3D deep convolutional neural network segmentation model for precipitate and porosity identification in synchrotron X-ray tomograms.

New developments at synchrotron beamlines and the ongoing upgrades of synchrotron facilities allow the possibility to study complex structures with a much better spatial and temporal resolution than ever before. However, the downside is that the data collected are also significantly larger (more than several terabytes) than ever before, and post-processing and analyzing these data is very challenging to perform manually. This issue can be solved by employing automated methods such as machine learning, which show significantly improved performance in data processing and image segmentation than manual methods. In this work, a 3D U-net deep convolutional neural network (DCNN) model with four layers and base-8 characteristic features has been developed to segment precipitates and porosities in synchrotron transmission X-ray micrograms. Transmission X-ray microscopy experiments were conducted on micropillars prepared from additively manufactured 316L steel to evaluate precipitate information. After training the 3D U-net DCNN model, it was used on unseen data and the prediction was compared with manual segmentation. A good agreement was found between both segmentations. An ablation study was performed and revealed that the proposed model showed better statistics than other models with lower numbers of layers and/or characteristic features. The proposed model is able to segment several hundreds of gigabytes of data in a few minutes and could be applied to other materials and tomography techniques. The code and the fitted weights are made available with this paper for any interested researcher to use for their needs (https://github.com/manasvupadhyay/erc-gamma-3D-DCNN).

Modulation of mtDNA copy number ameliorates the pathological consequences of a heteroplasmic mtDNA mutation in the mouse.

Heteroplasmic mtDNA mutations typically act in a recessive way and cause mitochondrial disease only if present above a certain threshold level. We have experimentally investigated to what extent the absolute levels of wild-type (WT) mtDNA influence disease manifestations by manipulating TFAM levels in mice with a heteroplasmic mtDNA mutation in the tRNAAla gene. Increase of total mtDNA levels ameliorated pathology in multiple tissues, although the levels of heteroplasmy remained the same. A reduction in mtDNA levels worsened the phenotype in postmitotic tissues, such as heart, whereas there was an unexpected beneficial effect in rapidly proliferating tissues, such as colon, because of enhanced clonal expansion and selective elimination of mutated mtDNA. The absolute levels of WT mtDNA are thus an important determinant of the pathological manifestations, suggesting that pharmacological or gene therapy approaches to selectively increase mtDNA copy number provide a potential treatment strategy for human mtDNA mutation disease.

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO ) and expected (HE ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

This corrects the article DOI: 10.1038/hdy.2016.79.

Need of The Ministry of Health in Federal Democratic Republic of Nepal.

The constitution of Nepal provides appointing a council of ministers both at federal and provincial levels without defining portfolios. There is a political agreement that MOH will be retained at the federal level. This article draws evidences around the world to meet health needs of Nepalese, the role of provincial ministry of health and coordinating structure at district/local level. The constitution emphasises on health and pronounced in 46 articles which provides guidance for the creation of federalized governance levels at federal, provincial and local levels. Retaining ministry of health at federal level without creating devolved structure at province and local levels in health sector will create difficulty in translating the spirit of the constitution and may not be effective in addressing health issues nationally and meeting global achievements like SDGs. It is suggested to establish an elaborate health system accordingly in Nepal to ensure constitutional mandate of health as a basic human right.

Stresses and Strains in Cruciform Samples Deformed in Tension.

The stress and strain relationship in the gauge region of six cruciform geometries is studied: the ISO standard geometry with slits in arms, two geometries with thinned gauge areas, two geometries with thinned gauge areas and slits in arms, and one modified ISO standard geometry with slits in arms and a thinned gauge area. For all the geometries, finite element simulations are performed under uniaxial loading to compare the plastic strain, the von Mises stress distribution and the in-plane stress evolution. Results show that less plastic strain can be achieved in the gauge of the two ISO standard geometries. For the remaining cruciform geometries, a strong non-linear coupling between applied forces in arms and gauge stresses is generated. The evolution of this non-linear coupling depends on the geometry type, applied biaxial load ratio and the elastic-plastic properties of the material. Geometry selection criteria are proposed to reduce this non-linear coupling.

