Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Profiles of the Response of Methicillin-Resistant Staphylococcus aureus to Pentacyclic Triterpenoids

Staphylococcus aureus is an important human pathogen in both hospital and the community that has demonstrated resistance to all currently available antibiotics over the last two decades. Multidrug-resistant isolates of methicillin-resistant S. aureus (MRSA) exhibiting decreased susceptibilities to glycopeptides has also emerged, representing a crucial challenge for antimicrobial therapy and infection control. The availability of complete whole-genome nucleotide sequence data of various strains of S. aureus presents an opportunity to explore novel compounds and their targets to address the challenges presented by antimicrobial drug resistance in this organism. Study compounds α-amyrin [3β-hydroxy-urs-12-en-3-ol (AM)], betulinic acid [3β-hydroxy-20(29)-lupaene-28-oic acid (BA)] and betulinaldehyde [3β-hydroxy-20(29)-lupen-28-al (BE)] belong to pentacyclic triterpenoids and were reported to exhibit antimicrobial activities against bacteria and fungi, including S. aureus. The MIC values of these compounds against a reference strain of methicillin-resistant S. aureus (MRSA) (ATCC 43300) ranged from 64 µg/ml to 512 µg/ml. However, the response mechanisms of S. aureus to these compounds are still poorly understood. The transcription profile of reference strain of MRSA treated with sub-inhibitory concentrations of the three compounds was determined using Affymetrix GeneChips. The findings showed that these compounds regulate multiple desirable targets in cell division, two-component system, ABC transporters, fatty acid biosynthesis, peptidoglycan biosynthesis, aminoacyl-tRNA synthetase, ribosome and β-lactam resistance pathways which could be further explored in the development of therapeutic agents for the treatment of S. aureus infections.
Supporting the identification of architecturally-relevant code anomalies

Code anomalies are likely to be critical to the systems' maintainability when they are related to architectural problems. Many tools have been developed to support the identification of code anomalies. However, those tools are restricted to only analyze source code structure and identify individual anomaly occurrences. These limitations are the main reasons why state-of-art tools are often unable to identify architecturally-relevant code anomalies, i.e. those related to architectural problems. To overcome these shortcomings we propose SCOOP, a tool that includes: (i) architecture-code traces in the analysis of the source code, and (ii) exploits relationships between multiple occurrences of code anomalies to detect the architecturally-relevant ones. Our preliminary evaluation indicated that SCOOP was able to detect anomalous code elements related to 293 out of 368 architectural problems found in 3 software systems.
Impact of Feature Selection Techniques on Bug Prediction Models

Several change metrics and source code metrics have been introduced and proved to be effective features in building bug prediction models. Researchers performed comparative studies of bug prediction models built using the individual metrics as well as combination of these metrics. In this paper, we investigate whether the prediction accuracy of bug prediction models is improved by applying feature selection techniques. We explore if there is one algorithm amongst ten popular feature selection algorithms that consistently fares better than others across sixteen bench marked open source projects. We also study whether the metrics in best feature subset are consistent across projects.
Fast phytoplankton classification from emission fluorescence spectra based on Self-Organizing Maps

Fluorescence spectroscopy is a powerful technique usually used to evaluate phytoplankton marine environments. In this study, a fast-technique for phytoplankton discrimination is presented based on the Self-Organizing Maps (SOM), evaluating its capability to achieve phytoplankton classification from its emission fluorescence spectra. The aim of this work is to reduce the acquisition time required for some of the existing techniques. Several cultures representing different algae groups were grown under the same conditions and their Emission spectra were measured every day. Finally, SOM analysis combined with derivative analysis was performed obtaining encouraging results.
Update on Metabolomics and Proteomics of Oxidative Stress Metabolic and Proteomic Markers for Oxidative Stress . New Tools for Reactive Oxygen Species Research 1 [ OA ]

