Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of conditions for cryopreservation of testicular tissue from immature mice.

BACKGROUND Cryopreservation of immature testicular tissue could be considered as a major step in fertility preservation for young boys with cancer. In the present study, eight different freezing protocols were evaluated in immature mice testis. METHODS Testis from six-day-old mice were frozen using either 1,2-propanediol (PROH) or dimethylsulphoxide (DMSO: D) at 1.5 M. Different cooling rate curves were tested: (i) controlled slow protocol with seeding (CS+) or (ii) without seeding (CS-), (iii) controlled rapid protocol and (iv) non-controlled protocol. Cryodamage of seminiferous cords was semi-quantitatively determined, establishing a scoring of alterations. Cell viability and apoptosis induction were assessed on testicular cell suspensions immediately after digestion (D0) and after a 20-h culture period (D1). Cells recovered after digestion of 100 mg tissue and the rate of living and non-apoptotic cells were quantified at D0 and D1. A long-term culture (9 days) of testis pieces was carried out for the protocol offering the best survival. Testosterone production, intratubular cell proliferation and tubule growth were assessed. RESULTS DMSO produced optimal results in the different cooling rate curves tested when compared with PROH. Optimal results were obtained for the DCS- procedure (P < 0.05). Testosterone production, tubule growth and cell proliferation of post-thaw pieces were similar to fresh samples. CONCLUSIONS Testis freezing with 1.5 M DMSO in a CS- procedure was found to maintain not only immature testicular tissue architecture, but also viability of testicular cells, endocrine and partial exocrine functions of the testis. Semi-quantitative evaluation of seminiferous cord cryodamage can be effectively used to rapidly screen optimal freezing conditions and as a possible quality control in a human application.
Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas

The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. These are currently annotated by visual inspection. In this paper, we describe automated approaches to analyze the images and their use to improve annotation. We began by training classifiers to recognize the annotated patterns. By ranking proteins according to the confidence of the classifier, we generated a list of proteins that were strong candidates for reexamination. In parallel, we applied hierarchical clustering to group proteins and identified proteins whose annotations were inconsistent with the remainder of the proteins in their cluster. These proteins were reexamined by the original annotators, and a significant fraction had their annotations changed. The results demonstrate that automated approaches can provide an important complement to visual annotation.
Clustering analysis based on genetic algorithms

Genetic algorithm is optimal mathematical search technique based on the principles of natural selection and genetic recombination. Therefore, to make clustering analysis process automation, a hybrid method combining genetic algorithm and clustering algorithm has been applied. Then, the best clustering result can be obtained. According to the simulation results, the proposed algorithm outperforms several existing approaches such as FCM, SOM.
Supporting Secure Authentication and Privacy in Wireless Computing

The IEEE 802.11 standard for wireless LAN communications introduced the Wired Equivalent Privacy(WEP) protocol in an attempt to bring the security level of wireless systems closer to that of wired ones. Unfortunately, WEP falls short of accomplishing its security goals. Despite employing the well-known and believed-secure RC4 cipher, WEP contains several major security flaws. The flaws give rise to a number of attacks, both passive and active, that allow eavesdropping on, and tampering with, wireless transmissions. The IEEE 802.1x framework, what was known to have improved the IEEE 802.11b¿s weakness in user authentication, is a port-based authentication protocol. The IEEE 802.1x does not specify an authentication method, although the most common approach for WLANs is EAP, which is a framework for a variety of authentication methods. However, the IEEE 802.1x is also vulnerable to Denial of service and session high-jacking attacks due to the lack of AP authentication and encryption mechanism. In this paper, we propose a Wireless LAN secure system that offers secure encrypted communication and user authentications. The purpose of the WLAN secure system that this study suggests is to improve the weakness in security of IEEE 802.1x and to guarantee a secure encrypted communication. The proposed system does not allow any faking of the identity by performing a thorough mutual authentication to all associated objects. Furthermore, it provides an integrity service by encrypting EAP-SUCCESS messages with distributed a new shared-key through the key distribution mechanism when an authentication process is executed, and securing the encrypted communication by using the 128 bit-length key.
A Security Framework for Service Overlays: Operating in the Presence of Compromised Nodes

In this paper we explore an important issue for many overlay networks the presence of compromised nodes and how they affect the operation of the system. In overlay networks, compromised nodes can drop, delay or in other ways subvert user traffic and break protocols required for the successful operation of the system. We take a game theoretic approach to model the characteristics of a compromised node and an altruistic legitimate node who wishes to identify the compromised node. We first prove that the damage that can be done by the attacker has an upper bound. We then describe the operation of the system that can operate in the presence of compromised nodes by enforcing this upper bound on attacker damage.
A Hyper-Solution Framework for SVM Classification: Application for Predicting Destabilizations in Chronic Heart Failure Patients