Intergranular Strain Evolution During Biaxial Loading: A Multiscale FE-FFT Approach.

Predicting the macroscopic and microscopic mechanical response of metals and alloys subjected to complex loading conditions necessarily requires a synergistic combination of multiscale material models and characterization techniques. This article focuses on the use of a multiscale approach to study the difference between intergranular lattice strain evolution for various grain families measured during in situ neutron diffraction on dog bone and cruciform 316L samples. At the macroscale, finite element simulations capture the complex coupling between applied forces and gauge stresses in cruciform geometries. The predicted gauge stresses are used as macroscopic boundary conditions to drive a mesoscale full-field elasto-viscoplastic fast Fourier transform crystal plasticity model. The results highlight the role of grain neighborhood on the intergranular strain evolution under uniaxial and equibiaxial loading.

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.

Teaching District Concept of BP Koirala Institute of Health Sciences: An Inter-disciplinary Community Based Medical Education and Health Service Delivery Model in Rural Nepal.

Community based education trains health professional students to deal with the community health problems. The attitude and skills they gain as planners for health care provision are applicable in both hospital and community settings. BP Koirala Institute of Health Sciences has implemented a model of Community based education which encompasses the health institutions, organisations and the communities of the sixteen districts in eastern Nepal and refers to this concept as the 'Teaching District" concept of B P Koirala Institute of Health Sciences. This paper seeks to describe the concept and its implementation. Almost 20 years have passed since first initiated; and pending a comprehensive evaluation, this concept has gathered a great deal of experience to serve as a model for partnership between academic health sciences institutions with the district health system of Nepal.

Monitoring the durability of long-lasting insecticidal nets in field conditions in Nepal.

Understanding and improving the durability of long-lasting insecticidal nets (LLINs) in the field is critical for the success of malaria prevention using mosquito nets, as well as contributing to procurement decisions based on the number of years of protection, rather than the current practice of unit cost. Using the recently published guidelines from the World Health Organization (WHO) some progress has been made in the monitoring and assessment of performance of nets in the field. This paper describes the protocol of an ongoing retrospective study of the attrition rate, physical integrity and bioefficacy of three polyester LLIN products that were distributed during 2010 to 2013 in Nepal. It is hoped that robust and auditable data on net survival (physical integrity and bioefficacy) of these three brands in different environments will assist the Nepal National Malaria Control Programme in planning future LLIN-replacement strategies, including behaviour-change communication about LLIN care and maintenance. The advantages and disadvantages of prospective and retrospective cross-sectional approaches are discussed, including appropriate strategies to validate the timing for mass distribution of nets. Similar studies should be done in other countries to (i) track LLIN durability to support management of resupply, and (ii) inform procurement decisions at the global level. New, more predictive, textile laboratory testing is also urgently needed.

Utilization of primary eye health services by people from a rural community of Nepal.

INTRODUCTION: Preventable and treatable eye diseases are still major causes of blindness in rural communities. OBJECTIVE: To find the factors influencing utilization of primary eye health services among the people in a rural community of Nepal. MATERIALS AND METHODS: This was a population-based study with a cross-sectional and descriptive design. Lete Ilaka in Mustang District of Nepal was the study site. Data of knowledge on eye diseases, availability of services and utilization of available services were obtained from female care takers. Association among variables was observed by bivariate analysis. RESULTS: A total of 216 female care takers participated in the study. The median age of the respondents was 39 years. Almost 80 % of the respondents had agriculture as their major occupation and more than a quarter were from lower castes (dalit) community. Low level of educational attainment (OR = 3.1, 95 % CI = 1.6-6.1) and poverty (OR = 2.0, 95 % CI = 1.13-3.43) among respondents were found to be significantly associated with a low level of awareness on eye diseases. The risk of not knowing about eye diseases increased more than 3.5 times when people were illiterate. Locally available eye health services and skills amongst the health workers were found inadequate. CONCLUSION: Low level of education, poor knowledge of eye diseases and great distance from home to health facilities were found to be factors on the demand side while inadequacy of eye health services and perceived inadequate skills among health workers were identified as factors in the supply side affecting utilization of eye health services among people of Mustang District.

