NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

<p>Abstract</p> <p>Background</p> <p>Nuclear localization signals (NLSs) are stretches of residues within a protein that are important for the regulated nuclear import of the protein. Of the many import pathways that exist in yeast, the best characterized is termed the 'classical' NLS pathway. The classical NLS contains specific patterns of basic residues and computational methods have been designed to predict the location of these motifs on proteins. The consensus sequences, or patterns, for the other import pathways are less well-understood.</p> <p>Results</p> <p>In this paper, we present an analysis of characterized NLSs in yeast, and find, despite the large number of nuclear import pathways, that NLSs seem to show similar patterns of amino acid residues. We test current prediction methods and observe a low true positive rate. We therefore suggest an approach using hidden Markov models (HMMs) to predict novel NLSs in proteins. We show that our method is able to consistently find 37% of the NLSs with a low false positive rate and that our method retains its true positive rate outside of the yeast data set used for the training parameters.</p> <p>Conclusion</p> <p>Our implementation of this model, NLStradamus, is made available at: <url>http://www.moseslab.csb.utoronto.ca/NLStradamus/</url></p

Evaluation of school health instruction in public primary schools in Bonny Local Government Area, Rivers state

Background: Effective school health instruction in primary schools is  essential in addressing the health risks and needs of school age children and adolescents. This study sought to evaluate the status of schoolhealth instruction in public primary schools in Bonny Local Government Area.Method: This is a cross sectional school based study carried out in 20 public primary schools in Bonny Local Government Area, Rivers State, in March 2006. The availability of the various components of the school health instruction programme was evaluated using an evaluation scale. Components had weighted scores. The minimum acceptable and maximumattainable scores for school health instruction were 31 and 47. Data was analyzed using SPSS version 11.Results: There were a total of 100 teachers in all the schools. The teacher population per school ranged from 2 to 13 with a mean of 5±2.77SD. The pupil population of the schools ranged between 100-1460 with a mean of352±336SD. Teacher/pupil ratio per school ranged from 1: 30 to 1: 128. Fourteen (70%) schools had teacher/pupil ratio less than 1:40. There was no professional health instructor in all the schools. Four schools (20%) allotted 3 periods per week to health teaching, while the rest (80%)  allotted less than 3 periods per week. HIV/AIDS was not in the health education curriculum being used. The only teaching method used by all the schools was the direct teaching method. No school used teaching aids; noschool went on field trips. Teachers did not receive in-service training on health education. No school attained the minimum acceptable score of 31 points using the evaluation scale.Conclusion: School health instruction was poorly implemented in the primary schools investigated. Teachers were not adequately prepared for health teaching and the classrooms were overcrowded.Keywords: School; Health instruction, Evaluatio

Hand washing practices amongst medical students in Port Harcourt, Nigeria

Background: Hand washing with soap and water is one of the most effective and inexpensive means of preventing infections. Rates of hand washing are low world wide even amongst health care workers who are should know about its importance. The aim of the study was to evaluate the knowledge, attitudes and hand washing practices both in and outside the hospital amongst medical students in Port Harcourt.Method: This was a descriptive cross sectional survey carried out amongst randomly selected fourth to sixth year medical students of the University of Port Harcourt. A simple questionnaire exploring perceptions, attitudes and self reported behavior was used. Information obtained included biodata, awareness information and practice. Data were analyzed using descriptive statistics.Results: Two hundred and sixty one students participated in the study with a M: F of 1.5:1. Diarrhea diseases were most commonly recognised as being associated with contaminated hands. 37.6% washed their hands regularly after interacting with their patients while 33.9% did so only after the days work. 58.3% and 58.9% washed hands before meals and after defecating respectively. Use of soap was generally low. The greatest motivation for hand washing was fear of contracting disease, whilst constraints included lack of soap, forgetfulness and inconveniently located sinks.Conclusion: Hand washing rates are low amongst medical students in Port Harcourt. There is need for regular education and re-education.Key words: Hand washing practices; medical students; Port Harcourt

Mothers' Perception of Fever Management in Children

Background: Fever is a common problem in childhood. Most febrile episodes are managed at home before consultation in a health facility. Caregivers' response to fever will depend on their perception of its cause and knowledge of its management. This study aimed to evaluate mothers' perceptions of fever and its management in childhood.Methods: This was a descriptive hospital based study. It involved the distribution of 11 itemed questionnaires on fever and related questions to 151 mothers who brought their children to the Paediatrics outpatient clinic of University of Port Harcourt Teaching Hospital. Data was analyzed using descriptive statistics.Results: A total of 151 mothers participated with age range 19 years to 54 years with mean of 31.4±5.7SD. One hundred and thirteen (74.8%) defined fever as hotness of the body. Commonest associated symptom with fever was loss of appetite (71.5%). Commonest identified cause of fever was malaria (71 (47%) mothers). 115 (76.2%) mothers measured their children's body temperature by touching their forehead, while 21 (13.9%) used thermometer. Commonest action taken when there was fever was to administer Paracetamol (107 (70.9%)). Commonest identified complication of fever was convulsion (86(67.7%)).Conclusion: Knowledge of fever is good amongst mothers in Port Harcourt; however there is need to educate them on the use of thermometer and appropriate use of drugs.Keywords: Mothers Perception; Fever; Childre

Prevalence of alcohol consumption among secondary school students in Port Harcourt, Southern Nigeria

