Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

Loss of heterozygosity (LOH) and copy number alteration (CNA) feature prominently in the somatic genomic landscape of tumors. As such, karyotypic aberrations in cancer genomes have been studied extensively to discover novel oncogenes and tumor-suppressor genes. Advances in sequencing technology have enabled the cost-effective detection of tumor genome and transcriptome mutation events at single-base-pair resolution; however, computational methods for predicting segmental regions of LOH in this context are not yet fully explored. Consequently, whole transcriptome, nucleotide-level resolution analysis of monoallelic expression patterns associated with LOH has not yet been undertaken in cancer. We developed a novel approach for inference of LOH from paired tumor/normal sequence data and applied it to a cohort of 23 triple-negative breast cancer (TNBC) genomes. Following extensive benchmarking experiments, we describe the nucleotide-resolution landscape of LOH in TNBC and assess the consequent effect of LOH on the transcriptomes of these tumors using RNA-seq-derived measurements of allele-specific expression. We show that the majority of monoallelic expression in the transcriptomes of triple-negative breast cancer can be explained by genomic regions of LOH and establish an upper bound for monoallelic expression that may be explained by other tumor-specific modifications such as epigenetics or mutations. Monoallelically expressed genes associated with LOH reveal that cell cycle, homologous recombination and actin-cytoskeletal functions are putatively disrupted by LOH in TNBC. Finally, we show how inference of LOH can be used to interpret allele frequencies of somatic mutations and postulate on temporal ordering of mutations in the evolutionary history of these tumors.
A model for the lowering of plant ethylene concentrations by plant growth-promoting bacteria

It was previously shown that a number of plant growth promoting rhizobacteria contain an enzyme, 1-aminocyclopropane-1-carboxylate deaminase, that catalyses the cleavage of 1-aminocyclopropane-1-carboxylate, the immediate precursor of ethylene in plants. Moreover, experimental evidence indicated that the activity of this enzyme was the key factor in the ability of plant growth promoting rhizobacteria to stimulate the elongation of plant roots. In the model presented in this manuscript we address the question of how the bacterial enzyme 1-aminocyclopropane-1-carboxylate deaminase, with a low affinity for 1-aminocyclopropane-1-carboxylate, can effectively compete with the plant enzyme 1-aminocyclopropane-1-carboxylate oxidase, which has a high affinity for the same substrate, 1-aminocyclopropane-1-carboxylate, with the result that the plant's endogenous ethylene concentration is reduced. It is argued that the simplest explanation for the observed biological activity of plant growth promoting rhizobacteria relates to the relative amounts of 1-aminocyclopropane-1-carboxylate deaminase and 1-aminocyclopropane-1-carboxylate oxidase in the system under consideration. For plant growth promoting rhizobacteria to be able to lower plant ethylene levels, the 1-aminocyclopropane-1-carboxylate deaminase level should be at least 100- to 1000-fold greater then the 1-aminocyclopropane-1-carboxylate oxidase level. This is likely to be the case, provided that the expression of 1-aminocyclopropane-1-carboxylate oxidase has not been induced.Copyright 1998 Academic Press Limited Copyright 1998 Academic Press Limited
Can we Leave it to Chance? New Learning Technologies and the Problem of Professional Competence

This paper describes two different university and school collaborations featuring teachers’ and students’ use of online environments. The first example involves a classroom application of a Learning Management System (LMS) to deliver a Year 8 Studies of Society Unit on ‘Rainforests’. This example serves to capture, bracket and examine the ways in which teachers have begun to redefine teaching practice, and to document the ways in which students experience this change in teaching. The second example documents feedback from a formal hands-on professional development program for teachers where follow up support was offered on-line, using the same LMS. Data presented here suggest that the on-line environment is not a panacea for better teaching and learning outcomes. Example one identifies the means by which the on-line environment is able to stimulate effective learning exchange, yet signposts to the teacher the ways in which the emerging ICT classroom will challenge the technology, logistics, organisation and delivery competencies of many teachers. In example two, technology is painted as a catalyst to other elements of school reform. In both examples, the value of the on-line environment lies in its capacity to enable our collaborative knowledge about teaching and learning to interact so that each becomes a structuring, and constitutive resource for the other.
Roles de género e instituciones políticas: el caso de los ayuntamientos de la Comunidad Autónoma de Canarias

