The weakness of senescent dermal fibroblasts.

Skin is the largest human organ with easily noticeable biophysical manifestations of aging. As human tissues age, there is chronological accumulation of biophysical changes due to internal and environmental factors. Skin aging leads to decreased elasticity and the loss of dermal matrix integrity via degradation. The mechanical properties of the dermal matrix are maintained by fibroblasts, which undergo replicative aging and may reach senescence. While the secretory phenotype of senescent fibroblasts is well studied, little is known about changes in the fibroblasts biophysical phenotype. Therefore, we compare biophysical properties of young versus proliferatively aged primary fibroblasts via fluorescence and traction force microscopy, single-cell atomic force spectroscopy, microfluidics, and microrheology of the cytoskeleton. Results show senescent fibroblasts have decreased cytoskeletal tension and myosin II regulatory light chain phosphorylation, in addition to significant loss of traction force. The alteration of cellular forces is harmful to extracellular matrix homeostasis, while decreased cytoskeletal tension can amplify epigenetic changes involved in senescence. Further exploration and detection of these mechanical phenomena provide possibilities for previously unexplored pharmaceutical targets against aging.

Correction: Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data.

[This corrects the article DOI: 10.1371/journal.pgen.1008698.].

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data.

Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and non-overlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.

Immunogenetics in stem cell donor registry work: The DKMS example (Part 1).

Currently, stem cell donor registries include more than 35 million potential donors worldwide to provide HLA-matched stem cell products for patients in need of an unrelated donor transplant. DKMS is a leading stem cell donor registry with more than 9 million donors from Germany, Poland, the United States, the United Kingdom, India and Chile. DKMS donors have donated hematopoietic stem cells more than 80,000 times. Many aspects of donor registry work are closely related to topics from immunogenetics or population genetics. In this two-part review article, we describe, analyse and discuss these areas of donor registry work by using the example of DKMS. Part 1 of the review gives a general overview on DKMS and includes typical donor registry activities with special focus on the HLA system: high-throughput HLA typing of potential stem cell donors, HLA haplotype frequencies and resulting matching probabilities, and donor file optimization with regard to HLA diversity.

Immunogenetics in stem cell donor registry work: The DKMS example (Part 2).

DKMS is a leading stem cell donor registry with more than 9 million donors. Donor registry activities share many touch points with topics from immunogenetics or population genetics. In this two-part review article, we deal with these aspects of donor registry work by using the example of DKMS. In the second part of the review, we focus on donor typing of non-HLA genes, the impact of donor age, gender and CMV serostatus on donation probabilities, the identification of novel HLA, KIR and MIC alleles by high-throughput donor typing, the activities of the Collaborative Biobank and pharmacogenetics in the donor registry context.

Actin depolymerisation and crosslinking join forces with myosin II to contract actin coats on fused secretory vesicles.

In many secretory cells actin and myosin are specifically recruited to the surface of secretory granules following their fusion with the plasma membrane. Actomyosin-dependent compression of fused granules is essential to promote active extrusion of cargo. However, little is known about molecular mechanisms regulating actin coat formation and contraction. Here, we provide a detailed kinetic analysis of the molecules regulating actin coat contraction on fused lamellar bodies in primary alveolar type II cells. We demonstrate that ROCK1 and myosin light chain kinase 1 (MLCK1, also known as MYLK) translocate to fused lamellar bodies and activate myosin II on actin coats. However, myosin II activity is not sufficient for efficient actin coat contraction. In addition, cofilin-1 and α-actinin translocate to actin coats. ROCK1-dependent regulated actin depolymerisation by cofilin-1 in cooperation with actin crosslinking by α-actinin is essential for complete coat contraction. In summary, our data suggest a complementary role for regulated actin depolymerisation and crosslinking, and myosin II activity, to contract actin coats and drive secretion.

Beyond bread and beer: whole cell protein extracts from baker's yeast as a bulk source for 3D cell culture matrices.

