Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyramidal Segmentation of Medical Images using Adversarial Training

Colorectal cancer is a severe health issue globally and a significant cause of cancer-related mortality, but it is treatable if found at an early stage. Early detection is usually done through a colonoscopy, where clinicians search for cancer precursors called polyps. Research has shown that clinicians miss between 14% and 30% of polyps during standard screenings of the gastrointestinal tract. Furthermore, once the polyps have been found, clinicians often overestimate the size of the polyps. In this respect, automatic analysis of medical images for detecting and locating polyps is a research area where machine learning has excelled in recent years. Still, current models have much room for improvement. In this paper, we propose a novel approach based on learning to segment within several grids, which we introduce to U-Net and Pix2Pix architectures. In short, we have experimented using several grid sizes, and using two open-source polyp segmentation datasets for cross-data training and testing. Our results suggest that segmentation at lower resolutions produces better results at the cost of less precision, which proved useful for the cases where higher precision segmentations gave limited results. Generally, compared to traditional U-Net and Pix2Pix, our grid-based approaches improve segmentation performance.
Calea funkiana (Compositae, Neurolaeneae), a New Endemic Species from Serra do Cipó, Minas Gerais, Brazil

Abstract A new species of Calea belonging to sect. Meyeria is described and named as an in memoriam tribute to Vicki Ann Funk (1947–2019), who dedicated her career to plant systematics, specially focusing on the Compositae. Calea funkiana resembles Calea triantha, but is distinguished by the slightly branched habit, apically acute leaves, glabrous ray florets, and, mainly, the villose indumentum of stems, leaves, peduncle, and outer phyllaries. The new species is described and illustrated, its geographic distribution is mapped, and its taxonomic affinities are discussed. Additionally, a key for the species of Calea from Serra do Cipó, Minas Gerais, Southeastern Brazil, is provided.
Study of Micro-Upsetting by Finite Element Simulation Based on Crystal Plasticity and Grain Boundary Strengthening Theories

The properties of individual grains affect the mechanical behaviors and response of materials in micro-scaled deformation, viz., microforming, and there are unknown phenomena and deformation behaviors existing and limiting the wide application of microforming due to size effect. In this paper, a composite model combining crystal plasticity and grain boundary strengthening theories was developed for numerical investigation into the effect of grain boundaries on the plastic deformation of copper micro-upsetting. By comparing the results with and without grain-boundary structure, it is revealed that grain boundaries, which act as the barriers of crystal slip, result in the enhanced flow stress and the discontinuous distribution of stress and strain. The grain size effect is also considered in this research, and the results show the coarse-grained material reduces the flow stress and enhances the inhomogeneous deformation.
High‐performance low bandgap thin film solar cells for tandem applications

Thin film tandem solar cells provide a promising approach to achieve high efficiencies. These tandem cells require at least a bottom low bandgap and an upper high bandgap solar cell. In this contribution, 2 high‐performance Cu(In,Ga)Se2 cells with bandgaps as low as 1.04 and 1.07 eV are presented. These cells have shown certified efficiencies of 15.7% and 16.6% respectively. Measuring these cells under a 780‐nm longpass filter, corresponding to the bandgap of a typical top cell in tandem applications (1.57 eV), they achieved efficiencies of 7.9% and 8.3%. Admittance measurements showed no recombination active deep defects. One additional high‐performance CuInSe2 thin film solar cell with bandgap of 0.95 eV and efficiency of 14.1% is presented. All 3 cells have the potential to be integrated as bottom low bandgap cells in thin film tandem applications achieving efficiencies around 24% stacked with an efficient high bandgap top cell.
Controlled chemical synthesis of CaO2 particles coated with polyethylene glycol: characterization of crystallite size and oxygen release kinetics

