Miracle-dz/UniFAR-FTUs huggingface dataset:
The sweetened actualities of neural membrane proteins: A computational structural analysis

In nature, every cell is coated by an array of complex molecules known as glycans, which are also known as sugars. Their intricacy makes them difficult to analyze and as a consequence little is known about their function. However, in the last decade, compounding evidence points to glycans participating in critical roles in every cell type, including neurons. In fact, altered glycosylation has been correlated to neural disorders such as Alzheimer’s and Parkinson's disease. To learn more about these molecules, we investigated two neural membrane glycoproteins: the type-A γ-aminobutyric acid (GABAA) and the human 5-hydroxytryptamine 2B (5-HT2B) receptors by computational methods. We examined if the glycan structures could physically interfere with the receptor active site. To answer this question, we modeled different glycans on each protein. The model shows that the active sites are heavily glycosylated and all or several glycans are either directly on or bracketing the active site. Furthermore, molecular dynamics simulations demonstrated these molecules to be highly dynamic and in the case of 5-HT2B receptor, capable of covering the entire active site region. Therefore, validating our hypothesis that at least physically, glycans partakes with the active site functions. Future experimental work needs to be done to reveal how the absence or structure changes in these molecules relate to disease. This information can be used for future neurological disease treatments and possible cures.
Characterizing the evolution of antibiotic resistance in commercial Lactobacillus strains

Throughout the world, millions of patients consume probiotic supplements and fermented foods for their perceived health benefits. Recent research suggests that the ingestion of bacteria commonly associated with probiotics negatively correlates with the prevalence of health conditions such as antibiotic-associated dysbiosis and can benefit immunocompromised patients through competitive inhibition. Therefore, healthcare providers often recommend co-administration of probiotics and antibiotics during treatment. Despite the benefits conferred by co-administration, the transfer of antibiotic-resistance genes from probiotics to pathogenic bacteria residing in the gut microbiome remains a significant risk to patient health, as many species are known to be resistant. We sought to determine how antibiotic resistance and its transferability developed among a commonly consumed species of probiotic, Lactobacillus. We hypothesized that these bacteria would demonstrate increased resistance to an antibiotic when administered over successive generations, that resistance would specifically develop during the first two generations of antibiotic exposure, and that antibiotic resistance could be modeled to predict future behavior in response to other antibiotics. We determined the transferability of antibiotic resistance by exposing Escherichia coli to resistant Lactobacillus and testing for antibiotic resistance. Our results demonstrated that Lactobacillus develops antibiotic resistance logarithmically with each generation and variably depending on the class of the antibiotic administered. Further, we created a model to predict how antibiotic resistance developed. Our findings may influence how healthcare providers evaluate the risks associated with probiotic co-administration in immunocompromised patients.
Identification of the Presence of the "Swollen Shoot" Disease in Endemic Areas in Côte d'Ivoire Via Convolutional Neural Networks

: The detection of Swollen Shoot disease and its control is one of the major objectives of research related to sustainable cocoa farming in Côte d'Ivoire. To contain the epidemic, the Cocoa Coffee Council (CCC) in collaboration with the National Agency for Support to Rural Development (ANADER) is responsible for prospecting and delimiting the infected areas as well as for uprooting suspect cocoa plants. since there is currently no cure for this virus. However, this monitoring is done with the naked eye and mobilizes many human resources (planters and plant pathologists). This process is delicate and time-consuming, resulting in significant economic losses for both planters and Côte d’Ivoire. Convolutional Neural Networks (CNN) emerged from the study of the visual cortex of the brain. CNNs are particularly used in image processing and offer many applications related to precision agriculture. Over the past few years, thanks to the increase in computing power, and the amount of training data available, CNNs have been capable of superhuman performance on complex visual tasks. They are at the heart of automatic image and video classification systems. The objective of the work presented in this article is to establish a collaborative solution between CNN-based image processing and plant pathology. The solution will reduce the human labor time required by using algorithms to facilitate the identification of swollen shoot disease in a cocoa plantation. The use of images collected from a drone on cocoa plantations as input information, allowed our learning model, based on CNNs, to guide a new approach for automating Swollen diagnosis. Shoot with our model, we have achieved a level of accuracy of 98% based on the known symptoms.
A study of pipe-soil-climate interaction of buried water and gas pipes

