Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Topology of Genetic Algorithms

Genetic algorithms are stochastic search heuristics which are popular for their broad applicability, especially in combinatorial search problems. The search mechanism relies on an abstraction of genetic evolution and selection as seen in nature. This paper introduces a topological structure for the search space which is consistent with existing theory and practice for genetic algorithms, namely forma analysis. A notion of convexity is defined within this context and connections between this definition and forma analysis are established. This framework provides an alternative perspective on the exploitation/exploration dilemma as well as population convergence, which relates directly to the genetic operators employed to drive the evolution process. It also provides a different interpretation of design constraints associated with genetic algorithm implementations. The intention is to provide a new analytical perspective for genetic algorithms, and to establish a connection with exact search methods through the concept of convexity.
Characterization of a WaaF (RfaF) Homolog Expressed by Haemophilus ducreyi

ABSTRACT Haemophilus ducreyi lipooligosaccharide (LOS) is capable of inducing an inflammatory response in skin (A. A. Campagnari, L. M. Wild, G. Griffiths, R. J. Karalus, M. A. Wirth, and S. M. Spinola, Infect. Immun. 59:2601–2608, 1991) and likely contributes to the virulence of this sexually transmitted pathogen (B. A. Bauer, M. K. Stevens, and E. J. Hansen, Infect. Immun. 68:4290–4298, 1998). An open reading frame in H. ducreyi 35000 was found to encode a predicted protein that was 59% identical to the protein product of the rfaF(waaF) gene of Salmonella typhimurium. TheH. ducreyi waaF gene was able to complement an S. typhimurium rfaF (waaF) mutant, a result which confirmed the identity of this gene. In contrast to therfaF (waaF) gene of enteric bacteria, theH. ducreyi waaF gene was not located adjacent to other genes involved in lipopolysaccharide expression. Inactivation of theH. ducreyi waaF gene by insertion mutagenesis resulted in expression of a LOS that migrated much faster than wild-type LOS in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The LOS of this mutant also did not bind a monoclonal antibody directed against a cell surface-exposed epitope of wild-type H. ducreyi LOS. Testing of the wild-type H. ducreyi strain and its isogenicwaaF mutant in the temperature-dependent rabbit model for dermal lesion production by H. ducreyi revealed that thiswaaF mutant was less virulent than the wild-type parent strain. Complementation of the H. ducreyi waaF mutant with the wild-type H. ducreyi waaF gene resulted in expression of both wild-type LOS and wild-type virulence by this mutant.
Red meat consumption and cancer: Reasons to suspect involvement of bovine infectious factors in colorectal cancer

An increased risk for colorectal cancer has been consistently reported for long‐time consumption of cooked and processed red meat. This has frequently been attributed to chemical carcinogens arising during the cooking process of meat. Long‐time fish or poultry consumption apparently does not increase the risk, although similar or higher concentrations of chemical carcinogens were recorded in their preparation for consumption. The geographic epidemiology of colorectal cancer seems to correspond to regions with a high rate of beef consumption. Countries with a virtual absence of beef in the diet (India) or where preferably lamb or goat meat is consumed (several Arabic countries) reveal low rates of colorectal cancer. In China, pork consumption has a long tradition, with an intermediate colorectal cancer rate. In Japan and Korea, large scale beef and pork imports started after World War II or after the Korean War. A steep rise in colorectal cancer incidence was noted after 1970 in Japan and 1990 in Korea. The consumption of undercooked beef (e.g., shabu‐shabu, Korean yukhoe and Japanese yukke) became very popular in both countries. The available data are compatible with the interpretation that a specific beef factor, suspected to be one or more thermoresistant potentially oncogenic bovine viruses (e.g., polyoma‐, papilloma‐ or possibly single‐stranded DNA viruses) may contaminate beef preparations and lead to latent infections in the colorectal tract. Preceding, concomitant or subsequent exposure to chemical carcinogens arising during cooking procedures should result in increased risk for colorectal cancer synergistic with these infections.
Stochastic cross-layer resource allocation for wireless networks using orthogonal access: Optimality and delay analysis

