Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Efficient Algorithm for the Gene-Team Problem on General Sequences

Identifying conserved gene clusters is an important step toward understanding the evolution of genomes and predicting the functions of genes. A famous model to capture the essential biological features of a conserved gene cluster is called the gene-team model. The problem of finding the gene teams of two general sequences is the focus of this paper. For this problem, He and Goldwasser had an efficient algorithm that requires O(mn) time using O(m + n) working space, where m and n are, respectively, the numbers of genes in the two given sequences. In this paper, a new efficient algorithm is presented. Assume m ≤ n. Let C = Σ<sub>αϵΣ</sub> o<sub>1</sub>(α)o<sub>2</sub>(α), where Σ is the set of distinct genes, and o<sub>1</sub>(α) and o<sub>2</sub>(a) are, respectively, the numbers of copies of a in the two given sequences. Our new algorithm requires O(min{C lg n,mn}) time using O(m + n) working space. As compared with He and Goldwasser's algorithm, our new algorithm is more practical, as C is likely to be much smaller than mn in practice. In addition, our new algorithm is output sensitive. Its running time is O(lg n) times the size of the output. Moreover, our new algorithm can be efficiently extended to find the gene teams of k general sequences in O(k C Ig (n<sub>1</sub>n<sub>2</sub>.n<sub>k</sub>)) time, where n<sub>i</sub> is the number of genes in the ith input sequence.
Onboard low-complexity compression of solar images

Acquiring and processing astronomical images is becoming increasingly important for accurate space weather prediction and expanding our understanding about the Sun and the Universe. These images are often rich in content, large in size and dynamic range. Efficient, low-complexity compression solutions are essential to reduce onboard storage, processing, and communication resources. Distributed compression is a promising technique for onboard coding of solar images by exploiting correlation between successively acquired images. In this paper we propose an adaptive distributed compression solution using particle filtering that tracks correlation, as well as performing disparity estimation, at the decoder side. The proposed algorithm is tested on the stereo solar images captured by the twin satellites system of NASA's STEREO project. Our experimental results show the significant PSNR improvement over traditional separate bit-plane decoding without dynamic correlation and disparity estimation.
Short- and long-term clinical outcome after Q wave and non-Q wave myocardial infarction in a large patient population.

Prognosis for patients with non-Q wave myocardial infarction is controversial although a number of studies have shown a less favorable outlook after hospital discharge for patients with non-Q wave than for those with Q wave infarction. Therefore, the in-hospital and 1-year prognosis was investigated in a sufficiently large patient population (n = 2,024) to allow stratification by subgroups, in particular by age and previous myocardial infarction. Patients with non-Q wave infarction (n = 444; 22% of the total study population) were somewhat older (65 vs. 63 years, p less than 0.001) and had an increased incidence of previous myocardial infarction (46% vs. 24%, p less than 0.001) and congestive heart failure (21% vs. 8%, p less than 0.001) than patients with Q wave infarction. In-hospital mortality of patients with non-Q wave infarction was lower (8.1% vs. 11.5%; p less than 0.06), whereas their 1-year mortality after hospital discharge was significantly higher (13.7% vs. 9.2%, p less than 0.05) than for patients with Q wave infarction. However, total mortalities at 1 year were nearly equal. When patients were subgrouped by presence or absence of a previous myocardial infarction, patients in both subgroups exhibited mortality patterns typical of the entire population with Q wave or non-Q wave infarction. However, when stratified by age and previous infarction, in-hospital mortality for patients with non-Q wave infarction was significantly lower only in patients older than 70 years of age. Similarly, the higher mortality after hospital discharge in patients with non-Q wave infarction occurred only in patients older than 70 years of age without previous myocardial infarction. (ABSTRACT TRUNCATED AT 250 WORDS)
Holocene development of subarctic permafrost peatlands in Finnmark, northern Norway

