Miracle-dz/UniFAR-FTUs huggingface dataset:
A Critical Interaction between NR2B and MAGUK in l-DOPA Induced Dyskinesia

Abnormal function of NMDA receptor has been suggested to be correlated with the pathogenesis of Parkinson’s disease (PD) as well as with the development of l-3,4-dihydroxyphenylalanine (l-DOPA)-induced dyskinesia. Here we show that NMDA receptor NR2 subunits display specific alterations of their subcellular distribution in striata from unilateral 6-hydroxydopamine-lesioned, l-DOPA-treated dyskinetic, and l-DOPA-treated nondyskinetic rats. Dyskinetic animals have significantly higher levels of NR2A subunit in the postsynaptic compartment than all other experimental groups, whereas NR2B subunit shows a significant reduction in both dopamine-denervated and dyskinetic rats. These events are paralleled by profound modifications of NMDA receptor NR2B subunit association with interacting elements, i.e., members of the membrane-associated guanylate kinase (MAGUK) protein family postsynaptic density-95, synapse-associated protein-97 and synapse-associated protein-102. Treatment of nondyskinetic animals with a synthetic peptide (TAT2B) able to affect NR2B binding to MAGUK proteins as well as synaptic localization of this subunit in nondyskinetic rats was sufficient to induce a shift of treated rats toward a dyskinetic motor behavior. These data indicate abnormal NR2B redistribution between synaptic and extrasynaptic membranes as an important molecular disturbance of the glutamatergic synapse involved in l-DOPA-induced dyskinesia.
Anomaly Detection Using Autoencoders with Nonlinear Dimensionality Reduction

This paper proposes to use autoencoders with nonlinear dimensionality reduction in the anomaly detection task. The authors apply dimensionality reduction by using an autoencoder onto both artificial data and real data, and compare it with linear PCA and kernel PCA to clarify its property. The artificial data is generated from Lorenz system, and the real data is the spacecrafts' telemetry data. This paper demonstrates that autoencoders are able to detect subtle anomalies which linear PCA fails. Also, autoencoders can increase their accuracy by extending them to denoising autoenconders. Moreover, autoencoders can be useful as nonlinear techniques without complex computation as kernel PCA requires. Finaly, the authors examine the learned features in the hidden layer of autoencoders, and present that autoencoders learn the normal state properly and activate differently with anomalous input.
Query revision during cluster based search on large unstructured corpora

We investigate a frequently occurring issue in search (retrieval) in the age of big unstructured data. Searches conducted on large unstructured corpora result in long results lists. Such results lists are often clustered and reranked for ease of navigation. Should a query be revised during time-critical examinations of such long cluster based reranked lists? This question arises naturally during early stages of commercially important applications of IR such as eDiscovery, but has not yet been given any research attention. Four factors compound the difficulty of this question in the setting of eDiscovery: (a) the query sources (the technical experts) are different from the legal staff that are actually executing the query and using the retrieval system, (b) the retrieved lists for each query tend to be very long, and (c) the user might be accessing these retrieved results through a clustering interface, and (c) all decisions must be transparent and easy to explain due to the litigious nature of the application. Analogous difficulties arise in other applications involving search over large unstructured corpora. We introduce a framework to help users make the decision of “whether to revise. ” Our framework consists of two components. First, we introduce a “limited view” which is a summary of a long cluster-based reranked list. This is the first input to the user. This provides the user a summary of the long cluster-based list. Second, we construct query predictors for this limited view, and provide their prediction as a second input to the user. This prediction is used to corroborate the inspection of the summary limited view. The proposed combination of a limited view and query performance prediction can assist search staff in determining whether to pursue an expensive query revision or not, as well as save precious time by precluding inspections of lists with very few relevant documents during the early stages of commercially important applications such as eDiscovery.
Luma Adjustment for High Dynamic Range Video

In this paper we present a solution to a luminance artifact problem that occurs when conventional non-constant luminance Y'CbCr and 4:2:0 subsampling is combined with the type of highly non-linear transfer functions typically used for High Dynamic Range (HDR) video. These luminance artifacts can be avoided by selecting a luma code value that minimizes the luminance error. Subjectively, the quality improvement is clearly visible even for uncompressed video. Improvements in tPSNR-Y of up to 20 dB have been observed, compared to conventional subsampling. Crucially, no change in the decoder is needed.
Approximate Max-Min Resource Sharing for Structured Concave Optimization