Efficient design of wireless networks requires implementation of cross-layer algorithms that exploit channel state information. Capitalizing on convex optimization and stochastic approximation tools, this paper develops a stochastic algorithm that allocates resources at network, link, and physical layers so that a sum-utility of the average end-to-end rates is maximized. Focus is placed on networks where interference is strong and nodes transmit orthogonally over a set of parallel channels. Convergence of the developed stochastic schemes is characterized, and the average queue delays are obtained in closed form.
Conduction Failure following Spinal Cord Injury: Functional and Anatomical Changes from Acute to Chronic Stages

In the majority of spinal cord injuries (SCIs), some axonal projections remain intact. We examined the functional status of these surviving axons since they represent a prime therapeutic target. Using a novel electrophysiological preparation, adapted from techniques used to study primary demyelination, we quantified conduction failure across a SCI and studied conduction changes over time in adult rats with a moderate severity spinal contusion (150 kdyn; Infinite Horizon impactor). By recording antidromically activated single units from teased dorsal root filaments, we demonstrate complete conduction block in ascending dorsal column axons acutely (1–7 d) after injury, followed by a period of restored conduction over the subacute phase (2–4 weeks), with no further improvements in conduction at chronic stages (3–6 months). By cooling the lesion site, additional conducting fibers could be recruited, thus revealing a population of axons that are viable but unable to conduct under normal physiological conditions. Importantly, this phenomenon is still apparent at the most chronic (6 month) time point. The time course of conduction changes corresponded with changes in behavioral function, and ultrastructural analysis of dorsal column axons revealed extensive demyelination during the period of conduction block, followed by progressive remyelination. A proportion of dorsal column axons remained chronically demyelinated, suggesting that these are the axons recruited with the cooling paradigm. Thus, using a clinically relevant SCI model, we have identified a population of axons present at chronic injury stages that are intact but fail to conduct and are therefore a prime target for therapeutic strategies to restore function.
Enabling Knowledge Management of Organizational Memory for groups through shared topic Maps

Managers are challenged to deal with ever increasing and interconnected web of knowledge and information. Competing for attention in an information rich environment requires the use of efficient mechanisms to abstract the underlying knowledge extracted from collaborative tasks and myriad sources. Moreover, building capabilities to access and reuse the knowledge is also important. The recent push toward service oriented architectures and enabling technologies have refocused attention on knowledge management and organizational memory. Managers and users rely on a variety of information and knowledge from many sources. Their ability to access, use, and repurpose the knowledge is critical, especially when decisions are made at the group and organizational level. Topic maps based systems provide a vehicle to carry out a solution. At group levels, the topic map supports dynamic changes to the structure through collaborative search and modification capabilities. We present a model of a topic map based system that uses these theories and illustrate its use by way of supporting a group search implementation. A prototype of the model is briefly discussed.
Internal thyroid doses to Fukushima residents—estimation and issues remaining

Enormous quantities of radionuclides were released into the environment following the disastrous accident at the Fukushima Daiichi Nuclear Power Plant (FDNPP) in March 2011. It is of great importance to determine the exposure doses received by the populations living in the radiologically affected areas; however, there has been significant difficulty in estimating the internal thyroid dose received through the intake of short-lived radionuclides (mainly, 131I), because of the lack of early measurements on people. An estimation by the National Institute of Radiological Sciences for 1 April 2012 to 31 March 2013 was thus performed using a combination of the following three sources: thyroid measurement data (131I) for 1080 children examined in the screening campaign, whole-body counter measurement data (134Cs, 137Cs) for 3000 adults, and atmospheric transport dispersion model simulations. In this study, the residents of Futaba town, Iitate village and Iwaki city were shown to have the highest thyroid equivalent dose, and their doses were estimated to be mostly below 30 mSv. However, this result involved a lot of uncertainties and provided only representative values for the residents. The present paper outlines a more recent dose estimation and preliminary analyses of personal behavior data used in the new method.
TACAGCTGGTCC ATCTYCGGTGTWACACCATC CCTYTDTCWGG TTRCHGGRTCTTGWTAAGAG ARGAGGAYGAGG GGYTGAATACAAGCTTCAAGGCC AGAYGCTAAYTGGC GRAASASCAWATAMAGCCAATTCC ATTTTRYTYGTCDTG ACACTACCYCTACAATAGCTGTC HAATGGTGTTAGGC TTAGTAACTAAWTTRTCTGGTKGCAC AGTTRCCTARTGC CTGACTTTGCAATRTTGGCRGC TWACACAGCAAG ACATCATCAAAGGCTCGCTTTAC 