Background: Consumption of alcohol by secondary school students is a major public health concern globally, but its prevalence is not known in secondary schools in Port Harcourt.Objective: To determine the prevalence and factors associated with alcohol use among secondary school students in Port Harcourt.Methods: This was a cross sectional school based study conducted in Port Harcourt in March 2014. A 20 itemed structured, self -administered questionnaire was distributed to 1080 senior secondary 1 to 3 students from 10 public secondary schools selected through Multistage Sampling technique. Questions asked covered drinking of alcohol, frequency of drinking and being drunk in the past 30 days before the survey. Other behaviours sought were smoking of cigarette, use of cocaine and going out in the evening for fun. Sociodemographic was also sought. Data was analyzed using SPSS version 20.Results: 1080 students participated in the study, mean age 16.09±6SD and male to female ratio of 0.9: 1. Prevalence of current drinking of alcohol was 30.6% and 38.1% of current drinkers were also drunk in the past 30 days, with 17.2 % being very frequently drunk. The behaviour which showed a strong association with drinking of alcohol, being drunk and the frequency of being drunk was going out in the evening for fun and recreation. Gender showed a positive association with drinking of alcohol, as more males drank alcohol with in the past 30 days compared to the females (p=0.000). Smoking of cigarette in the past 30 days and truancy were positively associated with being drunk, while academic grades showed an inverse relationship with consumption of alcohol. Majority of those who drank alcohol (42.6%) were experimenting with alcohol, though 5.4% drank due to addiction. Majority (39.3%) bought their drinks from stores and supermarkets. The most Common problems experienced by the drinkers were fatigue, alcohol made them behave in ways they later regretted and it hurt their relationships.Conclusion: Alcoholism is a serious problem with secondaryschool students in Port Harcourt. It is linked with truancy, poor academic achievement and other substances use. The most serious health and social problem experienced by the drinkers is addiction.Keywords: Prevalence, Alcohol, Secondary school, Consumption

Mothers’ recognition of newborn danger signs and health seeking behaviour

Background: Early recognition of neonatal illnesses followed by  care-seeking and intervention are key factors in improving neonatal health and survival.Objectives: To assess mothers’ ability to recognize newborn dangersigns and actions taken by mothers in the event of neonatal illness.Methods: The study was carried out in three health centres in Yenagoa Metropolis from April to May 2011. A 15 itemed Questionnaire based on the WHO/UNICEF IMCI programme handbook was administered to 146 mothers with infants younger than three months. The mothers were asked to identify danger signs of neonatal illness from a list of symptoms, to indicate which of the listed symptoms their babies experienced, to state what actions were taken in response to the symptoms and reasons for notutilizing orthodox healthcare.Results: None of the listed symptoms was recognized by up to halfthe mothers as danger signs of neonatal illness, the best being fast breathing by 66 (45.2%) mothers. Eighty two (56.2%) mothers reportedthat their children experienced some of the neonatal danger signs: the commonest were difficult breathing and convulsions in 8 (9.8%) cases each. Unconsciousness and excessive crying were thought to be caused by evil spirits and consultations sought with faith healers. The major constraint to utilization of health facilities was cost {45(29.8%)}.Conclusion: Mothers’ recognition of danger signs in the newborn was poor. Self-medication and the use of home remedies delayed timely  consultation. The commonest reason for non-utilization of health facilities was lack of money.Keywords: Mothers, Newborns, Danger signs, Recognition, Health seeking

Replacement of Goto Statements During Code Migration

This disclosure describes code conversion techniques for replacement of Goto statements in program code in a source language with equivalent constructs in a target language. Different types of equivalent code constructs are utilized to replace Goto statements in the source language, depending on the use of the Goto statement in the original code that is to be converted. Another option is to introduce a method-like syntax in the language. Backward jumps and forward jumps are handled by the addition of new do-while loops that start from or end at a label associated with the Goto statement. In some cases, code blocks are divided into closure methods such that every loop that includes a nested label is converted into a recursive method. On Error Goto statements are converted by utilizing try-catch blocks

WeatherProof: A Paired-Dataset Approach to Semantic Segmentation in Adverse Weather

The introduction of large, foundational models to computer vision has led to drastically improved performance on the task of semantic segmentation. However, these existing methods exhibit a large performance drop when testing on images degraded by weather conditions such as rain, fog, or snow. We introduce a general paired-training method that can be applied to all current foundational model architectures that leads to improved performance on images in adverse weather conditions. To this end, we create the WeatherProof Dataset, the first semantic segmentation dataset with accurate clear and adverse weather image pairs, which not only enables our new training paradigm, but also improves the evaluation of the performance gap between clear and degraded segmentation. We find that training on these paired clear and adverse weather frames which share an underlying scene results in improved performance on adverse weather data. With this knowledge, we propose a training pipeline which accentuates the advantages of paired-data training using consistency losses and language guidance, which leads to performance improvements by up to 18.4% as compared to standard training procedures

Quantitative characterization of optic nerve atrophy in patients with multiple sclerosis

Optic neuritis (ON) is one of the most common presentations of multiple sclerosis (MS). Magnetic resonance imaging (MRI) of the optic nerves is challenging because of retrobulbar motion, orbital fat and susceptibility artifacts from maxillary sinuses; therefore, axonal loss is investigated with the surrogate measure of a single heuristically defined point along the nerve as opposed to volumetric investigation.The objective of this paper is to derive optic nerve volumetrics along the entire nerve length in patients with MS and healthy controls in vivo using high-resolution, clinically viable MRI.An advanced, isotropic T2-weighted turbo spin echo MRI was applied to 29 MS patients with (14 patients ON+) or without (15 patients ON-) history of ON and 42 healthy volunteers. An automated tool was used to estimate and compare whole optic nerve and surrounding cerebrospinal fluid radii along the length of the nerve.Only ON+ MS patients had a significantly reduced optic nerve radius compared to healthy controls in the central segment of the optic nerve. Using clinically available MRI methods, we show and quantify ON volume loss for the first time in MS patients