Reactive oxygen species (ROS) play a significant role in plant growth, development, and interaction with biotic and abiotic environments (Alvarez et al., 1998; Blokhina et al., 2003). ROS have also been implicated as important regulatory and signaling elements in a variety of cellular processes (Foyer and Noctor, 2005). ROS are constantly produced during the course of photosynthesis and respiration, whereas redox homeostasis in the cell is tightly controlled by redundant protective mechanisms. Disruption of these protective mechanisms can cause oxidative stress, leading to oxidative damage and cell death. Measuring oxidative stress in the cell requires sensitive and robust assays for ROS detection, accurate quantitation, and measurements of intrinsic cell defense responses. Measurement of ROS in living organisms carries a significant analytical challenge. Most ROS are highly reactive and short lived and therefore hard to detect in complex biological matrices. Additionally, ROS often are produced and/or detoxified in subcellular compartments, which requires detectionmethods directed to specific subcellular localization. ROS can be measured either directly or indirectly following the formation of oxidative by-products of lipids, proteins, or nucleic acids (a technique often called fingerprinting). Techniques to measure these reactive intermediates have been extensively reviewed (for a recent review, see Halliwell and Whiteman, 2004; Tarpey et al., 2004). Here we mainly focus on recent applications of these techniques to measure ROS in plants. DIRECT MEASUREMENTS OF ROS BY ELECTRON PARAMAGNETIC RESONANCE
Introduction to time-delay and sampled-data systems

Time-delay naturally appears in many control systems, and it is frequently a source of instability. However, for some systems, the presence of delay can have a stabilizing effect. Therefore, stability and control of time-delay systems is of theoretical and practical importance. Modern control systems usually employ digital technology for controller implementation, i.e. sampled-data control. A time-delay approach to sampled-data control, where the system is modeled as a continuous-time system with the delayed control input became popular in the networked control systems, where the plant and the controller exchange data via communication network. In the present Tutorial, introduction to time-delay systems will be given together with some advanced results on the topic.
Improving Network Echo Cancellation in VoIP Using Packet Loss Concealment

This paper deals the problem of network echo in Voice over Internet Protocol (VoIP). Unfortunately, the presence of network echo due to the impedance mismatch in this network degrades the speech quality. Network Echo Canceller (NEC) based on adaptive filtering is generally used to remove this echo. Moreover, the performance of the NEC is dramatically degraded during Packet Loss (PL) situations in the VoIP network. In this work, we investigate a Packet Loss Concealment (PLC) method to improve the NEC performance in packet loss scenarios. This method consists of generating a synthetic speech signal to cover missing data in a received bit stream. Simulation results using speech signals issued from NOIZEUS dataset and echo path modeled by a sparse impulse response show a significant improvement in performance of NEC using PLC compared to NEC without PLC.
Subject independent EEG-based BCI decoding

In the quest to make Brain Computer Interfacing (BCI) more usable, dry electrodes have emerged that get rid of the initial 30 minutes required for placing an electrode cap. Another time consuming step is the required individualized adaptation to the BCI user, which involves another 30 minutes calibration for assessing a subject's brain signature. In this paper we aim to also remove this calibration proceedure from BCI setup time by means of machine learning. In particular, we harvest a large database of EEG BCI motor imagination recordings (83 subjects) for constructing a library of subject-specific spatio-temporal filters and derive a subject independent BCI classifier. Our offline results indicate that BCI-native users could start real-time BCI use with no prior calibration at only a very moderate performance loss.
Comparison of active and passive optical access networks

Active and passive optical networks are compared. Based on a reference model that covers AON and PON as well as the interfacing equipment, the different sites and locations in an access network are identified. Such a reference model is necessary in order to make a proper techno-economical comparison between the various optical access network architectures. Also, such a model makes it easier to compare functional differences between AON and PON. The reference model particularly focuses on identifying CAPEX contributions, but also OPEX contributions are regarded. Moreover, the definition of PON and AON has been refined in order to achieve a much more consistent terminology.
Myosin II is required for interkinetic nuclear migration of neural progenitors