We present a Lagrangian decomposition algorithm which uses logarithmic potential reduction to compute an $\varepsilon$-approximate solution of the general max-min resource sharing problem with M nonnegative concave constraints on a convex set B. We show that this algorithm runs in $O(M(\varepsilon^{-2}+{\rm ln} M))$ iterations, a data independent bound which is optimal up to polylogarithmic factors for any fixed relative accuracy $\varepsilon\in(0,1)$. In the block-angular case, B is the product of K convex sets (blocks) and each constraint function is block separable. For such models, an iteration of our method requires a $\Theta(\varepsilon)$-approximate solution of K independent block maximization problems which can be computed in parallel.
Assessing the Accuracy of Bone Resection by Cutting Blocks in Patient-Specific Total Knee Replacements

Introduction. The key to a successful total knee arthroplasty (TKA) is the restoration of the mechanical axis with balanced flexion and extension gaps. Patient-specific cutting block technique has been the latest development in total knee arthroplasty. This technique uses a magnetic resonance image (MRI) of the patient's symptomatic knee to create bone models and cutting jigs. This study was designed to evaluate the intraoperative accuracy of the patient-specific cutting block as compared to the preoperative template. Methods. Visionaire (Smith and Nephew, Genesis 2 Knee Arthroplasty) patient-specific TKA was used in all patients. An independent research officer was responsible for measuring all the resected articular surfaces of femur and tibia during surgery and compared it to the cutting block manufactured according to the preoperative template. Seven different measurements from each patient were obtained; four different measurements from the femur and three from the tibia were recorded. The differences between the actual resections made intraoperatively, as compared to the original pre-operative templates, were noted as the error. The surgical team was blinded to the measurements of the resections and the calculations of the errors. Results. Twenty-six Visionaire patient-specific TKA were included in the study. A total of 182 readings of bone resections made intraoperatively (seven for each patient). Eighty five percent of all collected readings were below the error margin of ≤1.5 mm. Size of resection had no effect on the error margin. All patients had satisfactory post-operative alignment, and at discharge all 26 patients achieved more than 90° of knee flexion. Conclusion. This observational study provides evidence that patient-specific TKA is comparable to other forms of TKA and may have some distinct advantages. In addition, we have shown that the cutting blocks are able to consistently deliver accurate cuts that are reproducible. We recommend intra-operative measurement of the bone resection and its comparison with the cutting block as a routine surgical step to confirm the MRI scan data, block placement, and instant validation of the bony resection before implant placement.
Measurement of jet charge in dijet events from with the ATLAS detector

The momentum-weighted sum of the charges of tracks associated to a jet is sensitive to the charge of the initiating quark or gluon. This paper presents a measurement of the distribution of momentum-weighted sums, called jet charge , in dijet events using 20 . 3 fb − 1 of data recorded with the ATLAS detector at ﬃﬃﬃ s p ¼ 8 TeV in pp collisions at the LHC. The jet charge distribution is unfolded to remove distortions from detector effects and the resulting particle-level distribution is compared with several models. The p T dependence of the jet charge distribution average and standard deviation are compared to predictions obtained with several leading-order and next-to-leading-order parton distribution functions. The data are also compared to different Monte Carlo simulations of QCD dijet production using various settings of the free parameters within these models. The chosen value of the strong coupling constant used to calculate gluon radiation is found to have a significant impact on the predicted jet charge. There is evidence for a p T dependence of the jet charge distribution for a given jet flavor. In agreement with perturbative QCD predictions, the data show that the average jet charge of quark-initiated jets decreases in magnitude as the energy of the jet increases.
The potential role of stratospheric ozone in the stratosphere‐ionosphere coupling during stratospheric warmings

The recent discovery of large ionospheric disturbances associated with sudden stratospheric warmings (SSW) has challenged the current understanding of mechanisms coupling the stratosphere and ionosphere. Non‐linear interaction of planetary waves and tides has been invoked as a primary mechanism for such coupling. Here we show that planetary waves may play a more complex role than previously thought. Planetary wave forcing induces a global circulation that leads to the build‐up of ozone density in the tropics at 30–50 km altitude, the primary region responsible for the generation of the migrating semidiurnal tide. The increase in the ozone density reaches 25% and lasts for ∼35 days following the SSW, long after the collapse of the planetary waves. Ozone enhancements are not only associated with SSW but are also observed after other amplifications in planetary waves. In addition, the longitudinal distribution of the ozone becomes strongly asymmetric, potentially leading to the generation of non‐migrating semidiurnal tides. We report a persistent increase in the variability of ionospheric total electron content that coincides with the increase in stratospheric ozone and we suggest that the ozone fluctuations affect the ionosphere through the modified tidal forcing.
An Approximation- Based Data Structure for Similarity Search

