scholarly journals WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences

2016 ◽  
Author(s):  
Ahmed A. Metwally ◽  
Yang Dai ◽  
Patricia W. Finn ◽  
David L. Perkins
Keyword(s):  
Computation Time ◽  
High Sensitivity ◽  
Shotgun Sequencing ◽  
Taxonomic Identification ◽  
Weighted Voting ◽  
Identification Methods ◽  
Taxonomic Profile ◽  
Abundance Profile ◽  
High Level ◽  
Automated Tool

AbstractMetagenome shotgun sequencing presents opportunities to identify organisms that may prevent or promote disease. The analysis of sample diversity is achieved by taxonomic identification of metagenomic reads followed by generating an abundance profile. Numerous tools have been developed based on different design principles. Tools achieving high precision can lack sensitivity in some applications. Conversely, tools with high sensitivity can suffer from low precision and require long computation time. In this paper, we present WEVOTE (WEighted VOting Taxonomic idEntification), a method that classifies metagenome shotgun sequencing DNA reads based on an ensemble of existing methods using k-mer-based, marker-based, and naive-similarity based approaches. Our evaluation on fourteen benchmarking datasets shows that WEVOTE improves the classification precision by reducing false positive annotations while preserving a high level of sensitivity. WEVOTE is an efficient and automated tool that combines multiple individual taxonomic identification methods to produce more precise and sensitive microbial profiles. WEVOTE is developed primarily to identify reads generated by MetaGenome Shotgun sequencing. It is expandable and has the potential to incorporate additional tools to produce a more accurate taxonomic profile. WEVOTE was implemented using C++ and shell scripting and is available at www.bitbucket.org/ametwally/wevote

scholarly journals Design Time Optimization for Hardware Watermarking Protection of HDL Designs

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
E. Castillo ◽  
D. P. Morales ◽  
A. García ◽  
L. Parrilla ◽  
E. Todorovich ◽  
...  
Keyword(s):  
Digital Signature ◽  
Computation Time ◽  
Original System ◽  
Combinational Logic ◽  
Time Optimization ◽  
Ip Cores ◽  
And Performance ◽  
High Level ◽  
Automated Tool ◽  
Selection Of

HDL-level design offers important advantages for the application of watermarking to IP cores, but its complexity also requires tools automating these watermarking algorithms. A new tool for signature distribution through combinational logic is proposed in this work. IPP@HDL, a previously proposed high-level watermarking technique, has been employed for evaluating the tool. IPP@HDL relies on spreading the bits of a digital signature at the HDL design level using combinational logic included within the original system. The development of this new tool for the signature distribution has not only extended and eased the applicability of this IPP technique, but it has also improved the signature hosting process itself. Three algorithms were studied in order to develop this automated tool. The selection of a cost function determines the best hosting solutions in terms of area and performance penalties on the IP core to protect. An 1D-DWT core and MD5 and SHA1 digital signatures were used in order to illustrate the benefits of the new tool and its optimization related to the extraction logic resources. Among the proposed algorithms, the alternative based on simulated annealing reduces the additional resources while maintaining an acceptable computation time and also saving designer effort and time.

Influence of Irrational Beliefs and Sensitivity to a Person on Future Psychology Students’ Propensity to Coercion or Nonviolence

2021 ◽  
pp. 143-165
Author(s):  
V.G. Maralov ◽  
◽  
V.A. Sitarov ◽  
Keyword(s):  
Irrational Beliefs ◽  
High Sensitivity ◽  
Daily Practice ◽  
Psychology Students ◽  
State Universities ◽  
Low Level ◽  
Level Of Understanding ◽  
Low Sensitivity ◽  
High Level ◽  
Dependent Type

