Miracle-dz/UniFAR-FTUs huggingface dataset:
ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis

Small-angle scattering (SAS) is frequently employed for screening large numbers of samples and for studying these samples under different conditions, including space- and time-resolved analysis. These measurements produce immense amounts of data, especially on modern high-flux and high-brilliance sources (e.g. third-generation synchrotrons). In biological SAS, like high-throughput macromolecular crystallography, large-scale analysis of proteins and macromolecular complexes is also emerging. Automation of data analysis becomes an indispensable prerequisite for adequate evaluation of high-throughput SAS experiments. Here a prototype of an automated data-analysis system for isotropic solution scattering based on the further development of the programs belonging to the package ATSAS 2.1 is reported. This system allows the major analysis tasks starting from the raw data processing and, for monodisperse systems, finishing with a three-dimensional model, to be performed automatically. Convenient web interfaces for the online use of individual ATSAS programs are also provided.
Detection of Sybil Attacks in Vehicular Ad Hoc Networks

Until recently vehicles and transportation systems were considered as the realm of mechanical engineers, but the need for the road safety and desire to be connected to the world, has broaden the industry scope. In order to do so Intelligent Transport System has been introduced and for few years, Vehicular Ad hoc Networks are getting much attention. The advance developments, wireless communication and life safety point towards to take into consideration the need of security in VANETs. In VANET, many attacks are possible and can cause serious damages to life. One such attack is Sybil attack. Sybil attacks have been regarded as a serious security threat to Ad hoc Networks and Sensor Networks. They may also damage the potential applications of Vehicular Ad hoc Networks (VANETs) by creating a deception of traffic congestion. Here we look on how the Sybil attack works and possible ways that an attacker can cause harm by launching these types of attacks in VANETS, along with the detection schemes that can be used to identify Sybil nodes and prevent the network from various hurtful effects.
Terminal Drought Stress Adaptability in Synthetic-derived Bread Wheat is Explained by Alleles of Major Adaptability Genes and Superior Phenology

Establishing the agronomic superiority of wheat germplasm derived from crop-wild introgressions under field stress conditions is of prime importance in breeding. Comparative performance between synthetic-derived bread wheat (SBW) and conventional bread wheat (CBW) under terminal drought stress condition was evaluated in this study. Evaluations were carried out under well-watered and drought stress conditions for two consecutive years at pre-anthesis stage of crop. Based on drought susceptibility index (DSI) values, the SBW genotypes SBW6, SBW8, SBW10, SBW13, SBW22, SBW23 and SBW24 had low values than the check varieties under drought stress. The genotypes exhibited narrow range of flowering time, however SBW with photoperiod insensitive (Ppd-D1a) and wild-type Rht-B1a/Rht-D1a alleles have clear yield advantage over CBW under terminal drought stress. Likewise, winter-type vrn-A1 and vrn-D1 alleles slightly increased heading time and enhanced yield in SBW. SSR based population structure inferred from Bayesian analysis and principal component analysis (PCA) dissected the population into 2 sub-groups, with most of the SBW in one sub-population and slight admixture between SBW and CBW. In conclusion, these results indicate the agronomic superiority of SBW under terminal drought stress is likely through retention of favorable alleles in SBW sub-population. Low DSI (DSI<1) values can be used as a selection criterion for increasing yields under terminal drought conditions. © 2018 Friends Science Publishers
Retrovirus-Induced Immunodeficiency Anchoring in T Cells Resist Mice with Disrupted Type I Protein Kinase A

Souad Rahmouni and Kjetil TaskenHeglind, Anja Ruppelt, Michel Moutschen, Sven Enerback, Randi Mosenden, Pratibha Singh, Isabelle Cornez, Mikaelol.1100003http://www.jimmunol.org/content/early/2011/03/21/jimmunJ Immunol€ published online 23 March 2011Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai. org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:
An adaptive replication scheme for elastic data stream processing systems