Mini-implants for retraction, intrusion and protraction in a Class II division 1 patient.

This case report demonstrates the clinical utility and versatility of mini-implants in carrying out different types of tooth movement in a 14-year-old boy with a 'severe' Class II division 1 malocclusion. Mini-implants were placed for 'en masse' retraction and intrusion of maxillary anterior teeth and for lower molar protraction. More than 11 mm of maxillary incisor retraction was achieved together with 3 mm of intrusion. There was significant reduction in the dentoalveolar protrusion and retraction of the upper lip, which resulted in decreased mentalis strain and improved chin projection. Cephalometric superimposition and panoramic radiographs showed no anchorage loss and good occlusion at the end of treatment.

Corneal ulceration in south-east Asia III: prevention of fungal keratitis at the village level in south India using topical antibiotics.

AIM: To determine whether topical antifungal prophylaxis distributed by paid village health workers (VHWs) in south India is necessary after corneal abrasion to prevent fungal keratitis in a population where half of the ulcers are fungal. METHODS: Two panchayaths (village administrative units in Madurai district with a combined population of 48 039 were followed prospectively for 18 months by 15 VHWs who were trained to identify post-traumatic corneal abrasions. Patients fulfilling the eligibility criteria were randomised into two groups and treated with either 1% chloramphenicol and 1% clotrimazole ointment or 1% chloramphenicol and a placebo ointment three times a day for 3 days. Patients, doctors and VHWs were blinded to treatment. RESULTS: During the 18-month period, 1365 people reported to VHWs with ocular injuries, of whom 374 with corneal abrasions were eligible for treatment. Of these, 368 (98.5%) abrasions healed without complications. Two patients had mild localised allergic reactions to the ointment, two dropped out and two patients in the placebo group developed microscopic culture-negative corneal stromal infiltrates that healed in 1 week with natamycin drops. CONCLUSIONS: Both fungal and bacterial ulcers that occur after traumatic corneal abrasions seem to be effectively prevented in a village setting using only antibiotic prophylaxis.

Corneal ulceration in South East Asia. II: a strategy for the prevention of fungal keratitis at the village level in Burma.

AIM: To prove that topical antifungal and antibiotic prophylaxis distributed by grass roots village health workers (VHWs) in Burma is an effective public health intervention for the prevention of post-traumatic microbial keratitis in a population where the majority of ulcers are fungal. METHODS: Three villages in Bago District with a combined population of 16,987 were selected for the study. This defined population was followed prospectively for 12 months by 15 VHWs who were trained to identify post-traumatic corneal abrasions with fluorescein dye and a blue torch and to administer 1% chloramphenicol and 1% clotrimazole ointment three times a day for 3 days to the eyes of individuals who fulfilled the eligibility criteria. RESULTS: During the 12 month period 273 individuals reported to VHWs with an ocular injury and 126 were found to have a corneal abrasion. All 126 were treated with 1% chloramphenicol and 1% clotrimazole ointment three times a day for 3 days, and all healed without sequelae. CONCLUSIONS: Both fungal and bacterial ulcers that occur following traumatic corneal abrasions can be effectively prevented in a village setting by using relatively simple measures that local volunteer public health workers can easily be taught to employ.

Corneal ulceration in South East Asia. I: a model for the prevention of bacterial ulcers at the village level in rural Bhutan.