En este articulo examinamos la relacion entre los roles de genero tradicionales y las responsabilidades politicas de las mujeres en los gobiernos locales de las Islas Canarias (88 municipios). El principal objetivo es analizar la situacion de las politicas dentro de los gobiernos municipales, centrandonos en la division de los roles de poder (segregacion vertical) y de las diferentes areas de gobierno (segregacion horizontal). Planteamos que el acercamiento de los roles/estereotipos de genero puede explicar la situacion de las mujeres en la politica formal y las desigualdades que podemos observar en la administracion publica local. Este acercamiento se combina con la teoria del poder. En este sentido, un factor clave para explicar ese panorama tambien es el papel dominante de los hombres en las estructuras de poder tradicionales.
Effect of volume and pH on surface receptor number in macrophages

Incubation of rabbit alveolar macrophages in hypo‐osmotic solutions transiently increases cell volume and inhibits membrane internalization, resulting in an increase in surface receptor number. Since recent reports suggest that hypo‐osmotic treatment decreases intracellular pH, and that reduced pH inhibits receptor internalization, pH was measured in hypo‐osmotically treated macro‐phages. We found that cells incubated in iso‐osmotic solutions of pH less than 7.2 exhibited a decrease in intracellular pH upon exposure to hypo‐osmotic solutions, while cells in iso‐osmotic solutions of pH greater than 7.2 had an increase in pH upon exposure to hypo‐osmotic solutions. The relative increase in surface receptor number was unaffected by the initial pH or by the direction of change in pH. Incubation of cells in high K+/low Na+ hypotonic buffers induced a persistent increase in cell volume and surface receptor number. Cell volume and surface receptor number fell to baseline values after restoration of isotonicity by the addition of hypertonic sucrose. These manipulations had little effect on intracellular pH. We conclude that the inhibition of membrane internalization observed in cells exposed to hypo‐osmotic solutions is independent of changes in intracellular pH. The inhibition of internalization observed in this system may be due directly to forces produced as a consequence of cell swelling.
Growth-related differences in maximum laterotrusion and retrusion between children and adults.

OBJECTIVE To test the null hypothesis that there are no differences between children and adults in maximum laterotrusion and maximum retrusion on the right and left sides. MATERIALS AND METHODS This population-based study included 81 randomly selected children between the ages of 6 and 10 years and 67 adults. Kinematic variables were measured with the ultrasonic JMA-System for registration. RESULTS The mean maximum laterotrusion of the children's group (10.6 +/- 1.5 mm on the left, 11.0 +/- 1.7 mm on the right) was significantly smaller than that of the adult group (11.7 +/- 2.0 mm on the left, 12.2 +/- 1.7 mm on the right). The maximum laterotrusion of the children's group corresponded to about 90% on the left and right sides of that of the adult group. The mean maximum retrusion of the children's group was significantly bigger than that of the adult group. There, the adult values corresponded to 66.7% on the left and 50% on the right side of the children's values. No significant difference in maximum laterotrusion and retrusion was noted on the right and left sides, and no significant differences according to gender specificities were observed in either group. CONCLUSIONS The hypothesis is rejected. In development of the temporomandibular joint, maximum laterotrusion on the right and left sides increases significantly with age, and maximum retrusion decreases significantly with age.
Non-convex compressed sensing CT reconstruction based on tensor discrete Fourier slice theorem