Here, we present a novel approach to form hydrogels from yeast whole cell protein. Countless hydrogels are available for sophisticated research, but their fabrication is often difficult to reproduce, with the gels being complicated to handle or simply too expensive. The yeast hydrogels presented here are polymerized using a four-armed, amine reactive crosslinker and show a high chemical and thermal resistance. The free water content was determined by measuring swelling ratios for different protein concentrations, and in a freeze-drying approach, pore sizes of up to 100 µm in the gel could be created without destabilizing the 3D network. Elasticity was proofed to be adjustable with the help of atomic force microscopy by merely changing the amount of used protein. Furthermore, the material was tested for possible cell culture applications; diffusion rates in the network are high enough for sufficient supply of human breast cancer cells and adenocarcinomic human alveolar basal epithelial cells with nutrition, and cells showed high viabilities when tested for compatibility with the material. Furthermore, hydrogels could be functionalized with RGD peptide and the optimal concentration for sufficient cell adhesion was determined to be 150 µM. Given that yeast protein is one of the cheapest and easiest available protein sources and that hydrogels are extremely easy to handle, the developed material has highly promising potential for both sophisticated cell culture techniques as well as for larger scale industrial applications.

Objective assessment of symptomatic vitreous floaters using optical coherence tomography: a case report.

BACKGROUND: Vitrectomy for symptomatic vitreous floaters carries significant risks. Justification of surgery is difficult, particularly in healthy eyes with normal visual acuity and without a posterior vitreous detachment. This is the first reported case of optical coherence tomography being utilized to objectively assess the impact of a vitreous opacity on the macula. CASE PRESENTATION: A 37-year-old Caucasian female complained of the sudden onset of a ring-like floater in the central visual field of her left eye. Visual acuity was 20/20, there was no intraocular inflammation and the posterior vitreous was not detached. Complete blood count with differential, serology screen (including cysticercosis and echinococcus), chest x-ray and abdominal ultrasound found no evidence of systemic infective or cystic disease. A color photograph and B-scan ultrasound confirmed a 4.31 mm free-floating semi-translucent vitreous cyst with a hyperechogenic, pigmented surface and faint internal strands suspended in the mid-vitreous cavity, in the visual axis. The cyst moved with ocular movements, but only within the vitreous lacuna it resided in. Humphrey and Goldmann visual fields were normal. However, spectral domain optical coherence tomography (OCT) demonstrated shadowing on either side of the fovea, consistent with the ring-like scotoma described by the patient. Removing the retinal layers from the 3D-reconstructed macular cube OCT revealed a circular shadow on the macula. The patient elected for conservative management and at 3-month follow-up her symptoms had almost fully resolved as the cyst migrated to the inferior vitreous cavity, no longer casting a shadow on the macula. CONCLUSION: To our knowledge, this is the first description of using OCT as an objective, qualitative assessment of symptoms caused by large vitreous opacities and may provide a simple yet useful adjunctive tool in evaluating the risk-benefit ratio of vitrectomy in patients with large symptomatic vitreous floaters.

Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing.

BACKGROUND: A close match of the HLA alleles between donor and recipient is an important prerequisite for successful unrelated hematopoietic stem cell transplantation. To increase the chances of finding an unrelated donor, registries recruit many hundred thousands of volunteers each year. Many registries with limited resources have had to find a trade-off between cost and resolution and extent of typing for newly recruited donors in the past. Therefore, we have taken advantage of recent improvements in NGS to develop a workflow for low-cost, high-resolution HLA typing. RESULTS: We have established a straightforward three-step workflow for high-throughput HLA typing: Exons 2 and 3 of HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 are amplified by PCR on Fluidigm Access Array microfluidic chips. Illumina sequencing adapters and sample specific tags are directly incorporated during PCR. Upon pooling and cleanup, 384 samples are sequenced in a single Illumina MiSeq run. We developed "neXtype" for streamlined data analysis and HLA allele assignment. The workflow was validated with 1140 samples typed at 6 loci. All neXtype results were concordant with the Sanger sequences, demonstrating error-free typing of more than 6000 HLA loci. Current capacity in routine operation is 12,000 samples per week. CONCLUSIONS: The workflow presented proved to be a cost-efficient alternative to Sanger sequencing for high-throughput HLA typing. Despite the focus on cost efficiency, resolution exceeds the current standards of Sanger typing for donor registration.

