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Frontiers in Neuroscience 2023To outline the complex biological rhythms underlying the time-to-action of goal-oriented behavior in the adult brain, we employed a Boolean Algebra model based on...
To outline the complex biological rhythms underlying the time-to-action of goal-oriented behavior in the adult brain, we employed a Boolean Algebra model based on Control Systems Theory. This suggested that "timers" of the brain reflect a metabolic excitation-inhibition balance and that healthy clocks underlying goal-oriented behavior (optimal range of signal variability) are maintained by XOR logic gates in parallel sequences between cerebral levels. Using truth tables, we found that XOR logic gates reflect healthy, regulated time-to-action events between levels. We argue that the brain clocks of time-to-action are active within multileveled, parallel-sequence complexes shaped by experience. We show the metabolic components of time-to-action in levels ranging from the atom level through molecular, cellular, network and inter-regional levels, operating as parallel sequences. We employ a thermodynamic perspective, suggest that clock genes calculate free energy versus entropy and derived time-to-action level-wise as a master controller, and show that they are receivers, as well as transmitters of information. We argue that regulated multileveled time-to-action processes correspond to Boltzmann's thermodynamic theorem of micro- and macro-states, and that the available metabolic free-energy-entropy matrix determines the brain's reversible states for its age-appropriate chrono-properties at given moments. Thus, healthy timescales are not a precise number of nano- or milliseconds of activity nor a simple phenotypic distinction between slow vs. quick time-to-action, but rather encompass a range of variability, which depends on the molecules' size and dynamics with the composition of receptors, protein and RNA isoforms.
PubMed: 37378011
DOI: 10.3389/fnins.2023.1171765 -
BMJ Open Sep 2022The aetiology of gastric cancer is still unclear but (HP) infection and chronic atrophic gastritis (AG) are recognised as two major risk factors for gastric cancer....
INTRODUCTION
The aetiology of gastric cancer is still unclear but (HP) infection and chronic atrophic gastritis (AG) are recognised as two major risk factors for gastric cancer. GastroPanel (GP) test is the first non-invasive diagnostic tool to detect AG and HP infection.The aim of the study is to conduct a systematic review and meta-analysis to review published literature about the GP test for diagnosing AG and HP infection, with the objective of estimating the diagnostic performance indices of GP for AG and HP infection.
METHODS AND ANALYSIS
This protocol of systematic review and meta-analysis is reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols statement guidelines. PubMed, Embase, Web of Science and Cochrane Library databases will be systematically searched from inception to March 2022 for eligible studies. No language limitations were imposed. The studies will be downloaded into the EndNote V.X9 software and duplicates will be removed. Two review authors independently screened the full text against the inclusion criteria, extracted the data from each included study by using a piloted data extraction form and conducted risk of bias assessment, resolving disagreement by discussion. Results will be synthesised narratively in summary tables, using a random-effect bivariate model, and we fit a hierarchical summary receiver operating characteristic curve.
ETHICS AND DISSEMINATION
This systematic review will include data extracted form published studies, therefore, does not require ethics approval. The results of this study will be submitted to a peer-reviewed journal.
PROSPERO REGISTRATION NUMBER
CRD42021282616.
Topics: Biomarkers; Gastritis, Atrophic; Helicobacter Infections; Helicobacter pylori; Humans; Meta-Analysis as Topic; Stomach Neoplasms; Systematic Reviews as Topic
PubMed: 36171026
DOI: 10.1136/bmjopen-2022-062849 -
Journal of Endourology Jun 2021Nonabsorbable monofilament suture is traditionally used to secure vaginal mesh for robot-assisted sacral colpopexy (RASC) but can become exposed postoperatively...
