital morbidity and mortality, one patient died postoperatively due to pulmonary infection and right heart failure (6.25%) and 6 patients suffered significant postoperative complications (37.5%; bleeding = 1, infection = 1, wound healing deficits = 3; dysrhythmia = 1). Conclusion: Our data show that major orthopedic surgery is feasible with satisfactory outcome even in cases of severe pulmonary hypertension by an individualized, disease-adapted interdisciplinary treatment concept.
Management of interface design in humanoid

Today's interface design tools either force designers to handle a tremendous number of design details, or limit their control over design decisions. Neither of these approaches taps the true strengths of either human designers or computers in the design process. This paper presents a human-computer collaborative system that uses a model-based approach for interface design to help designers on decision making, and utilizes the bookkeeping capabilities of computers for regular and tedious tasks. We describe (a) the underlying modeling technique and an execution environment that allows even incompletely-specified designs to be executed for evaluation and testing purposes, and (b) a tool that decomposes high-level design goals into the necessary implementation steps, and helps designers manage the myriad of details that arise during design.
Intermediated Trade

This paper develops a simple model of international trade with intermediation. We consider an economy with two islands and two types of agents, farmers and traders. Farmers can produce two goods, but in order to sell these goods in centralized (Walrasian) markets, they need to be matched with a trader, and this entails costly search. In the absence of search frictions, our model reduces to a standard Ricardian model of trade. We use this simple model to contrast the implications of changes in the integration of Walrasian markets, which allow traders from different islands to exchange their goods, and changes in the access to these Walrasian markets, which allow farmers to trade with traders from different islands. We find that intermediation always magnifies the gains from trade under the former type of integration, but leads to more nuanced welfare results under the latter, including the possibility of aggregate losses. These welfare losses may be circumvented, however, through policies that discriminate against foreign traders in a way that minimizes the margins charged by domestic traders.
Multilingual XML-Based Named Entity Recognition for E-Retail Domains

We describe the multilingual Named Entity Recognition and Classification (NERC) subpart of an e-retail product comparison system which is currently under development as part of the EU-funded project CROSSMARC. The system must be rapidly extensible, both to new languages and new domains. To achieve this aim we use XML as our common exchange format and the monolingual NERC components use a combination of rule-based and machine-learning techniques. It has been challenging to process web pages which contain heavily structured data where text is intermingled with HTML and other code. Our preliminary evaluation results demonstrate the viability of our approach.
Efficient Antibody Production upon Suppression of O Mannosylation in the Yeast Ogataea minuta

ABSTRACT When antibodies were expressed in the methylotrophic yeast Ogataea minuta, we found that abnormal O mannosylation occurred in the secreted antibody. Yeast-specific O mannosylation is initiated by the addition of mannose at serine (Ser) or threonine (Thr) residues in the endoplasmic reticulum via protein O mannosyltransferase (Pmt) activity. To suppress the addition of O-linked sugar chains on antibodies, we examined the possibility of inhibiting Pmt activity by the addition of a Pmt inhibitor during cultivation. The Pmt inhibitor was found to partially suppress the O mannosylation on the antibodies. Surprisingly, the suppression of O mannosylation was associated with an increased amount of assembled antibody (H2L2) and enhanced the antigen-binding activity of the secreted antibody. In this study, we demonstrated the expression of human antibody in O. minuta and elucidated the relationship between O mannosylation and antibody production in yeast.
On the Free Bridge Across the Digital Divide: Assessing the Quality of Facebook's Free Basics Service

Free Basics is an initiative backed by Facebook to provide users in developing countries free mobile Internet access to selected services. Despite its wide-spread deployment and its potential impact on bridging the digital divide, to date, few studies have rigorously measured the quality of the free Internet service offered by Free Basics. In this short paper, we characterize the quality of the Free Basics service offered in Pakistan and South Africa along three dimensions: (i) the selection of accessible Web services, (ii) the functionality of those services, and (iii) the network performance for those services. While preliminary, our findings show that data- driven studies are essential for having more informed public debates on the pros and cons of the current design of the Free Basics service.
Cross-Presentation by Osteoclasts Induces FoxP3 in CD8+ T Cells

Bone is remodeled throughout the life of an animal by the action of osteoclasts, which resorb bone, and osteoblasts, which form new bone. It has recently been recognized that T cells regulate osteoclasts by secreting a number of cytokines including type I and II IFNs and receptor activator of NF-κB ligand. In this study, we show that osteoclasts produce chemokines that recruit CD8+ T cells. Using transgenic OT-I mice, we found that in the presence of OVA, osteoclasts induced the secretion of IL-2, IL-6, and IFN-γ as well as the proliferation of CD8+ T cells. CD8+ T cells activated by osteoclasts expressed FoxP3, CTLA4, and receptor activator of NF-κB ligand. The FoxP3+CD8+ T cells were anergic and suppressed dendritic cell priming of naive responder CD8+ T cells. These results provide two novel observations for osteoimmunology: first, we demonstrate that osteoclasts can cross-present Ags to CD8+ T cells. Second, these data show that osteoclasts are not only regulated by T cells, but they also can regulate T cells forming a feedback control loop. The induction of FoxP3 in T cells through a MHC class I-dependent manner provides a new mechanism to peripherally produce a regulatory T cell. These observations open a new avenue of investigation for the pathogenesis of autoimmune-mediated inflammatory bone diseases.
HFE genotyping demonstrates a significant incidence of hemochromatosis in undifferentiated arthritis.

