Miracle-dz/UniFAR-FTUs huggingface dataset:
The Origin, Development, Application, Lessons Learned, and Future Regarding the Bayesian Network Relative Risk Model for Ecological Risk Assessment

In 2012, a regional risk assessment was published that applied Bayesian networks (BN) to the structure of the relative risk model. The original structure of the relative risk model (RRM) was published in the late 1990s and developed during the next decade. The RRM coupled with a Monte Carlo analysis was applied to calculating risk to a number of sites and a variety of questions. The sites included watersheds, terrestrial systems, and marine environments and included stressors such as nonindigenous species, effluents, pesticides, nutrients, and management options. However, it became apparent that there were limits to the original approach. In 2009, the relative risk model was transitioned into the structure of a BN. Bayesian networks had several clear advantages. First, BNs innately incorporated categories and, as in the case of the relative risk model, ranks to describe systems. Second, interactions between multiple stressors can be combined using several pathways and the conditional probability tables (CPT) to calculate outcomes. Entropy analysis was the method used to document model sensitivity. As with the RRM, the method has now been applied to a wide series of sites and questions, from forestry management, to invasive species, to disease, the interaction of ecological and human health endpoints, the flows of large rivers, and now the efficacy and risks of synthetic biology. The application of both methods have pointed to the incompleteness of the fields of environmental chemistry, toxicology, and risk assessment. The low frequency of exposure‐response experiments and proper analysis have limited the available outputs for building appropriate CPTs. Interactions between multiple chemicals, landscape characteristics, population dynamics and community structure have been poorly characterized even for critical environments. A better strategy might have been to first look at the requirements of modern risk assessment approaches and then set research priorities. Integr Environ Assess Manag 2021;17:79–94. © 2020 SETAC
Physical Fitness, Sex Considerations, and Academy Graduation for Law Enforcement Recruits.

Lockie, RG, Dawes, JJ, Dulla, JM, Orr, RM, and Hernandez, E. Physical fitness, sex considerations, and academy graduation for law enforcement recruits. J Strength Cond Res XX(X): 000-000, 2020-This study investigated the influence of fitness on academy graduation, and any between-sex differences, in law enforcement recruits. Data collected at the start of 4 training academies were retrospectively analyzed, including age, height, and body mass; waist circumference; waist-to-hip ratio; grip strength; vertical jump (VJ); 75-yard pursuit run; 2-kg medicine ball throw (MBT); push-ups, sit-ups, and arm ergometer revolutions in 60 seconds; and 20-m multistage fitness test (20MSFT) shuttles. Recruits were categorized into graduated (GRAD = 269) and separated (did not graduate; SEP = 42) groups. SEP recruits were not split according to separation reasons, just whether they did or not. This categorization also occurred for male subjects (GRAD = 228; SEP = 32) and female subjects (GRAD = 41; SEP = 10). Independent samples t-tests calculated between-group differences for all recruits combined, male subjects, and female subjects. Correlations and stepwise linear regression calculated relationships between the data and graduation. The t-test (p ≤ 0.016) and correlation (r = ±0.137-0.296; p < 0.05) data indicated that SEP recruits (both sexes combined) were older and performed poorer in every fitness test except grip strength and VJ. SEP male subjects were older and performed poorer in all tests except grip strength (p ≤ 0.009). SEP female subjects scored lower in the arm ergometer (p = 0.008). The regression equation for all recruits found that age, 20MSFT (aerobic fitness), MBT (upper-body power), and arm ergometer (upper-body endurance) were academy graduation predictors (r = 0.169; p < 0.001). For the male recruits, the predictors were age, MBT, and 20MSFT (r = 0.182; p ≤ 0.001), and for female recruits, arm ergometer and 20MSFT (r = 0.213; p ≤ 0.003). Recruits should improve multiple fitness aspects, including muscular endurance, power, and aerobic fitness, to enhance graduation potential.
Accurate Retinal Vessel Segmentation in Color Fundus Images via Fully Attention-Based Networks

