Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Diagnostics of Plant-Symbiotic and Phytopathogenic Bacteria

Rapid and reliable diagnostics and identification of pathogenic and symbiotic bacteria are at the top of the agenda. In the first case, they are important to control and prevent crop damages, and thus reduce economic losses. In the second, it's necessary to design and monitor quality of biofertilizer to raise its effectiveness and crop capacity. Development of accurately, rapidly, technically and commercially accessible methods remains a critical problem for the bacteria with comprehensive phylogenetic structure. In this work, we investigated pathogenic Xanthomonas and Ralstonia and symbiotic Sinorhizobium. The aim of this investigation was to examine the applicability of the novel methods for phylogenetic study, identification and diagnostics of closely related species of these genera. The conventional phenotypic and genotypic (16S rRNA, gyrB) methods were applied as referents. Novel polymerase chain reaction (PCR)-based approaches, single-adapter amplified fragment length polymorphism (saAFLP) and comparative analyses of hin-region and Xcc0006-0007 sequences, were first employed for the investigations. Phenotypic tests, 16S rRNA and gyrB analysis distinguished bacteria at the genus level, but failed to identify them to the species robustly. The new methods identified bacteria at the inter-species level more precisely. This identification agreed with the accepted genera's classifications. The only exceptions were X. fuscans & X. citri and X. perforance & X. euvesicatoria which clustered together. The further outcome of this study was achieved hin-region-based genus-specific PCR primers for the express-diagnostics of the genera. Summary, these new methods can be applied for genome-based phylogeny investigations and as convenient and accurate tools for identification and routine laboratory diagnostics of these comprehensive genera.
Implementation and Parallelization of a Reverse-Search Algorithm for Minkowski Sums

We present an implementation of a reverse-search algorithm of Fukuda for computing Minkowski sums of polytopes efficiently. The algorithm allows summing any number of polytopes in any dimension, and is complete in the sense that it does not assume general position. Its running time depends linearly on the size of the output. To the best of our knowledge, this is the only existing implementation that can efficiently compute Minkowski sums in higher dimensions. The implementation uses the exact arithmetic GMP, which ensures robustness of the program and exactness of the results. We furthermore present a parallel version of our implementation to demonstrate the simplicity and efficiency of performing the reverse search in parallel. The results of the performance tests show a near-linear acceleration of our parallel implementation.
Marginal Copper-Restricted Diets Produce Altered Cardiac Ultrastructure in the Rat

Abstract To determine if chronic ingestion of a diet containing a marginally low level of Cu could cause deleterious alterations in cardiac ultrastructure, male offspring were nursed by dams fed a diet containing either 6.7 or 2.8 mg Cu/kg from midgestation through lactation before weaning to the same diet. Conventional measures of Cu status, including growth, relative heart weight, tissue concentrations of Cu, ceruloplasmin activity, and tissue activity of Cu, Zn-superoxide dismutase (SOD) were similar in both dietary treatment groups at 5.5 months of age. However, significant increases in the number and volume of lipid droplets and an increased incidence of pathological abnormalities in mitochondria and basal laminae were observed in sections of hearts from rats chronically fed the diet containing 2.8 mg/kg Cu. Reduction of the dietary level of Cu from 2.8 to 1.3 mg/kg from 4 to 5.5 months of age caused significant reductions in the concentration of Cu in serum and liver, but Cu content, Cu, Zn-SOD activity, pathological scores, and morphometric parameters in hearts were not modified by the greater restriction of dietary Cu in adult rats. This study suggests that abnormalities in cardiac ultrastructure occurred in rats chronically fed diets marginally low in Cu, despite minimal changes in conventional biochemical indicators of Cu status.
Progression and prognosis in pure autonomic failure (PAF): comparison with multiple system atrophy

Objective: To clarify the progression of autonomic symptoms and functional deterioration in pure autonomic failure (PAF), particularly in comparison with multiple system atrophy (MSA). Methods: The investigation involved eight patients with PAF (M/F = 7/1; mean age at onset, 57 years) and 22 with probable MSA matched for age at onset (M/F = 14/8; onset 56 years). Subjects were followed up for neurological symptoms, activities of daily living, and autonomic function for more than seven years. Autonomic functional tests were carried out. Results: In PAF, fainting or sudomotor dysfunction occurred first, followed by constipation and syncope. Urinary dysfunction developed late, and respiratory dysfunction was not evident. This clinical course contrasted sharply with that in MSA, where early urinary dysfunction usually proceeded to sudomotor dysfunction or orthostatic hypotension (p = 0.004), followed by respiratory dysfunction (p = 0.0004). Results of pharmacological tests also distinguished PAF from MSA. Progression and prognosis in patients with PAF did not worsen, unlike the steady progressive autonomic dysfunction in MSA (p<0.0001, p<0.0001, p = 0.0009, and p = 0.003, for progression to modified Rankin scale grade III, IV, V, and death, respectively). Conclusions: The time course and pattern of progression of autonomic failure differed significantly between PAF and MSA. Patients with PAF had slower functional deterioration and a better prognosis.
Sulfamide-based inhibitors for carboxypeptidase A. Novel type transition state analogue inhibitors for zinc proteases.