OBJECTIVE Hereditary hemochromatosis is a common autosomal recessive disorder of iron metabolism. Among Northern Europeans the carrier frequency is estimated to be 1 in 10, while up to 1 in 200 is affected by the disease. Arthropathy is one early clinical manifestation of this disease, but the articular features are often misdiagnosed. In this study the two frequent mutations of the HLA-linked hemochromatosis gene (HFE) were investigated in a rheumatology clinic population. METHODS Two hundred and six consecutive patients (mean age 57.7 years; 38 male/168 female) attending a rheumatology clinic over a period of 14 months were screened for HFE mutations (C282Y and H63D). All standard diagnostic procedures were used to identify the aetiology of the arthropathy. Mutations were evaluated by separation on PAGE of digested PCR amplificates of DNA (by SnapI and Bcl-I, for C282Y and H63D, respectively) obtained from PBMCs. RESULTS The C282Y and H63D allele frequencies were 4.5 and 12.8 in patients with rheumatic diseases. Five patients were homozygote for H63D (2.4%), and one for C282Y (0.5%). Five patients were compound heterozygous (2.4%). The observed C282Y allele frequency in rheumatic patients with undifferentiated arthritis was 12.9 and exceeded that of healthy subjects (p = 0.01). CONCLUSIONS Determination of the HFE genotype is clinically useful in patients with arthritis of unknown origin, to allow early diagnosis of hemochromatosis.
Influenza Virus Hemagglutinin (H3 Subtype) Requires Palmitoylation of Its Cytoplasmic Tail for Assembly: M1 Proteins of Two Subtypes Differ in Their Ability To Support Assembly

ABSTRACT The influenza A virus hemagglutinin (HA) transmembrane domain boundary region and the cytoplasmic tail contain three cysteines (residues 555, 562, and 565 for the H3 HA subtype) that are highly conserved among the 16 HA subtypes and which are each modified by the covalent addition of palmitic acid. Previous analysis of the role of these conserved cysteine residues led to differing data, suggesting either no role for HA palmitoylation or an important role for HA palmitoylation. To reexamine the role of these residues in the influenza virus life cycle, a series of cysteine-to-serine mutations were introduced into the HA gene of influenza virus A/Udorn/72 (Ud) (H3N2) by using a highly efficient reverse genetics system. Mutant viruses containing HA-C562S and HA-C565S mutations had reduced growth and failed to form plaques in MDCK cells but formed wild-type-like plaques in an MDCK cell line expressing wild-type HA. In cell-cell fusion assays, nonpalmitoylated H3 HA, in both cDNA-transfected and virus-infected cells, was fully competent for HA-mediated membrane fusion. When the HA cytoplasmic tail cysteine mutants were examined for lipid raft association, using as the criterion Triton X-100 insolubility, loss of raft association did not show a direct correlation with a reduction in virus replication. However, mutant virus assembly was reduced in parallel with reduced virus replication. Additionally, a reassortant of strain A/WSN/33 (WSN), containing the Ud HA gene with mutations C555S, C562S, and C565S, produced virus that could form plaques on regular MDCK cells and had only moderately decreased replication, suggesting differences in the interactions between Ud and WSN HA and internal viral proteins. Analysis of M1 mutants containing substitutions in the six residues that differ between the Ud and WSN M1 proteins indicated that a constellation of residues are responsible for the difference between the M1 proteins in their ability to support virus assembly with nonpalmitoylated H3 HA.
The effects of doxycycline on reducing symptoms in knee osteoarthritis: results from a triple-blinded randomised controlled trial

Objectives Evidence suggests that doxycycline might have disease-modifying properties in osteoarthritis. However, the clinically relevant question as to whether doxycycline also modifies symptoms in knee osteoarthritis is unanswered. The objective of this study was to investigate the effectiveness of doxycycline on pain and daily functioning in symptomatic knee osteoarthritis. Methods A 24-week, randomised, triple-blind, placebo controlled trial on the symptomatic effectiveness of doxycycline twice a day 100 mg in knee osteoarthritis patients according to the clinical and radiological American College of Rheumatology classification criteria. The primary endpoint was the difference in the proportion of participants in both study groups achieving a clinical response defined by the OMERACT–OARSI set of responder criteria. Secondary endpoints included pain, stiffness, daily functioning, patient global assessment, quality of life, osteoarthritis-related medication and side effects. Results 232 patients were randomly assigned. At study end, 31% of participants met the primary endpoint in both groups. Except for more adverse events in the doxycycline group, no differences were also found on the secondary endpoints. Conclusions Doxycycline is not effective in reducing symptoms in knee osteoarthritis patients over a 24-week study period, but is associated with an increased risk of adverse events. Although a possible structure-modifying effect of doxycycline was previously suggested, this is not accompanied by symptom relief in the short and medium term. Dutch Trial Register no NTR1111.
Efficacy of a Nelfinavir- and Nevirapine-Containing Salvage Regimen