Interkinetic nuclear migration (INM) is a hallmark of the polarized stem and progenitor cells in the ventricular zone (VZ) of the developing vertebrate CNS. INM is responsible for the pseudostratification of the VZ, a crucial aspect of brain evolution. The nuclear migration toward the apical centrosomes in G2 is thought to be a dynein-microtubule-based process. By contrast, the cytoskeletal machinery involved in the basally directed nuclear translocation away from the centrosome in G1 has been enigmatic. Studying the latter aspect of INM requires manipulation of the cytoskeleton without impairing mitosis and cytokinesis. To this end, we have established a culture system of mouse embryonic telencephalon that reproduces cortical development, and have applied it to explore a role of actomyosin in INM. Using the nonmuscle myosin II inhibitor blebbistatin at a low concentration at which neither cell cycle progression nor cytokinesis is impaired, we show that myosin II is required for the apical-to-basal (ap→bl), ab-centrosomal INM. Myosin II activity is also necessary for the nuclear translocation during delamination of subventricular zone (SVZ) cells, a second, telencephalon-specific type of neural progenitor. Moreover, the inhibition of ab-centrosomal INM changes the balance between VZ and SVZ progenitor cell fate. Our data suggest a unifying concept in which the actomyosin contraction underlying ab-centrosomal INM sets the stage for the evolutionary increase in VZ pseudostratification and for SVZ progenitor delamination, a key process in cortical expansion.
A Novel Multimodal Deep Neural Network Framework for Extending Knowledge Base

Knowledge base is a very important database for knowledge management, which is very useful for Question Answering, Query Expansion and other AI tasks. However, due to the fast-growing knowledge on the web and not all common knowledge expressed in the text is explicit, the knowledge base always suffers from incompleteness. Recently many researchers are trying to solve the problem as link prediction, only using the existing knowledge base, however, it is just knowledge base completion without adding new entities, which emerges from unstructured text not in existing knowledge base. In this paper, we propose a multimodal deep neural network framework that trying to learn new entities from unstructured text and to extend the knowledge base. Experiments demonstrate the excellent performance.
Enhancing synchronizability of complex networks by community weakening

Many complex networks show community structure, i.e., fewer connections between different subgraphs than within each subgraph. In this paper, synchronization as an important dynamics of complex networks is studied. Inspired on the growth and preferential attachment, an evolving community network is proposed firstly. By exploiting the inner- and intercommunity connections, we find that weakening the community structure, that is, rewiring the inner-community connections into the inter-community ones, could efficiently improve the synchronizability of complex networks.
Learning to read alters cortico-subcortical cross-talk in the visual system of illiterates

As little as 6 months of literacy instruction leads to neuroplastic changes in deep structures of the brain of illiterate adults. Learning to read is known to result in a reorganization of the developing cerebral cortex. In this longitudinal resting-state functional magnetic resonance imaging study in illiterate adults, we show that only 6 months of literacy training can lead to neuroplastic changes in the mature brain. We observed that literacy-induced neuroplasticity is not confined to the cortex but increases the functional connectivity between the occipital lobe and subcortical areas in the midbrain and the thalamus. Individual rates of connectivity increase were significantly related to the individual decoding skill gains. These findings crucially complement current neurobiological concepts of normal and impaired literacy acquisition.
ECNU at TREC 2016: Web-based query expansion and experts diagnosis in Medical Information Retrieval

In this paper, we present our work in TREC 2016 Clinical Decision Support Track. Among ﬁve submitted runs, two of them are based on summary topics and the others on note topics. In summary version run, we expand the original text with exter-nal data on web. Note topics are much longer than the summary, which contain a signiﬁcant number of medical abbreviations as well as other linguistic jargon and style. An automatic method and a manual method are applied to process note topics. In the automatic method, we utilize KODA, a well-known knowledge drive annotator, to extract key information from the original text. In the manual one, we ask medical experts to diagnose and give their advice. For all of the ﬁve runs, we adopt Terrier search engine to implement various retrieval models. Furthermore, results combinations are applied to improve the performance of our model.
The RAID-6 Liberation Codes