N-Sulfamoylphenylalanine and its derivatives having varied alkyl groups on the terminal amino group were designed rationally as transition state analogue inhibitors for carboxypeptidase A (CPA) and synthesized. In CPA inhibitory assays the parent compound having the (S)-configuration, i.e., (S)-1a, showed potent inhibitory activity with the K(i) value of 0.64 microM. Its enantiomer was shown to be much less potent (K(i) = 470 microM). Introduction of an alkyl group such as methyl or isopropyl group on the terminal amino group of (S)-1a lowered the inhibitory potency drastically. Introduction of a methyl group on the internal amino group of (S)-1a also caused a drastic reduction of the inhibitory activity. The structure of the CPA x(S)-1a complex determined by single-crystal X-ray diffraction reveals that the sulfamoyl moiety interacts with the zinc ion and functional groups at the active site of CPA, which is reminiscent of the postulated stabilization mode of a tetrahedral transition state in the CPA-catalyzed hydrolysis of a peptide substrate. On the basis of the design rationale and the binding mode of (S)-1a to CPA shown by X-ray crystallographic analysis, the present inhibitors are inferred to be a novel type of transition state analogue inhibitor for CPA.
Decoding with Finite-State Transducers on GPUs

Weighted finite automata and transducers (including hidden Markov models and conditional random fields) are widely used in natural language processing (NLP) to perform tasks such as morphological analysis, part-of-speech tagging, chunking, named entity recognition, speech recognition, and others. Parallelizing finite state algorithms on graphics processing units (GPUs) would benefit many areas of NLP. Although researchers have implemented GPU versions of basic graph algorithms, no work, to our knowledge, has been done on GPU algorithms for weighted finite automata. We introduce a GPU implementation of the Viterbi and forward-backward algorithm, achieving speedups of up to 4x over our serial implementations running on different computer architectures and 3335x over widely used tools such as OpenFST.
Enhancement of harmonic content of speech based on a dynamic programming pitch tracking algorithm

For pitch tracking of a single speaker, a common requirement is to find the optimal path through a set of voiced or voiceless pitch estimates over a sequence of time frames. Dynamic programming (DP) algorithms have been applied before to this problem. Here, the pitch candidates are provided by a multi-channel autocorrelation-based estimator, and DP is extended to pitch tracking of multiple concurrent speakers. We use the resulting pitch information to enhance harmonic content in noisy speech and to obtain separations of target from interfering speech.
An Approach for Enhancing the Results of Detecting Foreground Objects and Their Moving Shadows in Surveillance Video

Automated surveillance system is becoming increasingly important especially in the fields of computer vision and video processing. This paper describes a novel approach for improving the results of detecting foreground objects and their shadows in indoor image sequences. Several previous techniques have been developed in the literature that deal with moving shadows. However, a comparative evaluation of the existing approaches shows that most of the methods are unable to extract and preserve the shape of the moving objects completely. Since accurately detecting the moving objects from the background scene is a crucial step in such system, we then design a method to improve the detection results by appropriately filling the regions that are erroneously removed from foreground regions. We propose to combine the classification result of the moving objects, object representation based on the cardboard and head detection technique for performing the improvement task.
A Programmable DataPath for MPEG-4 and Natural Hybrid Video Coding

A programmable data-path that supports MPEG standards Synthetic & Natural Hybrid video Coding (SNHC) is presented. It can support a maximum of 16 parallel SIMD integer operations and 2 parallel SIMD floating-point operations. Two new instructions were added in order to increase the execution of 3D graphics and SNHC as well as to speed up IDCT, FFT, and other media signal processing algorithms. These operations are implemented by re-using the hardware without significant increase in area and delay. The datapath has been modeled in Verilog using 0.25u CMOS library and synthesized using Synopsys. All operations are single-cycle running at 200 MHz.
NEFSC bycatch estimation methodology : allocation, precision, and accuracy