Nonabsorbable monofilament suture is traditionally used to secure vaginal mesh for robot-assisted sacral colpopexy (RASC) but can become exposed postoperatively requiring invasive vaginal removal. Polydioxanone delayed absorbable suture may avoid this. We sought to determine the objective and subjective impact of suture choice for mesh fixation. A cohort study was undertaken using a prospective registry and subjects were grouped based on type of suture at the time of RASC. Apical failure was defined as C point descent of >2 cm, anterior compartment failure was defined as pelvic organ prolapse quantification (POP-Q) Ba point of >0, and posterior compartment failure was defined as Bp point of >0. Patient-reported outcomes included urogenital distress inventory (UDI)-6 and QoL. Two-tailed -test and chi-squared were used for analysis. A total of 119 women underwent RASC between 2009 and 2016. Patients had similar preoperative characteristics (Table 1). All POP-Q, UDI-6, and quality of life (QoL) scores improved postoperatively (Tables 1 and 2). Apical failure was noted in 0, anterior failure was noted in 7 (average Ba +1.1 cm in failures), and posterior failure was noted in 4 (mean Bp +1.0 cm) at 16 months' follow-up. Failures in the anterior compartment were much more common in the nonabsorbable monofilament cohort (Table 2). Failures in the apical and posterior compartments were not significantly different between groups. Nine suture erosions were noted in the nonabsorbable monofilament cohort, five requiring excision in the clinic and two in the operating room. Two suture erosions were noted in the delayed absorbable cohort, 0 required excision. Postoperative UDI-6 and QoL scores did not vary significantly between groups (5.3 ± 4.0 5.1 ± 4.0, = not significant (NS), 2.8 ± 2.0 2.8 ± 2.2, = NS). [Table: see text] [Table: see text] Securing mesh with delayed absorbable monofilament did not appear to increase risk of failure in patients undergoing RASC and eliminates the need for suture excision postoperatively.
Topics: Cohort Studies; Female; Humans; Pelvic Organ Prolapse; Quality of Life; Robotic Surgical Procedures; Robotics; Surgical Mesh; Sutures; Treatment Outcome
PubMed: 32037875
DOI: 10.1089/end.2018.0029 -
Ecology and Evolution Apr 2019The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for...
The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here, we present a wrapper tool named EasyCodeML that provides a user-friendly graphical interface for using CodeML. EasyCodeML has a custom running mode in which parameters can be adjusted to meet different requirements. It also offers a preset running mode in which an evolutionary analysis pipeline and publication-quality tables can be exported by a single click. EasyCodeML allows visualized, interactive tree labelling, which greatly simplifies the use of the branch, branch-site, and clade models of selection. The program allows comparison of major codon-based models for analyses of selection. EasyCodeML is a stand-alone package that is supported in Windows, Mac, and Linux operating systems, and is freely available at https://github.com/BioEasy/EasyCodeML.
PubMed: 31015974
DOI: 10.1002/ece3.5015 -
The Cochrane Database of Systematic... May 2021Pressure ulcers (also known as injuries, pressure sores, decubitus ulcers and bed sores) are localised injuries to the skin or underlying soft tissue, or both, caused by... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Pressure ulcers (also known as injuries, pressure sores, decubitus ulcers and bed sores) are localised injuries to the skin or underlying soft tissue, or both, caused by unrelieved pressure, shear or friction. Reactive surfaces that are not made of foam or air cells can be used for preventing pressure ulcers.
OBJECTIVES
To assess the effects of non-foam and non-air-filled reactive beds, mattresses or overlays compared with any other support surface on the incidence of pressure ulcers in any population in any setting.
SEARCH METHODS
In November 2019, we searched the Cochrane Wounds Specialised Register; the Cochrane Central Register of Controlled Trials (CENTRAL); Ovid MEDLINE (including In-Process & Other Non-Indexed Citations); Ovid Embase and EBSCO CINAHL Plus. We also searched clinical trials registries for ongoing and unpublished studies, and scanned reference lists of relevant included studies as well as reviews, meta-analyses and health technology reports to identify additional studies. There were no restrictions with respect to language, date of publication or study setting.
SELECTION CRITERIA
We included randomised controlled trials that allocated participants of any age to non-foam or non-air-filled reactive beds, overlays or mattresses. Comparators were any beds, overlays or mattresses used.