Incorporating oxygen generating substances into tissue constructs is one of the methods for increasing cell survival under hypoxic condition. Calcium peroxide from alkaline earth metal peroxide groups has been proposed as an appropriate compound for supplying sufficient oxygen to cells within the scaffolds. The high surface-to-volume ratio of CaO2 particles can lead to an increase in oxygen generation ability over a particular time interval. One objective of this study was to decrease calcium peroxide crystallite size via changing the local supersaturation level by controlling the reactant addition rate during coprecipitation synthesis. Therefore, the effect of hydrogen peroxide addition rate on the crystallite size, particle size distribution, and CaO2 purity, which have not been studied before, were discussed. It was found that the crystallite size of CaO2 depends upon the reactant addition rate, and the crystallite size decreased from 111 to 37 nm when the addition rate increased from 0.29 to 0.88 ml min−1. Furthermore, after determining the hydrogen peroxide addition rate, a facile method was developed to prepare CaO2 particles with polyethylene glycol coating for the first time. The aim of PEG coating was to improve redispersion of the precipitated CaO2 particles. Thermogravimetric analysis was used to measure the content of adsorbed PEG on the surface of the particles. Eventually, the oxygen release profile of PEG-coated calcium peroxide particles demonstrated that the release kinetics is dependent on the pH value of the exterior medium, diffusion through the calcium carbonate product layer, and molar ratios of PEG to calcium.
Polarization and acoustic properties of barium-modified lead-free potassium–sodium niobate ceramics

Results of polarization and polarization switching in samples prepared by solid phase synthesis of the (1-х )(K 0.5 Na 0.5 )(Nb 0.93 Sb 0.07 )O 3 – x BaTiO 3 + 0.5mol%MnO 2 system at x = 0.01, 0.02, and 0.04 (KNNS7– x BT) studied over a wide range of temperatures are reported. The observed features of the dielectric nonlinearity at the ferroelectric and structural phase transitions in the materials are described. The dielectric response data of the samples of different contents of the admixture in the KNNS7– x В T ceramics are compared with the behaviour of their elastic properties.
Reaction induced interfacial instability of miscible fluids in a channel

Abstract When a less viscous miscible fluid displaces a more-viscous one under a pressure-driven channel flow, unstable Kelvin–Helmholtz (K–H)-type billows are formed at the miscible interface. In this paper, we investigate whether such instability can be induced by a simple ($\textbf {A}+ \textbf {B} \rightarrow \textbf {C}$)-type chemical reaction. Here a miscible solution of one reactant $\textbf {A}$ is displacing another isoviscous reactant $\textbf {B}$ and producing a more-viscous product $\textbf {C}$ at the reactive front. It is found that because of a local increase in viscosity gradient due to the formation of more-viscous product $\textbf {C}$, K–H-type billows are formed at the $\textbf {A}$–$\textbf {C}$ interface. The changes in dynamical properties of such billows are examined by varying the governing parameters such as the mobility ratio $R_{c}$, Damköhler number $Da$, Péclet number $Pe$ and Reynolds number $Re$. Interestingly, we have found that even at high reaction rates (sufficiently large $Da$) for $R_{c}=1$, the interface remains stable and for larger values of $R_{c} (=3, 5)$ the K–H billows are observed. It is also noticed that a laminar horseshoe-type vortex develops near the wall at the channel inlet where the less-viscous reactant pushes the more-viscous product. We have computed numerically the onset time ($t_{on}$) of instability to understand the early-stage developments of the K–H billows. For different values of $Da$, we have shown the unstable and stable time zones in the ($t_{on}$–$R_{c}$) space. The bipartite ($t_{on}$–$R_{c}$) space also depicts the critical ($Da$-, $Pe$- and $Re$-dependent) $R_{c}$ value for which instability can be triggered in a finite desirable time. The delay in the onset of instability is observed with increasing $Pe$. Further it is shown that $t_{on}$ can be linearly scaled with $Pe$ to have a modified onset time ($t^{*}_{on}$), which establishes a proportionate dynamics with respect to $Pe$ in the early stages of the instability. Moreover, a reverse dependency of onset on lower $R_{c}$ values for higher Reynolds numbers is observed.
Prevalence and seasonal variation of Fasciola hepatica in slaughtered cattle: the role of climate and environmental factors in Mexico