Assessment of Anatomical Morphology of the Ileocecal Junction and Ileocecal Valve by Dissection and Endoscopy.

INTRODUCTION: The ileocecal valve (ICV) guards the opening of the ileocecal junction (ICJ) and acts as a mechanical barrier to prevent the reflux of material from the colon into the ileum. The morphology of the ICV noted in living is different from that of cadavers. The ICV is better studied in the living by endoscopy. A study of variation in the gross anatomy of the ICV can help determine the factors responsible for its competency. MATERIALS AND METHODS: A descriptive study was conducted on a total of 85 (N) patients each in two groups over a period of two years. Group I: 85 specimens of the ileocecal region obtained during dissection; Group 2: 85 patients undergoing colonoscopic study undertaken in the Department of Medical Gastroenterology. In the dissection method, the apparently normal ICJ was inspected, photographed, and measured using Vernier calipers. In the colonoscopy method, the procedure was observed and while observing ICV, photos were taken. These photographs were later compared with other photographs in the literature to identify the morphology of ICV. The age, gender, location, and morphology of ICV were represented in percentile, and qualitative variables were analyzed by Pearson correlation coefficient. RESULTS: Out of 85 participants in Group A, 80% (68) were males and 20% (17) were females; in Group B, 58% (49) were males, and the remaining 42% (36) were females. In the dissection method out of 85 (N) patients, 98% had reverse S type terminal ileum, correlation of diameter of ICV with age p=0.003 and correlation of morphology of ICV with age p=0.006, and was statistically significant. In the colonoscopy method, 58% were males and 22% of them were 31-40 years. In 49% of patients, ICV was viewed from the left lateral position. The correlation of success of ileoscopy with age (p=0.608), gender (p=0.896), the position of the patient (p=0.236), and morphology of ICV (p=0.631) was not statistically significant. CONCLUSION: There were no age-related changes observed regarding the morphology of the ICJ. It was found that as age increases diameter of ICV increases. The success of ileoscopy was highest in 31-40 years of age.

Micronutrient deficiencies and anaemia associated with body mass index in Australian adults: a cross-sectional study.

AIM: To estimate the prevalence of micronutrient deficiencies and anaemia, and their association with body mass index (BMI) categories among Australian adults. METHOD: We analysed data from the 2011-2013 Australian Health Survey from 3539 participants aged 18 years and over (without known pregnancy) with measured weight and height, and nutrient biomarkers. To address complex sampling, survey weights were used when estimating the prevalence of micronutrient deficiencies (vitamin B12 deficiency; serum vitamin B12<145 pmol/L; iron deficiency; ferritin<30 µg/L and vitamin D deficiency; 25-hydroxyvitamin D<50 nmol/L) and anaemia (haemoglobin <120 g/L for females and <130 g/L for males) and when assessing associations with logistic regression models with adjusted ORs (AORs) for BMI categories: healthy weight (BMI 18.5 to <25.0 kg/m2), reference; overweight (BMI 25.0 to <30.0 kg/m2), obesity class I (BMI 30.0 to <35.0 kg/m2), obesity class II/III (BMI 35.0 kg/m2 or more). RESULT: The prevalence of vitamin B12 deficiency (range 0.9%─2.8%) and anaemia (range 3.9%─6.7%) were variable across BMI groups. The prevalence of iron deficiency in the obesity class I group was 12.0 percentage points lower than healthy weight group with an AOR of 0.50 (95% CI 0.30 to 0.83). The prevalence of vitamin D deficiency in the obesity class II/III group was 7.9 percentage points higher than the healthy weight group with an AOR of 1.62 (95% CI 1.01 to 2.60). Vitamin B12 deficiency and anaemia were not consistently associated with BMI groups. CONCLUSION: We found a consistent association between severe obesity and vitamin D deficiency in Australian adults. We also found obesity class I was negatively associated with iron deficiency, whereas there was no consistent association between BMI groups and vitamin B12 deficiency and anaemia. Public health strategies are needed to prevent vitamin D deficiency in this high-risk population.

