Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary ancestor inference via genome rearrangement

Inferring ancestral gene orders in a phylgenomic tree is an important topic in comparative genomics. In this thesis, three different approaches have been used to infer ancestors, first, using common intervals in a model-free approach and extending it to using common clusters and neighbourhood parameter; second, using double cut and join operation (DCJ); third, using breakpoint distance. A statistically fair comparison between the performance of DCJ and breakpoint criteria ends the thesis. Away from any assumptions or considerations, probabilistic or combinatorial, about specific processes involved in rearranging genomes, we present a new phylogenetic reconstruction method based solely on common intervals. The objective function to be optimized is simply the sum over the tree branches of the symmetric difference between the two sets of intervals associated with the genomes at the two ends of the branch. To achieve this goal, we use dynamic programming optimization to determine the presence of common intervals at the ancestral nodes of the phylogeny. Noticing the drawback that the concept of common intervals suffers from, we introduce the concept of generalized adjacency to find common clusters using a neighborhood parameter that turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. Again, we use dynamic programming optimization to determine the presence of individual edges at the ancestral nodes of the phylogeny. The DCJ (double cut and join) operation introduced by Yancopoulos et al. in 2005 is the most inclusive operation to date as it can generate all the movement rearrangements. One year later, Bergeron et al. restated the DCJ model and produced a simplified (linear) algorithm, which is now the most general existing algorithm to transform one genome into another using genome rearrangements events. Motivated by both, the most inclusive operation, DCJ, and its most general algorithm, we study the small phylogeny problem in the space of multichromosomal genomes under the DCJ metric. This is similar to the existing MGR (multiple genome rearrangements) approach, but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange.
EFFECTS OF PHOSPHORUS SUPPLY ON GROWTH, YIELD, AND YIELD COMPONENTS OF SAFFLOWER AND SUNFLOWER

This study comparatively evaluates the phosphorus (P) requirement of safflower (Carthamus tinctorius L.) and sunflower (Helianthus annuus L.) in view of identifying low input oil crops. Both species responded strongly to increasing P supply with respect to plant growth and yield. Yield component analysis revealed that oil yield in safflower was affected by P deficiency mainly via the number of capitula per plant followed, in consecutive order, by the number of achenes per capitulum and the single achene mass (SAM). The major yield component influencing oil yield of sunflower was the number of achenes per plant, followed by the SAM. Contribution of the seed oil concentration to overall yield variation was insignificant for both species. Path coefficient analyses indicate that in sunflower total nitrogen (N) accumulated was found to be most important, while in safflower this holds true for both the total P and N accumulated. It was concluded that safflower cannot be considered a low-input oil crop in terms of its P requirement.
Book reviews

Striving to De‐Exoticize Japanese Marriage Avoiders Beyond Common Sense: Sexuality and Gender in Contemporary Japan. By Wim Lunsing. London: Kegan Paul, 2001, 411 pages. Hardcover, $127.50. A Multicultural Feminist Perspective on Interpersonal Violence Against Lesbians and Gay Men The Spectacle of Violence: Homophobia, Gender, and Knowledge. By Gail Mason. London: Routledge, 2002, 170 pages. Paper, $22.95.
Bounds and algorithms for graph trusses

The $k$-truss, introduced by Cohen (2005), is a graph where every edge is incident to at least $k$ triangles. This is a relaxation of the clique. It has proved to be a useful tool in identifying cohesive subnetworks in a variety of real-world graphs. Despite its simplicity and its utility, the combinatorial and algorithmic aspects of trusses have not been thoroughly explored. We provide nearly-tight bounds on the edge counts of $k$-trusses. We also give two improved algorithms for finding trusses in large-scale graphs. First, we present a simplified and faster algorithm, based on approach discussed in Wang & Cheng (2012). Second, we present a theoretical algorithm based on fast matrix multiplication; this converts a triangle-generation algorithm of Bjorklund et al. (2014) into a dynamic data structure.
Going East: How Media Companies Successfully Enter the Eastern European Radio Market: A Case of Hungary

Expansion into Eastern European and Central European markets has begun in the media sector. Above all, US, English, French, and German companies are active in the radio sector in the East. Nevertheless, the Hungarian example shows that market entry does not always run smoothly and that economic success is by no means a given. This study investigates the factors for a successful entry into the Hungarian radio market for western investors. Findings include the selection of a low capital and low risk market entry strategy with a local partner, exact research into and incorporation of the peculiarities of the Hungarian radio market, clear content positioning in order to be clearly noticed in the highly competitive Budapest radio market, localization of the product, entry into partnerships to consolidate the market as well as finding a suitable strategy for dealing with the media regulatory body Országos Rádío És Televízió Testület [ORTT].
Relationship between Tobacco and Human Immunodeficiency Virus Infection: A Review