A major challenge for cloud-based systems is to be fault tolerant to cope with an increasing probability of faults in cloud environments. This is especially true for in-memory computing solutions like data stream processing systems, where a single host failure might result in an unrecoverable information loss. In state of the art data streaming systems either active replication or upstream backup are applied to ensure fault tolerance, which have a high resource overhead or a high recovery time respectively. This paper combines these two fault tolerance mechanisms in one system to minimize the number of violations of a user-defined recovery time threshold and to reduce the overall resource consumption compared to active replication. The system switches for individual operators between both replication techniques dynamically based on the current workload characteristics. Our approach is implemented as an extension of an elastic data stream processing engine, which is able to reduce the number of used hosts due to the smaller replication overhead. Based on a real-world evaluation we show that our system is able to reduce the resource usage by up to 19% compared to an active replication scheme.
New party performance after breakthrough

Parliamentary entry on the national level is a crucial achievement for any new party. But its repercussions are not necessarily beneficial. This article assesses the electoral consequences of parliamentary breakthrough by theorizing factors that shape (a) a new party organization’s capacity to cope with pressures generated by parliamentary entry and (b) the relative intensity of the new functional pressures a new party is exposed to after breakthrough. To test our hypotheses derived from these two rationales, we apply multilevel analyses to a new data set covering 135 organizationally new parties that entered national parliament across 17 advanced democracies over nearly five decades (1968–2015). Our findings stress the importance of party organizational characteristics (party origin, time for party building and leadership continuity) for parties’ capacity to sustain electoral support after breakthrough. In contrast, the intensity of functional pressures as generated by government participation immediately after breakthrough does not have significant effects on parties’ performance at the follow-up election.
Global Prescribed Mean Curvature foliations in cosmological spacetimes with matter, Part II

This second part is devoted to the investigation of global properties of Prescribed Mean Curvature (PMC) foliations in cosmological spacetimes with local U (1) × U (1) symmetry and matter described by the Vlasov equation. It turns out, that these spacetimes admit a global foliation by PMC surfaces, as well, but the techniques to achieve this goal are more complex than in the cases considered in part I.
Stability of the max-weight routing and scheduling protocol in dynamic networks and at critical loads

We study the stability of the max-weight protocol for combined routingand scheduling in communication networks. Previous work has shownthat this protocol is stable for adversarial multicommodity trafficin subcritically loaded static networks and for single-commoditytraffic in critically loaded dynamic networks. We show: The max-weight protocol is stable for adversarial multicommodity traffic in adversarial dynamic networks whenever the network is subcriticallyloaded. The max-weight protocol is stable for fixed multicommodity trafficin fixed networks even if the network is critically loaded. The latter result has implications for the running time of themax-weight protocol when it is used to solve multicommodity flowproblems. In particular, for a fixed problem instance we show thatif the value of the optimum solution is known, the max-weight protocolfinds a flow that is within a (1-ε)-factor of optimal in time O(1/ε) (improving the previous bound of O(1/ε2)). If thevalue of the optimum solution is not known, we show how to apply themax-weight algorithm in a binary search procedure that runs in O(1/ε) time.
Bioimaging of Nucleolin Aptamer-Containing 5-(N-benzylcarboxyamide)-2′-deoxyuridine More Capable of Specific Binding to Targets in Cancer Cells

Chemically modified nucleotides have been developed and applied into SELEX procedure to find a novel type of aptamers to fit with targets of interest. In this study, we directly performed chemical modification of 5-(N-benzylcarboxyamide)-2′-deoxyuridine (called 5-BzdU) in the AS1411 aptamer, which binds to the nucleolin protein expressed in cancer cells. Forty-seven compounds of AS1411-containing Cy3-labeled 5-BzdU (called Cy3-(5-BzdU)-modified-AS1411) were synthesized by randomly substituting thymidines one to twelve in AS1411 with Cy3-labeled 5-BzdU. Both statistically quantified fluorescence measurements and confocal imaging analysis demonstrated at least three potential compounds of interest: number 12, 29 and 41 that significantly increased the targeting affinity to cancer cells but no significant activity from normal healthy cells. These results suggest that the position and number of substituents in AS1411 are critical parameters to improve the aptamer function. In this study, we demonstrated that chemical modification of the existing aptamers enhanced the binding and targeting affinity to targets of interest without additional SELEX procedures.
Design space exploration of an NVM-based memory hierarchy