Abstract The objective of this study is to determine the prevalence of Fasciola hepatica infection in cattle slaughterhouses, as well as its association with climatic/environmental factors (derived from satellite data), seasonality and climate regions in two states in Mexico. Condemned livers from slaughtered animals were obtained from three abattoirs in the states of Puebla and Veracruz. The overall prevalence of the parasite in cattle between January and December of 2017 was 20.6% (1407 out of 6834); the highest rate of condemnation was observed in Veracruz (26.3%; tropical climate), and the lowest rate was found in Puebla (15.5%; temperate climate). The seasonal prevalence of fluke infection was 18.6%, 14.8% and 28.4% during the wet season, and 17.1%, 12.4% and 22.8% during the dry season in the three abattoir sites, located in the districts of Zacatlán, Teziutlán and Ciudad Alemán, respectively. Liver condemnations due to bovine fasciolosis were prevalent in the Zacatlán, Teziutlán and Ciudad Alemán districts during summer, autumn and summer, respectively. Using generalized estimating equations analysis, we determined six variables – rainfall (wet/dry), land surface temperature day, land surface temperature night, normalized difference vegetation index, seasonality and climate regions (temperate/tropical) – to be significantly associated with the prevalence of condemned livers. Climate region was the variable most strongly associated with F. hepatica infection (odds ratio (OR) 266.59; 95% confidence interval (CI): 241.90–353.34), followed by wet and dry seasons (OR 25.56; 95% CI: 20.56–55.67).
A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activates defence responses

Cysteine-rich receptor-like kinases (CRKs) are a large family of plasma membrane-bound receptors ubiquitous in higher plants. They are transcriptionally regulated by a wide variety of environmental cues and stresses, however their precise biological roles remain largely unknown. Here we report a novel mutant isolated for the CYSTEINE-RICH RECEPTOR-LIKE KINASE 10 (CRK10) of Arabidopsis thaliana which harbours the substitution of alanine 397 by a threonine in the αC-helix of its kinase domain and which we registered as crk10-A397T in the community database. In situ phosphorylation assays with the His-tagged wild type (WT) and crk10-A397T versions of the CRK10 kinase domain revealed that both alleles are active kinases capable of auto-phosphorylation with the newly introduced threonine acting as an additional phosphorylation site in crk10-A397T. Phenotypically the mutant is a dwarf and the analysis of thin cross sections with light and transmission electron microscopy revealed that collapsed xylem vessels in roots and hypocotyls are very likely the cause for this reduction in stature. Transcriptomic analysis of WT and mutant hypocotyls revealed that predominantly biotic and abiotic stress-responsive genes are constitutively up-regulated in the mutant. Root-infection assays with the vascular pathogen Fusarium oxysporum demonstrated that the crk10-A397T mutant has enhanced resistance to this pathogen compared to WT plants. Taken together our results suggest that crk10-A397T is a gain-of-function allele of CRK10 and open up new avenues for the investigation of this elusive receptor-like kinase family.
AMPing up the search: An in silico approach to identifying Antimicrobial Peptides (AMPs) with potential anti-biofilm activity