It is expected that the adverse effects of tobacco use is associated with more adverse health outcomes. Nicotine dependency and depression are hurdles to tobacco cessation among adolescents and adult smokers. Epigenetic changes lead to depression, schizophrenia and drug addiction. Increase in pain in any form, increases tobacco abuse. The issues faced by males and females and their causes leading to addictions are not always the same. Hence gender based interventions are needed. Counseling for tobacco cessation is imperative for such patients. There is a lack of such a session in the Indian centers where Anti Retroviral Therapy drugs or testing is carried out. Health education is very essential to achieve the desired results. Rather than a simple curative procedure, there is a need to have an “inclusive approach” towards tobacco cessation programmes, with main focus on the rural and the illiterate population. This review highlights a few of the reasons related to tobacco abuse among the Human Immunodeficiency Virus infected patients and the role that a dentist can play in tobacco cessation for these patients.
Evaluation of an authentic bi-directional promoter in a new transfer vector for generating LSDV recombinants

Lumpy skin disease virus (LSOV), a member of the Capripoxvirus genus, is one of the poxviruses currently being investigated as a live recombinant system for expressing foreign genes. The strict tropism of the virus, limited to ungulates, renders it very promising as a vector for veterinary vaccine purposes. Poxvirus recombinants are generated by a process of homologous recombination, mediated by using specific transfer vectors. In this study a new transfer vector pHSWF was evaluated for its ability to generate stable LSOV recombinants that would express foreign genes from an authentic bi-directional LSOV promoter. A reporter gene, the E. coli LacZ-gene encoding the p-galactosidase (p-gal) enzyme, was used in initial studies. It was placed under control of either the early or the late promoter by constructing two different transfer plasm ids pHSWFILacE and pHSWFILacL. These were used to generate LSOVILacE and LSOVILacL recombinants in fetal bovine testis (FBT) cells. Southern blot analysis confirmed that the LacZ-gene was stably integrated into an intergenic region of the LSOV genome. Expression of the LacZ-gene from both the early and late promoters was confirmed by monitoring the p-gal enzyme activity in infected cells. Similar intensities of blue stained foci , indicative of p-gal activity, was observed in FBT-cells infected with the respective recombinants. This suggested that similar high levels of expression were induced by both the early and the late promoters. The results on the LacZ recombinants confirmed that the new transfer vector may indeed be used to generate stable recombinants and that foreign genes are expressed at high levels. The transfer vector was then used to generate LSOV recombinants that express an immunological important gene, the VP7 gene of AHSV from the LSOV early promoter. The VP7 protein encodes the major group-specific antigen of AHSV and is a possible candidate for use in recombinant vaccines. Expression of the VP7 protein in the recombinant LSOV system was confirmed by SOS-PAGE analysis and radioactive labelling of proteins in infected cells. Characteristically, high levels of VP7 expression leads to its assembly in flat hexagonal crystals in infected cells . This property was analysed by cryoelectron microscopy. Crystal formation was indeed observed, confirming
Sudden Intraoperative Hyperkalemia during Laparoscopic Radical Nephrectomy in a Patient with Underlying Renal Insufficiency

We experienced a case of severe intraoperative hyperkalemia during laparoscopic radical nephrectomy in a 60-year-old male patient with renal insufficiency, whose hypertension had been managed by preoperative angiotensin II receptor blocker (ARB) and adrenergic beta-antagonist. After renal vessel ligation, his intraoperative potassium concentration suddenly increased to 7.0 mEq/L, but his electrocardiography (ECG) did not show any significant change. While preoperative ARB therapy has been regarded as a contributing factor for further aggravation of underlying renal insufficiency, we assumed that nephrectomy itself and rhabdomyolysis caused by surgical trauma also aggravated the underlying renal dysfunction and resulted in sudden hyperkalemia. Hyperkalemia was managed successfully with calcium gluconate, insulin, furosemide and crystalloid loading during the intraoperative and immediate postoperative periods, and potassium concentration decreased to 5.0 mEq/L at 8 hours after the operation. The patient’s hospital course was uncomplicated, but his renal function deteriorated further.
Multiple Viewpoint Systems: Time Complexity and the Construction of Domains for Complex Musical Viewpoints in the Harmonization Problem

