Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Insights into Taste Perception of the Invasive Pest Drosophila suzukii

Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here, we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D. suzukii and in its close relative D. biarmipes. We then analyzed the evolution, in terms of size, of each gene family as well of the molecular evolution of the genes in a 14 Drosophila species phylogenetic framework. We show that the overall evolution of GRs parallels that of dIRs not only in D. suzukii, but also in all other analyzed Drosophila. Our results reveal an unprecedented burst of gene family size in the lineage leading to the suzukii subgroup, as well as genomic changes that characterize D. suzukii, particularly duplications and strong signs of positive selection in the putative bitter-taste receptor GR59d. Expression studies of duplicate genes in D. suzukii support a spatio-temporal subfunctionalization of the duplicate isoforms. Our results suggest that D. suzukii is not characterized by gene loss, as observed in other specialist Drosophila species, but rather by a dramatic acceleration of gene gains, compatible with a highly generalist feeding behavior. Overall, our analyses provide candidate taste receptors specific for D. suzukii that may correlate with its specific behavior, and which may be tested in functional studies to ultimately enhance its control in the field.
The Road Map to KM Evaluation in Organization: A Holistic Framework

Knowledge Management (KM) has the real staying power and the potential to become the significant and permanent part of management's tool box. However, many organizations failed to realize the potential of marrying Information & Communications Technology (ICT) and KM theory to build Knowledge Management System (KMS). To meet the benefits from KM to expectations and reach KMS to its real potential, it is seriously needed to establish the evaluation and measurement framework for KMS. Based on metrics identified in literature, this paper proposes a holistic evaluation framework and a evaluation matrix, which provide a road map to KM evaluation in organization, and are applicable to plan the assessment of KM and systems holistically and effectively in organization
IR evaluation methods for retrieving highly relevant documents

This paper proposes evaluation methods based on the use of non-dichotomous relevance judgements in IR experiments. It is argued that evaluation methods should credit IR methods for their ability to retrieve highly relevant documents. This is desirable from the user point of view in modern large IR environments. The proposed methods are (1) a novel application of P-R curves and average precision computations based on separate recall bases for documents of different degrees of relevance, and (2) two novel measures computing the cumulative gain the user obtains by examining the retrieval result up to a given ranked position. We then demonstrate the use of these evaluation methods in a case study on the effectiveness of query types, based on combinations of query structures and expansion, in retrieving documents of various degrees of relevance. The test was run with a best match retrieval system (In-Query1) in a text database consisting of newspaper articles. The results indicate that the tested strong query structures are most effective in retrieving highly relevant documents. The differences between the query types are practically essential and statistically significant. More generally, the novel evaluation methods and the case demonstrate that non-dichotomous relevance assessments are applicable in IR experiments, may reveal interesting phenomena, and allow harder testing of IR methods.
Novel psychrotolerant picocyanobacteria isolated from Chesapeake Bay in the winter

Picocyanobacteria are major primary producers in the ocean, especially in the tropical or subtropical oceans or during warm seasons. Many “warm” picocyanobacterial species have been isolated and characterized. However, picocyanobacteria in cold environments or cold seasons are much less studied. In general, little is known about the taxonomy and ecophysiology of picocyanobacteria living in the winter. In this study, 17 strains of picocyanobacteria were isolated from Chesapeake Bay, a temperate estuarine ecosystem, during the winter months. These winter isolates belong to five distinct phylogenetic lineages, and are distinct from the picocyanobacteria previously isolated from the warm seasons. The vast majority of the winter isolates were closely related to picocyanobacteria isolated from other cold environments like Arctic or subalpine waters. The winter picocyanobacterial isolates were able to maintain slow growth or prolonged dormancy at 4°C. Interestingly, the phycoerythrin‐rich strains outperformed the phycocyanin‐rich strains at cold temperature. In addition, winter picocyanobacteria changed their morphology when cultivated at 4°C. The close phylogenetic relationship between the winter picocyanobacteria and the picocyanobacteria living in high latitude cold regions indicates that low temperature locations select specific ecotypes of picocyanobacteria.
Brief History