Support Vector Machines (SVMs) represent a powerful learning paradigm able to provide accurate and reliable decision functions in several application fields. In particular, they are really attractive for application in medical domain, where often a lack of knowledge exists. Kernel trick, on which SVMs are based, allows to map non-linearly separable data into potentially linearly separable one, according to the kernel function and its internal parameters value. During recent years non-parametric approaches have also been proposed for learning the most appropriate kernel, such as linear combination of basic kernels. Thus, SVMs classifiers may have several parameters to be tuned and their optimal values are usually difficult to be identified a-priori. Furthermore, combining different classifiers may reduce risk to perform errors on new unseen data. For such reasons, we present an hyper-solution framework for SVM classification, based on meta-heuristics, that searches for the most reliable hyper-classifier (SVM with a basic kernel, SVM with a combination of kernel, and ensemble of SVMs), and for its optimal configuration. We have applied the proposed framework on a critical and quite complex issue for the management of Chronic Heart Failure patient: the early detection of decompensation conditions. In fact, predicting new destabilizations in advance may reduce the burden of heart failure on the healthcare systems while improving quality of life of affected patients. Promising reliability has been obtained on 10-fold cross validation, proving our approach to be efficient and effective for an high-level analysis of clinical data.
GRAPES: A Software for Parallel Searching on Biological Graphs Targeting Multi-Core Architectures

Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP), offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential. As a consequence, such software implementations (i) do not fully exploit available parallel computing power and (ii) they do not scale with respect to the size of graphs in the database. We present GRAPES, software for parallel searching on databases of large biological graphs. GRAPES implements a parallel version of well-established graph searching algorithms, and introduces new strategies which naturally lead to a faster parallel searching system especially for large graphs. GRAPES decomposes graphs into subcomponents that can be efficiently searched in parallel. We show the performance of GRAPES on representative biological datasets containing antiviral chemical compounds, DNA, RNA, proteins, protein contact maps and protein interactions networks.
Repetition Suppression and Expectation Suppression Are Dissociable in Time in Early Auditory Evoked Fields

Repetition of a stimulus, as well as valid expectation that a stimulus will occur, both attenuate the neural response to it. These effects, repetition suppression and expectation suppression, are typically confounded in paradigms in which the nonrepeated stimulus is also relatively rare (e.g., in oddball blocks of mismatch negativity paradigms, or in repetition suppression paradigms with multiple repetitions before an alternation). However, recent hierarchical models of sensory processing inspire the hypothesis that the two might be separable in time, with repetition suppression occurring earlier, as a consequence of local transition probabilities, and suppression by expectation occurring later, as a consequence of learnt statistical regularities. Here we test this hypothesis in an auditory experiment by orthogonally manipulating stimulus repetition and stimulus expectation and, using magnetoencephalography, measuring the neural response over time in human subjects. We found that stimulus repetition (but not stimulus expectation) attenuates the early auditory response (40–60 ms), while stimulus expectation (but not stimulus repetition) attenuates the subsequent, intermediate stage of auditory processing (100–200 ms). These findings are well in line with hierarchical predictive coding models, which posit sequential stages of prediction error resolution, contingent on the level at which the hypothesis is generated.
Concentric layout, a new scientific data layout for matrix data-set in Hadoop file system

Due to the explosive growth in the size of scientific data-sets, data-intensive computing and analysing are an emerging trend in computational science. In these applications, data pre-processing is widely adopted because it can optimise the data layout or format beforehand to facilitate the future data access. On the other hand, current research shows an increasing popularity of MapReduce framework for large-scale data processing. However, the data access patterns which are generally applied to scientific data-set are not supported by current MapReduce framework directly. This gap motivates us to provide support for these scientific data access patterns in MapReduce framework. In our work, we study the data access patterns in matrix files and propose a new concentric data layout solution to facilitate matrix data access and analysis in MapReduce framework. Concentric data layout is a data layout which maintains the dimensional property in chunk level. Contrary to the continuous data layout adopted in the current Hadoop framework, concentric data layout stores the data from the same sub-matrix into one chunk. This layout can guarantee that the average performance of data access is optimal regardless of the various access patterns. The concentric data layout requires reorganising the data before it is being analysed or processed. Our experiments are launched on a real-world halo-finding application; the results indicate that the concentric data layout improves the overall performance by up to 38%.
A new march sequence to fit DDR SDRAM test in burst mode