Abstract Purpose: In this study, our purpose was to assess the efficacy of nelfinavir- and nevirapine-containing salvage regimens in nonnucleoside reverse transcriptase inhibitor (NNRTI)-naive patients virologically failing a protease inhibitor (PI)-based combination. Method: A retrospective case note review of all patients virologically failing their PI-based combination who were switched to a regimen containing both nelfinavir (1 g t.d.s.) and nevirapine (200 mg b.d.). CD4 cell counts and viral loads were monitored. Genotypic analysis was performed using RT-PCR sequencing. Results: Nineteen patients commenced a salvage regimen containing nelfinavir and nevirapine. Five patients also changed at least one nucleoside reverse transcriptase inhibitor (NRTI), although in one case this represented recycling. Thirty-eight percent (6/16) of patients achieved a viral load below the level of detection (BLD; <200 copies/mL; complete responders [CR]), 3 achieved <20 copies/mL. Five patients achieved ≥ 1 log drop (partial responders [PR]) that was not sustained over follow-up, and five failed to respond to therapy (nonresponders [NR]). CRs tended to have wild-type NNRTI and PI sequences relative to PRs and NRs. Conclusion: In heavily pretreated patients, a nelfinavir-and nevirapine-containing salvage regimen resulted in a virological response in 38% of patients that was sustained in 31% over 63 weeks.
An Approach for Search Based Testing of Null Pointer Exceptions

Uncaught exceptions, and in particular null pointer exceptions (NPEs), constitute a major cause of crashes for software systems. Although tools for the static identification of potential NPEs exist, there is need for proper approaches able to identify system execution scenarios causing NPEs. This paper proposes a search-based test data generation approach aimed at automatically identify NPEs. The approach consists of two steps: (i) an inter-procedural data and control flow analysis-relying on existing technology-that identifies paths between input parameters and potential NPEs, and (ii) a genetic algorithm that evolves a population of test data with the aim of covering such paths. The algorithm is able to deal with complex inputs containing arbitrary data structures. The approach has been evaluated on to test class clusters from six Java open source systems, where NPE bugs have been artificially introduced. Results show that the approach is, indeed, able to identify the NPE bugs, and it outperforms random testing. Also, we show how the approach is able to identify real NPE bugs some of which are posted in the bug-tracking system of the Apache libraries.
Negative Selection during the Peripheral Immune Response to Antigen

Thymic selection depends on positive and negative selective mechanisms based on the avidity of T cell interaction with antigen–major histocompatibility complex complexes. However, peripheral mechanisms for the recruitment and clonal expansion of the responding T cell repertoire remain obscure. Here we provide evidence for an avidity-based model of peripheral T cell clonal expansion in response to antigenic challenge. We have used the encephalitogenic, H-2 Au-restricted, acetylated NH2-terminal nonameric peptide (Ac1-9) epitope from myelin basic protein as our model antigen. Peptide analogues were generated that varied in antigenic strength (as assessed by in vitro assay) based on differences in their binding affinity for Au. In vivo, these analogues elicited distinct repertoires of T cells that displayed marked differences in antigen sensitivity. Immunization with the weakest (wild-type) antigen expanded the high affinity T cells required to induce encephalomyelitis. In contrast, immunization with strongly antigenic analogues led to the elimination of T cells bearing high affinity T cell receptors by apoptosis, thereby preventing disease development. Moreover, the T cell repertoire was consistently tuned to respond to the immunizing antigen with the same activation threshold. This tuning mechanism provides a peripheral control against the expansion of autoreactive T cells and has implications for immunotherapy and vaccine design.
SNS-based issue detection and related news summarization scheme

Due to the unprecedented popularity of social network services (SNSs), such as Twitter and Facebook, means that a huge number of user documents are created and shared constantly via SNSs. Given the volume of user documents, browsing documents in a selective manner based on personal interests is a time-consuming and laborious task. Therefore, in the case of Twitter, trend keyword lists are provided for the user's convenience. However, it is still not easy to determine the details based on a few simple keywords. The keywords usually relate to the hot issues at any time so many documents will contain pertinent details, such as news on the Internet. Thus, to provide detailed information about an issue, it is necessary to identify relationships among them. In this study, we developed a SNS-based issue detection and related news summarization scheme. To evaluate the effectiveness of our scheme, we implemented a prototype system and performed various experiments. We present some of the results.