HISTORICAL BACK GROUND The College of Humanities and Social Sciences (CHSS) is one of the six Colleges of the University of Nairobi. Like the other five, it was established following the recommendations of the 1985 Presidential Visitation Committee headed by Mr. Geoffrey Kariithi. The College comprises one faculty, four schools and five institutes and a centre. CHSS is the largest College of the University with over fifty percent of the total student enrolment and staff. The College operates in several locations namely, Main, Parklands, Lower Kabete, Mombasa and Kisumu campuses and at the National Museum. The faculties, schools, institutes and centres offer a wide array of academic and research programmes. The mandate of the College is to coordinate the implementation of University policies [8] and programmes in the humanities and social sciences. Milestones The College was established in 1985 The College introduced self sponsored programmes in 1998 The College opened its satellite campus in Mombasa in 2005 and Kisumu in 2007 Distance Learning (Module III) was launched in the Faculty of Arts and School of Business in 2007 Previous Principals Prof. Onesmas Mutungi (1982-1992) [9] Prof. Joseph N. Nyasani (1992-1997) [10] Prof. Francis N. Kibera [11] (1997-2002) Prof. Isaac Meroka Mbeche (2002-2011) [12] Prof. Njeru Enos H. Nthia (2011 To date) [13]
Verifying Outsourced Inner Product Computation via Vector Aggregation in Cloud Computing

Outsourced computation has been extensively studied in a number of computer application fields with the increasing prevalence of cloud computing. As the basis and the fundamental operation, inner product computation of vectors, has also been put forwarded. As the service provider of the cloud computing may not be trustworthy, the correctness of the computation results can be corrupted if the service provider is with random fault or not honest (e.g., lazy, malicious, etc). Therefore, it is necessary for the client to verify the correctness of inner product of vectors. Existing verification mechanisms are almost built on the Merkle tree structure and signature chain mechanism, which lack efficiency on both storage and computation aspects. The existing aggregate verification scheme based on algebraic properties is able to ease such problem, however, there exist some serious design defects and lack important details. In order to solve such problems, in this paper we propose the sound inner product verification schemes based on the algebraic properties. Specifically, we first propose the simple aggravate framework, then we analyze its serious defects under smart cloud attack. Furthermore, we design the local aggregate and random aggregate framework to solve the problems respectively. Finally, we provide analysis of the proposed verification schemes in this paper.
Analysis and Improvement of Data Extraction Technology on the Web

the paper introduces an improved technology and infrastructure to support the effective flow of information among the sources and services on the Web and their interconnection with legacy systems that were designed to operate with traditional relational databases. This technology is designed to work as a relational front-end to semi-structured data sources. It extracts data from web pages using declarative specification files that define extraction rules expressed in regular expressions.
Fragmented query parse tree based SQL injection detection system for web applications

Increasing use of database driven web applications every day causes attacks on those web applications are also increasing. The common web application attack is SQL Injection attack or code injection or insertion of SQL query via input data from the client to the application. There are many detection techniques focused on the SQL structure at the application level are available. Those techniques failed to detect some of the attacks at the database level. Many existing approaches were proposed to detect the attack at the database level. The existing approach uses SVM classification for classification, which is the supervised learning algorithm, uses the syntactic and semantic features of the query parse tree. It takes more time for preprocessing of the query parse tree. In this paper, we fragmented the query parse tree to increase the speed of the preprocessing. The internal query tree can be obtained from the database log. To get instances for classification, the query tree is converted to n - dimensional feature vector by using multi - dimensional sequence. The semantic features are used as the component of feature vectors. And also the syntactic and semantic features are used to generate multi - dimensional sequences. Then the extracted feature is converted into a numeric value, if the feature contains any string value. Experimental results show that the proposed approach is more accurate and fast in detecting the attacks than existing approaches.
Rapyuta: The RoboEarth Cloud Engine

In this paper we present the design and implementation of Rapyuta1, the RoboEarth Cloud Engine. Rapyuta is an open source Platform-as-a-Service (PaaS) framework designed specifically for robotics applications. Rapyuta helps robots to offload heavy computation by providing secured customizable computing environments in the cloud. The computing environments also allow robots to easily access the RoboEarth knowledge repository. Furthermore, these computing environments are tightly interconnected, paving the way for deployment of robotic teams. We also describe specific use case configurations and present some performance results.
Histologic Disorderliness in the Arrangement of Tumor Cells as an Objective Measure of Tumor Differentiation

Background Inter-observer and intra-observer variation in histologic tumor grading are well documented. To determine whether histologic disorderliness in the arrangement of tumor cells may serve as an objective criterion for grading, we tested the hypothesis the degree of disorderliness is related to the degree of tumor differentiation on which tumor grading is primarily based. Methods Borrowing from the statistical thermodynamic definition of entropy, we defined a novel mathematical formula to compute the relative degree of histologic disorderliness of tumor cells. We then analyzed a total of 51 photomicrographs of normal colorectal mucosa and colorectal adenocarcinoma with varying degrees of differentiation using our formula. Results A one-way analysis of variance followed by post hoc pairwise comparisons using Bonferroni correction indicated that the mean disorderliness score was the lowest for the normal colorectal mucosa and increased with decreasing tumor differentiation. Conclusions Disorderliness, a pathologic feature of malignant tumors that originate from highly organized structures is useful as an objective tumor grading proxy in the field of digital pathology.
Characterization of the work–time relationship during cross-country ski ergometry