This work is focused on DDR SDRAM test based on data word burst-oriented access. Existent March algorithms are not efficient to detect static unlinked faults (as Coupling and Address Decoder faults) in burst-mode operation. We propose to modify the March X algorithm to overcome its weakness. The proposed algorithm can reduce the total test time over 30% by using burst-mode data access in the DDR SDRAM test. The new algorithm has a length of (6 + BL)N, were BL is the burst-length used in data access. Results show that the proposed method detects errors produced by address decoder faults in word-oriented memories using burst mode operation, which is characteristic of DDR SDRAMs. We also propose to implement the new March algorithm into built-in self-test (BIST) modules for external memory testing.
A new microcomputer-based direct torque control system for three-phase induction motor

A microcomputer-based direct primary flux and torque control system for three-phase induction motors is presented, showing that the instantaneous primary flux of the induction motor can be calculated by means of computer software. The control algorithm can be implemented online with only a 1 K ROM memory. The controller, therefore, can be quite compact, and both the hardware and software implementation are easy to achieve. A full digital controller using a 16-bit microcomputer is developed. The experimental results are presented and agree with the theory. It is shown that by selecting a space nonzero voltage vector and its time width the amplitude of the primary flux can be controlled, and by selecting a space zero voltage vector and its time width the amplitude of the electromagnetic torque can be controlled. Therefore, flux and torque control can be achieved independently. <<ETX>>
Conflicts of interest and spin in reviews of psychological therapies: a systematic review

Objective To explore conflicts of interest (COI) and their reporting in systematic reviews of psychological therapies, and to evaluate spin in the conclusions of the reviews. Methods MEDLINE and PsycINFO databases were searched for systematic reviews published between 2010 and 2013 that assessed effects of psychological therapies for anxiety, depressive or personality disorders, and included at least one randomised controlled trial. Required COI disclosure by journal, disclosed COI by review authors, and the inclusion of own primary studies by review authors were extracted. Researcher allegiance, that is, that researchers concluded favourably about the interventions they have studied, as well as spin, that is, differences between results and conclusions of the reviews, were rated by 2 independent raters. Results 936 references were retrieved, 95 reviews fulfilled eligibility criteria. 59 compared psychological therapies with other forms of psychological therapies, and 36 psychological therapies with pharmacological interventions. Financial, non-financial, and personal COI were disclosed in 22, 4 and 1 review, respectively. 2 of 86 own primary studies of review authors included in 34 reviews were disclosed by review authors. In 15 of the reviews, authors showed an allegiance effect to the evaluated psychological therapy that was never disclosed. Spin in review conclusions was found in 27 of 95 reviews. Reviews with a conclusion in favour of psychological therapies (vs pharmacological interventions) were at high risk for a spin in conclusions (OR=8.31 (1.41 to 49.05)). Spin was related in trend to the inclusion of own primary studies in the systematic review (OR=2.08 (CI 0.83 to 5.18) p=0.11) and researcher allegiance (OR=2.63 (0.84 to 8.16) p=0.16). Conclusions Non-financial COI, especially the inclusion of own primary studies into reviews and researcher allegiance, are frequently seen in systematic reviews of psychological therapies and need more transparency and better management.
How Critical are Critical Reviews? The Box Office Effects of Film Critics, Star Power, and Budgets

The authors investigate how critics affect the box office performance of films and how the effects may be moderated by stars and budgets. The authors examine the process through which critics affect box office revenue, that is, whether they influence the decision of the film going public (their role as influencers), merely predict the decision (their role as predictors), or do both. They find that both positive and negative reviews are correlated with weekly box office revenue over an eight-week period, suggesting that critics play a dual role: They can influence and predict box office revenue. However, the authors find the impact of negative reviews (but not positive reviews) to diminish over time, a pattern that is more consistent with critics’ role as influencers. The authors then compare the positive impact of good reviews with the negative impact of bad reviews to find that film reviews evidence a negativity bias; that is, negative reviews hurt performance more than positive reviews help performance, but only during the first week of a film's run. Finally, the authors examine two key moderators of critical reviews, stars and budgets, and find that popular stars and big budgets enhance box office revenue for films that receive more negative critical reviews than positive critical reviews but do little for films that receive more positive reviews than negative reviews. Taken together, the findings not only replicate and extend prior research on critical reviews and box office performance but also offer insight into how film studios can strategically manage the review process to enhance box office revenue.
Intercultural communication in online social networking discourse