Many similarity measures for multimedia retrieval, decision support, and data mining are based on underlying vector spaces of high dimensionality. Data-partitioning index methods for such spaces (e.g. grid-les, quad-trees, R-trees, X-trees, etc.) generally work well for low-dimensional spaces, but perform poorly as dimensionality increases|a phenomenon which has become known as thèdimensional curse'. In this paper, we rst provide an analysis of the nearest-neighbor search problem in high-dimensional vector spaces. Under the assumptions of uniformity and independence, we establish bounds on the average performance of three important classes of data-partitioning techniques. We then introduce the vector-approximation le (VA-File), a method which overcomes the diiculties of high dimensionality by following not the data-partitioning approach of conventional index methods, but rather a lter-based approach. A VA-File contains a compact, geometric approximation for each vector. By rst scanning these smaller approximations, only a small fraction of the vectors themselves must be visited. Thus, the VA-File acts as a simple lter, much as a signature le is a lter. Performance is evaluated on the basis of both synthetic and real data sets, and compared to that of the R ? -tree and the X-tree. We show that performance does not degrade, and even improves with increased dimensionality. Both our analytical and our experimental results suggest that the VA-File is generally the preferred method for similarity search over moderate and large data sets with dimensionality in excess of around ten.
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main questions explored in studies to date have been about the effects of using sparse data, adding new taxa, including more characters from genome sequences and using different (or concatenated) locus regions. These questions can be reduced to more fundamental ones about the assessment of data quality and the design guidelines of taxon sampling in phylogenetic inference experiments. This review summarizes progress to date in understanding the impact of taxon sampling on the accuracy of phylogenetic analysis.
Towards a Unified Metrics Suite for JUnit Test Cases

This paper aims at proposing a unified metrics suite that can be used to quantify different perspectives related to the code of JUnit test cases. We extended existing JUnit test case metrics by introducing two new metrics. We analyzed the code of JUnit test cases of two open source Java software systems (ANT and JFREECHART). We used in total five metrics. We used the Principal Component Analysis (PCA) method in order: (1) to better understand the underlying orthogonal dimensions captured by the suite of unit test case metrics, and (2) to find whether the metrics are independent or are measuring similar structural aspects of the JUnit test code. Overall, results show that: (1) the new introduced unit test case metrics are relevant, (2) the studied unit test case metrics are not independent, and (3) the best subset (a couple) of unit test case metrics that maximizes the variance varies from one system to the other. The new introduced metrics are, however, each in the best subset of unit test case metrics that provide the best independent information that maximizes the variance for each system.
Dose–volume analysis of predictors for chronic gastrointestinal complications in patients with cervical cancer treated with postoperative concurrent chemotherapy and whole-pelvic radiation therapy

The purpose of this study is to evaluate dose–volume histogram (DVH) predictors for the development of chronic gastrointestinal (GI) complications in patients with cervical cancer who have undergone postoperative concurrent chemotherapy and whole-pelvic radiation therapy (WPRT). The subjects were 135 patients who had undergone postoperative WPRT with concurrent nedaplatin-based chemotherapy between 2000 and 2014. Associations between selected DVH parameters and the incidence of chronic GI complications of G3 or higher were evaluated. Chronic GI complications of severity G3 occurred in 18 (13%) patients. Patients with GI complications had significantly greater V5–V45, mean dose and the generalized equivalent uniform dose (gEUD) of the small bowel loops, compared with those without GI complications. V30–V45, mean dose and gEUD of the bowel bag also showed significant differences between patients with and without GI complications. In contrast, no parameter for the large bowel loop was correlated with GI complications. Receiver operating characteristics curve analysis indicated that V30–V45 of the small bowel loops were better predictors than these respective parameters for the bowel bag. Next, patients were divided into four groups based on the median V15 and V40 of the small bowel loops. The group with both a high V15 and a high V40 showed a significantly higher probability of chronic GI complications. In conclusion, the small bowel loops are better predictors of chronic GI complications compared with the bowel bag, and a relatively high-dose volume (e.g. V40) of the small bowel loops is a useful predictor of chronic GI complications.
CFD simulation of blood flow inside the corkscrew collaterals of the Buerger’s disease

Introduction: Buerger’s disease is an occlusive arterial disease that occurs mainly in medium and small vessels. This disease is associated with Tobacco usage. The existence of corkscrew collateral is one of the established characteristics of the Buerger’s disease. Methods: In this study, the computational fluid dynamics (CFD) simulation of blood flow within the corkscrew artery of the Buerger’s disease is conducted. The geometry of the artery is constructed based on the actual corkscrew artery of a patient diagnosed with the Buerger’s disease. The blood properties are the same as the actual blood properties of the patient. The blood flow rate is taken from the available experimental data in the literature. Results: The local velocity patterns, pressure and kinematic viscosity distributions in different segments of the corkscrew collateral artery was demonstrated and discussed for the first time for this kind of artery. The effects of non-Newtonian consideration for the blood viscosity behavior were investigated in different segments of the artery. Moreover, the variations of the blood flow patterns along the artery were investigated in details for each segment. Conclusion: It was found that the flow patterns were affected by the complex geometry of this artery in such a way that it could lead to the presence of sites that were prone to the accumulation of the flowing particles in blood like nicotine. Furthermore, due to the existence of many successive bends in this artery, the variations of kinematic viscosity along this artery were significant, therefore the non-Newtonian behavior of the blood viscosity must be considered.
Secure Multi-Player Protocols: Fundamentals, Generality, and Efficiency