Automatic retinal vessel segmentation is important for the diagnosis and prevention of ophthalmic diseases. The existing deep learning retinal vessel segmentation models always treat each pixel equally. However, the multi-scale vessel structure is a vital factor affecting the segmentation results, especially in thin vessels. To address this crucial gap, we propose a novel Fully Attention-based Network (FANet) based on attention mechanisms to adaptively learn rich feature representation and aggregate the multi-scale information. Specifically, the framework consists of the image pre-processing procedure and the semantic segmentation networks. Green channel extraction (GE) and contrast limited adaptive histogram equalization (CLAHE) are employed as pre-processing to enhance the texture and contrast of retinal blood images. Besides, the network combines two types of attention modules with the U-Net. We propose a lightweight dual-direction attention block to model global dependencies and reduce intra-class inconsistencies, in which the weights of feature maps are updated based on the semantic correlation between pixels. The dual-direction attention block utilizes horizontal and vertical pooling operations to produce the attention map. In this way, the network aggregates global contextual information from semantic-closer regions or a series of pixels belonging to the same object category. Meanwhile, we adopt the selective kernel (SK) unit to replace the standard convolution for obtaining multi-scale features of different receptive field sizes generated by soft attention. Furthermore, we demonstrate that the proposed model can effectively identify irregular, noisy, and multi-scale retinal vessels. The abundant experiments on DRIVE, STARE, and CHASE_DB1 datasets show that our method achieves state-of-the-art performance.
Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events.

AIMS Cardiac electrical activity is extraordinarily robust. However, when it goes wrong it can have fatal consequences. Electrical activity in the heart is controlled by the carefully orchestrated activity of more than a dozen different ion conductances. Whilst there is considerable variability in cardiac ion channel expression levels between individuals, studies in rodents have indicated that there are modules of ion channels whose expression co-vary. The aim of this study was to investigate whether meta-analytic co-expression analysis of large-scale gene expression data sets could identify modules of co-expressed cardiac ion channel genes in human hearts that are of functional importance. METHODS AND RESULTS Meta-analysis of 3653 public human RNA-seq datasets identified a strong correlation between expression of CACNA1C (L-type calcium current, ICaL) and KCNH2 (rapid delayed rectifier K+ current, IKr), which was also observed in human adult heart tissue samples. In silico modeling suggested that co-expression of CACNA1C and KCNH2 would limit the variability in action potential duration seen with variations in expression of ion channel genes and reduce susceptibility to early afterdepolarizations, a surrogate marker for pro-arrhythmia. We also found that levels of KCNH2 and CACNA1C expression are correlated in human induced pluripotent stem cell derived cardiac myocytes and the levels of CACNA1C and KCNH2 expression were inversely correlated with the magnitude of changes in repolarization duration following inhibition of IKr. CONCLUSIONS Meta-analytic approaches of multiple independent human gene expression datasets can be used to identify gene modules that are important for regulating heart function. Specifically, we have verified that there is co-expression of CACNA1C and KCNH2 ion channel genes in human heart tissue, and in silico analyses suggest that CACNA1C-KCNH2 co-expression increases the robustness of cardiac electrical activity. TRANSLATIONAL PERSPECTIVE Here, we show, using meta-analysis of multiple independent human gene expression datasets, that there is co-expression of KCNH2-CACNA1C in human heart tissue which was then confirmed in human cardiac myocytes derived from induced pluripotent stem cells. Both in silico and functional studies show that the co-expression of CACNA1C and KCNH2 increases the robustness of cardiac electrical signalling. Our data also suggest that those patients who express higher levels of CACNA1C and KCNH2 are likely to be more susceptible to arrhythmias when exposed to drugs that block IKr, the major cause of drug-induced cardiac arrhythmias.
Molecular basis for histone H3 “K4me3-K9me3/2” methylation pattern readout by Spindlin1

