Improving the Segmentation of Anatomical Structures in Chest Radiographs using U-Net with an ImageNet Pre-trained Encoder

Accurate segmentation of anatomical structures in chest radiographs is essential for many computer-aided diagnosis tasks. In this paper we investigate the latest fully-convolutional architectures for the task of multi-class segmentation of the lungs field, heart and clavicles in a chest radiograph. In addition, we explore the influence of using different loss functions in the training process of a neural network for semantic segmentation. We evaluate all models on a common benchmark of 247 X-ray images from the JSRT database and ground-truth segmentation masks from the SCR dataset. Our best performing architecture, is a modified U-Net that benefits from pre-trained encoder weights. This model outperformed the current state-of-the-art methods tested on the same benchmark, with Jaccard overlap scores of 96.1% for lung fields, 90.6% for heart and 85.5% for clavicles.Comment: Presented at the First International Workshop on Thoracic Image Analysis (TIA), MICCAI 201

Generation and chromosome mapping of expressed sequence tags (ESTs) from a human infant thymus

In an effort to identify novel genes that are expressed differentially in an infant thymus, we constructed an oligo-d(T) primed cDNA library from a human infant thymus followed by single-run partial sequencing to generate expressed sequence tags (ESTs). Characterization of more than 1400 sequences enabled us to convert human thymus transcripts into 1223 useful ESTs. These ESTs consisted of 613 (50.1%) showing homology to known human genes, 51 (4.2%) matching to genes from other species, 289 (23.6%) matching ESTs of unknown functions, and 182 (14.9%) being novel transcripts. The expression profile of an infant thymus features a high number of genes related to cell division-DNA synthesis and gene-protein expression, indicating the active growth stage of an infant thymus. To identify the chromosomal localization of 43 thymus ESTs, PCR-based mapping was performed using a human-rodent somatic cell hybrid or radiation hybrid mapping panel. The results indicated that several novel genes were determined to be located in the vicinity of previously mapped disease loci; histidinemia loci, plasminogen Tochigi disease loci, Ehlers-Danlos syndrome, hypertriglyceridemia, thyroid resistance locus, ocular albinism, galactosemia, porphyria variegata, Charcot-Marie-tooth disease, FEOM (fibrosis of extraocular muscles), Prader-Willi syndrome.published_or_final_versio

Rapid diagnostic tests for molecular surveillance of Plasmodium falciparum malaria -assessment of DNA extraction methods and field applicability

Background: The need for new malaria surveillance tools and strategies is critical, given improved global malaria control and regional elimination efforts. High quality Plasmodium falciparum DNA can reliably be extracted from malaria rapid diagnostic tests (RDTs). Together with highly sensitive molecular assays, wide scale collection of used RDTs may serve as a modern tool for improved malaria case detection and drug resistance surveillance. However, comparative studies of DNA extraction efficiency from RDTs and the field applicability are lacking. The aim of this study was to compare and evaluate different methods of DNA extraction from RDTs and to test the field applicability for the purpose of molecular epidemiological investigations. Methods: DNA was extracted from two RDT devices (Paracheck-PfW and SD Bioline Malaria Pf/Pan (R)), seeded in vitro with 10-fold dilutions of cultured 3D7 P. falciparum parasites diluted in malaria negative whole blood. The level of P. falciparum detection was determined for each extraction method and RDT device with multiple nested-PCR and real-time PCR assays. The field applicability was tested on 855 paired RDT (Paracheck-Pf) and filter paper (Whatman (R) 3MM) blood samples (734 RDT negative and 121 RDT positive samples) collected from febrile patients in Zanzibar 2010. RDT positive samples were genotyped at four key single nucleotide polymorphisms (SNPs) in pfmdr1 and pfcrt as well as for pfmdr1 copy number, all associated with anti-malarial drug resistance. Results: The P. falciparum DNA detection limit varied with RDT device and extraction method. Chelex-100 extraction performed best for all extraction matrixes. There was no statistically significant difference in PCR detection rates in DNA extracted from RDTs and filter paper field samples. Similarly there were no significant differences in the PCR success rates and genotyping outcomes for the respective SNPs in the 121 RDT positive samples. Conclusions: The results support RDTs as a valuable source of parasite DNA and provide evidence for RDT-DNA extraction for improved malaria case detection, molecular drug resistance surveillance, and RDT quality control.ACT Consortium through Bill and Melinda Gates Foundation; Swedish International Development Agency (SIDA) [SWE 2009-193]; Swedish Civil Contingencies Agency (MSB) [2010-7991]; Swedish Medical Research Council (VR) [2009-3785]; Goljes Foundationinfo:eu-repo/semantics/publishedVersio

Tracing the evolution of dust-obscured activity using sub-millimetre galaxy populations from STUDIES and AS2UDS

We analyse the physical properties of 121 SNR ≥ 5 sub-millimetre galaxies (SMGs) from the STUDIES 450 μm survey. We model their UV-to-radio spectral energy distributions using MAGPHYS+photo-z and compare the results to similar modelling of 850 μm-selected SMG sample from AS2UDS, to understand the fundamental physical differences between the two populations at the observed depths. The redshift distribution of the 450-μm sample has a median of z = 1.85 ± 0.12 and can be described by strong evolution of the far-infrared luminosity function. The fainter 450-μm sample has ∼14 times higher space density than the brighter 850-μm sample at z ≲ 2, and a comparable space density at z = 2–3, before rapidly declining, suggesting LIRGs are the main obscured population at z ∼ 1–2, while ULIRGs dominate at higher redshifts. We construct rest-frame ∼180-μm-selected and dust-mass-matched samples at z = 1–2 and z = 3–4 from the 450 and 850-μm samples, respectively, to probe the evolution of a uniform sample of galaxies spanning the cosmic noon era. Using far-infrared luminosity, dust masses, and an optically thick dust model, we suggest that higher redshift sources have higher dust densities due to inferred dust continuum sizes which are roughly half of those for the lower redshift population at a given dust mass, leading to higher dust attenuation. We track the evolution in the cosmic dust mass density and suggest that the dust content of galaxies is governed by a combination of both the variation of gas content and dust destruction time-scale