Subarctic permafrost peatlands are important soil organic carbon pools, and improved knowledge about peat properties and peatland sensitivity to past climate change is essential when predicting future response to a warmer climate and associated feedback mechanisms. In this study, Holocene peatland development and permafrost dynamics of four subarctic peat plateaus in Finnmark, northern Norway have been investigated through detailed analyses of plant macrofossils and geochemical properties. Peatland inception occurred around 9800 cal. yr BP and 9200 cal. yr BP at the two continental sites Suossjavri and Iskoras. Younger basal peat ages were found at the two coastal locations Lakselv and Karlebotn, at least partly caused by the time lag between deglaciation and emergence of land by isostatic uplift. Here, peatland development started around 6150 cal. yr BP and 5150 cal. yr BP, respectively. All four peatlands developed as wet fens throughout most of the Holocene. Permafrost aggradation, causing frost heave and a shift in the vegetation assemblage from wet fen to dry bog species, probably did not occur until during the last millennium, ca. 950 cal. yr BP in Karlebotn and ca. 800 cal. yr BP in Iskoras, and before ca. 150 cal. yr BP in Lakselv and ca. 100 cal. yr BP in Suossjavri. In Karlebotn, there are indications of a possible earlier permafrost phase around 2200 cal. yr BP due to climatic cooling at the late Subboreal to early Subatlantic transition. The mean long-term Holocene carbon accumulation rate at all four sites was 12.3 ± 4.1 gC m−2 yr−1 (±SD) and the mean soil organic carbon storage was 97 ± 46 kgC m−2.
Mapping Tree Canopy Cover and Aboveground Biomass in Sudano-Sahelian Woodlands Using Landsat 8 and Random Forest

Accurate and timely maps of tree cover attributes are important tools for environmental research and natural resource management. We evaluate the utility of Landsat 8 for mapping tree canopy cover (TCC) and aboveground biomass (AGB) in a woodland landscape in Burkina Faso. Field data and WorldView-2 imagery were used to assemble the reference dataset. Spectral, texture, and phenology predictor variables were extracted from Landsat 8 imagery and used as input to Random Forest (RF) models. RF models based on multi-temporal and single date imagery were compared to determine the influence of phenology predictor variables. The effect of reducing the number of predictor variables on the RF predictions was also investigated. The model error was assessed using 10-fold cross validation. The most accurate models were created using multi-temporal imagery and variable selection, for both TCC (five predictor variables) and AGB (four predictor variables). The coefficient of determination of predicted versus observed values was 0.77 for TCC (RMSE = 8.9%) and 0.57 for AGB (RMSE = 17.6 tons∙ha−1). This mapping approach is based on freely available Landsat 8 data and relatively simple analytical methods, and is therefore applicable in woodland areas where sufficient reference data are available.
Send Orders of Reprints at Reprints@benthamscience.org Should Posterior Vitrectomy Be Made a Priority in Ophthalmic Facilities of Sub Sahara Africa?

Background: Posterior vitrectomy facilities are lacking in Sub Sahara Africa due to paucity of trained personnel in vitreo retinal subspecialty. More cases are seen needing vitrectomy, especially cases with vitreous opacities and complications of cataract surgery as more residents are being trained. The review will aim to determine whether vitrectomy facility should be a priority as part of ophthalmic facility in the region. Method: A 3 year review was carried out. All cases of posterior vitrectomy performed at the retinal unit of the University College Hospital, Ibadan, Africa between 2008 and 20011 were retrieved. Indications, and visual outcome were documented. Proportions and percentages were used to analyse the data. Results: Sixty six posterior vitrectomies were performed during the period. The most common indication for vitrectomy was vitreous hemorrhage n=30 [45.5%]. Complication of cataract surgery such as dropped intraocular lens 7 [10.7%], sclera fixated intra ocular lens 6 [9.2%], and dropped nucleus 5 [7.5%] were emerging indications. Other indications noted include complicated retinal detachments 4 (6.1%), membranectomy for posterior capsule opacity from pediatric cataract surgery 3 (4.5%) and congenital lens subluxation 2 (3.0%). Improved visual outcome was noted after surgery. Forty nine [75%] eyes were blind [visual acuity of < 3/60] before vitrectomy. This proportion dropped to 24 [37%] after vitrectomy with an additional 24% regaining navigational vision [visual acuity of 3/60 to Counting fingers at 1meter]. Conclusion: Vitrectomy should be an integral part of eye care and its availability should be made a priority in ophthalmic facilities of Sub Sahara Africa, especially those involved in ophthalmology training.
Energy Harvesting From Piezoelectric Materials Fully Integrated in Footwear