DATA COLLECTION AND ANALYSIS
At least two review authors independently assessed studies using predetermined inclusion criteria. We carried out data extraction, 'Risk of bias' assessment using the Cochrane 'Risk of bias' tool, and the certainty of the evidence assessment according to Grading of Recommendations, Assessment, Development and Evaluations methodology. If a non-foam or non-air-filled surface was compared with surfaces that were not clearly specified, then the included study was recorded and described but not considered further in any data analyses.
MAIN RESULTS
We included 20 studies (4653 participants) in this review. Most studies were small (median study sample size: 198 participants). The average participant age ranged from 37.2 to 85.4 years (median: 72.5 years). Participants were recruited from a wide range of care settings but were mainly from acute care settings. Almost all studies were conducted in Europe and America. Of the 20 studies, 11 (2826 participants) included surfaces that were not well described and therefore could not be fully classified. We synthesised data for the following 12 comparisons: (1) reactive water surfaces versus alternating pressure (active) air surfaces (three studies with 414 participants), (2) reactive water surfaces versus foam surfaces (one study with 117 participants), (3) reactive water surfaces versus reactive air surfaces (one study with 37 participants), (4) reactive water surfaces versus reactive fibre surfaces (one study with 87 participants), (5) reactive fibre surfaces versus alternating pressure (active) air surfaces (four studies with 384 participants), (6) reactive fibre surfaces versus foam surfaces (two studies with 228 participants), (7) reactive gel surfaces on operating tables followed by foam surfaces on ward beds versus alternating pressure (active) air surfaces on operating tables and subsequently on ward beds (two studies with 415 participants), (8) reactive gel surfaces versus reactive air surfaces (one study with 74 participants), (9) reactive gel surfaces versus foam surfaces (one study with 135 participants), (10) reactive gel surfaces versus reactive gel surfaces (one study with 113 participants), (11) reactive foam and gel surfaces versus reactive gel surfaces (one study with 166 participants) and (12) reactive foam and gel surfaces versus foam surfaces (one study with 91 participants). Of the 20 studies, 16 (80%) presented findings which were considered to be at high overall risk of bias.
PRIMARY OUTCOME
Pressure ulcer incidence We did not find analysable data for two comparisons: reactive water surfaces versus foam surfaces, and reactive water surfaces versus reactive fibre surfaces. Reactive gel surfaces used on operating tables followed by foam surfaces applied on hospital beds (14/205 (6.8%)) may increase the proportion of people developing a new pressure ulcer compared with alternating pressure (active) air surfaces applied on both operating tables and hospital beds (3/210 (1.4%) (risk ratio 4.53, 95% confidence interval 1.31 to 15.65; 2 studies, 415 participants; I = 0%; low-certainty evidence). For all other comparisons, it is uncertain whether there is a difference in the proportion of participants developing new pressure ulcers as all data were of very low certainty. Included studies did not report time to pressure ulcer incidence for any comparison in this review. Secondary outcomes Support-surface-associated patient comfort: the included studies provide data on this outcome for one comparison. It is uncertain if there is a difference in patient comfort between alternating pressure (active) air surfaces and reactive fibre surfaces (one study with 187 participants; very low-certainty evidence). All reported adverse events: there is evidence on this outcome for one comparison. It is uncertain if there is a difference in adverse events between reactive gel surfaces followed by foam surfaces and alternating pressure (active) air surfaces applied on both operating tables and hospital beds (one study with 198 participants; very low-certainty evidence). We did not find any health-related quality of life or cost-effectiveness evidence for any comparison in this review.
AUTHORS' CONCLUSIONS
Current evidence is generally uncertain about the differences between non-foam and non-air-filled reactive surfaces and other surfaces in terms of pressure ulcer incidence, patient comfort, adverse effects, health-related quality of life and cost-effectiveness. Reactive gel surfaces used on operating tables followed by foam surfaces applied on hospital beds may increase the risk of having new pressure ulcers compared with alternating pressure (active) air surfaces applied on both operating tables and hospital beds. Future research in this area should consider evaluation of the most important support surfaces from the perspective of decision-makers. Time-to-event outcomes, careful assessment of adverse events and trial-level cost-effectiveness evaluation should be considered in future studies. Trials should be designed to minimise the risk of detection bias; for example, by using digital photography and adjudicators of the photographs being blinded to group allocation. Further review using network meta-analysis will add to the findings reported here.