The relevance of the problem is due to the importance of identifying factors that determine the propensity of students to coercion or nonviolence, creating psychological and pedagogical conditions for the formation of the socionomic sphere of nonviolent competencies for future specialists at universities. The theoretical basis of the study was the position of nonviolence as a daily practice of interaction, by which we understand the ability of a person to choose from a number of possible alternatives that carry the least charge of coercion. The aim of the work was to study the influence of irrational beliefs and sensitivity to a person (interest, empathy, understanding and assistance) on the students’ tendency to coercion, manipulation, non-violence and non-interference in the processes of interaction with people. The hypothesis was tested that the tendency of students to coercion, manipulation, and noninterference will be due to expressed irrational beliefs and low level of sensitivity to a person and the tendency to non-violence will be explained by the absence of irrational beliefs and a high level of sensitivity to a person. The study involved 125 students of pedagogical and psychological faculties of the Moscow Humanitarian and Cherepovets State universities. The authors used questionnaires to identify the positions of interaction among students and sensitivity to a person, as well as a list of irrational beliefs proposed by A. Beck and A. Freeman. It is established that the tendency to both coercion and manipulation are determined by the beliefs of anti-social type and low sensitivity to the person. The tendency to manipulate the narcissistic beliefs, high interest in people and understanding them, at the same time the tendency to non-violence and non-interference are determined by beliefs of avoidant and dependent types with a low level of understanding people. And a tendency to non-interference is determined by beliefs of dependent type with unexpressed orientation on helping. The tendency to nonviolence is determined by the high sensitivity to a person and the absence of irrational beliefs of antisocial, passive-aggressive and narcissistic types. As a result, the conclusion is made about the need to form purposefully the ability to nonviolent interaction among students, which should include the work on awareness and overcoming irrational beliefs and the development of sensitivity to a person. The obtained results can be used in practical work with students on the formation of their nonviolent competencies.

scholarly journals Automated monitoring system for events detection in sewer network by distribution temperature sensing data measurement

2018 ◽  
Vol 78 (7) ◽  
pp. 1499-1508
Author(s):  
Abdelhak Kessili ◽  
Jes Vollertsen ◽  
Asbjørn Haaning Nielsen
Keyword(s):  
Large Data ◽  
Temperature Sensing ◽  
Wastewater Discharge ◽  
Sewer Pipe ◽  
Temperature Changes ◽  
Set Up ◽  
Comparison Of The Results ◽  
Events Detection ◽  
High Level ◽  
Automated Tool

Abstract This study is related to distribution temperature sensing (DTS) in sewers for tracing illicit or unintended inflows to foul sewers. A DTS measurement is performed with a fiber optic cable that is installed at the invert of a sewer pipe in combination with a standalone laser/computer instrument. This set-up generates in-sewer temperature measurements with high resolutions in time (every minute) and space (every metre) along the cable over long periods of time (weeks on end). The prolonged monitoring period in combination with the high level of detail in the dataset allows the study of anomalies (i.e., unexpected temperatures and/or temperature variations at certain locations), even if these only occur very infrequently. The objective of this paper is to develop an automated tool to analyze the large data masses and identify anomalies caused by illicit or unintended inflows. In this study, an algorithm for detecting the temperature changes that are caused by both wastewater discharge and inflow of stormwater are developed. A comparison of the results of the automated procedure to the results of a manual assessment of the datasets (Elmehaven, Denmark) shows that the automated procedure performs very well.

Hardware Context Switch-based Cryptographic Accelerator for Handling Multiple Streams

2021 ◽  
Vol 14 (3) ◽  
pp. 1-25
Author(s):  
Arif Sasongko ◽  
I. M. Narendra Kumara ◽  
Arief Wicaksana ◽  
Frédéric Rousseau ◽  
Olivier Muller
Keyword(s):  
Computation Time ◽  
Multiple Streams ◽  
Original Algorithm ◽  
Context Switching ◽  
Mode Of Operation ◽  
Synthesis Tool ◽  
Block Level ◽  
Key Block ◽  
Symmetric Key ◽  
High Level