In the last few years, there has been an increasing demand for low-power and portable-energy sources due to the development and mass consumption of portable electronic devices. Furthermore, the portable-energy sources must be associated with environmental issues and imposed regulations. These demands support research in the areas of portable-energy generation methods. In this scope, piezoelectric materials become a strong candidate for energy generation and storage in future applications. This paper describes the use of piezoelectric polymers in order to harvest energy from people walking and the fabrication of a shoe capable of generating and accumulating the energy. In this scope, electroactive ß-polyvinylidene fluoride used as energy harvesting element was introduced into a bicolor sole prepared by injection, together with the electronics needed to increase energy transfer and storage efficiency. An electrostatic generator was also included in order to increase energy harvesting.
Overexpression of an Orchid (Dendrobium nobile) SOC1/TM3-Like Ortholog, DnAGL19, in Arabidopsis Regulates HOS1-FT Expression

Flowering in the appropriate season is critical for successful reproduction in angiosperms. The orchid species, Dendrobium nobile, requires vernalization to achieve flowering in the spring, but the underlying regulatory network has not been identified to date. The MADS-box transcription factor DnAGL19 was previously identified in a study of low-temperature treated D. nobile buds and was suggested to regulate vernalization-induced flowering. In this study, phylogenetic analysis of DnAGL9 and the MADS-box containing proteins showed that DnAGL19 is phylogenetically closely related to the SOC1-like protein from orchid Dendrobium Chao Parya Smile, DOSOC1. The orchid clade closed to but is not included into the SOC1-1/TM3 clades associated with either eudicots or monocots, suggesting that DnAGL19 is an SOC1-1/TM3-like ortholog. DnAGL19 was found to be highly expressed in pseudobulbs, leaves, roots, and axillary buds but rarely in flowers, and to be substantially upregulated in axillary buds by prolonged low-temperature treatments. Overexpression of DnAGL19 in Arabidopsis thaliana resulted in a small but significantly reduced time to bolting, suggesting that flowering time was slightly accelerated under normal growth conditions. Consistent with this, the A. thaliana APETELA1 (AP1) gene was expressed at an earlier stage in transgenic lines than in wild type plants, while the FLOWERING LOCUS T (FT) gene was suppressed, suggesting that altered regulations on these transcription factors caused the weak promotion of flowering. HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1) was slightly activated under the same conditions, suggesting that the HOS1-FT module may be involved in the DnAGL19-related network. Under vernalization conditions, FT expression was significantly upregulated, whereas HOS1 expression in the transgenic A. thaliana has a level similar to that in wild type. Taken together, these results suggest that DnAGL19 controls the action of the HOS1-FT module depending on temperature cues, which could contribute to regulation of D. nobile flowering time. These data provide insights into how flowering is fine-tuned in D. nobile to acclimate the plant to seasonal changes in temperature.
Recurrent Networks as Models of Short Term Memory