The purpose of this study was to examine the validity and reliability of estimated parameters of the work–time relationship during cross-country ski ergometry using the traditional multi-trial critical power (CP) test and a 3 min ‘all-out’ test (3MT). Fourteen recreationally active male participants (mean±SD; age: 22.14 ± 2.85 yrs; height: 177.09 ± 6.57 cm; weight: 85.68 ± 13.56 kg) completed three testing visits. All testing was conducted using an upper-body ergometer (SkiErg, Concept2, Inc., Morrisville, VT). A graded exercise test was used to determined maximal oxygen uptake (VO2peak). Two separate 3MT sessions were used to determine oxygen uptake (VO23MT), end-test power (EP), work above end-test power (WEP) and end stroke rate (ESR). Additionally, three time trials completed in a single day at simulated distances of 300 m, 650 m and 1000 m were used to estimate CP, W′ and critical stroke rate (CSR). VO2peak (3.65 ± 0.50l ⋅ min−1) and VO23MT (3.59 ± 0.4 l ⋅ min−1) were not significantly different (p = 0.162). Intraclass correlation coefficients for EP, WEP and ESR were 0.809, 0.611 and 0.783, respectively. EP (148 ± 33 W) and CP (157 ± 49 W), were not significantly different between the testing methodologies (p = 0.290) and were highly correlated (r = 0.780). WEP (8.4 ± 3.0 kJ) and W′ (8.3 ± 3.0 kJ) were similar (p = 0.947) but not related (r = 0.119), while ESR (45 ± 7 spm) and CSR (47 ± 7 spm) values were not significantly different (p = 0.238) and moderately correlated (r = 0.498). The 3MT using ski ergometry was shown to produce concurrently valid results with the traditional multi-trial CP test for CP and CSR, but not W′, and elicited similar maximal oxygen uptake values when compared to a graded exercise test.
Bayesian learning of visual chunks by human observers

Efficient and versatile processing of any hierarchically structured information requires a learning mechanism that combines lower-level features into higher-level chunks. We investigated this chunking mechanism in humans with a visual pattern-learning paradigm. We developed an ideal learner based on Bayesian model comparison that extracts and stores only those chunks of information that are minimally sufficient to encode a set of visual scenes. Our ideal Bayesian chunk learner not only reproduced the results of a large set of previous empirical findings in the domain of human pattern learning but also made a key prediction that we confirmed experimentally. In accordance with Bayesian learning but contrary to associative learning, human performance was well above chance when pair-wise statistics in the exemplars contained no relevant information. Thus, humans extract chunks from complex visual patterns by generating accurate yet economical representations and not by encoding the full correlational structure of the input.
The Pre-NH2-Terminal Domain of the Herpes Simplex Virus 1 DNA Polymerase Catalytic Subunit Is Required for Efficient Viral Replication

ABSTRACT The catalytic subunit of herpes simplex virus 1 DNA polymerase (HSV-1 Pol) has been extensively studied; however, its full complement of functional domains has yet to be characterized. A crystal structure has revealed a previously uncharacterized pre-NH2-terminal domain (residues 1 to 140) within HSV-1 Pol. Due to the conservation of the pre-NH2-terminal domain within the herpesvirus Pol family and its location in the crystal structure, we hypothesized that this domain provides an important function during viral replication in the infected cell distinct from 5′-3′ polymerase activity. We identified three pre-NH2-terminal Pol mutants that exhibited 5′-3′ polymerase activity indistinguishable from that of wild-type Pol in vitro: deletion mutants PolΔN43 and PolΔN52 that lack the extreme N-terminal 42 and 51 residues, respectively, and mutant PolA6, in which a conserved motif at residues 44 to 49 was replaced with alanines. We constructed the corresponding pol mutant viruses and found that the polΔN43 mutant displayed replication kinetics similar to those of wild-type virus, while polΔN52 and polA6 mutant virus infection resulted in an 8-fold defect in viral yield compared to that achieved with wild type and their respective rescued derivative viruses. Additionally, both polΔN52 and polA6 viruses exhibited defects in viral DNA synthesis that correlated with the observed reduction in viral yield. These results strongly indicate that the conserved motif within the pre-NH2-terminal domain is important for viral DNA synthesis and production of infectious virus and indicate a functional role for this domain.
Depth estimation from a video sequence with moving and deformable objects