Unhealthy Diet Pattern Mediates the Disproportionate Prevalence of Obesity among Adults with Socio-Economic Disadvantage: An Australian Representative Cross-Sectional Study.

The role of unhealthy dietary pattern in the association between socio-economic factors and obesity is unclear. The aim was to examine the association between socio-economic disadvantage and obesity and to assess mediation effect of unhealthy dietary pattern defined using the Mediterranean diet criteria. The data source was the Australian National Nutrition and Physical Activity Survey. The study sample included 7744 participants aged 18 years and over, 28% of whom had obesity. We used the Australian Socio-Economic Indexes for Areas (SEIFA) classification system for categorizing socio-economic disadvantage; calculated the Mediterranean Diet Score (MDS) using standard criteria; and used measured body mass index to define obesity. We conducted a mediation analysis using log-binomial models to generate the prevalence ratio for obesity and the proportion mediated by the MDS. The most disadvantaged group was associated with higher level of obesity after controlling for covariates (1.40, 95% CI 1.25, 1.56) compared to the least disadvantaged group, and in a dose-response way for each decreasing SEIFA quintile. The relationship between socio-economic disadvantage and obesity was mediated by the MDS (4.0%, 95% CI 1.9, 8.0). Public health interventions should promote healthy dietary patterns, such as the Mediterranean diet, to reduce obesity, especially in communities with high socio-economic disadvantage.

Limits and convergence properties of the sequentially Markovian coalescent.

Several methods based on the sequentially Markovian coalescent (SMC) make use of full genome sequence data from samples to infer population demographic history including past changes in population size, admixture, migration events and population structure. More recently, the original theoretical framework has been extended to allow the simultaneous estimation of population size changes along with other life history traits such as selfing or seed banking. The latter developments enhance the applicability of SMC methods to nonmodel species. Although convergence proofs have been given using simulated data in a few specific cases, an in-depth investigation of the limitations of SMC methods is lacking. In order to explore such limits, we first develop a tool inferring the best case convergence of SMC methods assuming the true underlying coalescent genealogies are known. This tool can be used to quantify the amount and type of information that can be confidently retrieved from given data sets prior to the analysis of the real data. Second, we assess the inference accuracy when the assumptions of SMC approaches are violated due to departures from the model, namely the presence of transposable elements, variable recombination and mutation rates along the sequence, and SNP calling errors. Third, we deliver a new interpretation of SMC methods by highlighting the importance of the transition matrix, which we argue can be used as a set of summary statistics in other statistical inference methods, uncoupling the SMC from hidden Markov models (HMMs). We finally offer recommendations to better apply SMC methods and build adequate data sets under budget constraints.

Is the Mediterranean Diet Pattern Associated with Weight Related Health Complications in Adults? A Cross-Sectional Study of Australian Health Survey.

We hypothesized that unhealthy dietary pattern would be associated with weight related complications among overweight. We analysed data from the Australian Health Survey conducted from 2011 to 2013. A total of 5055 adults with at least overweight (body mass index ≥25 kg/m2) were analysed. We used logistic regression to assess the association between unhealthy dietary pattern, defined by low adherence to Mediterranean Diet Score (MDS), and weight related complications, defined by the Edmonton Obesity Staging System (EOSS). We repeated the logistic regression models by age and socio-economic disadvantage strata in sensitivity analyses. We also repeated the main analysis on a propensity score matched dataset (n = 3364). Complications by EOSS ≥2 was present in 3036 (60.1%) participants. There was no statistically significant association between unhealthy dietary pattern and weight related complication (odds ratio 0.98 (95%confidence interval: 0.85, 1.12)). The null association remained the same after repeating the analysis on three age and five socio-economic indexes for areas strata. The finding persisted after the analysis was repeated on a propensity score matched dataset. We found no evidence to support the hypothesis that unhealthy dietary pattern was associated with weight related complications in this cross-sectional study of the Australian population with overweight or obesity.