The class of recurrent networks known as attractor networks is known to exhibit behaviors relevant to modeling human memory processes – notably content -addressable memory, storage of repeated inputs as stable patterns (under Hebbian learning), and maintenance of information (as activity) over time. In addition, these networks provide a natural account of the effect of similarity on interference in recall. However when looked at in finer detail there are some ways in which traditional attractor networks fail as models of human short-term memory. In particular, information in human short-term memory decays over time unless it is rehearsed, rather than remaining indefinitely. Also, under Hebbian learning traditional attractor networks have particular trouble learning correlated patterns. Here we investigate some variations on the classic framework which make it more appropriate for modeling human STM. We show (1) how adjusting the threshold of continuously-valued units can lead to networks which maintain activity information temporarily, but decay over time, (2) how noise in learning and/or input leads the similarity structure of the set of stored patterns to be reflected in the distribution of recall errors, and (3) how adding a timedelayed anti-correlative component to the learning rule provides robustness against highly correlated patterns and varying levels of input. These ideas have been incorporated in a model of serial recall that explains many aspects of human behavior on that task, and have also been used in newer simulations that learn temporal properties of the environment.
Multi-party Password-Authenticated Key Exchange Scheme with Privacy Preservation for Mobile Environment

Communications among multi-party must be fast, cost effective and secure. Today’s computing environments such as internet conference, multi-user games and many more applications involve multi-party. All participants together establish a common session key to enable multi-party and secure exchange of messages. Multi-party password-based authenticated key exchange scheme allows users to communicate securely over an insecure network by using easy-to-remember password. Kwon et al. proposed a practical three-party password-based authenticated key exchange (3-PAKE) scheme to allow two users to establish a session key through a server without pre-sharing a password between users. However, Kwon et al."s scheme cannot meet the security requirements of key authentication, key confirmation and anonymity. In this paper, we present a novel, simple and efficient multi-party password-based authenticated key exchange (M-PAKE) scheme based on the elliptic curve cryptography for mobile environment. Our proposed scheme only requires two round-messages. Furthermore, the proposed scheme not only satisfies security requirements for PAKE scheme but also achieves efficient computation and communication.
Original Antibacterial Activityof AntibacterialCuttingBoards in Household Kitchen

We examined antibacterial cutting boards with antibacterial activity values of either "2" or " 4" in compliance with the JIS Z 2801 standard, and compared their findings with those of cutting boards with no antibacterial activity. These cutting boards were used in ten different households, and we measured changes in the viable cell counts of several types of bacteria with the drop plate method. We also identified the detected bacterial flora and measured the minimum antimicrobial concentrations of several commonly used antibacterial agents against the kinds of bacteria identified to determine the expected antibacterial activity of the respective agents. Cutting boards with activity values of both "2" and "4" proved to be antibacterial in actual use, although no correlation between the viable cell counts and the antibacterial activity values was observed. In the kitchen environment, large quantities of Pseudomonas, Flavobacterium, Micrococcus, and Bacillus were detected, and it was confirmed that common antibacterial agents used in many antibacterial products are effective against these bacterial species. In addition, we measured the minimum antimicrobial concentrations of the agents against lactobacillus, a typical good bacterium, and discovered that this bacterium is less sensitive to these antibacterial agents compared to more common bacteria.
Multipole Vector Anomalies in the First-Year WMAP Data: A Cut-Sky Analysis

We apply the recently defined multipole vector framework to the frequency-specific first-year WMAP sky maps, estimating the low-l multipole coefficients from the high-latitude sky by means of a power equalization filter. While most previous analyses of this type have considered only heavily processed (and foreground-contaminated) full-sky maps, the present approach allows for greater control of residual foregrounds and therefore potentially also for cosmologically important conclusions. The low-l spherical harmonic coefficients and corresponding multipole vectors are tabulated for easy reference. Using this formalism, we reassess a set of earlier claims of both cosmological and noncosmological low-l correlations on the basis of multipole vectors. First, we show that the apparent l = 3 and 8 correlation claimed by Copi and coworkers is present only in the heavily processed map produced by Tegmark and coworkers and must therefore be considered an artifact of that map. Second, the well-known quadrupole-octopole correlation is confirmed at the 99% significance level and shown to be robust with respect to frequency and sky cut. Previous claims are thus supported by our analysis. Finally, the low-l alignment with respect to the ecliptic claimed by Schwarz and coworkers is nominally confirmed in this analysis, but also shown to be very dependent on severe a posteriori choices. Indeed, we show that given the peculiar quadrupole-octopole arrangement, finding such a strong alignment with the ecliptic is not unusual.
Automatic Recognition of Dutch Sign Language Keywords : sign language , automatic recognition , classification , pattern recognition , markov model

