Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis C virus: The role of molecular mimicry in response to interferon treatment

Chronic hepatitis C virus (HCV) infection is one of the major causes of chronic liver disease worldwide. In order for HCV to persist, the virus must escape immune recognition or inhibit the host immune response. The NS5A protein contains the interferon sensitivity‐determining region (ISDR) and is able to repress dsRNA‐dependent protein kinase (PKR) thus influencing the response to interferon (IFN) therapy. Patients who respond to IFN therapy have stronger antibody reactivity against the NS5A compared to IFN non‐responders. Therefore, given the possible role for the ISDR in IFN resistance and differential antibody reactivity, it is possible that variation in ISDR may be involved in viral immune escape and development of persistent HCV infection employing aspects of host mimicry. In this study, pre‐treatment samples obtained from HCV infected patients were used to investigate the effect of different NS5A ISDR variants on the IFN antiviral response and their involvement in immune evasion. The NS5A was identified as a homologue of the variable region of immunoglobulins (Ig). The IFN resistant genotypes had higher levels of similarity to Ig compared to IFN sensitive genotypes. Expression of NS5A‐6003 (HCV genotype 1b) and NS5A‐6074 (HCV genotype 2a) was able to rescue vesicular stomatitis virus (VSV) from IFN inhibition and restore luciferase activity. A correlation between Ig‐like NS5A structure and also antibody response with the outcome of IFN treatment was observed. J. Med. Virol. 84:1571–1585, 2012. © 2012 Wiley Periodicals, Inc.
Surgical Treatment for Occlusion of Graft Arteriovenous Fistula in Patients Undergoing Hemodialysis

Background Maintenance of adequate vascular access for hemodialysis is important in patients with end-stage renal disease. Once arteriovenous fistula (AVF) occlusion occurs, the patient should be treated with rescue therapy. This study was performed to evaluate the results of a rescue therapy for AVF occlusion. Methods From January 2008 to December 2012, 47 patients who underwent surgical rescue therapy for AVF occlusion after graft AVF formation, were enrolled in this study. The patients were divided into two groups, namely the graft repair group (group A, n=19) and the thrombectomy group (group B, n=28). Postoperative results of both groups were analyzed retrospectively. Results There were no statistically significant differences in the clinical characteristics between the two groups. In terms of the duration of AVF patency after the first rescue therapy, group A showed a longer AVF patency duration than group B (24.5±21.9 months versus 17.7±13.6 months), but there was no statistically significant difference (p=0.310). In terms of the annual frequency of AVF occlusion after the rescue therapy of group A was lower than that of group B (0.59 versus 0.71), but there was no statistically significant difference (p=0.540). The AVF patency rates at 1, 2, 3, and 5 years after the first rescue therapy in group A were 52.6%, 31.5%, 21.0%, and 15.7%, respectively, and those in group B, they were 32.1%, 25.0%, 17.8%, and 7.14%, respectively. There was no statistically significant difference (p=0.402). Conclusion Graft repair revealed comparable results. Although there was no statistically significant difference, the patent duration and annual frequency of AVF occlusion of group A were better than those of group B. Therefore, graft repair is considered as a safe and useful procedure for maintaining graft AVF.
TrACS: transceiver architecture and wireless channel simulator

This paper presents the design of a system-level simulator for radio receivers, including receiver circuits, in Matlab. The system level outlook offers a better characterization of circuit design, as the signal processing in the digital receiver is asymmetric across topologies. Also, circuit models in the simulator make it more precise and realistic compared to baseband models, which assume a single-step error-free down conversion. This interpretation is especially relevant in the design of energy-constrained wireless sensor network solutions. The simulator results for binary FSK in AWGN confirm the importance of system level simulation.
An optimal task decision method for a warehouse robot with multiple tasks based on linear temporal logic

Currently, the robot is playing an increasingly significant role in managing a warehouse. This paper proposes an optimal method to help a warehouse robot make task decisions, which aims at minimizing the whole cost of completing multiple tasks. Firstly, Abstract Transition System (ATS) is used to model the warehouse environment, and Linear Temporal Logic (LTL) formula is used to formulate the tasks of warehouse robot. Then based on the ATS and the Büchi automaton translated from the LTL formula, a Min-cost Task Decision Algorithm is proposed to obtain the task decision for the warehouse robot. The decision points out the optimal order and path for the robot to do its tasks. The effectiveness of the proposed method is validated through case studies with two kinds of tasks.
Second-line systemic treatment for advanced cholangiocarcinoma.