Histone recognition by “reader” modules serves as a fundamental mechanism in epigenetic regulation. Previous studies have shown that Spindlin1 is a reader of histone H3K4me3 as well as “K4me3-R8me2a” and promotes transcription of rDNA or Wnt/TCF4 target genes. Here we show that Spindlin1 also acts as a potent reader of histone H3 “K4me3-K9me3/2” bivalent methylation pattern. Calorimetric titration revealed a binding affinity of 16 nm between Spindlin1 and H3 “K4me3-K9me3” peptide, which is one to three orders of magnitude stronger than most other histone readout events at peptide level. Structural studies revealed concurrent recognition of H3K4me3 and H3K9me3/2 by aromatic pockets 2 and 1 of Spindlin1, respectively. Epigenomic profiling studies showed that Spindlin1 colocalizes with both H3K4me3 and H3K9me3 peaks in a subset of genes enriched in biological processes of transcription and its regulation. Moreover, the distribution of Spindlin1 peaks is primarily associated with H3K4me3 but not H3K9me3, which suggests that Spindlin1 is a downstream effector of H3K4me3 generated in heterochromatic regions. Collectively, our work calls attention to an intriguing function of Spindlin1 as a potent H3 “K4me3-K9me3/2” bivalent mark reader, thereby balancing gene expression and silencing in H3K9me3/2-enriched regions.
Remodeling the Skeletal Muscle Extracellular Matrix in Older Age—Effects of Acute Exercise Stimuli on Gene Expression

With advancing age, the skeletal muscle extracellular matrix (ECM) undergoes fibrotic changes that may lead to increased muscle stiffness, injury susceptibility and strength loss. This study tested the potential of different exercises to counter these changes by stimulating the activity of genes associated with ECM remodeling. Twenty-six healthy men (66.9 ± 3.9 years) were stratified to two of four groups, performing unilateral (i) conventional resistance exercise, (ii) conventional resistance exercise followed by self-myofascial release (CEBR), (iii) eccentric-only exercise (ECC) or (iv) plyometric jumps (PLY). The non-trained leg served as control. Six hours post-exercise, vastus lateralis muscle biopsy samples were analyzed for the expression of genes associated with ECM collagen synthesis (COL1A1), matrix metallopeptidases (collagen degradation; MMPs) and peptidase inhibitors (TIMP1). Significant between-group differences were found for MMP3, MMP15 and TIMP1, with the greatest responses in MMP3 and TIMP1 seen in CEBR and in MMP15 in ECC. MMP9 (3.24–3.81-fold change) and COL1A1 (1.47–2.40-fold change) were increased in CEBR and PLY, although between-group differences were non-significant. The expression of ECM-related genes is exercise-specific, with CEBR and PLY triggering either earlier or stronger remodeling than other stimuli. Training studies will test whether execution of such exercises may help counter age-associated muscle fibrosis.
Six Sigma for workplace safety improvement: improving hazards and unsafe conditions in a metallic packaging manufacturing company

Six Sigma has been applied as a business process improvement strategy in many companies worldwide with great results. On the other hand, workplace safety constitutes a key issue for company managers due to their responsibility. The aim of this article is to demonstrate how using Six Sigma can reduce accidents. A case study is conducted on a large European metallic packaging manufacturing company. As a result, the company presented a reduction of lost time accidents from 97 to 30 that saved a lot of time and cost. The σ value achieved was 4.24. This project shows the effectiveness of Six Sigma as an improvement tool in the human resources area, despite most of the previous Six Sigma research being focused on manufacturing aspects. The case studied can be useful either for large companies or small and medium-sized companies interested in improving safety.
Preparation of Hybrid Alginate-Chitosan Aerogel as Potential Carriers for Pulmonary Drug Delivery

This study aims to prepare hybrid chitosan-alginate aerogel microparticles without using additional ionic crosslinker as a possible pulmonary drug delivery system. The microparticles were prepared using the emulsion gelation method. The effect of the mixing order of the biopolymer within the emulsion and the surfactant used on final particle properties were investigated. Physicochemical characterizations were performed to evaluate particle size, density, morphology, surface area, surface charge, and the crystallinity of the preparation. The developed preparation was evaluated for its acute toxicity in adult male Sprague-Dawley rats. Measurements of zeta potential suggest that the surface charge depends mainly on the surfactant type while the order of biopolymer mixing has less impact on the surface charge. Chitosan amphiphilic properties changed the hydrophilic-lipophilic balance (HLB) of the emulsifying agents. The specific surface area of the prepared microparticles was in the range of (29.36–86.20) m2/g with a mesoporous pore size of (12.48–13.38) nm and pore volume of (0.09–0.29) cm3/g. The calculated aerodynamic diameter of the prepared particles was in the range of (0.17–2.29 µm). Toxicity studies showed that alginate-chitosan carrier developed herein caused mild lung inflammation with some renal and hepatic toxicities.
On higher order computations, rewiring the connectome, and non-von Neumann computer architecture.