In this paper we present an algorithm for depth estimation from a monocular video sequence containing moving and deformable objects. The method is based on a coded aperture system (i.e., a conventional camera with a mask placed on the main lens) and it takes a coded video as input to provide a sequence of dense depth maps as output. To deal with nonrigid deformations, our work builds on the state-of-the-art single-image depth estimation algorithm. Since singleimage depth estimation is very ill-posed, we cast the reconstruction task as a regularized algorithm based on nonlocal-means filtering applied to both the spatial and temporal domain. Our assumption is that regions with similar texture in the same frame and in neighbouring frames are likely to belong to the same surface. Moreover, we show how to increase the computational efficiency of the method. The proposed algorithm has been successfully tested on challenging real scenarios.
Variants of Plane Diameter Completion

The {\sc Plane Diameter Completion} problem asks, given a plane graph $G$ and a positive integer $d$, if it is a spanning subgraph of a plane graph $H$ that has diameter at most $d$. We examine two variants of this problem where the input comes with another parameter $k$. In the first variant, called BPDC, $k$ upper bounds the total number of edges to be added and in the second, called BFPDC, $k$ upper bounds the number of additional edges per face. We prove that both problems are {\sf NP}-complete, the first even for 3-connected graphs of face-degree at most 4 and the second even when $k=1$ on 3-connected graphs of face-degree at most 5. In this paper we give parameterized algorithms for both problems that run in $O(n^{3})+2^{2^{O((kd)^2\log d)}}\cdot n$ steps.
Possible role of pectin-containing mucilage and dew in repairing embryo DNA of seeds adapted to desert conditions.

BACKGROUND AND AIMS Repair of damage to DNA of seed embryos sustained during long periods of quiescence under dry desert conditions is important for subsequent germination. The possibility that repair of embryo DNA can be facilitated by small amounts of water derived from dew temporarily captured at night by pectinaceous surface pellicles was tested. These pellicles are secreted during early seed development and form mucilage when hydrated. METHODS Seeds of Artemisia sphaerocephala and Artemisia ordosica were collected from a sandy desert. Their embryos were damaged by gamma radiation to induce a standard level of DNA damage. The treated seeds were then exposed to nocturnal dew deposition on the surface of soil in the Negev desert highlands. The pellicles were removed from some seeds and left intact on others to test the ability of mucilage to support repair of the damaged DNA when night-time humidity and temperature favoured dew formation. Repair was assessed from fragmentation patterns of extracted DNA on agarose gels. KEY RESULTS For A. sphaerocephala, which has thick seed pellicles, DNA repair occurred in seeds with intact pellicles after 50 min of cumulative night dew formation, but not in seeds from which the pellicles had been removed. For A. ordosica, which has thin seed pellicles, DNA repair took at least 510 min of cumulative night dewing to achieve partial recovery of DNA integrity. The mucilage has the ability to rehydrate after daytime dehydration. CONCLUSIONS The ability of seeds to develop a mucilaginous layer when wetted by night-time dew, and to repair their DNA under these conditions, appear to be mechanisms that help maintain seed viability under harsh desert conditions.
Representation and Evolution of Lego-Based Assemblies

This research presents an approach to the automatic generation of electromechanical engineering designs. Our intent is to apply the Messy Genetic Algorithm optimization techniques to the evolution of assemblies composed of the Lego structures. Each design is represented as a labeled assembly graph. Designs are evaluated based on a set of behavior and structural equations, which we are trying to optimize. Our eventual goal is to introduce a simulation of electromechanical devices into our evaluation functions. The initial populations are generated at random. The design candidates for subsequent generations are produced by user specified selection technique. Crossovers are applied by using cut and splice operators at the random points of the chromosomes; random mutations are applied to modify the graph with a certain low probability. This cycle will continue until a suitable design is found. The research contributions in this work include the development of a new GA encoding scheme for mechanical assemblies (Legos), as well as the creation of selection criteria for this domain. We believe that this research creates a foundation for future work and it will apply GA techniques to the evolution of more complex and realistic electromechanical structures.
Increasing the Lifetime of Mobile WSNs via Dynamic Optimization of Sensor Node Communication Activity

In this paper, a simple and flexible method for increasing the lifetime of fixed or mobile wireless sensor networks is proposed. Based on past residual energy information reported by the sensor nodes, the sink node or another central node dynamically optimizes the communication activity levels of the sensor nodes to save energy without sacrificing the data throughput. The activity levels are defined to represent portions of time or time-frequency slots in a frame, during which the sensor nodes are scheduled to communicate with the sink node to report sensory measurements. Besides node mobility, it is considered that sensors’ batteries may be recharged via a wireless power transmission or equivalent energy harvesting scheme, bringing to the optimization problem an even more dynamic character. We report large increased lifetimes over the non-optimized network and comparable or even larger lifetime improvements with respect to an idealized greedy algorithm that uses both the real-time channel state and the residual energy information.