Antibiotic resistance is a public health threat, and the rise of multidrug-resistant bacteria, including those that form protective biofilms, further compounds this challenge. Antimicrobial peptides (AMPs) have been recognized for their anti-infective properties, including their ability to target processes important for biofilm formation. However, given the vast array of natural and synthetic AMPs, determining potential candidates for anti-biofilm testing is a significant challenge. In this study, we present an in silico approach, based on open-source tools, to identify AMPs with potential anti-biofilm activity. This approach is developed using the sortase-pilin machinery, important for adhesion and biofilm formation, of the multidrug-resistant, biofilm-forming pathogen C. striatum as the target. Using homology modeling, we modeled the structure of the C. striatum sortase C protein, resembling the semi-open lid conformation adopted during pilus biogenesis. Next, we developed a structural library of 5544 natural and synthetic AMPs from sequences in the DRAMP database. From this library, AMPs with known anti-Gram positive activity were filtered, and 100 select AMPs were evaluated for their ability to interact with the sortase C protein using in-silico molecular docking. Based on interacting residues and docking scores, we built a preference scale to categorize candidate AMPs in order of priority for future in vitro and in vivo biofilm studies. The considerations and challenges of our approach, and the resources developed, which includes a search-enabled repository of predicted AMP structures and protein-peptide interaction models relevant to biofilm studies (B-AMP), can be leveraged for similar investigations across other biofilm targets and biofilm-forming pathogens.
Evidence of multiple genome duplication events in Mytilus evolution

Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.
Differences in working memory coding of biological motion attributed to oneself and others

The question how the brain distinguishes between information about oneself and the rest of the world is of fundamental interest to both philosophy and neuroscience. This question can be approached empirically by investigating how associating stimuli with oneself leads to differences in neurocognitive processing. However, little is known about the brain network involved in forming such self-associations for, specifically, bodily stimuli. In this fMRI study, we sought to distinguish the neural substrates of representing a full-body movement as one’s movement and as someone else’s movement. Participants performed a delayed match-to-sample working memory task where a retained full-body movement (displayed using point-light walkers) was arbitrarily labelled as one’s own movement or as performed by someone else. By using arbitrary associations we aimed to address a limitation of previous studies, namely that our own movements are more familiar to us than movements of other people. A searchlight multivariate decoding analysis was used to test where information about types of movement and about self-association was coded. Movement specific activation patterns was found in a network of regions also involved in perceptual processing of movement stimuli, however not in early sensory regions. Information about whether a memorized movement was associated with the self or with another person was found to be coded by activity in the left middle frontal gyrus (MFG), left inferior frontal gyrus (IFG), bilateral supplementary motor area, and (at reduced threshold) in the left temporoparietal junction (TPJ). These areas are frequently reported as involved in action understanding (IFG, MFG) and domain-general self/other distinction (TPJ). Finally, in univariate analysis we found that selecting a self-associated movement for retention was related to increased activity in the ventral medial prefrontal cortex.
Light-emitting diodes as light sources for spectroscopy: Sensitivity to temperature

Understanding of light-emitting diode lamp behaviour is essential to support the use of these devices as illumination sources in near infrared spectroscopy. Spectral variation in light-emitting diode peak output (680, 700, 720, 735, 760, 780, 850, 880 and 940 nm) was assessed over time from power up and with variation in environmental temperature. Initial light-emitting diode power up to full intensity occurred within a measurement cycle (12 ms), then intensity decreased exponentially over approximately 6 min, a result ascribed to an increase in junction temperature as current is passed through the light-emitting diode. Some light-emitting diodes displayed start-up output characteristics on their first use, indicating the need for a short light-emitting diode ‘burn in’ period, which was less than 24 h in all cases. Increasing the ambient temperature produced a logarithmic decrease in overall intensity of the light-emitting diodes and a linear shift to longer wavelength of the peak emission. This behaviour is consistent with the observed decrease in the IAD Index (absorbance difference between 670 nm and 720 nm, A670–A720) with increased ambient temperature, as measured by an instrument utilising light-emitting diode illumination (DA Meter). Instruments using light-emitting diodes should be designed to avoid or accommodate the effect of temperature. If accommodating temperature, as light-emitting diode manufacturer specifications are broad, characterisation is recommended.
Hierarchical Bayesian models of transcriptional and translational regulation processes with delays