Structural plasticity in the brain (i.e. rewiring the connectome) may be viewed as mechanisms for dynamic reconfiguration of neural circuits. First order computations in the brain are done by static neural circuits, whereas higher order computations are done by dynamic reconfigurations of the links (synapses) between the neural circuits. Static neural circuits correspond to first order computable functions. Synapse creation (activation) between them correspond to the mathematical notion of function composition. Functionals are higher order functions that take functions as their arguments. The construction of functionals is based on dynamic reconfigurations of function compositions. Perhaps the functionals correspond to rewiring mechanisms of the connectome. The architecture of human mind is different than the von Neumann computer architecture. Higher order computations in the human brain (based on functionals) may suggest a non-von Neumann computer architecture, a challenge posed by John Backus in 1977 \cite{Backus}. The presented work is a substantial extension and revision of the paper published in Proc. ICANN2016.
Population genomics of parallel adaptation

Parallel evolution is one of the striking patterns in nature. The presence of repeated evolution of the same phenotypes, suites of traits, and adaptations suggests a strong role for natural selection in shaping biological diversity. The reasoning is straightforward: each instance of repeated evolution makes it less likely that these features evolved neutrally or due to stochastic forces in each population or species. With the growing sequencing capability, we are now poised to examine the genetic basis of parallel evolution in model and nonmodel systems. On pages 4102‐4117 of this issue of Molecular Ecology, van Boheemen and Hodgins (2020) provide an exemplar study of this kind, using common ragweed (Ambrosia artemisiifolia; Figure 1a). Their study is noteworthy and ambitious in many respects, and we think will serve as a model for studying parallel adaptation, even in nonmodel species.
When dispatcher assistance is not saving lives: assessment of process compliance, barriers and outcomes in out-of-hospital cardiac arrest in a metropolitan city in China

Background Several Chinese cities have implemented dispatcher-assisted cardiopulmonary resuscitation (DA-CPR), although out-of-hospital cardiac arrest (OHCA) survival rates remain low. We aimed to assess the process compliance, barriers and outcomes of OHCA in one of the earliest implemented (DA-CPR) programmes in China. Methods We retrospectively reviewed OHCA emergency dispatch records of Suzhou emergency medical service from 2014 to 2015 and included adult OHCA victims (>18 years) with a bystander-witnessed atraumatic OHCA that was subsequently confirmed by on-site emergency physician. The circumstances and DA-CPR process related to the OHCA event were analysed. Dispatch audio records were reviewed to identify potential barriers to implementation during the DA-CPR process. Results Of the 151 OHCA victims, none survived. The median time from patient collapse to call for emergency services and that from call to provision of cardiopulmonary resuscitation instructions was 30 (IQR 20–60) min and 115 (IQR 90–153) s, respectively. Only 110 (80.3%) bystanders/rescuers followed the dispatcher instructions; of these, 51 (46.3%) undertook persistent chest compressions. Major barriers to following the DA-CPR instructions were present in 104 (68.9%) cases, including caller disconnection of the call, distraught mood or refusal to carry out either compressions or ventilations. Conclusions The OHCA survival rate and the DA-CPR process were far from optimal. The zero survival rate is disproportionally low compared with survival statistics in high-income countries. The prolonged delay in calling the emergency services negated and rendered futile any DA-CPR efforts. Thus, efforts targeted at developing public awareness of OHCA, calling for help and competency in DA-CPR should be increased.
Gene transfer in AAV seropositive rhesus macaques following rapamycin treatment and subcutaneous delivery of AAV6 but not retargeted AAV6 vectors.