AIM: To prove that antibiotic distribution by grassroots volunteer village health workers (VVHWs) in Bhutan is an effective and efficient public health intervention for the prevention of post-traumatic corneal ulceration. METHODS: 55 villages in two districts in Bhutan were selected for the study. A defined population of 10 139 individuals was followed prospectively for 18 months by 31 VVHWs who were trained to identify post-traumatic corneal abrasions with fluorescein dye and a blue torch and to administer 1% chloramphenicol ointment three times a day for 3 days to the eyes of individuals who fulfilled the eligibility criteria. RESULTS: During the 18 month period 135 individuals reported to VVHWs with an ocular injury and 115 were found to have a corneal abrasion. All 115 were treated with 1% chloramphenicol ointment three times a day for 3 days and all healed without sequelae CONCLUSIONS: Corneal ulcers that occur following traumatic corneal abrasions can be effectively prevented, even in the setting of isolated rural conditions such as those that exist in villages in Bhutan, by using relatively simple preventative measures that local VVHWs can easily be taught to employ.

Cling wrap, an innovative intervention for temperature maintenance and reduction of insensible water loss in very low-birthweight babies nursed under radiant warmers: a randomized, controlled trial.

AIM: The value of polythene film ('cling wrap') to improve thermal control and reduce postnatal weight loss in preterm, very low-birthweight babies was investigated. METHODS: Consecutively born babies with birthweights between 750 and 1500 g were stratified by birthweight (<1250 g, 1251-1500 g) and randomised either to the cling wrap (CW) or no cling wrap (NCW) group. The baby bassinette of the RW was covered with cling wrap up to the level of the neck in the CW group for the 1st 7 days. The primary outcome variables were the incidence of hypothermia (axillary temperature < or = 36 degrees C) after initial stabilisation during the first 7 days and cumulative weight loss (percentage of birthweight) at 48 hours of age. RESULTS: Of 51 babies, 26 were randomised to the CW and 25 to the NCW group. None of the babies in the CW group developed hypothermia in the 1st 7 days but 36% in the NCW group (p = 0.001) did. Babies who were hypothermic on admission took less time to reach normal temperature in the CW group. Cumulative weight loss in the 1st 48 hours was 5.0 + 5.6% in the CW group and 8.6 + 7.0% in the NCW group (p = 0.06). CONCLUSION: Use of CW might be a simple method of maintaining temperature in very low-birthweight babies in developing countries.

Measuring the burden of ocular morbidity.

This hospital-based study highlights the spectrum of eye ailments in 35,273 patients who attended the Department of Ophthalmology at the B P Koirala Institute of Health Sciences, Eastern Nepal, during a 5-year period with varied clinical diagnosis. The attendance each year showed a progressive increase with a male preponderance. More than 13% of the patients were children. Cataract was the most common problem for which patients needed ophthalmic advice; diabetic and hypertensive retinopathy were frequent occurrences and infection was a common problem. Over 21% of the eyes examined had a refractive error: as high as 2.54% were amyblyopic caused by non-correction of refractive errors. Allergic conjunctivitis was frequently encountered. As shown by the magnitude of the problem, the existing eye care facilities must be enhanced and new strategies developed.

Corneal blindness: a global perspective.

Diseases affecting the cornea are a major cause of blindness worldwide, second only to cataract in overall importance. The epidemiology of corneal blindness is complicated and encompasses a wide variety of infectious and inflammatory eye diseses that cause corneal scarring, which ultimately leads to functional blindness. In addition, the prevalence of corneal disease varies from country to country and even from one population to another. While cataract is responsible for nearly 20 million of the 45 million blind people in the world, the next major cause is trachoma which blinds 4.9 million individuals, mainly as a result of corneal scarring and vascularization. Ocular trauma and corneal ulceration are significant causes of corneal blindness that are often underreported but may be responsible for 1.5-2.0 million new cases of monocular blindness every year. Causes of childhood blindness (about 1.5 million worldwide with 5 million visually disabled) include xerophthalmia (350,000 cases annually), ophthalmia neonatorum, and less frequently seen ocular diseases such as herpes simplex virus infections and vernal keratoconjunctivitis. Even though the control of onchocerciasis and leprosy are public health success stories, these diseases are still significant causes of blindness--affecting a quarter of a million individuals each. Traditional eye medicines have also been implicated as a major risk factor in the current epidemic of corneal ulceration in developing countries. Because of the difficulty of treating corneal blindness once it has occurred, public health prevention programmes are the most cost-effective means of decreasing the global burden of corneal blindness.