The confidentiality and integrity of a stream has become one of the biggest issues in telecommunication. The best available algorithm handling the confidentiality of a data stream is the symmetric key block cipher combined with a chaining mode of operation such as cipher block chaining (CBC) or counter mode (CTR). This scheme is difficult to accelerate using hardware when multiple streams coexist. This is caused by the computation time requirement and mainly by management of the streams. In most accelerators, computation is treated at the block-level rather than as a stream, making the management of multiple streams complex. This article presents a solution combining CBC and CTR modes of operation with a hardware context switching. The hardware context switching allows the accelerator to treat the data as a stream. Each stream can have different parameters: key, initialization value, state of counter. Stream switching was managed by the hardware context switching mechanism. A high-level synthesis tool was used to generate the context switching circuit. The scheme was tested on three cryptographic algorithms: AES, DES, and BC3. The hardware context switching allowed the software to manage multiple streams easily, efficiently, and rapidly. The software was freed of the task of managing the stream state. Compared to the original algorithm, about 18%–38% additional logic elements were required to implement the CBC or CTR mode and the additional circuits to support context switching. Using this method, the performance overhead when treating multiple streams was low, and the performance was comparable to that of existing hardware accelerators not supporting multiple streams.

scholarly journals A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Felix M. Kibegwa ◽  
Rawlynce C. Bett ◽  
Charles K. Gachuiri ◽  
Francesca Stomeo ◽  
Fidalis D. Mujibi
Keyword(s):  
Next Generation Sequencing ◽  
Metagenomic Data ◽  
Diversity Analysis ◽  
Taxonomic Identification ◽  
Sequencing Platforms ◽  
High Level ◽  
Small Holder ◽  
Generation Sequencing ◽  
Bacterial Domain

Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines. These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis. In this study, we compared two commonly used pipelines for shotgun metagenomic analysis: MG-RAST and Kraken 2, in terms of taxonomic classification, diversity analysis, and usability using their primarily default parameters. Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken 2 and MG-RAST, respectively. 933 species were detected by the two algorithms. Kraken 2 solely detected 3550 species, while MG-RAST identified 557 species uniquely. For archaea, Kraken 2 generated 105 and 236 genera and species, respectively, while MG-RAST detected 60 genera and 88 species. 54 genera and 72 species were commonly detected by the two methods. Kraken 2 had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample. This study revealed that Kraken 2 and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected. However, Kraken 2 generated a more accurate taxonomic identification given the higher number of “Unclassified” reads in MG-RAST. The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data. The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of the combined pipelines.

scholarly journals Prognostic Metrics Associated with Inflammation and Atherosclerosis Signaling Evaluate the Burden of Adverse Clinical Outcomes in Ischemic Stroke Patients

2020 ◽  
Vol 66 (11) ◽  
pp. 1434-1443
Author(s):  
Daoxia Guo ◽  
Zhengbao Zhu ◽  
Chongke Zhong ◽  
Aili Wang ◽  
Xuewei Xie ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Clinical Outcomes ◽  
Pathway Analysis ◽  
Primary Outcome ◽  
Extreme Case ◽  
High Sensitivity ◽  
Additional Information ◽  
Reactive Protein ◽  
Significant Enrichment ◽  
High Level