This series is a secondary scientific series designed to assure the long-term documentation and to enable the timely transmission of research results by Center and/or non-Center researchers, where such results bear upon the research mission of the Center (see the outside back cover for the mission statement). These documents receive internal scientific review but no technical or copy editing. The National Marine Fisheries Service does not endorse any proprietary material, process, or product mentioned in these documents. All documents issued in this series since April 2001, and several documents issued prior to that date, have been copublished in both paper and electronic versions. To access the electronic version of a document in this series, go to Summary of fleet sectors, by species group, that are imputed and not imputed; blank cells indicate no fleet activity . point estimates of the coefficient of variation of the discard to kept ratio for New England groundfish caught with otter trawl gear, and the expected coefficient of variation of the discard to kept ratio over a range of sample sizes. 43 Figure 12. The 2003/2004 point estimates of the coefficient of variation of the discard to kept ratio for New England groundfish caught with gillnet gear, and the expected coefficient of variation of the discard to kept ratio over a range of sample sizes. 44 v Executive Summary This report describes the standardized methodology used to estimate bycatch rates of finfish by commercial fisheries in the Northeast. In this report, bycatch is defined as the observed discarded catch, summed over from eleven different groundfish species. Estimates of unobserved discards are not considered. All retained catches are included whether or not the catches were incidental to the target species. Emphasis is placed on the methods used to define the sampling frame (i.e., the population of commercial fishing trips to be sampled), appropriate stratification, and efficient allocation of sampling effort to these strata. Efficient allocation of sampling effort within a stratified survey design improves the precision of the estimate of overall discard rates. Accuracy of sample estimates is evaluated by comparing various performance measures (e.g., landings, trip duration) between vessels with and without observers present. Although formal statistical distinctions between accuracy and bias of estimators and estimates can be made, in this report we use the terms interchangeably and less formally. A biased estimator is inaccurate; an accurate estimator is unbiased. This report focuses on bycatch …
Fast and Easy: Approximating Uniform Information Density in Language Production

A model of sentence production is presented, which implements a strategy that produces sentences with more uniform surprisal profiles, as compared to other strategies, and in accordance to the Uniform Information Density Hypothesis (Jaeger, 2006; Levy & Jaeger, 2007). The model operates at the algorithmic level combining information concerning word probabilities and sentence lengths, representing a first attempt to model UID as resulting from underlying factors during language production. The sentences produced by this model showed indeed the expected tendency, having more uniform surprisal profiles and lower average word surprisal, in comparison to other production strategies.
Multi-criteria Group Decision Making Using A Modified Fuzzy TOPSIS Procedure

In this paper we propose a modified fuzzy technique for order performance by similarity to ideal solution (modified fuzzy TOPSIS) for the multi-criteria decision making (MCDM) problem when there is a group of decision makers. Regarding the value of the truth that a fuzzy number is greater than or equal to another fuzzy number, a new distance measure is proposed in this paper. This distance measure calculates the distance of each fuzzy number from both fuzzy positive ideal solution (FPIS) and fuzzy negative ideal solution (FNIS). Then, the alternative which is simultaneously closer to FPIS and farther from FNIS would be selected as the best choice. To clarify our proposed procedure, a numerical example is discussed
Management of multiple tasks: cockpit task management errors

It is argued that a flightcrew has not only to perform tasks, but to manage them as well, and that proper task management can be crucial to the successful completion of the flight mission. From this perspective, a framework for cockpit task management (CTM) has been proposed. Based on this framework, a set of CTM errors is being derived from aircraft accident/incident reports and flight simulator experiments. The results of a preliminary analysis of 14 air accident reports are presented. It is found that not correctly initiating a task contributes to over one third of the errors in these accidents. An initial attempt to derive the cause of such errors indicates that the pilot's knowledge of the aircraft or the procedures is usually limited in those tasks when abnormal conditions occurred. A preliminary set of specifications for a pilot-vehicle interface is proposed on the basis of the preliminary results. <<ETX>>
S2S: a peer to peer protocol for participative sensing

Participatory sensing represents a promising perspective in the worldwide diffusion of smarter and smarter mobile devices. This paper proposes s2s, a peer-to-peer protocol to increase precision and effectiveness, as well as to reduce resources consuming on a system for participative sensing of noise pollution by means of common smartphones. S2s has been conceived with the aim to obtain an optimal scheme to lookup and query neighbors' information for improving quality of sensing and reducing data exchanges through the Net.
Secure Self-Destruction of Shared Data in Multi-CloudIoT

Due to its flexibility and efficiency, cloud computing becomes a typical infrastructure for storing, processing, and sharing a large amount of Internet of Things (IoT) data collected from devices and sensors. However, data sent to the Cloud may be used incorrectly or copied without permission. To allow owner of data sent to the Cloud to grant access to a specific set of captured data fields for a set of users and prevent that access to others using minimum number of keys; Our approach proposes encryption of data by access. Our solution also allows data owner to restrict access to certain period by destroying data and keys after this time in order to change them; In addition, our approach improves availability, integrity and confidentiality of information stored in the cloud by building a Cloud of Clouds (multi-cloud).
Comparison of Two Sampling Methods for Assessing Halyomorpha halys (Hemiptera: Pentatomidae) Numbers in Soybean Fields