BACKGROUND Gemcitabine plus platinum (GEM-P) combination chemotherapy is standard treatment for first-line advanced cholangiocarcinoma (aCC). GEM-P first-line therapy reports a progression-free survival (PFS) of 8 months and overall survival (OS) of 11.7 months. Treatment in the second-line setting is less clear. Five-year survival for aCC remains dismal at 5-10%. The purpose of this study was to describe the outcomes with second-line systemic treatment at our institution. METHODS This study was a single institution retrospective chart review of aCC patients who initiated second-line systemic treatment during 1/1/2009 to 12/31/2012. The primary objective was to evaluate PFS with second-line systemic treatment. Secondary objectives were OS and disease control rate. Second-line systemic regimens were classified into four treatment groups: GEM-P, gemcitabine + fluoropyrimidine (GEM-FU), other FU combination (FU-combo), and others. RESULTS Fifty-six patients were included and the majority had intrahepatic aCC. A total of 80% received first-line gemcitabine-based therapy. Second-line therapy consisted of GEM-P (19.6%), GEM-FU (28.6%), FU-combo (37.5%), and others (14.3%). Median PFS was 2.7-month (95% CI, 2.3-3.8 months) with a median OS of 13.8 months (95% CI, 12-19.3 months) and a disease control rate of 50%. No significant difference in survival was identified between the four treatment groups. CONCLUSIONS This study revealed a 2.7-month PFS, 50% disease control rate, and potential survival benefit with second-line treatment. Options for second-line systemic therapy include GEM-FU, FU-combo, GEM-P if not given in the first-line setting. Targeted therapy with erlotinib or bevacizumab could be considered in addition to chemotherapy.
Estimating Sparse Signals with Smooth Support via Convex Programming and Block Sparsity

Conventional algorithms for sparse signal recovery and sparse representation rely on l1-norm regularized variational methods. However, when applied to the reconstruction of sparse images, i.e., images where only a few pixels are non-zero, simple l1-norm-based methods ignore potential correlations in the support between adjacent pixels. In a number of applications, one is interested in images that are not only sparse, but also have a support with smooth (or contiguous) boundaries. Existing algorithms that take into account such a support structure mostly rely on nonconvex methods and-as a consequence-do not scale well to high-dimensional problems and/or do not converge to global optima. In this paper, we explore the use of new block l1-norm regularizers, which enforce image sparsity while simultaneously promoting smooth support structure. By exploiting the convexity of our regularizers, we develop new computationally-efficient recovery algorithms that guarantee global optimality. We demonstrate the efficacy of our regularizers on a variety of imaging tasks including compressive image recovery, image restoration, and robust PCA.
ASPIRATION , SYMPATHY AND MAXMIN OUTCOME

This paper rigorously examines a dynamic behavioral foundation of the Rawlsian criterion, that selects a social outcome which maximizes the payoff of the worst off agent. In order to understand how the behavior of individual agents shapes up this social norm through repeated long term interactions among agents, we analyze a dynamic matching process in which a long term relationship is embedded. A society is populated with a finite number players with two different roles, say row and column players. Two players are matched, and initiate the long term relationship if both players agree to do so, which is then subject to a small probability of break-up to dump the players back to the matching process. We focus on the outcomes sustained by the decision rule consistent with the satisficing behavior à la Simon (1987), slightly perturbed to incorporate sympathy in the spirit of Hume (1978). For a general class of two person games, as the probability of continuing the long term relationship converges to 1, all agents in the economy almost always play the most egalitarian outcome among Pareto efficient outcome, which is the efficient Rawlsian outcome. The Rawlsian criterion is generated through repeated long term interactions among agents in a decentralized fashion.
Inbreeding and risk of late onset complex disease

23 For example, a 4- 5% increase in childhood mortality has been found in the offspring of first cousin marriages, and similar results have been reported in other species. 245 However, the effects of inbreeding on late onset disorders are largely unknown, despite the fact that deleterious effects of inbreeding in other species are known to increase with age, as predicted by selection theory. 67 The reported finding of greater inbreeding effects for traits such as blood pressure and serum cholesterol in middle age compared with early adult life is consistent with this. 8
Assessment of Turbulent Wake Behind two Wind Turbines Using Multi-Fractal Analysis

In this paper we present preliminary results of the multi-fractal analysis for describing the behavior of turbulence evolution in the wake behind two model wind turbines using the program ImaCal. The wind energy is an important component of renewable energy sources. Nowadays the research community focuses on studying the turbulent wakes behind wind turbines and its interactions with the Atmospheric Boundary Layer. For finding the fractal dimension a multi-fractal analysis was performed using the results of a numerical simulation of the flow over two model wind turbines. The latter was carried out by means of the Large Eddy method with the Lagrangian Dynamic Smagorinsky subgrid model. The SOWFA library was employed as a part of OpenFoam software to perform the simulation.
Reference Frames for Spatial Frequency in Face Representation Differ in the Temporal Visual Cortex and Amygdala