Abstract We discuss the problem of automatic four-part harmonization: given a soprano part, add alto, tenor and bass in accordance with the compositional practices of a particular musical era. In particular, we focus on the development of representational and modelling techniques, within the framework of multiple viewpoint systems and Prediction by Partial Match (PPM), for the creation of statistical models of four-part harmony by machine learning. Our ultimate goal is to create better models, according to the information theoretic measure cross-entropy, than have yet been produced. We use multiple viewpoint because of their ability to represent both surface and underlying musical structure, and because they have already been successfully applied to melodic modelling. To allow for the complexities of harmony, however, the framework must be extended; for example, we begin by predicting complete chords, and then extend the framework to allow part by part prediction. As the framework is extended and generalized, the viewpoints become more complex. This article discusses matters related to viewpoint domains (alphabets), such as their size and consequent effect on run time; and presents methods for their reliable construction. We also present an empirical analysis of the time complexity of our computer implementation.
Noise Reduction Headphones and Autism: A Single Case Study

The purpose of this single-subject study was to investigate whether decreasing auditory sensation with the use of noise reduction headphones would impact attention to task in a child with auditory defensiveness. An A–B–B–A design was employed for 10 sessions using duration of attention to task as an index of behavior. In addition, classroom ambient sound levels were recorded. Visual analysis of the data was conducted by graphing baseline compared with intervention phases of task attention. Results showed ambient sound levels at or above recommended levels for an occupied classroom. Within this auditory environment, the participant demonstrated longer and more consistent attention to task with the use of the headphones. The results provide documented evidence for the use of noise reduction headphones for task attention.
Importance of Cognitive Screening and Management in Multiple Sclerosis Care—Reflection on the Recent Recommendations

Support: No funding was received in the publication of this article. The importance of recognizing and including cognition as a key factor to consider when ensuring comprehensive care for individuals with multiple sclerosis (MS) cannot be over emphasized. Unfortunately, despite it being accepted as a common symptom, cognitive function in MS is still not openly discussed, routinely assessed, or optimally treated. In an expert interview, Rosalind Kalb describes the background and crucial recent steps taken to tackle this issue, starting with a convening of the National MS Society’s National Medical Advisory Committee and leading to published recommendations for cognitive screening and management in MS care.
Preface

Selective breeding has generated an amazing array of plant varieties suited to production of food and fiber for humans. Over millennia, crop varieties have been a target for exploitation by a host of opportunists that have also found the fruits of this labor to be an attractive food source. These ‘pest’ organisms have been an antagonistic force in the struggle to raise crop productivity. Pest control has been among the many innovations that have sustained continual increases in crop productivity including irrigation, fertilizers and advanced breeding programs. While the term pesticide invokes for many the concept of a broadly toxic, synthetic chemical, the Gram-positive bacterium Bacillus thuringiensis (Bt) serves as a striking counterexample. This work seeks to illustrate the impact of Bt on pest control technology, and some of the related issues that surround its use. Development, use, and management of Bt derived technologies are covered in this set of papers, through a series of reviews and original research articles. Deployment of genetically engineered crops has been challenged by many health, economic, environmental, and social concerns. Many of these concerns, but not all, can be addressed with the material presented here. Since its discovery about a century ago, Bt has developed into an important tool for pest control. Unlike many synthetic chemicals, Bt’s mechanism of insecticidal activity is highly specific. Certain strains of the bacterium, and the associated insecticidal crystal proteins (ICPs), are effective against only certain insects. Typically the range of activity for any single Bt isolate is restricted to one of the orders Lepidoptera
Epidemiology of vector-borne diseases in cattle from SE Uganda.

Vector-borne diseases, (VBD), are amongst the most important constraints to animal production in tropical and sub-tropical regions of the world, including sub-Saharan Africa, (SSA). Losses due to these diseases are estimated to be up to 25% of the region's annual livestock production total. Some of the diseases are also zoonotic and therefore contribute to human health problems. The most important VBD are caused by the protozoa: Anaplasma, Cowdria, Babesia, Theileria and Trypanosoma parasites. Anaplasma, Cowdria, Babesia and Theileria are transmitted by ticks while trypanosomes are transmitted by tsetse flies in humans and animals in Africa. Control of these diseases in SSA is non-sustainable, mainly because of ineffective disease surveillance, poor diagnostic capacity and inadequate control measures largely due to economic constraints of the affected governments. Two of the most commonly used diagnostic methods, microscopy and molecular techniques for pathogen detection and species characterization, were evaluated for their sensitivity and specificity. The results showed that the two techniques have very low diagnostic agreement in detecting all the three species of trypanosomes, (kappa values < 0.02). The sensitivity of PCR amplification in detecting trypanosomes in cattle blood was found to be 5-10 times higher than microscopy. The specificity ofmicroscopy was found to be poor, in relation to PCR amplification as it mis-diagnosed many cases as having T. vivax while PCR showed that they were T. brucei. The study showed that Theileria species were more prevalent in Tororo than in Busia (60% vs. 38%). Molecular based methods revealed that Theileria mutans was the predominant species in cattle, at 42% prevalence while the overall prevalence of Theileria species was found to be 66% in Tororo district. The prevalence of trypanosome species was found to be 10 times higher than previously recorded in this region. The study revealed that isometamidium chloride (Samorin) treatment of cattle did not protect the animals from infection with any of the three trypanosome species for more than three months. While Samorin treatment appeared to control trypanosomiasis in areas with low prevalence, the drug had no effect in controlling the disease in high prevalence areas. It would therefore be necessary to combine the use of drug intervention with other methods such as vector control, to reduce the prevalence, in order to realize effective control of trypanosomiasis. The results further show that Samorin treatment did not offer protection against T. brucei
Perceived Premarital Counseling Outcomes Among Recently Married Army Personnel