Non-volatile memory (NVM) technologies support both byte addressability (like DRAM) and non-volatility (like disks). This characteristic makes it feasible for NVM to be employed at any layer of the memory hierarchy including CPU cache, main memory, file cache, storage, and hybrid memory. In this paper, we explore new challenges and opportunities that arise when NVM is introduced as a file cache in the memory hierarchy. One opportunity is that cache does not require long-term non-volatility since data are replaced when working sets are changed. This feature is well matched with NVM, which has limited retention time. In addition, the retention time of NVM is inverse proportional to the write latency, giving a chance to optimize the write performance. However, the limited retention time raises a new challenge that it may cause the hit ratio reduction and lead to cache performance degradation. To tackle this challenge, we propose a new inter-reference gap (IRG) based cache management scheme that writes data with different retention times according to their IRGs. Our proposal builds on the fact that block accesses of typical workloads show unique and regular patterns in terms of access intervals. Experimental results show that our scheme enhances system performance by up to 42% (33% on average), compared with the conventional LRU based cache management scheme.
NOVEL APPROACH TO TROPOSPHERIC NO 2 RETRIEVAL FOR TROPOMI

The current retrieval of tropospheric NO 2 data from satellite measurements – called DOMINO for OMI data and TM4NO2A for GOME, SCIAMACHY and GOME2 data – will be continued and improved in the light of the forthcoming Tropospheric Monitoring Instrument (TROPOMI), aboard the Sentinel-5 Precursor mission, which is due for lauch in March 2015. The DOMINO / TM4NO2A processing applies a DOAS retrieval on the satellite data and to determine the tropospheric NO 2 column it uses an AMF look-up table and a data assimilation system. For the latter a number of improvements are already planned. This paper describes the possible replacement of the DOAS retrieval and AMF look-up table by a novel retrieval method, called DISMAS, which potentially provides a better data product: more accurate tropospheric NO2 data, with better error estimates. Results of some first sensitivity tests of DISMAS retrievals using simulated data are presented as well.
Detecting Promotion Campaigns in Query Auto Completion

Query Auto Completion (QAC) aims to provide possible suggestions to Web search users from the moment they start entering a query, which is thought to reduce their physical and cognitive efforts in query formulation. However, the QAC has been misused by malicious users, being transformed into a new form of promotion campaign. These malicious users attack the search engines to replace legitimate auto-completion candidate suggestions with manipulated contents. Through this way, they provide a new malicious advertising service to promote their customers' products or services in QAC. To our best knowledge, we are among the first to investigate this new type of Promotion Campaign in QAC (PCQ). Firstly, we look into the causes of PCQ based on practical commercial search query logs. We found that various queries containing certain promotion intents are submitted multiple times to search engines to promote their rankings in QAC. Secondly, an effective promotion query detection framework is proposed by promotion intent propagation on query-user bipartite graph, which takes into account the behavioral characteristics of promotion campaigns. Finally, we extend the query detection framework to promotion target detection to identify the consistent promotion target which is the inherent goal of the promotion campaign. Large-scale manual annotations on practical data set convey both the effectiveness of our proposed algorithm, and an in-depth understanding of PCQ.
From Problems or Solutions to Problems and Solutions: Integrating the MRI and Solution-Focused Models of Brief Therapy

It is the purpose of this article to demonstrate how two popular brief therapy models, specifically solution-focused brief therapy (SFBT) and problem-focused brief therapy (PFBT), complement one another and how they can be integrated to provide clinicians with a systematic approach to brief therapy that encompasses a wider range of therapeutic options.
The direct healthcare costs associated with psychological distress and major depression: A population-based cohort study in Ontario, Canada