Social communication in nonhuman primates and humans is strongly affected by facial information from other individuals. Many cortical and subcortical brain areas are known to be involved in processing facial information. However, how the neural representation of faces differs across different brain areas remains unclear. Here, we demonstrate that the reference frame for spatial frequency (SF) tuning of face-responsive neurons differs in the temporal visual cortex and amygdala in monkeys. Consistent with psychophysical properties for face recognition, temporal cortex neurons were tuned to image-based SFs (cycles/image) and showed viewing distance-invariant representation of face patterns. On the other hand, many amygdala neurons were influenced by retina-based SFs (cycles/degree), a characteristic that is useful for social distance computation. The two brain areas also differed in the luminance contrast sensitivity of face-responsive neurons; amygdala neurons sharply reduced their responses to low luminance contrast images, while temporal cortex neurons maintained the level of their responses. From these results, we conclude that different types of visual processing in the temporal visual cortex and the amygdala contribute to the construction of the neural representations of faces.
The perception of two linguistic functions of prosody in Danish

This paper examines the prosodic perceptual ability of listeners (n=22) in tasks involving global intonation contours and local voice pitch variation. The signaling of utterance type was tested with speech material that included read and non-scripted questions and statements. Local variation was tested with an identification task where the level of prominence of an anaphor signaled either the subject or non-subject of a preceding sentence. Logistic regression revealed that question and statement identification differed between read and non-scripted material and was not linked to performance on the subject/non-subject task. A response bias was also observed in the vocoded condition towards statements. We conclude that performance differences between the two tasks may be due either to the task-related language ability of the listener or to differences in the perception of global and local prosody.
Towards security in sharing data on cloud-based social networks

Nowadays, ubiquitous sensor devices such as mobile phones, laptops, GPSes, etc. allow one to access not only his own data but also others' on cloud servers. To enhance security, data is usually encrypted before sending to the servers. However, making use of others' ones encrypted data without decryption keys is very challenging. In this paper, we suggest a framework that allows users of cloud-based social networks to share their private data in a secure manner. In our framework, every user in a group has his own secret key to encrypt and decrypt data. The key will be revoked if the user leaves the group. Using proxy re-encryption schemes, the framework helps any user be able to access others' data in the same group.
Beliefs, Coordination and Media Focus

News media provide an editorial service for their audiences by monitoring a large number of events and by selecting the most newsworthy of these to report. Using a Latent Dirichlet Allocation topic model to classify news articles we document the editorial function of US newspapers. We nd that, while dierent newspapers tend to report on dierent topics to dierent degrees, news coverage becomes more homogenous across newspapers after major events. We present a simple theoretical model that can match this fact and then use it to analyze the implications of the editorial function of news providers for agents' beliefs and their ability to coordinate. We show that, compared to a setting where agents choose ex ante what to get information about, their actions become more correlated when they rely on the editorial function of news providers. Information about large events is closer to common knowledge than information about small events. As a consequence, agents respond more than proportionally to large events, and in expectations, do not respond at all to events that are small enough.
Early evidence for syntactic bootstrapping : 15-month-olds use sentence structure in verb learning

Infant language-learners receive input consisting of word sequences paired with world scenes. Based on these data, they start learning to understand sentences early in the second year, and ultimately build a lexicon and grammar that support broad generalization. Accounts of how they do so necessarily begin with the extra-linguistic world: The true novice, not yet knowing the words or syntax, must try to link input sentences with aspects of accompanying scenes. Top-down knowledge derived from the scene then ‘supervises’ word and syntax learning, investing words and their combinations with meaning. Views of language acquisition of all theoretical stamps thus assume that knowledge of word and sentence meaning drives syntax acquisition (e.g., Pinker, 1984; Tomasello, 2003). However, aspects of verb meanings in particular challenge the assumption that children can recover word and sentence meanings based only on understanding scenes, and thus in turn challenge our theories of syntax acquisition (Gleitman et al., 2005). Verbs do not simply label events; rather, they denote abstract construals of them. To illustrate, pairs of verbs such as feed and eat, give and receive, take different perspectives on the same events. Scene feedback thus provides equivocal evidence for verb and sentence meaning (Gillette et al., 1999). The syntactic-bootstrapping theory proposes that children use knowledge of syntax itself to decode sentence and verb meanings (e.g., Gleitman et al., 2005). Syntactic bootstrapping relies on tight links between verb syntax and meaning (Fisher et al., 1991; Levin & Rappaport-Hovav, 2005; Pinker, 1989). Part of the meaning of a verb is a semantic predicate-argument structure specifying the number and type of arguments that the verb’s meaning implies. This semantic structure partly determines the syntactic structures licensed by the verb. For example, verbs entailing one argument take intransitive frames, with one noun phrase (NP) (It fell); verbs entailing two arguments take transitive frames, with two NPs (I dropped it). Toddlers use these links, assigning different meanings to verbs in different syntactic structures (Arunachalam & Waxman, 2010; Fisher, 1996; Naigles, 1990, 1996; Yuan & Fisher, 2009; Yuan et al., 2012).
Homology Parameters for Large Axisymmetric Shaped Dual-Reflector Antennas