Motivation Simultaneous recordings of gene network dynamics across large populations have revealed that cell characteristics vary considerably even in clonal lines. Inferring the variability of parameters that determine gene dynamics is key to understanding cellular behavior. However, this is complicated by the fact that the outcomes and effects of many reactions are not observable directly. Unobserved reactions can be replaced with time delays to reduce model dimensionality and simplify inference. However, the resulting models are non-Markovian, and require the development of new inference techniques. Results We propose a non-Markovian, hierarchical Bayesian inference framework for quantifying the variability of cellular processes within and across cells in a population. We illustrate our approach using a delayed birth-death process. In general, a distributed delay model, rather than a popular fixed delay model, is needed for inference, even if only mean reaction delays are of interest. Using in silico and experimental data we show that the proposed hierarchical framework is robust and leads to improved estimates compared to its non-hierarchical counterpart. We apply our method to data obtained using time-lapse microscopy and infer the parameters that describe the dynamics of protein production at the single cell and population level. The mean delays in protein production are larger than previously reported, have a coefficient of variation of around 0.2 across the population, and are not strongly correlated with protein production or growth rates. Availability Accompanying code in Python is available at https://github.com/mvcortez/Bayesian-Inference. Contact kresimir.josic@gmail.comkresimir.josic@gmail.com, jaekkim@kaist.ac. kr jaekkim@kaist.ac. kr, cbskust@korea.ac. kr cbskust@korea.ac. kr
A novel power-amplified jumping behavior in larval beetles (Coleoptera: Laemophloeidae)

Larval insects use many methods for locomotion. Here we describe a previously unknown jumping behavior in a group of beetle larvae (Coleoptera: Laemophloeidae). We analyze and describe this behavior in Laemophloeus biguttatus and provide information on similar observations for another laemophloeid species, Placonotus testaceus. Laemophloeus biguttatus larvae prelude jumps by arching their body while gripping the substrate with their legs over a period of 0.22 ± 0.17s. This is followed by a rapid ventral curling of the body after the larvae releases its grip that launches them into the air. Larvae reached takeoff velocities of 0.47 ± 0.15 m s-1 and traveled 11.2 ± 2.8 mm (1.98 ± 0.8 body lengths) horizontally and 7.9 ± 4.3 mm (1.5 ± 0.9 body lengths) vertically during their jumps. Conservative estimates of power output revealed that not all jumps can be explained by direct muscle power alone, suggesting Laemophloeus biguttatus uses a latch-mediated spring actuation mechanism (LaMSA) in which interaction between the larvae’s legs and the substrate serves as the latch. MicroCT scans and SEM imaging of larvae did not reveal any notable modifications that would aid in jumping. Although more in-depth experiments could not be performed to test hypotheses on the function of these jumps, we posit that this behavior is used for rapid locomotion which is energetically more efficient than crawling the same distance to disperse from their ephemeral habitat. We also summarize and discuss jumping behaviors among insect larvae for additional context of this behavior in laemophloeid beetles.
Additive Antiviral Effects of Lamivudine and α-Interferon in Chronic Hepatitis B Infection

α-Interferon has limited efficacy against chronic hepatitis B virus (HBV) infection. Nucleoside analogues may confer greater benefits, however, it is likely that combination therapies will be required for effective control of this infection. We investigated the antiviral effect of lamivudine and interferon therapy in eight patients with high HBV-DNA levels. Six patients received lamivudine/interferon combination therapy followed, after a 6-month drug-free period, with lamivudine monotherapy. Mean HBV viral load (copies/ml) reduction was significantly greater after 4 months of combination therapy (4.3x103) compared to an equivalent period of lamivudine monotherapy (2.9x102) (P=0.03). Two patients were given 6 months of lamivudine/interferon combination therapy followed immediately by lamivudine monotherapy. Cessation of interferon in these patients led to a rapid 1–2 log10 increase in HBV viral load. These findings suggest that α-interferon has a direct antiviral effect on chronic HBV infection, which may be additive to, or synergistic with lamivudine.