Topics: Adult; Aged; Aged, 80 and over; Bedding and Linens; Beds; Bias; Elasticity; Humans; Incidence; Middle Aged; Pressure Ulcer; Randomized Controlled Trials as Topic; Viscoelastic Substances; Water
PubMed: 34097764
DOI: 10.1002/14651858.CD013623.pub2 -
Frontiers in Robotics and AI 2021Modern Advanced Driver-Assistance Systems (ADAS) combine critical real-time and non-critical best-effort tasks and messages onto an integrated multi-core multi-SoC...
Modern Advanced Driver-Assistance Systems (ADAS) combine critical real-time and non-critical best-effort tasks and messages onto an integrated multi-core multi-SoC hardware platform. The real-time safety-critical software tasks have complex interdependencies in the form of end-to-end latency chains featuring, e.g., sensing, processing/sensor fusion, and actuating. The underlying real-time operating systems running on top of the multi-core platform use static cyclic scheduling for the software tasks, while the communication backbone is either realized through PCIe or Time-Sensitive Networking (TSN). In this paper, we address the problem of configuring ADAS platforms for automotive applications, which means deciding the mapping of tasks to processing cores and the scheduling of tasks and messages. Time-critical messages are transmitted in a scheduled manner via the timed-gate mechanism described in IEEE 802.1Qbv according to the pre-computed Gate Control List (GCL) schedule. We study the computation of the assignment of tasks to the available platform CPUs/cores, the static schedule tables for the real-time tasks, as well as the GCLs, such that task and message deadlines, as well as end-to-end task chain latencies, are satisfied. This is an intractable combinatorial optimization problem. As the ADAS platforms and applications become increasingly complex, such problems cannot be optimally solved and require problem-specific heuristics or metaheuristics to determine good quality feasible solutions in a reasonable time. We propose two metaheuristic solutions, a Genetic Algorithm (GA) and one based on Simulated Annealing (SA), both creating static schedule tables for tasks by simulating Earliest Deadline First (EDF) dispatching with different task deadlines and offsets. Furthermore, we use a List Scheduling-based heuristic to create the GCLs in platforms featuring a TSN backbone. We evaluate the proposed solution with real-world and synthetic test cases scaled to fit the future requirements of ADAS systems. The results show that our heuristic strategy can find correct solutions that meet the complex timing and dependency constraints at a higher rate than the related work approaches, i.e., the jitter constraints are satisfied in over 6 times more cases, and the task chain constraints are satisfied in 41% more cases on average. Our method scales well with the growing trend of ADAS platforms.
PubMed: 35059441
DOI: 10.3389/frobt.2021.762227 -
The Cochrane Database of Systematic... Sep 2014Intracranial vascular malformations (brain or pial/dural arteriovenous malformations/fistulae, and aneurysms) are the leading cause of intracerebral haemorrhage (ICH) in... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Intracranial vascular malformations (brain or pial/dural arteriovenous malformations/fistulae, and aneurysms) are the leading cause of intracerebral haemorrhage (ICH) in young adults. Early identification of the intracranial vascular malformation may improve outcome if treatment can prevent ICH recurrence. Catheter intra-arterial digital subtraction angiography (IADSA) is considered the reference standard for the detection an intracranial vascular malformation as the cause of ICH. Computed tomography angiography (CTA) and magnetic resonance angiography (MRA) are less invasive than IADSA and may be as accurate for identifying some causes of ICH.
OBJECTIVES
To evaluate the diagnostic test accuracy of CTA and MRA versus IADSA for the detection of intracranial vascular malformations as a cause of ICH.