X-ray computed tomography (CT) scanners provide clinical value through high resolution and fast imaging. However, achievement of higher signal-to-noise ratios generally requires emission of more X-rays, resulting in greater dose delivered to the body of the patient. This is of concern, as higher dose leads to greater risk of cancer, particularly for those exposed at a younger age. Therefore, it is desirable to achieve comparable scan quality while limiting X-ray dose. One means to achieve this compound goal is the use of compressed sensing (CS). A novel framework is presented to combine CS theory with X-ray CT. According to the tensor discrete Fourier slice theorem, the 1-D DFT of discrete Radon transform data is exactly mapped on a Cartesian 2-D DFT grid. The nonuniform random density sampling of Fourier coefficients is made feasible by uniformly sampling projection angles at random. Application of the non-convex CS model further reduces the sufficient number of measurements by enhancing sparsity. The numerical results show that, with limited projection data, the non-convex CS model significantly improves reconstruction performance over the convex model.
Serious fun in computer science

Computer Science has been in crisis for several years. Interest in studying it has dropped dramatically. We can wring our hands, or we can do something about it. Computer Science needs to engage with pure outreach: selling the subject (for free). Our approach has been to do this by just going out and having innovative fun. This is more effective than selling specific courses or institutions. CS is after all a naturally exciting, innovative and thought-provoking subject (Oh, and by the way there are good jobs at the end too). We see it as a Renaissance subject (so who cares what it's called or which variation the future depends on). It sits in a unique position, centrally connected to all of the sciences, arts and humanities. We are passionate about science generally, so we go out and spread that enthusiasm about it all. What have we been doing? There is cs4fn (www.cs4fn.org) a website and magazine that we've been writing for the sheer enjoyment of it; Sodarace (www.sodarace.net) where over 130 000 registered humans and computers compete in an online Olympics; Brain Academy (www.brainacademy.qmul.ac.uk), the Compute-Ability competition with career enhancing prizes; research talks for kids on Artificial Intelligence, women in technology, disability and mutant super-hero powers (actually its about search algorithms) and so on; a Computer Science Magic show (you have to promise not to tell anyone the secrets); and exhibits at the Royal Society Summer Exhibition on mathematical illusions and their link to computer science (www.cs4fn.org/illusions). We build brains that play Snap from rope and toilet roll, and introduce a piece of paper more intelligent than anyone in the room. Kids act out Turing Tests (can you tell the human from the robot? ), and we challenge them to solve puzzles with CS twists. We do real research too of course: a spin-out of our EPSRC funded research project on Human Error and Interactive Systems includes an online SpaceInvaders game-experiment (www.cs4fn.org/humanerror) the data from which helps us understand the causes of human error: can you consistently avoid making the mistake that will blow up your ship and lose all your points? What age group should we be targeting? Sixth formers? A major issue is that school ICT, vital as it is, gives a poor impression of how being a computer scientist is about being an innovative, creative, computational thinker. By the sixth form it is too late. It is the younger kids we have to get the message to. An early experiment has been teaching a version of a graduate level course on usability evaluation to primary school kids (www.cs4fn.org/manorside). They proved to be very innovative and "amazing", "will stay in my mind forever", "I want to teach others in the school what we did" were some of their comments. Our approach works: teachers, industry and the International Review of ICT have commended us & and we have seen an increase in undergraduate applications of over 130% in 2 years. Not bad when we are just having fun: serious fun.
Vegetarian diets and bone status 1-3

Osteoporosis is a common chronic condition associated with progressive loss of bone mineral density (BMD) and compromised bone strength, with increasing risk of fracture over time. Vegetarian diets have been shown to contain lower amounts of calcium, vitamin D, vitamin B-12, protein, and n–3 (v-3) fatty acids, all of which have important roles in maintaining bone health. Although zinc intakes are not necessarily lower quantitatively, they are considerably less bioavailable in vegetarian diets, which suggests the need for even higher intakes to maintain adequate status. At the same time, healthy vegetarian diets tend to contain more of several protective nutrients, including magnesium, potassium, vitamin K, and antioxidant and anti-inflammatory phytonutrients. On balance, there is evidence that vegetarians, and particularly vegans, may be at greater risk of lower BMD and fracture. Attention to potential shortfall nutrients through the careful selection of foods or fortified foods or the use of supplements can help ensure healthy bone status to reduce fracture risk in individuals who adhere to vegetarian diets. Am J Clin Nutr 2014;100(suppl):329S–35S.
A comparison between HMLP and HRBF for attitude control