The objective of our study was to estimate direct healthcare costs incurred by a population-based sample of people with psychological distress or depression. We used the 2002 Canadian Community Health Survey on Mental Health and Well Being and categorized individuals as having psychological distress using the Kessler-6, major depressive disorder (MDD) using DSM-IV criteria and a comparison group of participants without MDD or psychological distress. Costs in 2013 USD were estimated by linking individuals to health administrative databases and following them until March 31, 2013. Our sample consisted of 9,965 individuals, of whom 651 and 409 had psychological distress and MDD, respectively. Although the age-and-sex adjusted per-capita costs were similarly high among the psychologically distressed ($3,364, 95% CI: $2,791, $3,937) and those with MDD ($3,210, 95% CI: $2,413, $4,008) compared to the comparison group ($2,629, 95% CI: $2,312, $2,945), the population-wide excess costs for psychological distress ($441 million) were more than twice that for MDD ($210 million) as there was a greater number of people with psychological distress than depression. We found substantial healthcare costs associated with psychological distress and depression, suggesting that psychological distress and MDD have a high cost burden and there may be public health intervention opportunities to relieve distress. Further research examining how individuals with these conditions use the healthcare system may provide insight into the allocation of limited healthcare resources while maintaining high quality care.
Age , provenance and tectonic setting of the high-grade Jequitinhonha Complex , Araçuaí Orogen , eastern Brazil Idade

2Département des Sciences de la Terre et de l’Atmosphère, GEOTOP, Université du Québec à Montréal, Montréal, Québec, Canada. E-mail: stevenson.ross@uqam.ca 3Geological Survey of Brazil, CPRM-SUREG-BH, Belo Horizonte (MG), Brazil. E-mail: luiz.silva@cprm.gov. br 4Universidade Federal de Ouro Preto, Departamento de Geologia, Morro do Cruzeiro, Ouro Preto (MG), Brazil. E-mail: alkmim@degeo.ufop. br 5IG-Laboratório de Geocronologia, Universidade de Brasília, Asa Norte, Brasília (DF), Brazil. E-mail: marcio@unb.br, marcio.pimentel@ufrgs.br
Differentiation of morphology, genetics and electric signals in a region of sympatry between sister species of African electric fish (Mormyridae)

Mormyrid fishes produce and sense weak electric organ discharges (EODs) for object detection and communication, and they have been increasingly recognized as useful model organisms for studying signal evolution and speciation. EOD waveform variation can provide important clues to sympatric species boundaries between otherwise similar or morphologically cryptic forms. Endemic to the watersheds of Gabon (Central Africa), Ivindomyrus marchei and Ivindomyrus opdenboschi are morphologically similar to one another. Using morphometric, electrophysiological and molecular characters [cytochrome b sequences and amplified fragment length polymorphism (AFLP) genotypes], we investigated to what extent these nominal mormyrid species have diverged into biological species. Our sampling covered the known distribution of each species with a focus on the Ivindo River, where the two taxa co‐occur. An overall pattern of congruence among datasets suggests that I. opdenboschi and I. marchei are mostly distinct. Electric signal analysis showed that EODs of I. opdenboschi tend to have a smaller initial head‐positive peak than those of I. marchei, and they often possess a small third waveform peak that is typically absent in EODs of I. marchei. Analysis of sympatric I. opdenboschi and I. marchei populations revealed slight, but significant, genetic partitioning between populations based on AFLP data (FST ≈ 0.04). Taken separately, however, none of the characters we evaluated allowed us to discriminate two completely distinct or monophyletic groups. Lack of robust separation on the basis of any single character set may be a consequence of incomplete lineage sorting due to recent ancestry and/or introgressive hybridization. Incongruence between genetic datasets in one individual, which exhibited a mitochondrial haplotype characteristic of I. marchei but nevertheless fell within a genetic cluster of I. opdenboschi based on AFLP genotypes, suggests that a low level of recent hybridization may also be contributing to patterns of character variation in sympatry. Nevertheless, despite less than perfect separability based on any one dataset and inconclusive evidence for complete reproductive isolation between them in the Ivindo River, we find sufficient evidence to support the existence of two distinctive species, I. opdenboschi and I. marchei, even if not ‘biological species’ in the Mayrian sense.
Enrichment of methylated molecules using enhanced-ice-co-amplification at lower denaturation temperature-PCR (E-ice-COLD-PCR) for the sensitive detection of disease-related hypermethylation.