We extend the concept of best-fitting paraboloids for large single and dual reflectors with conic-section surfaces to best-fit shaped surface for large dual reflectors shaped for uniform amplitude distribution. The point focus of the paraboloidal main reflector is replaced by focal lines for the main reflector and the primary subreflector focus, whereas the secondary subreflector point focus at the feed is kept. The reflector surfaces are shaped, and all rays from the main-reflector aperture to the feed meet an equal-path-length condition. This condition may be represented by a set of “homology parameters” determined by a least-squares method. Finally, we calculate the homology parameters and the root mean square of surface errors for an 8-m dual-reflector system including gravity effects for the antenna pointed toward zenith and the horizon.
Novel End Point Analytic Techniques and Interpreting Shifts Across the Entire Range of Outcome Scales in Acute Stroke Trials

Background and Purpose— Stroke treatments are generally not curative, but rather alter patient outcome over the entire range of functional measures. Dichotomizing outcome scales reduces computational complexity, but discards substantial outcome information, artificially privileges only a single health state transition as clinically meaningful, and often reduces study power. Newer approaches to endpoint analysis have several advantageous properties. Summary of Review— The global statistic assesses treatment effects on multiple outcome measures simultaneously. However, translating the global statistic multidimensional vector effect at the population level into benefit or harm expected in the individual patient is problematic. Responder analysis adjusts outcome thresholds to patient stroke severity at study entry, identifying achievable goals for each patient. However, responder analysis still discards substantial outcome information. Shift analysis gauges change in outcome distributions over the full range of ascertained outcomes, incorporating benefit and harm at all health state transitions valued by patients and clinicians, and often increasing study power. Translation of findings of shift analyses into clinically accessible terms may be accomplished using the recently developed joint outcome table specification technique, which yields the following values for the number needed to treat for 1 patient to improve in a clinically important manner: nimodipine in subarachnoid hemorrhage, 6.8; coiling over clipping, 5.9; intra-arterial pro-urokinase in acute cerebral ischemia, 4.8; intravenous tissue plasminogen activator, 3.3. Conclusions— Dichotomized, global statistic, responder, and shift analyses each offer distinctive benefits and drawbacks. Choice of primary end point analytic technique should be tailored to the study population, expected treatment response, and study purpose. Shift analysis generally provides the most comprehensive index of a treatment's clinical impact.
Expression-Invariant 3D Face Recognition Using Patched Geodesic Texture Transform

Numerous methods have been proposed for the expression-invariant 3D face recognition, but a little attention is given to the local-based representation for the texture of the 3D images. In this paper, we propose an expression-invariant 3D face recognition approach based on the locally extracted moments of the texture when only one exemplar per person is available. We use a geodesic texture transform accompanied by Pseudo Zernike Moments to extract local feature vectors from the texture of a face. An extensive experimental investigation is conducted using publicly available BU-3DFE face databases covering face recognition under expression variations. The performance of the proposed method is compared with the performance of two benchmark approaches. The encouraging experimental results demonstrate that the proposed method can be used for 3D face recognition in single model databases.
Phylogenetic Comparison of Human and Mouse Promoter Regions and Visualization of a Variety of Conserved Elements

To extract biologically functional information from promoter regions is a difficult problem. Searching for potential Transcription factor binding sites (TFBS) by using TRANSFAC database [2] is a widely used method, but it is not so effective because the majority of obtained candidates seem to be false positives. Eugene et al. developed CONREAL algorithm [1], which can reduce the false positives of the TFBS search by finding a series of TFBSs that are arranged in the same order in an orthologous pairs of sequences. In compensation for the specificity, however, the CONREAL algorithm neglects TFBSs that are changed in the order in the query sequences. Although there are pioneering studies phylogenetically comparing genomic sequences [5], or comparison of human and mouse promoter regions [4], our understanding of the structures of promoter regions is still at a very primitive stage. To see what kind of characteristics tends to be conserved, we compared human and mouse orthologous promoter sequences, and visualized various types of data.