Article history: Received 29 March 2017 Received in revised form 5 May 2017 Accepted 7 May 2017 Available online 08 May 2017 Avian infectious bronchitis virus (IBV) is highly prevalent in chicken populations and is responsible for severe economic losses to poultry industry worldwide. In this study, we report the complete genome sequences of two IBV field strains, CU/1/2014 and CU/4/2014, isolated from vaccinated chickens in Egypt in 2014. The genome lengths of the strains CU/1/2014 and CU/4/2014 were 27,615 and 27,637 nucleotides, respectively. Both strains have a common genome organization in the order of 5′-UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-UTRpoly(A) tail-3′. Interestingly, strain CU/1/2014 showed a novel 15-nt deletion in the 4b-4c gene junction region. Phylogenetic analysis of the full S1 genes showed that the strains CU/1/2014 and CU/4/2014 belonged to IBV genotypes GI-1 lineage andGI-23 lineage, respectively. The genome of strain CU/1/2014 is closely related to vaccine strain H120 but showed genome-wide point mutations that lead to 27, 14, 11, 1, 1, 2, 2, and 2 amino acid differences between the two strains in 1a, 1b, S, 3a, M, 4b, 4c, and N proteins, respectively, suggesting that strain CU/1/ 2014 is probably a revertant of the vaccine strain H120 and evolved by accumulation of pointmutations. Recombination analysis of strain CU/4/2014 showed evidence for recombination fromat least three different IBV strains, namely, the Italian strain 90254/2005 (QX-like strain), 4/91, andH120. These results indicate the continuing evolution of IBV field strains by genetic drift and by genetic recombination leading to outbreaks in the vaccinated chicken populations in Egypt. © 2017 Published by Elsevier B.V.
Representations of the Deformed U(su(2)) and U(osp(1,2)) Algebras

The polynomial deformations of the Witten extensions of the U(su(2)) and U(osp(1,2)) algebras are three generator algebras with normal ordering, admitting a two generator subalgebra. The modules and the representations of these algebras are based on the construction of Verma modules, which are quotient modules, generated by ideals of the original algebra. This construction unifies a large number of the known algebras under the same scheme. The finite dimensional representations show new features such as the multiplicity of representations of the same dimensionality, or the existence of finite dimensional representations only for some dimensions.
The Nocebo Effect on the Web: An Analysis of Fake Anti-Virus Distribution

We present a study of Fake Anti-Virus attacks on the web. Fake AV software masquerades as a legitimate security product with the goal of deceiving victims into paying registration fees to seemingly remove malware from their computers. Our analysis of 240 million web pages collected by Google's malware detection infrastructure over a 13 month period discovered over 11,000 domains involved in Fake AV distribution. We show that the Fake AV threat is rising in prevalence, both absolutely, and relative to other forms of web-based malware. Fake AV currently accounts for 15% of all malware we detect on the web. Our investigation reveals several characteristics that distinguish Fake AVs from other forms of web-based malware and shows how these characteristics have changed over time. For instance, Fake AV attacks occur frequently via web sites likely to reach more users including spam web sites and on-line Ads. These attacks account for 60% of the malware discovered on domains that include trending keywords. As of this writing, Fake AV is responsible for 50% of all malware delivered via Ads, which represents a fivefold increase from just a year ago.
Does self-management education benefit all populations with arthritis? A randomized controlled trial in a primary care physician network.

