In most biomedical labs, researchers gather metadata (
., all details about the experimental data) in paper notebooks, spreadsheets, or, sometimes, electronic notebooks. When data analyses occur, the ...related details usually go into other notebooks or spreadsheets, and more metadata are available. The whole thing rapidly becomes very complex and disjointed, and keeping track of all these things can be daunting. Organizing all the relevant data and related metadata for analysis, publication, sharing, or deposit into archives can be time-consuming, difficult, and prone to errors. By having metadata in a centralized system that contains all details from the start, the process is greatly simplified. While lab management software is available, it can be costly and inflexible. The system described here is based on a popular, freely available, and open-source wiki platform. It provides a simple but powerful way for biomedical research labs to set up a metadata management system linking the whole research process. The system enhances efficiency, transparency, reliability, and rigor, which are key factors to improving reproducibility. The flexibility afforded by the system simplifies implementation of specialized lab requirements and future needs. The protocol presented here describes how to create the system from scratch, how to use it for gathering basic metadata, and provides a fully functional version for perusal by the reader.
Lab Metadata Management System.
Rodents use their whiskers to explore the environment, and the superior colliculus is part of the neural circuits that process this sensorimotor information. Cells in the intermediate layers of the ...superior colliculus integrate trigeminotectal afferents from trigeminal complex and corticotectal afferents from barrel cortex. Using histological methods in mice, we found that trigeminotectal and corticotectal synapses overlap somewhat as they innervate the lower and upper portions of the intermediate granular layer, respectively. Using electrophysiological recordings and optogenetics in anesthetized mice in vivo, we showed that, similar to rats, whisker deflections produce two successive responses that are driven by trigeminotectal and corticotectal afferents. We then employed in vivo and slice experiments to characterize the response properties of these afferents. In vivo, corticotectal responses triggered by electrical stimulation of the barrel cortex evoke activity in the superior colliculus that increases with stimulus intensity and depresses with increasing frequency. In slices from adult mice, optogenetic activation of channelrhodopsin-expressing trigeminotectal and corticotectal fibers revealed that cells in the intermediate layers receive more efficacious trigeminotectal, than corticotectal, synaptic inputs. Moreover, the efficacy of trigeminotectal inputs depresses more strongly with increasing frequency than that of corticotectal inputs. The intermediate layers of superior colliculus appear to be tuned to process strong but infrequent trigeminal inputs and weak but more persistent cortical inputs, which explains features of sensory responsiveness, such as the robust rapid sensory adaptation of whisker responses in the superior colliculus.
Assessment of Rehabilitation Infrastructure in Peru Fuhs, Amy K; LaGrone, Lacey N; Moscoso Porras, Miguel G ...
Archives of physical medicine and rehabilitation,
06/2018, Letnik:
99, Številka:
6
Journal Article
Recenzirano
Odprti dostop
To assess rehabilitation infrastructure in Peru in terms of the World Health Organization (WHO) health systems building blocks.
Anonymous quantitative survey; questions were based on the WHO's ...Guidelines for Essential Trauma Care and rehabilitation professionals' input.
Large public hospitals and referral centers and an online survey platform.
Convenience sample of hospital personnel working in rehabilitation and neurology (N=239), recruited through existing contacts and professional societies.
Not applicable.
Outcome measures were for 4 WHO domains: health workforce, health service delivery, essential medical products and technologies, and health information systems.