This paper describes the recognition of isolated Dutch sign language signs. Data is gathered with one digital camera. Head and hands are tracked, and the values are categorised to produce a linguistically inspired feature vector. With this feature vector, classification is performed. We build left-to-right Markov chain models without skips or loops to represent single signs. As an alternative, we use a classification method that compares vectors present in a sign, without regard for order. Due to the strictness of the left-to-right requirement, classification with the Markov models often fails. Classification with the alternative method yields reasonable results, supporting the notion that the linguistic feature vector is suitable for classification. More knowledge on morphology of signs would help to make more appropriate models for sign recognition.
Circulating endothelial cells and rheumatoid arthritis: relationship with plasma markers of endothelial damage/dysfunction.

OBJECTIVES RA is associated with endothelial cell dysfunction (ECD) and increased cardiovascular mortality and morbidity. Circulating endothelial cells (CECs) are a novel marker of severe endothelial damage. We hypothesized altered CECs in patients with RA compared with community controls (CCs) and hospital controls (HCs, with diabetes and hypertension) correlate with established plasma markers of inflammation and of ECD. METHODS CECs (CD146-immunobeads), von Willebrand factor, soluble E-selectin, soluble intercellular adhesion molecule-1, soluble vascular endothelial adhesion molecule-1 (sVCAM, all ELISA) and C-reactive protein (CRP, immunonephelometry) were measured in 57 patients with RA, 45 CC and 23 HC patients. RESULTS CECs in RA [median/interquartile range 8 (5-13.5) cells/ml] were elevated compared with either CC [4 (2-8.5) cells/ml] or HC [4 (1-8) cells/ml] (both P < 0.001). Levels of CECs did not correlate with other markers of ECD or of inflammation but did correlate inversely with sVCAM. CONCLUSION Evidence of endothelial damage in the form of mildly increased numbers of CECs is present in RA and is independent of plasma markers of inflammation and of ECD.
Reactive Oxygen Species and Nitric Oxide Control Early Steps of the Legume – Rhizobium Symbiotic Interaction

The symbiotic interaction between legumes and nitrogen-fixing rhizobium bacteria leads to the formation of a new organ, the nodule. Early steps of the interaction are characterized by the production of bacterial Nod factors, the reorientation of root-hair tip growth, the formation of an infection thread (IT) in the root hair, and the induction of cell division in inner cortical cells of the root, leading to a nodule primordium formation. Reactive oxygen species (ROS) and nitric oxide (NO) have been detected in early steps of the interaction. ROS/NO are determinant signals to arbitrate the specificity of this mutualistic association and modifications in their content impair the development of the symbiotic association. The decrease of ROS level prevents root hair curling and ITs formation, and that of NO conducts to delayed nodule formation. In root hairs, NADPH oxidases were shown to produce ROS which could be involved in the hair tip growth process. The use of enzyme inhibitors suggests that nitrate reductase and NO synthase-like enzymes are the main route for NO production during the early steps of the interaction. Transcriptomic analyses point to the involvement of ROS and NO in the success of the infection process, the induction of early nodulin gene expression, and the repression of plant defense, thereby favoring the establishment of the symbiosis. The occurrence of an interplay between ROS and NO was further supported by the finding of both S-sulfenylated and S-nitrosylated proteins during early symbiotic interaction, linking ROS/NO production to a redox-based regulation of the symbiotic process.