The attitude control problem of a rigid body, such as a spacecraft, in three-dimensional space is approached by introducing two new control strategies developed in hypercomplex algebra. The proposed approaches are based on two parallel controllers both derived in quaternion algebra. The first one is a feedback controller of PD type, while the second is a feedforward controller, which is implemented either by means of a hypercomplex multilayer perceptron (HMLP) neural network or by means of a hypercomplex radial basis function (HRBF) neural network. Several simulations show the performance of the two approaches. The results are also compared with a classical PD controller and with an adaptive controller, showing the improvements due to the use of the neural networks, especially when an external disturbance acts on the rigid body.
Algorithm to solve a chance‐constrained network capacity design problem with stochastic demands and finite support

We consider the problem of determining the capacity to assign to each arc in a given network, subject to uncertainty in the supply and/or demand of each node. This design problem underlies many real‐world applications, such as the design of power transmission and telecommunications networks. We first consider the case where a set of supply/demand scenarios are provided, and we must determine the minimum‐cost set of arc capacities such that a feasible flow exists for each scenario. We briefly review existing theoretical approaches to solving this problem and explore implementation strategies to reduce run times. With this as a foundation, our primary focus is on a chance‐constrained version of the problem in which α% of the scenarios must be feasible under the chosen capacity, where α is a user‐defined parameter and the specific scenarios to be satisfied are not predetermined. We describe an algorithm which utilizes a separation routine for identifying violated cut‐sets which can solve the problem to optimality, and we present computational results. We also present a novel greedy algorithm, our primary contribution, which can be used to solve for a high quality heuristic solution. We present computational analysis to evaluate the performance of our proposed approaches. © 2016 Wiley Periodicals, Inc. Naval Research Logistics 63: 236–246, 2016
Cardiovascular and Splenic Responses to Exercise in Humans.

To investigate splenic erythrocyte volume after exercise and the effect on hematocrit- and hemoglobin-based plasma volume equations, nine men cycled at an intensity of 60% maximal O(2) uptake for 5-, 10-, or 15-min duration, followed by an incremental ride to exhaustion. The reduction in spleen volume, calculated using (99m)Tc-labeled erythrocytes, was not significantly different among the three submaximal rides (5 min = 28%, 10 min = 30%, 15 min = 36%; P = 0.26). The incremental ride to exhaustion resulted in a 56% reduction in spleen volume, which recovered to baseline levels within 20 min. Plasma catecholamines were inversely related to spleen volume after exercise (r = 0.70-0.84; P < 0.0001). There were no differences in red cell or total blood volume pre- to postexercise; however, a significant reduction in plasma volume was observed (18.9%; P < 0.01). There was no difference between the iodinated albumin and the hematocrit and hemoglobin methods of assessing plasma volume changes. These results suggest that the spleen regulates its volume in response to an intensity-dependent signal, and plasma catecholamines appear partially responsible. Splenic release of erythrocytes has no effect on indirect measures of plasma volume.
Trichomonas vaginalis infection and human immunodeficiency virus acquisition in African women.