Clinical significance of hypoalbuminemia in outcome of patients with scrub typhus

<p>Abstract</p> <p>Background</p> <p>This study was designed to investigate the clinical significance of hypoalbuminemia as a marker of severity and mortality in patients with Scrub typhus.</p> <p>Methods</p> <p>The patients with scrub typhus were divided into two groups based on the serum albumin levels; Group I (serum albumin <3.0 g/dL) and Group II (serum albumin ≥3.0 g/dL). The outcome of patients with hypoalbuminemia was compared with that of normoalbuminemia.</p> <p>Results</p> <p>Of the total 246 patients who underwent the study, 84 patients (34.1%) were categorized as Group I and 162 patients were (65.9%) as Group II. Group I showed significantly higher incidence of confusion (24.6% vs. 5.3%, <it>p </it>< 0.001), pulmonary edema (15.8% vs. 3.2%, <it>p </it>= 0.002), pleural effusion (22.8% vs. 11.1%, <it>p </it>= 0.03), arrhythmia (12.3% vs. 2.6%, <it>p </it>= 0.008) and non-oliguric acute renal failure (40.4% vs. 11.1%, <it>p </it>< 0.001) compared to group II. Hypoalbuminemic group had a higher APACHE II score (11.37 ± 5.0 vs. 6.94 ± 4.2, <it>p </it>< 0.001), longer hospital stay (19.9 ± 42.1 days vs 7.5 ± 13.8 days, <it>p </it>= 0.012), and higher hospital cost compared to Group II.</p> <p>Conclusions</p> <p>This study showed hypoalbuminemia in scrub typhus was closely related to the frequency of various complication, longer hospital stay, consequently the higher medical cost, necessitating more efficient management of patients, including medical resources.</p

Home healthcare services in Taiwan: a nationwide study among the older population

<p>Abstract</p> <p>Background</p> <p>Home healthcare services are important in aging societies worldwide. The present nationwide study of health insurance data examined the utilization and delivery patterns, including diagnostic indications, for home healthcare services used by seniors in Taiwan.</p> <p>Methods</p> <p>Patients ≥65 years of age who received home healthcare services during 2004 under the Taiwanese National Health Insurance Program were identified and reimbursement claims were analyzed. Age, gender, disease diagnoses, distribution of facilities providing home healthcare services, and patterns of professional visits, including physician and skilled nursing visits, were also explored.</p> <p>Results</p> <p>Among 2,104,978 beneficiaries ≥65 years of age, 19,483 (0.9%) patients received 127,753 home healthcare visits during 2004 with a mean number of 6.0 ± 4.8 visits per person. The highest prevalence of home healthcare services was in the 75-84 year age group in both sexes. Females received more home healthcare services than males in all age groups. Cerebrovascular disease was the most frequent diagnosis in these patients (50.7%). More than half of home healthcare visits and around half of the professional home visits were provided by community home nursing care institutions. The majority of the home skilled nursing services were tube replacements, including nasogastric tubes, Foley catheter, tracheostomy, nephrostomy or cystostomy tubes (95%).</p> <p>Conclusions</p> <p>Nine out of 1,000 older patients in Taiwan received home healthcare services during 2004, which was much lower than the rate of disabled older people in Taiwan. Females used home healthcare services more frequently than males and the majority of skilled nursing services were tube replacements. The rate of tube replacement of home healthcare patients in Taiwan deserves to be paid more attention.</p

East London’s Homeless: a retrospective review of an eye clinic for homeless people

Background There is very little published work on the visual needs of homeless people. This paper is the first study to investigate the visual needs of homeless people in the UK. Although similar work has been done in other countries, this study is unique because the United Kingdom is the only country with a National Health Service which provides free healthcare at the point of access. This study analysed the refractive status of the sample used, determined the demographics of homeless people seeking eye care and established if there is a need for community eye health with access to free spectacle correction in East London. Methods This retrospective case study analysed the clinical records of 1,141 homeless people using the Vision Care for Homeless People services at one of their clinics in East London. All eye examinations were carried out by qualified optometrists and, where appropriate, spectacles were dispensed to patients. Data captured included age, gender, ethnicity and refractive error. Results were analysed using two-sample t-tests with Excel and Minitab. Results Demographics of age, gender and ethnicity are described. Spherical equivalents (SE) were calculated from prescription data available for 841 clinic users. Emmetropia was defined as SE–0.50DS to +1DS, myopia as SE  +1DS. The majority of clinic users were male (79.2 %, n = 923). Approximately 80 % (n = 583) of clinic users were white, 10 % (n = 72) were ‘black’, 4 % (n = 29) ‘Asian’ and the remaining 5.6 % (n = 40) were of ‘mixed ethnicity’ and ‘other’ groups. The mean age of females attending the clinic was significantly lower than that of males (45.9 years, SD = 13.8 vs’ 48.4 years, SD = 11.8) when analysed using a two-sample t-test (t (317) = 2.44, p = 0.02). One third of service users were aged between 50–59 years. Myopia and hyperopia prevalence rates were 37.0 % and 21.0 % respectively. A total of 34.8 % of homeless people were found to have uncorrected refractive error, and required spectacle correction. Conclusions This study has identified a high proportion of uncorrected refractive error in this sample and therefore a need for regular eye examinations and provision of refractive correction for homeless people