Abstract Background Conventional prognostic risk factors can only partly explain the adverse clinical outcomes after ischemic stroke. We aimed to establish a set of prognostic metrics and evaluate its public health significance on the burden of adverse clinical outcomes of ischemic stroke. Methods All patients were from the China Antihypertensive Trial in Acute Ischemic Stroke (CATIS). We established prognostic metrics of ischemic stroke from 20 potential biomarkers in a propensity-score-matched extreme case sample (n = 146). Pathway analysis was conducted using Ingenuity Pathway Analysis. In the whole CATIS population (n = 3575), we evaluated effectiveness of these prognostic metrics and estimated their population-attributable fractions (PAFs) related to the risk of clinical outcomes. The primary outcome was a composite outcome of death or major disability (modified Rankin Scale score ≥3) at 3 months after stroke. Results Matrix metalloproteinase-9 (MMP-9), S100A8/A9, high-sensitivity C-reactive protein (hsCRP), and growth differentiation factor-15 (GDF-15) were selected as prognostic metrics for ischemic stroke. Pathway analysis showed significant enrichment in inflammation and atherosclerosis signaling. All 4 prognostic metrics were independently associated with poor prognosis of ischemic stroke. Compared with patients having 1 or 0 high-level prognostic metrics, those with 4 had higher risk of primary outcome (OR: 3.84, 95%CI: 2.67–5.51; PAF: 37.4%, 95%CI: 19.5%–52.9%). Conclusion The set of prognostic metrics, enriching in inflammation and atherosclerosis signaling, could effectively predict the prognosis at 3 months after ischemic stroke and would provide additional information for the burden of adverse clinical outcomes among patients with ischemic stroke.

Signal coding in cockroach photoreceptors is tuned to dim environments

2012 ◽  
Vol 108 (10) ◽  
pp. 2641-2652 ◽  
Author(s):  
K. Heimonen ◽  
E.-V. Immonen ◽  
R. V. Frolov ◽  
I. Salmela ◽  
M. Juusola ◽  
...  
Keyword(s):  
Information Transfer ◽  
Periplaneta Americana ◽  
Single Photon ◽  
Signal To Noise Ratio ◽  
Temporal Integration ◽  
High Sensitivity ◽  
Single Photons ◽  
Low Frequencies ◽  
Whole Cell Patch Clamp ◽  
High Level

In dim light, scarcity of photons typically leads to poor vision. Nonetheless, many animals show visually guided behavior with dim environments. We investigated the signaling properties of photoreceptors of the dark active cockroach ( Periplaneta americana) using intracellular and whole-cell patch-clamp recordings to determine whether they show selective functional adaptations to dark. Expectedly, dark-adapted photoreceptors generated large and slow responses to single photons. However, when light adapted, responses of both phototransduction and the nontransductive membrane to white noise (WN)-modulated stimuli remained slow with corner frequencies ∼20 Hz. This promotes temporal integration of light inputs and maintains high sensitivity of vision. Adaptive changes in dynamics were limited to dim conditions. Characteristically, both step and frequency responses stayed effectively unchanged for intensities >1,000 photons/s/photoreceptor. A signal-to-noise ratio (SNR) of the light responses was transiently higher at frequencies <5 Hz for ∼5 s after light onset but deteriorated to a lower value upon longer stimulation. Naturalistic light stimuli, as opposed to WN, evoked markedly larger responses with higher SNRs at low frequencies. This allowed realistic estimates of information transfer rates, which saturated at ∼100 bits/s at low-light intensities. We found, therefore, selective adaptations beneficial for vision in dim environments in cockroach photoreceptors: large amplitude of single-photon responses, constant high level of temporal integration of light inputs, saturation of response properties at low intensities, and only transiently efficient encoding of light contrasts. The results also suggest that the sources of the large functional variability among different photoreceptors reside mostly in phototransduction processes and not in the properties of the nontransductive membrane.

scholarly journals Differential Involvement of Histidine Kinase Receptors in Pseudohyphal Development, Stress Adaptation, and Drug Sensitivity of the Opportunistic Yeast Candida lusitaniae

2007 ◽  
Vol 6 (10) ◽  
pp. 1782-1794 ◽  
Author(s):  
Florence Chapeland-Leclerc ◽  
Paméla Paccallet ◽  
Gwenaël Ruprich-Robert ◽  
David Reboutier ◽  
Christiane Chastin ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Histidine Kinase ◽  
High Sensitivity ◽  
Triple Mutant ◽  
Mating Ability ◽  
Reverse Transcription Pcr ◽  
Moderate Sensitivity ◽  
Candida Lusitaniae ◽  
High Level