Regarding the domain of health workforce, 47% of physical therapists, 50% of occupational therapists, and 22% of physiatrists never see inpatients. Few reported rehabilitative nurses (15%) or prosthetist/orthotists (14%) at their hospitals. Even at the largest hospitals, most reported ≤3 occupational therapists (54%) and speech-language pathologists (70%). At hospitals without speech-language pathologists, physical therapists (49%) or nobody (34%) perform speech-language pathology roles. At hospitals without occupational therapists, physical therapists most commonly (59%) perform occupational therapy tasks. Alternate prosthetist/orthotist task performers are occupational therapists (26%), physical therapists (19%), and physicians (16%). Forty-four percent reported interdisciplinary collaboration. Regarding the domain of health services, the most frequent inpatient and outpatient rehabilitation barriers were referral delays (50%) and distance/transportation (39%), respectively. Regarding the domain of health information systems, 28% reported rehabilitation service data collection. Regarding the domain of essential medical products and technologies, electrophysical agents (88%), gyms (81%), and electromyography (76%) were most common; thickened liquids (19%), swallow studies (24%), and cognitive training tools (28%) were least frequent.
Rehabilitation emphasis is on outpatient services, and there are comparatively adequate numbers of physical therapists and physiatrists relative to rehabilitation personnel. Financial barriers seem low for accessing existing services. There appear to be shortages of inpatient rehabilitation, specialized services, and interdisciplinary collaboration. These may be addressed by redistributing personnel and investing in education and equipment for specialized services. Further examination of task sharing's role in Peru's rehabilitation services is necessary to evaluate its potential to address deficiencies.
Background
Evidence for the positive impact of quality improvement (QI) programs on morbidity, mortality, patient satisfaction, and cost is strong. Data regarding the status of QI programs in low- ...and middle-income countries, as well as in-depth examination of barriers and facilitators to their implementation, are limited.
Methods
This cross-sectional, descriptive study employed a mixed-methods design, including distribution of an anonymous quantitative survey and individual interviews with healthcare providers who participate in the care of the injured at ten large hospitals in Lima, Peru.
Results
Key areas identified for improvement in morbidity and mortality (M&M) conferences were the standardization of case selection, incorporation of evidence from the medical literature into case presentation and discussion, case documentation, and the development of a clear plan for case follow-up. The key barriers to QI program implementation were a lack of prioritization of QI, lack of sufficient human and administrative resources, lack of political support, and lack of education on QI practices.
Conclusions
A national program that makes QI a required part of all health providers’ professional training and responsibilities would effectively address a majority of identified barriers to QI programs in Peru. Specifically, the presence of basic QI elements, such as M&M conferences, should be required at hospitals that train pre-graduate physicians. Alternatively, short of this national-level organization, efforts that capitalize on local examples through apprenticeships between institutions or integration of QI into continuing medical education would be expected to build on the facilitators for QI programs that exist in Peru.
The objective of this research was to compare the healthy behaviors and caries index of young people in school to obtain an overview of their lifestyles, which would enable the development of ...educational programs for the promotion of oral health. The study design was carried out using a descriptive, cross-sectional, and observational methodology with a mixed approach. 380 twelve-year-old students participated in this research conducted in the city of Riobamba-Ecuador. The techniques used were observational and surveys with their respective instruments, the Dental Clinical History, and the Health Behavior in School-aged Children 2014-Spain questionnaire. The community index of the Decayed, Missing due to caries, and Filled Teeth (DMFT) reflected a high level (6.47) in the study subjects. A variety of foods such as fruits, chips, vegetables, candy, sugar-containing drinks, meat, fish, dairy, and cereals were consumed at least once a week by most students. Two statistically significant associations were demonstrated in this investigation. The first one was between fruit consumption and the DMFT index, the second one was between vegetable consumption and the DMFT index. Both associations showed significant values (
) of 0.049 and 0.028, respectively; these were not determining indicators since caries is a multifactorial pathology, which can develop not only as a product of poor eating habits.
•Novel high resolution finite volume schemes on moving nonconforming unstructured meshes.•Significantly improved robustness in shear flows compared to conforming ALE schemes.•Locally and globally ...conservative ALE schemes that respect the geometric conservation law (GCL).•The fully discrete one-step scheme can be derived from a space-time conservation formalism.•Well-balanced for non-trivial stationary solutions of the governing PDE.