Adeno-associated virus (AAV) vectors such as AAV6, which shows tropism for primary human CD4+ T cells in vitro, are being explored for delivery of anti-HIV therapeutic modalities in vivo. However, pre-existing immunity and sequestration in non-target organs can significantly hinder their performance. To overcome these challenges, we investigated whether immunosuppression would allow gene delivery by AAV6 or targeted AAV6 derivatives in seropositive rhesus macaques. Animals were immune suppressed with rapamycin prior to intravenous (IV) or subcutaneous (SC) delivery of AAV, and we monitored vector biodistribution, gene transfer and safety. Macaques received either PBS, AAV6 alone, or an equal dose of AAV6 and an AAV6-55.2 vector retargeted to CD4 via a direct ankyrin repeat protein (DARPin). AAV6 and AAV6-55.2 vector genomes were found in PBMCs and most organs up to 28 days post administration, with the highest levels seen in liver, spleen, lymph nodes, and muscle, suggesting that retargeting did not prevent vector sequestration. Despite vector genome detection, gene expression from AAV6-55.2 was not detected in any tissues. SC injection of AAV6 facilitated efficient gene expression in muscle adjacent to the injection site, plus low-level gene expression in spleen, lymph nodes, and liver, whereas gene expression following IV injection of AAV6 was predominantly seen in the spleen. AAV vectors were well tolerated, although elevated liver enzymes were detected in 3 of 4 AAV treated animals 14 days after rapamycin withdrawal. One SC injected animal had muscle inflammation proximal to the injection site, plus detectable T cell responses against transgene and AAV6 capsid at study finish. Overall, our data suggests that rapamycin treatment may offer a possible strategy to express anti-HIV therapeutics such as broadly neutralizing antibodies from muscle. This study provides important safety and efficacy data that will aid study design for future anti-HIV gene therapies.
Inertial flywheel knee- and hip-dominant hamstring strength exercises in professional soccer players: Muscle use and velocity-based (mechanical) eccentric overload

The primary aim of the present study was to analyze mechanical responses during inertial knee- and hip-dominant hamstring strengthening exercises (flywheel leg-curl and hip-extension in conic-pulley), and the secondary aim was to measure and compare regional muscle use using functional magnetic resonance imaging. Mean power, peak power, mean velocity, peak velocity and time in the concentric (CON) and eccentric (ECC) phases were measured. The transverse relaxation time (T2) shift from pre- to post-exercise were calculated for the biceps femoris long (BFl) and short (BFs) heads, semitendinosus (ST) and semimembranosus (SM) muscles at proximal, middle and distal areas of the muscle length. Peak and mean power in flywheel leg-curl were higher during the CON than the ECC phase (p<0.01). ECC peak power was higher than CON phase (p<0.01) in conic-pulley hip-extension exercise, while mean power was higher during the CON than ECC phase (p<0.01). Flywheel leg-curl showed a higher T2 values in ST and BFs and BFl (p<0.05), while the conic-pulley hip-extension had a higher T2 values in the proximal region of the ST and BFl (p<0.05). In conclusion, ECC overload was only observed in peak power during the conic-pulley hip-extension exercise. Flywheel leg-curl involved a greater overall use of the 4 muscle bellies, more specifically in the ST and BFs, with a selective augmented activity (compared with the conic-pulley) in the 3 regions of the BFs, while conic-pulley hip-extension exercise selectively targeted the proximal and medial regions of the BFl. Physiotherapists and strength and conditioning coaches should consider this when optimizing the training and recovery process for hamstring muscles, especially after injury.
Supervised Descent Learning for Thoracic Electrical Impedance Tomography

Objective: The absolute image reconstruction problem of electrical impedance tomography (EIT) is ill-posed. Traditional methods usually solve a nonlinear least squares problem with some kind of regularization. These methods suffer from low accuracy, poor anti-noise performance, and long computation time. Besides, the integration of a priori information is not very flexible. This work tries to solve EIT inverse problem using a machine learning algorithm for the application of thorax imaging. Methods: We developed the supervised descent learning EIT (SDL-EIT) inversion algorithm based on the idea of supervised descent method (SDM). The algorithm approximates the mapping from measured data to the conductivity image by a series of descent directions learned from training samples. We designed a training data set in which the thorax contour, and some general structure of lungs, and heart are embedded. The algorithm is implemented in both two-, and three-dimensional cases, and is evaluated using synthetic, and measured thoracic data. Results, and conclusion: For synthetic data, SDL-EIT shows better accuracy, and anti-noise performance compared with traditional Gauss–Newton inversion (GNI) method. For measured data, the result of SDL-EIT is reasonable compared with computed tomography (CT) scan image. Significance: Using SDL-EIT, prior information can be easily integrated through the specifically designed training data set, and the image reconstruction process can be accelerated. The algorithm is effective in inverting measured thoracic data. It is a potential algorithm for human thorax imaging.