Clinical usefulness of brief screening tool for activating weight management discussions in primary cARE (AWARE): A nationwide mixed methods pilot study.

OBJECTIVE: The Edmonton Obesity Staging System (EOSS) is based on weight related health complications among individuals with overweight and obesity requiring clinical intervention. We aimed to assess the clinical usefulness of a new screening tool based on the EOSS for activating weight management discussions in general practice. METHODS: We enrolled five General Practitioners (GPs) and 25 of their patients located nationwide in metropolitan areas of Australia to test the feasibility, acceptability, and accuracy of the new 'EOSS-2 Risk Tool', using cross-sectional and qualitative study designs. Diagnostic accuracy of the tool for the presence of EOSS ≥2 criteria was based on clinical information collected prospectively. To assess feasibility and applicability, we explored the views of GP and patient participants by thematic analysis of transcribed verbatim and de-identified data collected by semi-structured telephone interviews. RESULTS: Nineteen (76%) patients were aged ≥45 years, five (20%) were male, and 20 (80%) were classified with obesity. All 25 patients screened positive for EOSS ≥2 criteria by the tool. Interviews with patients continued until data saturation was reached resulting in a total of 23 interviews. Our thematic analysis revealed five themes: GP recognition of obesity as a health priority (GPs expressed strong interest in and understanding of its importance as a health priority); obesity stigma (GPs reported the tool helped them initiate health based and non-judgmental conversations with their patients); patient health literacy (GPs and patients reported increased awareness and understanding of weight related health risks), patient motivation for self-management (GPs and patients reported the tool helped focus on self-management of weight related complications), and applicability and scalability (GPs stated it was easy to use, relevant to a range of their patient groups, and scalable if integrated into existing patient management systems). CONCLUSION: The EOSS-2 Risk Tool is potentially clinically useful for activating weight management discussions in general practice. Further research is required to assess feasibility and applicability.

Association of husbands' education status with unintended pregnancy in their wives in southern Ethiopia: A cross-sectional study.

BACKGROUND: Unintended pregnancy rates are substantially higher in developing regions, have significant health consequences, and disproportionately affect subgroups with socio-economic disadvantage. We aimed to examine whether there is an association between husbands' education status and their wives unintended pregnancy in southern Ethiopia. METHODS: The data source for this study was from a cross-sectional study on iron-folate supplementation and compliance in Wolaita, South Ethiopia. Data were collected from October to November 2015 in 627 married pregnant women regarding their husbands' education status, socio-demographic characteristics, and if they wanted to become pregnant at the time of survey using an interviewer administered questionnaire. Logistic regression was used to estimate Odds Ratios (ORs) with associated z-tests and 95% Confidence Intervals (95% CI) for variables associated with unintended pregnancy. RESULTS: The proportion of unintended pregnancy in this sample was 20.6%. Husbands' education status, age, residence, and using family planning methods were associated with unintended pregnancy (all P-values < 0.05). Multivariable models consistently showed that being married to a husband with at least some college or university education was associated with a decreased OR for unintended pregnancy after controlling for age and use of family planning at conception period (OR 0.36 [95%CI: 0.17, 0.82]) and age and rural residence (OR 0.40 [95%CI: 0.18, 0.90]). CONCLUSION: Unintended pregnancy among Ethiopian woman was consistently associated with being married to least educated husbands in southern Ethiopia. Increasing age and living in a rural vs urban area were also independently associated with unintended pregnancy. Strategies for addressing family planning needs of women with poorly educated husbands should be the subject of future research.

Predictive analytics on open big data for supporting smart transportation services.