In this paper, we present a novel second-order accurate Arbitrary-Lagrangian-Eulerian (ALE) finite volume scheme on moving nonconforming polygonal grids, in order to avoid the typical mesh distortion caused by shear flowsin Lagrangian-type methods. In our new approach the nonconforming element interfaces are not defined by the user, but they are automatically detected by the algorithm if the tangential velocity difference across an element interface is sufficiently large. The grid nodes that are sufficiently far away from a shear wave are moved with a standard node solver, while at the interface we insert a new set of nodes that can slide along the interface in a nonconforming manner. In this way, the elements on both sides of the shear wave can move with a different velocity, without producing highly distorted elements.
The core of the proposed method is the use of a space-time conservation formulation in the construction of the final finite volume scheme, which completely avoids the need of an additional remapping stage, hence the new method is a so-called direct ALE scheme. For this purpose, the governing PDE system is rewritten at the aid of the space-time divergence operator and then a fully discrete one-step discretization is obtained by integrating over a set of closed space-time control volumes. The nonconforming sliding of nodes along an edge requires the insertion or the deletion of nodes and edges, and in particular the space-time faces of an element can be shared between more than two cells.
Due to the space-time conservation formulation, the geometric conservation law (GCL) is automatically satisfied by construction, even on moving nonconforming meshes. Moreover, the mesh quality remains high and, as a direct consequence, also the time step remains almost constant in time, even for highly sheared vortex flows. In this paper we focus mainly on logically straight slip-line interfaces, but we show also first results for general slide lines that are not logically straight. Second order of accuracy in space and time is obtained by using a MUSCL-Hancock strategy, together with a Barth and Jespersen slope limiter.
The accuracy of the new scheme has been further improved by incorporating a special well balancing technique that is able to maintain particular stationary solutions of the governing PDE system up to machine precision. In particular, we consider steady vortex solutions of the shallow water equations, where the pressure gradient is in equilibrium with the centrifugal forces.
A large set of different numerical tests has been carried out in order to check the accuracy and the robustness of the new method for both smooth and discontinuous problems. In particular we have compared the results for a steady vortex in equilibrium solved with a standard conforming ALE method (without any rezoning technique) and with our new nonconforming ALE scheme, to show that the new nonconforming scheme is able to avoid mesh distortion in vortex flows even after very long simulation times.
This paper is devoted to benchmarking the Multilayer-HySEA model using laboratory
experimental data for landslide-generated tsunamis.
This article deals with rigid slides, and the second part, in a ...companion paper,
addresses granular slides.
The US National Tsunami Hazard and Mitigation Program (NTHMP) has proposed the experimental data used
and established for the NTHMP Landslide Benchmark Workshop, held in January 2017 at Galveston (Texas).
The first three benchmark problems proposed in this workshop deal with rigid slides. Rigid slides must be simulated as a moving
bottom topography, and, therefore, they must be modeled as a prescribed boundary condition.
These three benchmarks are used here to validate the Multilayer-HySEA model.
This new HySEA model consists of an efficient hybrid finite-volume–finite-difference implementation on GPU architectures of a non-hydrostatic multilayer model.
A brief description of model equations, dispersive properties, and the numerical scheme is included.
The benchmarks are described and the numerical results compared against the lab-measured data for each of them.
The specific aim is to validate this new code for tsunamis generated by rigid slides.
Nevertheless, the overall objective of the current benchmarking effort is to produce a ready-to-use numerical
tool for real-world landslide-generated tsunami hazard assessment.
This tool has already been used to reproduce the Port Valdez, Alaska, 1964 and Stromboli, Italy, 2002 events.