OBJECTIVE Studies have suggested that the Arthritis Self-Management Program (ASMP) course is effective at reducing arthritis pain and health care costs in volunteer participants. There have been no reports of trials of the ASMP in the context of primary care physicians' practices, where the potential for spreading the program may be greatest. We conducted a randomized controlled trial of the ASMP course in a large primary care physician network. METHODS Patients with osteoarthritis, rheumatoid arthritis, or fibromyalgia were recruited for the study. Subjects in the intervention practices received the 6 week course and those in the control practices received only the ASMP book, without course. Disability, pain, self-efficacy, mental health, and satisfaction were measured using validated instruments at baseline and at 4 months. RESULTS One hundred thirteen patients were recruited for the ASMP course (intervention) and completed baseline and 4 month followup questionnaires. Eighty-four percent completed at least 4 of 6 classes. Seventy-four patients received the ASMP manual (controls) and completed both questionnaires. Patients in the intervention and control groups had similar baseline pain (p = 0.94), self-efficacy to control pain (p = 0.90), mental health (p = 0.10), and vitality scores (p = 0.21), but those in the intervention arm had slightly less disability (p = 0.04). At 4 months, there was no significant improvement from baseline in any endpoint and no difference between patients in the intervention and control groups (all p > 0.2). Patient satisfaction with arthritis care and outcomes was no different for intervention and control patients (all p > 0.3). All types of health care resource use were similar at baseline and followup for both intervention and control groups (all p > 0.2). CONCLUSION While the ASMP course has been found to be effective in other patient groups, there were no significant clinical benefits noted at 4 months in patients recruited from primary care practices.
Socially transmitted gut microbiota protect bumble bees against an intestinal parasite

Populations of important pollinators, such as bumble bees and honey bees, are declining at alarming rates worldwide. Parasites are likely contributing to this phenomenon. A distinct resident community of bacteria has recently been identified in bumble bees and honey bees that is not shared with related solitary bee species. We now show that the presence of these microbiota protects bee hosts against a widespread and highly virulent natural parasite (Crithidia bombi) in an experimental setting. We add further support to this antagonistic relationship from patterns found in field data. For the successful establishment of these microbiota and a protective effect, exposure to feces from nest mates was needed after pupal eclosion. Transmission of beneficial gut bacteria could therefore represent an important benefit of sociality. Our results stress the importance of considering the host microbiota as an “extended immune phenotype” in addition to the host immune system itself and provide a unique perspective to understanding bees in health and disease.
Quality Assessment of Color Images Based on DSF in MPEG-21

A new method to evaluate the quality of color images is proposed in this paper, i.e. DSF (definition, error sensitivity and objective fidelity), which would combine the definition, error sensitivity and objective fidelity through utilizing the vision properties of human eyes and redundant color information fully. For the existence of color redundancy and structural similarity between three different frames, the definition of color images would be evaluated by the way based on 3D SIT (submatrix integration transform), in which three color components of color image is integrated into one model and color redundancy can be exploited well. The experimental results show that the assessment method is very effective and can give the objective evaluation relatively in accord with vision properties
Lung Cancer Detectability by Test, Histology, Stage, and Gender: Estimates from the NLST and the PLCO Trials