ABSTRACT Fungal histidine kinase receptors (HKRs) sense and transduce many extracellular signals. We investigated the role of HKRs in morphogenetic transition, osmotolerance, oxidative stress response, and mating ability in the opportunistic yeast Candida lusitaniae. We isolated three genes, SLN1, NIK1, and CHK1, potentially encoding HKRs of classes VI, III, and X, respectively. These genes were disrupted by a transformation system based upon the “URA3 blaster” strategy. Functional analysis of disruptants was undertaken, except for the sln1 nik1 double mutant and the sln1 nik1 chk1 triple mutant, which are not viable in C. lusitaniae. The sln1 mutant revealed a high sensitivity to oxidative stress, whereas both the nik1 and chk1 mutants exhibited a more moderate sensitivity to peroxide. We also showed that the NIK1 gene was implicated in phenylpyrrole and dicarboximide compound susceptibility while HKRs seem not to be involved in resistance toward antifungals of clinical relevance. Concerning mating ability, all disruptants were still able to reproduce sexually in vitro in unilateral or bilateral crosses. The most important result of this study was that the sln1 mutant displayed a global defect of pseudohyphal differentiation, especially in high-osmolarity and oxidative-stress conditions. Thus, the SLN1 gene could be crucial for the C. lusitaniae yeast-to-pseudohypha morphogenetic transition. This implication is strengthened by a high level of SLN1 mRNAs revealed by semiquantitative reverse transcription-PCR when the yeast develops pseudohyphae. Our findings highlight a differential contribution of the three HKRs in osmotic and oxidant adaptation during the morphological transition in C. lusitaniae.

scholarly journals Nonradioactive in situ hybridization for detection of mRNAs encoding for peroxisomal proteins: heterogeneous hepatic lobular distribution after treatment with a single dose of bezafibrate.

1996 ◽  
Vol 44 (8) ◽  
pp. 825-834 ◽  
Author(s):  
A Schad ◽  
H D Fahimi ◽  
A Völkl ◽  
E Baumgart
Keyword(s):  
Single Dose ◽  
High Sensitivity ◽  
Fold Increase ◽  
Urate Oxidase ◽  
Dot Blot ◽  
Liver Lobule ◽  
Perfusion Fixation ◽  
High Level ◽  
Parenchymal Cells ◽  
Dot Blot Analysis

We present a nonradioactive in siru hybridization (ISH) protocol for detection of mRNAs in rat liver encoding for three peroxisomal proteins: catalase and urate oxidase as representatives of high-level abundance mRNAs and trifunctional protein (PH) as that of low-level abundance mRNAs. In addition to normal rats, animals treated for 24 hr with a single dose of bezafibrate were studied. The use of perfusion-fixation with 4% depolymerized paraformaldehyde/0.05% glutaraldehyde combined with paraffin embedding and the application of digoxigenin-labeled cRNA probes provided optimal cytological resolution and high sensitivity comparable to that of radioactive ISH. In parallel experiments, the same digoxigenin-labeled cRNA probes were used for Northern and semiquantitative dot-blot analysis of isolated RNAs. In control animals, the mRNAs for catalase and urate oxidase were uniformly distributed across the liver lobule and were confined to liver parenchymal cells. The bile duct epithelial and the sinusoidal cells remained negative. The specificity and the high resolution of our protocol were further substantiated by reciprocal localization of transcripts for albumin and glyceraldehyde-3-phosphate dehydrogenase in different regions of the liver lobule and for catalase in the proximal tubules of the renal cortex. Whereas in control livers the transcripts for PH were barely detectable, a strong signal was found in pericentral hepatocytes of bezafibratetreated animals, corresponding to an 8-10-fold increase of mRNA detected in dot-blots. In contrast, the urate oxidase mRNA was reduced by more than 50%, with diminution of staining in pericentral regions of the liver lobule. The mRNA encoding for catalase was only slightly affected. Further applications of this protocol should be helpful in elucidation of the cell-specific transcriptional regulation of peroxisomal proteins in various organs under normal and pathological conditions.

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