SEARCH METHODS
We searched MEDLINE (1948 to August 2013), EMBASE (1980 to August 2013), MEDION (August 2013), the Database of Abstracts of Reviews of Effects (DARE; August 2013), the Health Technology Assessment Database (HTA; August 2013), ClinicalTrials.gov (August 2013), and WHO ICTRP (International Clinical Trials Register Portfolio; August 2013). We also performed a cited reference search for forward tracking of relevant articles on Google Scholar (http://scholar.google.com/), screened bibliographies, and contacted authors to identify additional studies.
SELECTION CRITERIA
We selected studies reporting data that could be used to construct contingency tables that compared CTA or MRA, or both, with IADSA in the same patients for the detection of intracranial vascular malformations following ICH.
DATA COLLECTION AND ANALYSIS
Two authors (CBJ and RA-SS) independently extracted data on study characteristics and measures of test accuracy. Two authors (CBJ and PMW) independently extracted data on test characteristics. We obtained data restricted to the subgroup undergoing IADSA in studies using multiple reference standards. We combined data using the bivariate model. We generated forest plots of the sensitivity and specificity of CTA and MRA and created a summary receiver operating characteristic plot.
MAIN RESULTS
Eleven studies (n = 927 participants) met our inclusion criteria. Eight studies compared CTA with IADSA (n = 526) and three studies compared MRA with IADSA (n = 401). Methodological quality varied considerably among studies, with partial verification bias in 7/11 (64%) and retrospective designs in 5/10 (50%). In studies of CTA, the pooled estimate of sensitivity was 0.95 (95% confidence interval (CI) 0.90 to 0.97) and specificity was 0.99 (95% CI 0.95 to 1.00). The results remained robust in a sensitivity analysis in which only studies evaluating adult patients (≥ 16 years of age) were included. In studies of MRA, the pooled estimate of sensitivity was 0.98 (95% CI 0.80 to 1.00) and specificity was 0.99 (95% CI 0.97 to 1.00). An indirect comparison of CTA and MRA using a bivariate model incorporating test type as one of the parameters failed to reveal a statistically significant difference in sensitivity or specificity between the two imaging modalities (P value = 0.6).
AUTHORS' CONCLUSIONS
CTA and MRA appear to have good sensitivity and specificity following ICH for the detection of intracranial vascular malformations, although several of the included studies had methodological shortcomings (retrospective designs and partial verification bias in particular) that may have increased apparent test accuracy.
Topics: Adolescent; Adult; Cerebral Angiography; Cerebral Hemorrhage; Female; Humans; Intracranial Arteriovenous Malformations; Magnetic Resonance Angiography; Male; Middle Aged; Randomized Controlled Trials as Topic; Sensitivity and Specificity; Tomography, X-Ray Computed
PubMed: 25177839
DOI: 10.1002/14651858.CD009372.pub2 -
PloS One 2020Acute infections of the middle ear are the most commonly treated childhood diseases. Because complications affect children's language learning and cognitive processes,...
Acute infections of the middle ear are the most commonly treated childhood diseases. Because complications affect children's language learning and cognitive processes, it is essential to diagnose these diseases in a timely and accurate manner. The prevailing literature suggests that it is difficult to accurately diagnose these infections, even for experienced ear, nose, and throat (ENT) physicians. Advanced care practitioners (e.g., nurse practitioners, physician assistants) serve as first-line providers in many primary care settings and may benefit from additional guidance to appropriately determine the diagnosis and treatment of ear diseases. For this purpose, we designed a content-based image retrieval (CBIR) system (called OtoMatch) for normal, middle ear effusion, and tympanostomy tube conditions, operating on eardrum images captured with a digital otoscope. We present a method that enables the conversion of any convolutional neural network (trained for classification) into an image retrieval model. As a proof of concept, we converted a pre-trained deep learning model into an image retrieval system. We accomplished this by changing the fully connected layers into lookup tables. A database of 454 labeled eardrum images (179 normal, 179 effusion, and 96 tube cases) was used to train and test the system. On a 10-fold cross validation, the proposed method resulted in an average accuracy of 80.58% (SD 5.37%), and maximum F1 score of 0.90 while retrieving the most similar image from the database. These are promising results for the first study to demonstrate the feasibility of developing a CBIR system for eardrum images using the newly proposed methodology.