BACKGROUND Trichomoniasis vaginalis is the most common nonviral sexually transmitted infection (STI) worldwide, with a particularly high prevalence in regions of human immunodeficiency virus (HIV) endemicity. However, its impact as a cofactor for HIV acquisition is poorly understood. METHODS Samples from 213 women who experienced HIV seroconversion (cases) during a longitudinal study involving 4450 women in Uganda and Zimbabwe were matched with samples from HIV-uninfected women (controls). All samples underwent polymerase chain reaction (PCR) analysis for Trichomonas vaginalis DNA. For cases, analyzed samples were from the visit in which HIV seroconversion was detected and the visit preceding detection of seroconversion; for controls, one analyzed sample was from the visit matched by follow-up duration to the cases' seroconversion visit, and the other sample was from the visit immediately preceding the matched visit. RESULTS The prevalence of T. vaginalis infection before HIV infection was 11.3% in cases and 4.5% in controls (P = .002). In multivariable analysis controlling for hormonal contraception, other STIs, behavioral, and demographic factors, the adjusted odds ratio for HIV acquisition was 2.74 (95% confidence interval, 1.25-6.00) for T. vaginalis-positive cases. The presence of behavioral risk factors for HIV infection, study recruitment from a referral population at high-risk for HIV, primary sex partner-associated risk for HIV infection, and herpes simplex virus type 2 seropositivity were also predictive of incident HIV infection. CONCLUSIONS T. vaginalis infection is strongly associated with an increased risk for HIV infection in this general population of African women. Given the high prevalence of T. vaginalis infection in HIV-endemic areas, T. vaginalis control may have a substantial impact on preventing HIV acquisition among women.
Ertapenem in the treatment of multidrug-resistant tuberculosis: first clinical experience

Treatment of multidrug-resistant (MDR) tuberculosis (TB) (defined as resistance to at least isoniazid and rifampicin, two core first-line drugs for TB treatment) and extensively drug-resistant (XDR)-TB (defined as resistance to isoniazid and rifampicin plus any fluoroquinolone and at least one of the injectable drugs amikacin, capreomycin or kanamycin) are a challenge for both clinicians and public health specialists [1–5]. Treatment outcomes of difficult-to-treat MDR-TB cases (e.g. those with an extensive resistance pattern) are still unsatisfactory, adverse events frequent and severe, and the necessary drugs expensive [6]. Ertapenem may be useful for MDR/XDR-TB to simplify administration of carbapenem when the patient is at home http://ow.ly/Snx69
Telecommunications Technology as an Aid to Family Caregivers of Persons With Dementia

Objective The aging of the population implies that an increased number of people are going to need some form of care or assistance. Caregiving poses a range of physical, emotional, and financial demands and often causes burden and stress for family members. This article describes how technology can be used to provide support to caregivers and increase the quality of life for both caregivers and care recipients. Preliminary data from an ongoing study of dementia caregivers is provided to demonstrate the feasibility of using technological interventions for this population. Methods The intervention involves a telecommunications system designed to augment a family therapy intervention by enhancing access to formal and informal support services. Specifically the system is intended to facilitate linkages between caregivers and other family members, friends, and other caregivers as well as to facilitate access to information on available resources. A total of 76 caregivers of dementia patients, including Cuban American and white American caregivers, received the telecommunications intervention. Data include real-time usage data and measures of usability at 6 months, 12 months, and 18 months after the initiation of the intervention. Results The data reported in this article are based on responses to the usability questionnaire at 6 months from a sample of 44 caregivers. Overall the results indicate that the system is easy to use and the caregivers find it valuable. The most common reason that the caregivers use the system is to communicate with other caregivers, especially those who are not nearby. The caregivers, especially the Cuban Americans, reported that the system facilitated their ability to communicate with family members and their therapist. The caregivers also indicated that they found participation in the “online discussion” groups to be very valuable and also found the “online resource guide”useful. Conclusions The results demonstrate how current information and communication technologies can be used to help caregivers meet the challenges of caregiving and improve the quality of life for caregivers. The potential benefit of this type of technology for health care providers is also discussed.
Estimation of User Specific Parameters in One-class Problems

In this paper, we propose a method to find and use user-dependant parameters to increase the performance of a keystroke dynamic system. These parameters include the security threshold and fusion weights of different classifiers. We have determined a set of global parameters which increase the performance of some keystroke dynamics methods. Our experiments show that parameter personalization greatly increases the performance. The main problem is how to estimate the parameters from only a user training set containing ten login sequences. This problem is a promising way to increase performance in biometric but it is still an open path