Background: Implementing optimal lung cancer screening programs requires knowledge of the natural history and detectability of lung cancer. This information can be derived from the results of clinical trials with the aid of microsimulation models. Methods: Data from the Surveillance, Epidemiology, and End Results (SEER) program and individual-level data from the National Lung Screening Trial (NLST) and the Prostate, Lung, Colon, and Ovarian Cancer Screening trial (PLCO) were used to investigate the sensitivity (by histology and stage) of CT and chest radiography (CXR) and the mean preclinical sojourn time (MPST) of lung cancer (by gender, histology, and stage). The MISCAN-Lung model was used to reproduce the lung cancer incidence by method of detection (clinically or screen-detected), gender, histology, and stage in both trials and SEER, by calibrating CT and CXR sensitivity and natural history parameters. Results: CT sensitivity ranges from 8.83% to 99.35% and CXR sensitivity from 2.51% to 97.31%, depending on histology and stage. CT sensitivity for stage IA is more than 3-fold higher compared with CXR, for all histologies. The total MPST estimates for lung cancer progressing through preclinical stages IA to IV range from 3.09 to 5.32 years for men and 3.35 to 6.01 years for women. The largest difference in total MPST between genders was estimated for adenocarcinoma. Conclusions: We estimate longer MPSTs for lung cancer compared with previous research, suggesting a greater window of opportunity for lung cancer screening. Impact: This study provides detailed insights into the natural history of lung cancer and CT screening effectiveness. Cancer Epidemiol Biomarkers Prev; 24(1); 154–61. ©2014 AACR.
Craniofacial morphometric analysis of individuals with X-linked hypohidrotic ectodermal dysplasia

Hypohidrotic ectodermal dysplasia (HED) is the most prevalent type of ectodermal dysplasia (ED). ED is an umbrella term for a group of syndromes characterized by missing or malformed ectodermal structures, including skin, hair, sweat glands, and teeth. The X‐linked recessive (XL), autosomal recessive (AR), and autosomal dominant (AD) types of HED are caused by mutations in the genes encoding ectodysplasin (EDA1), EDA receptor (EDAR), or EDAR‐associated death domain (EDARADD). Patients with HED have a distinctive facial appearance, yet a quantitative analysis of the HED craniofacial phenotype using advanced three‐dimensional (3D) technologies has not been reported. In this study, we characterized craniofacial morphology in subjects with X‐linked hypohidrotic ectodermal dysplasia (XLHED) by use of 3D imaging and geometric morphometrics (GM), a technique that uses defined landmarks to quantify size and shape in complex craniofacial morphologies. We found that the XLHED craniofacial phenotype differed significantly from controls. Patients had a smaller and shorter face with a proportionally longer chin and midface, prominent midfacial hypoplasia, a more protrusive chin and mandible, a narrower and more pointed nose, shorter philtrum, a narrower mouth, and a fuller and more rounded lower lip. Our findings refine the phenotype of XLHED and may be useful both for clinical diagnosis of XLHED and to extend understanding of the role of EDA in craniofacial development.
Anaesthetic management in a child with an atypical triad for reconstructive scoliosis surgery

Scoliosis may be of varied aetiology and may be associated with severe congenital anomalies. It often poses a challenge in its anaesthetic management. We present anaesthetic management of a child who underwent scoliosis reconstruction with a rare triad of cerebral palsy, glucose-6-phosphate dehydrogenase deficiency and severe mitral regurgitation. Anaesthetic management in these patients should focus primarily on associated co-morbidities and congenital anomalies affecting the course of the perioperative management and thereafter comprehensive pre-operative strategies must be executed to enhance the safety profile during the surgery.
A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4

Early prediction of xenobiotic metabolism is essential for drug discovery and development. As the most important human drug-metabolizing enzyme, cytochrome P450 3A4 has a large active cavity and metabolizes a broad spectrum of substrates. The poor substrate specificity of CYP3A4 makes it a huge challenge to predict the metabolic site(s) on its substrates. This study aimed to develop a mechanism-based prediction model based on two key parameters, including the binding conformation and the reaction activity of ligands, which could reveal the process of real metabolic reaction(s) and the site(s) of modification. The newly established model was applied to predict the metabolic site(s) of steroids; a class of CYP3A4-preferred substrates. 38 steroids and 12 non-steroids were randomly divided into training and test sets. Two major metabolic reactions, including aliphatic hydroxylation and N-dealkylation, were involved in this study. At least one of the top three predicted metabolic sites was validated by the experimental data. The overall accuracy for the training and test were 82.14% and 86.36%, respectively. In summary, a mechanism-based prediction model was established for the first time, which could be used to predict the metabolic site(s) of CYP3A4 on steroids with high predictive accuracy.