Topics: Adult; Algorithms; Child; Databases as Topic; Deep Learning; Humans; Image Processing, Computer-Assisted; Information Storage and Retrieval; Reproducibility of Results; Tympanic Membrane
PubMed: 32413096
DOI: 10.1371/journal.pone.0232776 -
BMJ Open Aug 2018This study aimed to assess the accuracy of staging liver fibrosis in patients with non-alcoholic fatty liver disease (NAFLD) usingpoint shear wave elastography (pSWE)... (Meta-Analysis)
Meta-Analysis Review
Diagnostic accuracy of point shear wave elastography and transient elastography for staging hepatic fibrosis in patients with non-alcoholic fatty liver disease: a meta-analysis.
OBJECTIVE
This study aimed to assess the accuracy of staging liver fibrosis in patients with non-alcoholic fatty liver disease (NAFLD) usingpoint shear wave elastography (pSWE) and transient elastography (TE).
SETTING
Relevant records on NAFLD were retrieved from PubMed, Embase, Web of Science and the China National Knowledge Infrastructure databases up to 20 December 2017. A bivariate mixed-effects model was conducted to combine sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and area under the summary receiver operating characteristic curve (AUC) between pSWE and TE. A sensitivity analysis was implemented to explore the source of heterogeneity.
PARTICIPANTS
Patients with NAFLD who had a liver stiffness measurement using pSWE and TE before liver biopsy were enrolled according to the following criteria: 2×2 contingency tables can be calculated via the reported number of cases; sensitivity and specificity were excluded according to the following criteria: history of other hepatic damage, such as chronic hepatitis C, concurrent active hepatitis B infection, autoimmune hepatitis, suspicious drug usage and alcohol abuse.
RESULTS
Nine pSWE studies comprising a total of 982 patients and 11 TE studies comprising a total of 1753 patients were included. For detection of significant fibrosis, advanced fibrosis and cirrhosis, the summary AUC was 0.86 (95% CI 0.83 to 0.89), 0.94 (95% CI 0.91 to 0.95) and 0.95 (95% CI 0.93 to 0.97) for pSWE, and the summary AUC was 0.85 (95% CI 0.82 to 0.88), 0.92 (95% CI 0.89 to 0.94) and 0.94 (95% CI 0.93 to 0.97) for TE, respectively. The proportion of failure measurement was over tenfold as common with TE using an M probe compared with pSWE.
CONCLUSION
pSWE and TE, providing precise non-invasive staging of liver fibrosis in NAFLD, are promising techniques, particularly for advanced fibrosis and cirrhosis.
Topics: Elasticity Imaging Techniques; Humans; Liver Cirrhosis; Non-alcoholic Fatty Liver Disease; Severity of Illness Index
PubMed: 30139901
DOI: 10.1136/bmjopen-2018-021787 -
Bioinformatics (Oxford, England) Jan 2010Exploratory Gene Association Networks (EGAN) is a Java desktop application that provides a point-and-click environment for contextual graph visualization of...
UNLABELLED
Exploratory Gene Association Networks (EGAN) is a Java desktop application that provides a point-and-click environment for contextual graph visualization of high-throughput assay results. By loading the entire network of genes, pathways, interactions, annotation terms and literature references directly into memory, EGAN allows a biologist to repeatedly query and interpret multiple experimental results without incurring additional delays for data download/integration. Other compelling features of EGAN include: support for diverse -omics technologies, a simple and interactive graph display, sortable/searchable data tables, links to external web resources including > or = 240 000 articles at PubMed, hypergeometric and GSEA-like enrichment statistics, pipeline-compatible automation via scripting and the ability to completely customize and/or supplement the network with new/proprietary data.
AVAILABILITY
Runs on most operating systems via Java; downloadable from http://akt.ucsf.edu/EGAN/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Computational Biology; Databases, Genetic; Gene Regulatory Networks; Software
PubMed: 19933825
DOI: 10.1093/bioinformatics/btp656