The RAID-6 specification calls for a storage system with multiple storage devices to tolerate the failure of any two devices. Numerous erasure coding techniques have been developed that can implement RAID-6; however, each has limitations. In this paper, we describe a new class of RAID-6 codes called the Liberation Codes. These codes encode, update and decode either optimally or close to optimally. Their modification overhead is lower than all other RAID-6 codes, and their encoding performance is often better as well. We provide an exact specification of the Liberation Codes and assess their performance in relation to other RAID-6 coding techniques. In the process, we describe an algorithm called bit matrix scheduling, which improves the performance of decoding drastically. Finally, we present a freely available library which facilitates the use of Liberation Codes in RAID-6 sytems.
Datagram Transport Layer Security Version 1.2

This document specifies version 1.2 of the Datagram Transport Layer Security (DTLS) protocol. The DTLS protocol provides communications privacy for datagram protocols. The protocol allows client/server applications to communicate in a way that is designed to prevent eavesdropping, tampering, or message forgery. The DTLS protocol is based on the Transport Layer Security (TLS) protocol and provides equivalent security guarantees. Datagram semantics of the underlying transport are preserved by the DTLS protocol. This document updates DTLS 1.0 to work with TLS version 1.2. [STANDARDS-TRACK]
To Permit or Not to Permit, That is the Usability Question: Crowdsourcing Mobile Apps’ Privacy Permission Settings

Abstract Millions of apps available to smartphone owners request various permissions to resources on the devices including sensitive data such as location and contact information. Disabling permissions for sensitive resources could improve privacy but can also impact the usability of apps in ways users may not be able to predict. We study an efficient approach that ascertains the impact of disabling permissions on the usability of apps through large-scale, crowdsourced user testing with the ultimate goal of making recommendations to users about which permissions can be disabled for improved privacy without sacrificing usability. We replicate and significantly extend previous analysis that showed the promise of a crowdsourcing approach where crowd workers test and report back on various configurations of an app. Through a large, between-subjects user experiment, our work provides insight into the impact of removing permissions within and across different apps (our participants tested three apps: Facebook Messenger (N=218), Instagram (N=227), and Twitter (N=110)). We study the impact of removing various permissions within and across apps, and we discover that it is possible to increase user privacy by disabling app permissions while also maintaining app usability.
Counter Attack against Free-Riders : Filling a Security Hole in Bittorrent Protocol

eer-to-Peer(P2P) networks are powerful distributed solutions which do not rely on external servers and gather required resources from their users. Therefor fairness is an important feature for designers of these networks. To have a fair network we always want to prevent free-riding. One of the most important file-sharing protocols in P2P is Bittorrent. What separates Bittorrent from other P2P protocols is its unique way of uploading process and its novel approach to fairness. For the first time by implementing eminent game theory strategy, "tit-for-tat" for its protocol, Bittorrent made a breakthrough on fairness for P2P networks. But unfortunately it did not take long for researchers to find security holes in its approach. It was proven several times that by making specific clients which do not follow Bittorrent algorithms and rules, we can easily achieve free-riding. In this paper by taking a simple yet efficient approach and without changing original protocol we make free-riding a much harder process. This will be achieved by changing the role of Tracker from an indexing server to a much more intelligent entity which makes free-riding a much harder process.
Some thoughts on the use of InSAR data to constrain models of surface deformation: Noise structure and data downsampling

Repeat‐pass Interferometric Synthetic Aperture Radar (InSAR) provides spatially dense maps of surface deformation with potentially tens of millions of data points. Here we estimate the actual covariance structure of noise in InSAR data. We compare the results for several independent interferograms with a large ensemble of GPS observations of tropospheric delay and discuss how the common approaches used during processing of InSAR data affects the inferred covariance structure. Motivated by computational concerns associated with numerical modeling of deformation sources, we then combine the data‐covariance information with the inherent resolution of an assumed source model to develop an efficient algorithm for spatially variable data resampling (or averaging). We illustrate these technical developments with two earthquake scenarios at different ends of the earthquake magnitude spectrum. For the larger events, our goal is to invert for the coseismic fault slip distribution. For smaller events, we infer the hypocenter location and moment. We compare the results of inversions using several different resampling algorithms, and we assess the importance of using the full noise covariance matrix.
Modeling agents and their environment in Multi-Level-DEVS