AIM The detection of specific DNA methylation patterns bears great promise as biomarker for personalized management of cancer patients. Co-amplification at lower denaturation temperature-PCR (COLD-PCR) assays are sensitive methods, but have previously only been able to analyze loss of DNA methylation. MATERIALS & METHODS Enhanced (E)-ice-COLD-PCR reactions starting from 2 ng of bisulfite-converted DNA were developed to analyze methylation patterns in two promoters with locked nucleic acid (LNA) probes blocking amplification of unmethylated CpGs. The enrichment of methylated molecules was compared to quantitative (q)PCR and quantified using serial dilutions. RESULTS E-ice-COLD-PCR allowed the multiplexed enrichment and quantification of methylated DNA. Assays were validated in primary breast cancer specimens and circulating cell-free DNA from cancer patients. CONCLUSION E-ice-COLD-PCR could prove a useful tool in the context of DNA methylation analysis for personalized medicine.
A self-testing and calibration method for embedded successive approximation register ADC

This paper presents a self-testing and calibration method for the embedded successive approximation register (SAR) analog-to-digital converter (ADC). We first propose a low cost design-for-test (DfT) technique which tests a SAR ADC by characterizing its digital-to-analog converter (DAC) capacitor array. Utilizing DAC major carrier transition testing, the required analog measurement range is just 4 LSBs; this significantly lowers the test circuitry complexity. Then, we develop a fully-digital missing code calibration technique that utilizes the proposed testing scheme to collect the required calibration information. Simulation results are presented to validate the proposed technique.
The role of the basolateral amygdala in the perception of faces in natural contexts

The amygdala is a complex structure that plays its role in perception and threat-related behaviour by activity of its specific nuclei and their separate networks. In the present functional magnetic resonance imaging study, we investigated the role of the basolateral amygdala in face and context processing. Five individuals with focal basolateral amygdala damage and 12 matched controls viewed fearful or neutral faces in a threatening or neutral context. We tested the hypothesis that basolateral amygdala damage modifies the relation between face and threatening context, triggering threat-related activation in the dorsal stream. The findings supported this hypothesis. First, activation was increased in the right precentral gyrus for threatening versus neutral scenes in the basolateral amygdala damage group compared with the control group. Second, activity in the bilateral middle frontal gyrus, and left anterior inferior parietal lobule was enhanced for neutral faces presented in a threatening versus neutral scene in the group with basolateral amygdala damage compared with controls. These findings provide the first evidence for the neural consequences of basolateral amygdala damage during the processing of complex emotional situations.
The complete genome sequence of cucumopine-type Agrobacterium rhizogenes strain K599 (NCPPB2659), a nature's genetic engineer inducing hairy roots.

Agrobacterium rhizogenes induces hairy roots from the infection site, when transferred DNA (T-DNA) in Ri plasmid inserted and integrated into host plant cell genome. Cucumopine-type A. rhizogenes strain K599 (NCPPB2659) has particularly high ability to induce hairy root. Here, using next-generation and third generation sequencing technologies, we do novo assembled the whole genome of K599. The genome is 5,114,385 bp and consists of one circular chromosome of 2,622,758 bp, one linear chromosome of 2,289,334 bp, and one Ri plasmid (pRi2659) of 202,292 bp. It contains 4716 protein-coding and 70 RNA genes, including 54 tRNAs, 12 rRNAs, and 4 ncRNAs. The genetic information of K599 exhibits the prediction of prophage regions and virulent genes, which is critical for DNA transfer to the host plant genome. © 2018 Friends Science Publishers