Data from 1,285 recently married soldiers who participated in the 1989 Army Family Research Program survey indicated that pre-marital counseling by itself had little effect on subsequent marital satisfaction. However, those who had premarital counseling were more likely to use marital and family therapy services, at both sub-clinical and clinical levels of distress, than others who had not had such counseling before marriage.
Ostracism

Abstract The literature suggests that ostracism coerces conformity to group norms: It maintains the stability, cohesion and safety of the group, and therefore helps maintain the smooth functioning of a group. To this end, a wide range of punishing behaviours may first be employed but if these are not successful, the individual may be permanently excluded. Therefore a person may be the subject of ostracism even if not excluded from the group: Where the punishing behaviours of the group persuade an individual to change their behaviour, the process will have served its function and will cease. The possibility that some bullying at school may be the result of this process emerged during the qualitative analysis of retrospective accounts from adults who are deaf. This resulted in a review of the relevant literature and a set of codes which were employed to reanalyse the data. The findings suggest that some bullying in groups can indeed be understood as ostracism.
Abstracts of papers and posters presented at the 2001 Annual Conference of the Society for Reproductive and Infant Psychology

The aim of this study is to identify patterns of thinking with regard to childcare for the under 2 year olds, amongst mothers. 40 women in two towns of similar demography in the Netherlands and England were interviewed, using a semi-structured interview. The discourse analysis method was used for the transcripts. Three ideologies were identified, namely "the ideology of the Good Mother" , " what the young child Needs" and "the ideology of Female Employment in this day and age" . Each of the ideologies comprised of 3 to 4 dilemmas mothers are faced with when deciding about childcare, like 'Mother’s Needs versus Child’s Needs’. Dutch mothers seemed to think that it is better to start using childcare when the child is as young as possible, whilst the English mothers thought the opposite. These dilemmas can be seen as part of a wider conflict of women’s (and child’s) needs.
BOOK REVIEWS

Abstract WHY PEOPLE DIE BY SUICIDE. Thomas Joiner. Cambridge, MA: Harvard University Press (2005), 276 pages. ISBN: 0-674-1901-6. List Price: $24.96. Hardcover. Reviewed by Ameda A. Manetta. MORE THAN A PARTING PRAYER: LESSONS IN CARE-GIVING FOR THE DYING. William H. Griffith. Valley Forge, PA: Judson Press (2004), 157 pages. ISBN: 0-8170-1480-2. List Price: $12.00. Paperback. Reviewed by Deana F. Morrow. GRIEF AND LOSS: THEORIES AND SKILLS FOR HELPING PROFESSIONALS. Katherine Walsh-Burke. Boston, MA: Pearson/Allyn and Bacon (2006), 144 pages. ISBN: 0-205-3881-2. List Price: $33.40. Paperback. Reviewed by Patrick Shannon.
Video Summaries for Science Talks

We generate video summaries for science talks by illustrating the main topics addressed in a physics lecture through the use of scientific documentaries. We drive content selection by the text stream. As such, we use a summarized transcript of a physics lecture to select topic-related content from a collection of documentaries. The issue of coherence is addressed as a consequence of the content selection process, as well as by means of video composition techniques via content organization. We conducted a preliminary study intended to assess the behavior of films and documentaries in summarization. Documentaries achieve higher performance in comparison to films, comparing the generated summaries against abstracts using the ROUGE metrics. For science talks videos, our results concern data from human subjective judgments. Video composition performed using ranking achieves higher ratings than simplicial curves for retaining the topics of the original document and overall quality. We show that none of the composition techniques actually addresses coherence, as perceived by the viewers.