Summary Background Cancer of unknown primary ranks in the top ten cancer presentations and has an extremely poor prognosis. Identification of the primary tumour and development of a tailored ...site-specific therapy could improve the survival of these patients. We examined the feasability of using DNA methylation profiles to determine the occult original cancer in cases of cancer of unknown primary. Methods We established a classifier of cancer type based on the microarray DNA methylation signatures (EPICUP) in a training set of 2790 tumour samples of known origin representing 38 tumour types and including 85 metastases. To validate the classifier, we used an independent set of 7691 known tumour samples from the same tumour types that included 534 metastases. We applied the developed diagnostic test to predict the tumour type of 216 well-characterised cases of cancer of unknown primary. We validated the accuracy of the predictions from the EPICUP assay using autopsy examination, follow-up for subsequent clinical detection of the primary sites months after the initial presentation, light microscopy, and comprehensive immunohistochemistry profiling. Findings The tumour type classifier based on the DNA methylation profiles showed a 99·6% specificity (95% CI 99·5–99·7), 97·7% sensitivity (96·1–99·2), 88·6% positive predictive value (85·8–91·3), and 99·9% negative predictive value (99·9–100·0) in the validation set of 7691 tumours. DNA methylation profiling predicted a primary cancer of origin in 188 (87%) of 216 patients with cancer with unknown primary. Patients with EPICUP diagnoses who received a tumour type-specific therapy showed improved overall survival compared with that in patients who received empiric therapy (hazard ratio HR 3·24, p=0·0051 95% CI 1·42–7·38; log-rank p=0·0029). Interpretation We show that the development of a DNA methylation based assay can significantly improve diagnoses of cancer of unknown primary and guide more precise therapies associated with better outcomes. Epigenetic profiling could be a useful approach to unmask the original primary tumour site of cancer of unknown primary cases and a step towards the improvement of the clinical management of these patients. Funding European Research Council (ERC), Cellex Foundation, the Institute of Health Carlos III (ISCIII), Cancer Australia, Victorian Cancer Agency, Samuel Waxman Cancer Research Foundation, the Health and Science Departments of the Generalitat de Catalunya, and Ferrer.
Background Although still uncommon, pregnancy frequency in women on maintenance hemodialysis therapy has increased in the past 20 years. Most published reports suggest that intensified hemodialysis ...regimens result in better pregnancy outcomes. The small number of patients investigated in all reported series is the main limitation of the available studies. Study Design Retrospective case series. Setting & Participants Data for all pregnancies that occurred in 1988-2008 in women undergoing maintenance hemodialysis (52 pregnancies) at the São Paulo University Medical School (São Paulo, Brazil). Outcomes & Measurements We analyzed maternal and fetal outcomes of 52 pregnancies, as well as their relationship with various clinical, laboratory, and hemodialysis parameters, such as pre-eclampsia, pregnancy before or after dialysis therapy, hemodialysis dose, polyhydramnios, anemia, and predialysis serum urea level. In addition, logistic regression models for a composite adverse fetal outcome (perinatal death or extremely premature delivery) and linear regression models for birth weight were built. Results 87% overall rate of successful delivery, with a mean gestational age of 32.7 ± 3.1 weeks. Pre-eclampsia was associated with a poor prognosis compared with pregnancies without pre-eclampsia: a successful delivery rate of 60% versus 92.9% ( P = 0.02), extremely premature delivery rate of 77.8% versus 3.3% ( P < 0.001), lower gestational age ( P < 0.001), and birth weight ( P < 0.001). Patients with an adverse composite fetal outcome had a higher frequency of pre-eclampsia ( P < 0.001), lower frequency of polyhydramnios ( P = 0.03), lower third-trimester hematocrit ( P = 0.03), and higher predialysis serum urea level ( P = 0.03). The same results were seen for birth weight. Limitations Retrospective data analysis. The absence of creatinine clearance measurements did not allow evaluation of the impact of residual renal function on fetal outcome. Conclusions Outcomes of pregnancy in women undergoing hemodialysis often are good. Pre-eclampsia, third-trimester hematocrit, polyhydramnios, and predialysis serum urea level are important variables associated with fetal outcome and birth weight.
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