In the current era of big data, huge quantities of valuable data, which may be of different levels of veracity, are being generated at a rapid rate. Embedded into these big data are implicit, previously unknown and potentially useful information and valuable knowledge that can be discovered by data science solutions, which apply techniques like data mining. There has been a trend that more and more collections of these big data have been made openly available in science, government and non-profit organizations so that people could collaboratively study and analysis these open big data. In this article, we focus on open big data for public transit because public transit (e.g., bus) as a means of transportation is a vital part of many people's lives. As time is a precious resource, bus delays could negatively affect commuters' plans. Unfortunately, they are inevitable. Hence, many existing works focused on predicting bus delays. However, predicting on-time or early buses is also important. For instance, commuters who come to a bus stop on time may still miss their buses if the buses leave early. So, in this article, we examine open big data about bus performance (e.g., early, on-time, and late stops). We analyze the data with frequent pattern mining and make predictions with decision-tree based classification. For illustration, we perform predictive analytics on real-life open big data available on Winnipeg Open Data Portal, about bus performance from Winnipeg Transit. It shows the benefits of predictive analytics on open big data for supporting smart transportation services.

Improving the improvisational pelvic circumferential compression technique for open-book pelvic fractures using a simulation model and a sphygmomanometer.

BACKGROUND: Open-book pelvic fractures are associated with significant mortality. Emergency management may require a commercial pelvic circumferential compression device to reduce the fracture and compress haemorrhaging pelvic vasculature. Standard, commercial, twin-sized bedsheets are acceptable should commercial devices be unavailable. However, obese victims or personnel with insufficient body strength may impede successful reduction. OBJECTIVE: To demonstrate the value of an improvisational windlass (intravenous pole) in improving the ability to reduce an open-book pelvic fracture. METHODS: The Institutional Review Board-approved study involved 28 diverse healthcare students and emergency medicine residents. Each participant's demographic information and physical characteristics were recorded. A METIman was prepared with knee and ankle binding and a sphygmomanometer set at 40 mm Hg placed over the symphysis pubis. Two-person teams were randomly selected to place a bedsheet at greater trochanter level and atop the sphygmomanometer. The bedsheet was secured with maximum effort by the pairs and the pressure recorded. Following this, the pairs inserted an intravenous pole in the knot and torqued the pole to maximum effort and a repeat pressure recorded. RESULTS: The mean increase in pressure using only the bedsheet was 106.43 mm Hg per team. With bedsheet and intravenous pole, the mean pressure increase was 351.79 mm Hg per team. The difference was statistically significant (independent samples t-test: t = 17.177, p < 0.001, 95% CI (216.65 to 274.07 mm Hg). There was no correlation between pressure increases and the individual physical characteristics of the subjects (r = - 0.183, p = 0.352). CONCLUSIONS: Regardless of personnel's physical attributes, the addition of an improvisational windlass to a pelvic circumferential compression bedsheet can improve the ability to reduce an open-book fracture, especially in obese victims.

[TRANSDISCIPLINARITY A NEW STATUS OF THE SUBJECT IN HEALTH? EPISTEMOLOGICAL AND ETHICAL QUESTIONS]. / Chapitre 2 LA TRANSDISCIPLINARITÉ: UN NOUVEAU STATUT DU SUJET EN SANTÉ? QUESTIONNEMENT ÉPISTÉMOLOGIQUE ET ÉTHIQUE.

The discoveries in human genetics regularly question the meaning and limits of our interventions. In fact, to intervene on the physical nature challenges their ethical framework. However a gap exists between a medicine treating biological imbalances, diseases with organics repercussions and the psychological, social and cultural reality of the treated human persons. This gap hopes to fade with bioethics, word that has, in its vocation, the desire to meet the "bios" (biology's techniques and knowledge) and ethics. Ethics therefore refers to the "self", to what has an independent existence, contrary to the quest for universality of science and technology. The same difference is suggested by the genome, which includes universal elements essential to the coding transmission and the development of life in general as well as the inscription and the manifestation of individual characters. Between the universal and the singular, unmasks the issue of the different levels of human reality. Each has its own laws making the genetic or bioethics questioning not only scientific or moral but also phenomenological, epistemological and logical. Transdisciplinarity in these areas could foster debate and open up innovative perspectives on the question of the subject into, through and beyond disease.