While classically cryptography is concerned with the problem of private communication among two entities, say players, in modern cryptography multi-player protocols play an important role. And among these, it is probably fair to say that secret sharing, and its stronger version verifiable secret sharing (VSS), as well as multi-party computation (MPC) belong to the most appealing and/or useful ones. The former two are basic tools to achieve better robustness of cryptographic schemes against malfunction or misuse by " decentralizing " the security from one single to a whole group of individuals (captured by the term threshold cryptography). The latter allows—at least in principle—to execute any collaboration among a group of players in a secure way that guarantees the correctness of the outcome but simultaneously respects the privacy of the participants. In this work, we study three aspects of secret sharing, VSS and MPC, which we denote by fundamentals, generality, and efficiency. By fundamentals we mean the quest for understanding why a protocol works and is secure in abstract (and hopefully simple) mathematical terms. By generality we mean generality with respect to the underlying mathematical structure, in other words, minimizing the mathematical axioms required to do some task. And efficiency of course deals with the improvement of protocols with respect to some meaningful complexity measure. We briefly summarize our main results. (1) We give a complete characterization of black-box secret sharing in terms of simple algebraic conditions on the integer sharing coefficients, and we propose a black-box secret sharing scheme with minimal expansion factor. Note that, in contrast to the classical field-based secret sharing schemes, a black-box secret sharing scheme allows to share a secret sampled from an arbitrary Abelian group and requires only black-box access to the group operations and to random group elements. Such a scheme may be very useful in the construction of threshold cryptosystems based on groups with secret order (like RSA). (2) We show that without loss of efficiency, MPC can be based on arbitrary finite rings. This is in sharp contrast to the literature where essentially all MPC protocols require a much stronger mathematical structure, namely a field. Apart from its theoretical value, this can lead to efficiency improvements since it allows a greater freedom in the (mathematical) representation of the task that needs to be securely executed. (3) We propose a unified treatment of perfectly secure linear VSS and distributed commitments (a weaker version …
How Deviations from Performance Norms Impact Charitable Donations

Although the actions of others can influence a consumer's behavior, these actions are often at odds with performance norms. For example, charities can experience relatively low rates of support (resulting in a negative deviation from a performance norm) or relatively high rates of support (resulting in a positive deviation from a performance norm). Previous research provides evidence of the equivocal effects of these deviations, with both positive and negative deviations motivating prosocial behaviors. The current research reconciles these competing findings by introducing construal as a moderator. Across four studies, the authors find that positive deviations from performance norms motivate prosocial behavior for independent donors, whereas negative deviations from performance norms motivate prosocial behavior for interdependent donors. They further show that these effects are driven by a prevention focus associated with interdependent consumers and a promotion focus associated with independent consumers. The article concludes with implications for the marketing of charities and prosocial behaviors.
NBS1 Expression as a Prognostic Marker in Uveal Melanoma

Purpose: Up to half of uveal melanoma patients die of metastatic disease. Treatment of the primary eye tumor does not improve survival in high-risk patients due to occult micrometastatic disease, which is present at the time of eye tumor diagnosis but is not detected and treated until months to years later. Here, we use microarray gene expression data to identify a new prognostic marker. Experimental Design: Microarray gene expression profiles were analyzed in 25 primary uveal melanomas. Tumors were ranked by support vector machine (SVM) and by cytologic severity. Nbs1 protein expression was assessed by quantitative immunohistochemistry in 49 primary uveal melanomas. Survival was assessed using Kaplan-Meier life-table analysis. Results: Expression of the Nijmegen breakage syndrome (NBS1) gene correlated strongly with SVM and cytologic tumor rankings (P < 0.0001). Further, immunohistochemistry expression of the Nbs1 protein correlated strongly with both SVM and cytologic rankings (P < 0.0001). The 6-year actuarial survival was 100% in patients with low immunohistochemistry expression of Nbs1 and 22% in those with high Nbs1 expression (P = 0.01). Conclusions: NBS1 is a strong predictor of uveal melanoma survival and potentially could be used as a clinical marker for guiding clinical management.