Abstract Sampling soybean fields for the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera: Pentatomidae), can be challenging. Both adults and nymphs have a “startle response” and drop to the ground with even the slightest disturbance. This behavior could reduce the effectiveness of the traditional sweep net and ground cloth sampling methods. In 2013 and 2014, in Virginia, Delaware, and Maryland, we evaluated a visual plant inspection method that consisted of counting the number of brown marmorated stink bug nymphs and adults seen on soybean plants in a 2-min inspection period while walking carefully between two rows. After a 30-min interval, which allowed the stink bugs to reposition in the canopy, the area was resampled using 15 sweeps with a 38-cm-diameter sweep net. In total, 76 soybean fields and 2,042 paired comparisons were used to determine a strong linear relationship between sampling methods (y = 0.984x + 0.4359, R2 = 0.6934, where y = brown marmorated stink bugs/2-min visual count and x = brown marmorated stink bugs/15 sweeps). An average visual count of 5.4 brown marmorated stink bugs in 2 min was estimated as being equivalent to the current economic threshold of 5 stink bugs per 15 sweeps. Visual inspection appears to be an effective method for assessing brown marmorated stink bug populations in soybeans.
Mechanisms for segregating T cell receptor and adhesion molecules during immunological synapse formation in Jurkat T cells

T cells interacting with antigen-presenting cells (APCs) form an “immunological synapse” (IS), a bull's-eye pattern composed of a central supramolecular activation cluster enriched with T cell receptors (TCRs) surrounded by a ring of adhesion molecules (a peripheral supramolecular activation cluster). The mechanism responsible for segregating TCR and adhesion molecules remains poorly understood. Here, we show that immortalized Jurkat T cells interacting with a planar lipid bilayer (mimicking an APC) will form an IS, thereby providing an accessible model system for studying the cell biological processes underlying IS formation. We found that an actin-dependent process caused TCR and adhesion proteins to cluster at the cell periphery, but these molecules appeared to segregate from one another at the earliest stages of microdomain formation. The TCR and adhesion microdomains attached to actin and were carried centripetally by retrograde flow. However, only the TCR microdomains penetrated into the actin-depleted cell center, whereas the adhesion microdomains appeared to be unstable without an underlying actin cytoskeleton. Our results reveal that TCR and adhesion molecules spatially partition from one another well before the formation of a mature IS and that differential actin interactions help to shape and maintain the final bull's-eye pattern of the IS.
An overview of the phylogeny and diversity of eukaryotes

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eu- karyotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predomi- nantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the pro- posed relationships of these groups to each other.
A Hybrid Generative/Discriminative Framework to Train a Semantic Parser from an Un-annotated Corpus

We propose a hybrid generative/discriminative framework for semantic parsing which combines the hidden vector state (HVS) model and the hidden Markov support vector machines (HM-SVMs). The HVS model is an extension of the basic discrete Markov model in which context is encoded as a stack-oriented state vector. The HM-SVMs combine the advantages of the hidden Markov models and the support vector machines. By employing a modified K-means clustering method, a small set of most representative sentences can be automatically selected from an un-annotated corpus. These sentences together with their abstract annotations are used to train an HVS model which could be subsequently applied on the whole corpus to generate semantic parsing results. The most confident semantic parsing results are selected to generate a fully-annotated corpus which is used to train the HM-SVMs. The proposed framework has been tested on the DARPA Communicator Data. Experimental results show that an improvement over the baseline HVS parser has been observed using the hybrid framework. When compared with the HM-SVMs trained from the fully-annotated corpus, the hybrid framework gave a comparable performance with only a small set of lightly annotated sentences.
Interleukin-17 and interleukin-23 in patients with polymyositis and dermatomyositis

Objective: To analyse the concentration of interleukin (IL)-17 and IL-23 in serum and ex vivo culture supernatant of peripheral blood mononuclear cells (PBMCs) from patients with polymyositis (PM) and dermatomyositis (DM) compared with healthy controls (HC). Methods: Enzyme-linked immunosorbent assay (ELISA) was used to analyse the concentration of IL-17 and IL-23 from 25 patients with PM, 21 patients with DM, and 12 HC in serum or ex vivo culture supernatant of PBMCs following stimulation ex vivo with anti-CD3/CD28 for 72 h. Results: The levels of IL-23 increased in the serum and culture supernatant of patients with PM and patients with DM compared with HC. By contrast, concentrations of IL-17 in supernatants from patients with PM and DM were not significantly higher than those from HC. We subdivided the group of DM and PM patients into those with early disease versus those with established disease and found that the levels of IL-17 and IL-23 were much higher in early stage compared to established disease. Conclusion: We have demonstrated that stimulated PBMCs from DM and PM patients produce increased levels of IL-23 as compared to HC. IL-17 and IL-23 levels are increased in early as compared to established disease. This provides further evidence that IL-17/IL-23 may play a crucial role in autoimmune diseases.