Environments play an important role in multi-agent systems. They present the context agents operate in. When testing multi-agent systems by simulation, the environment and partly agents have to be modeled. We explore the potential of Multi-Level-DEVS to serve as a modeling formalism for agents, their environment, and the interaction between them. Multi-Level-DEVS combines a modular, hierarchical modeling with variable structures, dynamic interfaces, and explicit means for describing up- and downward causation between different levels of the compositional hierarchy. The modeling in Multi-Level-DEVS emphasizes the role of the environment to provide information for and enforce constrains on the situated agents. A smart meeting room scenario is modeled, and an approach aimed at recognizing user activities in smart environments is tested and evaluated in a simulation study.
Intraoperative use of the vacuum bell for elevating the sternum during the Nuss procedure.

OBJECTIVE To evaluate the routine use of the vacuum bell for elevating the sternum during minimally invasive repair of pectus excavatum (MIRPE) (the Nuss procedure). SUBJECTS AND METHODS This was a retrospective evaluation of a prospective database including all patients who underwent MIRPE at our institution between 2005 and 2010. Data included the patient's demographic characteristics, age at surgery, gender, Haller index, duration of surgery, and intraoperative complications. RESULTS Fifty patients from 9 to 28 years old (average, 14.95 years) were observed, including 39 males and 11 females. The preoperative Haller index was between 3.25 and 7.4 (average, 5.05). Mean duration of surgery was 58 minutes (range, 45-92 minutes). The use of the vacuum bell led to a clear elevation of the sternum as confirmed by thoracoscopy. Advancement of the pectus introducer and placement of the pectus bar were safe, successful, and uneventful in all patients. No cardial and/or pericardial lesion was noted as well as no lesion of the mammary vessels. CONCLUSIONS The intraoperative use of the vacuum bell during the MIRPE is safe and effective as it facilitates the retrosternal dissection and the insertion of the pectus bar. If available, we recommend the routine use of this device for MIRPE.
High frequency of loss of heterozygosity in imprinted, compared with nonimprinted, genomic regions in follicular thyroid carcinomas and atypical adenomas.

CONTEXT Many mammalian genes that are imprinted regulate cell growth, differentiation, and apoptosis. Because imprinting silences one of the two alleles, resulting in functional haploinsufficiency, we hypothesized that loss of heterozygosity (LOH) at an imprinted locus may result in the deletion of the only functional copy of an imprinted tumor suppressor gene. OBJECTIVE The goal of this study was to specifically address this hypothesis that in thyroid neoplasias loss of imprinted loci becomes enriched during oncogenesis. DESIGN In total, thyroid tissue was obtained from 72 patients with thyroid neoplasias comprising 34 follicular thyroid carcinomas (FTCs) and 38 follicular adenomas. We performed PCR-based LOH analysis of DNA from paired normal-tumor samples using 18 markers mapped to imprinted regions (IR) and 13 markers in nonimprinted regions (NIR). RESULTS Overall LOH frequencies for the IR markers were 26% for the adenomas and 38% for the carcinomas. In the NIR, the overall LOH frequency was 23 and 26% for adenomas and FTCs, respectively. The difference in LOH frequencies between IR and NIR was statistically significant only for the carcinomas (P = 0.001), although there was a similar trend for the atypical adenomas (ATY, P = 0.06). CONCLUSIONS Our observations suggest that IRs are more prone to genomic instability in FTCs. The fact that the ATY trended toward differential IR/NIR LOH, similar to FTC, may suggest that loss of IR might be instrumental in the adenoma-carcinoma sequence in thyroid carcinogenesis and that ATY could be an important intermediate in this pathway.