ABSTRACT This article presents a case study that examines how an online social networking community is constituted through intercultural discourse on the part of one learner sojourning in the US. Using Byram’s model of intercultural communicative competence, this study examines the learner’s naturalistic communication in a social networking site (SNS). The qualitative analysis indicates that the learner acted upon the affordances of SNSs to reflect on her intercultural experiences and displayed evidence of intercultural understanding during her study abroad years. The learner’s intercultural knowledge, attitudes, and discovery are shown to be co-constructed by her and other members in the online discourse. This study indicates that computer-mediated communities like SNSs provide the learner with a space in which she documented her cultural experience and reflected on those experiences in real-time exchanges with multilingual, multicultural users. Pedagogical implications are discussed.
A framework of teleoperated and stereo vision guided mobile manipulation for industrial automation

Smart and flexible manufacturing requests the adoption of industrial mobile manipulators in factory. The goal of autonomous mobile manipulation is the execution of complex manipulation tasks in unstructured and dynamic environments. It is significant that a mobile manipulator is able to detect and grasp the object in a fast and accurate manner. In this research, we developed a stereo vision system providing qualified point cloud data of the object. A modified and improved iterative closest point algorithm is applied to recognize the targeted object greatly avoiding the local minimum in template matching. Moreover, a stereo vision guided teleoperation control algorithm using virtual fixtures technology is adopted to enhance robot teaching ability. Combining these two functions, the mobile manipulator is able to learn semi-autonomously and work autonomously. The key components and the system performance are then tested and proved in both simulation and experiments.
on CMS information server CMS NOTE 1999 / 054 The Compact Muon Solenoid Experiment

In its current state, the Muon Trigger Track Finder in the ben ding plane achieves a coarse η-resolution, derived from the position where the muon crossed detector wh eel boundaries. In this paper, an improvement of theη-assignment is discussed: by using the θ-Super Layer of the muon stations, tracks are found standalone in the z-projection and matched to the t racks found in the bending plane. Moreover, the output format of the θ-Trigger Server is described and impacts of the missing θ-Super Layer in station MB4 are shown.
APOBEC4 Enhances the Replication of HIV-1

APOBEC4 (A4) is a member of the AID/APOBEC family of cytidine deaminases. In this study we found a high mRNA expression of A4 in human testis. In contrast, there were only low levels of A4 mRNA detectable in 293T, HeLa, Jurkat or A3.01 cells. Ectopic expression of A4 in HeLa cells resulted in mostly cytoplasmic localization of the protein. To test whether A4 has antiviral activity similar to that of proteins of the APOBEC3 (A3) subfamily, A4 was co-expressed in 293T cells with wild type HIV-1 and HIV-1 luciferase reporter viruses. We found that A4 did not inhibit the replication of HIV-1 but instead enhanced the production of HIV-1 in a dose-dependent manner and seemed to act on the viral LTR. A4 did not show detectable cytidine deamination activity in vitro and weakly interacted with single-stranded DNA. The presence of A4 in virus producer cells enhanced HIV-1 replication by transiently transfected A4 or stably expressed A4 in HIV-susceptible cells. APOBEC4 was capable of similarly enhancing transcription from a broad spectrum of promoters, regardless of whether they were viral or mammalian. We hypothesize that A4 may have a natural role in modulating host promoters or endogenous LTR promoters.
Online Learning with Feedback Graphs: Beyond Bandits

We study a general class of online learning problems where the feedback is specified by a graph. This class includes online prediction with expert advice and the multi-armed bandit problem, but also several learning problems where the online player does not necessarily observe his own loss. We analyze how the structure of the feedback graph controls the inherent difficulty of the induced $T$-round learning problem. Specifically, we show that any feedback graph belongs to one of three classes: strongly observable graphs, weakly observable graphs, and unobservable graphs. We prove that the first class induces learning problems with $\widetilde\Theta(\alpha^{1/2} T^{1/2})$ minimax regret, where $\alpha$ is the independence number of the underlying graph; the second class induces problems with $\widetilde\Theta(\delta^{1/3}T^{2/3})$ minimax regret, where $\delta$ is the domination number of a certain portion of the graph; and the third class induces problems with linear minimax regret. Our results subsume much of the previous work on learning with feedback graphs and reveal new connections to partial monitoring games. We also show how the regret is affected if the graphs are allowed to vary with time.
Audio watermarking algorithm for real-time speech integrity and authentication

Data integrity and source origin authentication are essential topics for real-time multimedia systems. But traditional method, such as MAC, is not very applicable to overcome the distortion introduced in real-time multimedia communication. In this paper a new integrity mechanics deploying speech watermarking is presented. The advocated approach adopts public key encryption to efficiently generate non-repudiate speech. In the last part of the article, a speech watermarking algorithm incorporating with GSM 610 full-rate coder is proposed.