In Australia, buried water and gas pipes are reported to have more frequent failures in hot and dry summers, which suggests that soil shrinkage and thermal effects are the main factors associated with pipe failure. Shrinkage and swelling are common behaviours of soils especially for reactive clays due to seasonal variation of soil moisture content. As a result, the differential soil movement beneath buried pipe can lead to flexural bending and circumferential fracture of the pipe. In addition, seasonal variation of soil moisture content can cause cyclic upward and downward pipe bending and ultimately lead to fatigue failure. However, the relationships between pipe failure, soil behaviour and seasonal climatic change have not been studied in detail. Consequently, the effect of soil moisture content variation on the performance of buried pipes is not clear. This research study is aimed at extending the current knowledge on the interaction between pipes, soils and climate. Field instrumentation was undertaken to study the behaviour of buried cast iron pipes in the natural environment. The collected data confirmed that significant flexural stress was induced by the soil movement on the buried pipe due to the seasonal variation of soil moisture content. Upward and downward bending of the pipe was found to occur at wet and dry seasons, respectively. Regional field measurements of soil moisture content were undertaken in conjunction with field instrumentation to study the seasonal variation of soil moisture content at sites with different soil profiles and geological formations. The 23 sites considered in the study were classified into three categories based on the geological profiles. The study showed that change in soil moisture content was associated with rainfalls and the geological profiles of the site. Variations of soil moisture content can lead to swelling and shrinking of soils and corresponding bending of buried pipes. These data provided the necessary information to understand the likely behaviour of pipes buried in different types of soils. The ground-atmosphere models were used for prediction of soil moisture content variation of the field sites. The Winkler spring models were used to simulate the pipe-soil interaction, and in conjunction with the long term moisture content variation, pipe flexural stress was calculated. Taking into account the deterioration of cast iron pipe strength with time, the relationship between pipe failure probability and pipe age was obtained. This research provides a prediction tool for pipe failure associated with soil behaviour and seasonal climate change. The prediction model can be used to plan for asset management and rehabilitation of the buried pipe networks, thus providing savings on repair of unexpected pipe failures and consequence loss of water and gas services to the communities.
Becker Digital

CD36 mediates the transfer of fatty acids (FAs) across the plasma membranes of muscle and adipose cells, thus playing an important role in regulating peripheral FA metabolism in vivo. In the proximal intestine, CD36 is localized in abundant quantities on the apical surface of epithelial cells, a pattern similar to that of other proteins implicated in the uptake of dietary FAs. To define the role of CD36 in the intestine, we examined FA utilization and lipoprotein secretion by WT and CD36-null mice in response to acute and chronic fat feeding. CD36-null mice given a fat bolus by gavage or fed a high-fat diet accumulated neutral lipid in the proximal intestine, which indicated abnormal lipid processing. Using a model in which mice were equipped with lymph fistulae, we obtained evidence of defective lipoprotein secretion by directly measuring lipid output. The secretion defect appeared to reflect an impaired ability of CD36-null enterocytes to efficiently synthesize triacylglycerols from dietary FAs in the endoplasmic reticulum. In the plasma of intact mice, the reduced intestinal lipid secretion was masked by slow clearance of intestine-derived lipoproteins. The impaired clearance occurred despite normal lipoprotein lipase activity and likely reflected feedback inhibition of the lipase by FAs due to their defective removal from the plasma. We conclude that CD36 is important for both secretion and clearance of intestinal lipoproteins. CD36 deficiency results in hypertriglyceridemia both in the postprandial and fasting states and in humans may constitute a risk factor for diet-induced type 2 diabetes and cardiovascular disease.
A Robust Method to Filter Various Types of Artifacts on Long Duration Eeg Recordings

—The EEG is a system to measure electrical brain activity using multiple electrodes placed on the scalp. Unfortunately , the signal can be easily contaminated by a lot of noises called artifacts. These can be generated by various actions such as eye blinks, eye movements, muscle activities or small electrode movements. This paper presents a global artifact removal method corresponding to an evolution of the AFOP method (Adaptive Filtering by Optimal Projection) in order to improve its stability. This evolution automatically filters ocular, muscular and heart beat artifacts. The results are validated on long duration EEG recordings containing pathological activity. An expert analysis shows that the cerebral signal is well conserved while a lot of artifacts are removed.
Do Attractants Bias the Results of Malaise Trap Research?

The study of biodiversity is crucial to the stability of the planet as it assists scientists with the knowledge and tools necessary to maintain a functional and sustainable environment. Previous research has utilized malaise traps to collect insects in order to study trends in biodiversity. However, malaise traps may have a potential for bias, depending on the type of attractant used, given that flies are attracted to rotting, fermented fruit. This study aims to test whether inadequate sampling occurs during the collection of flying insects. We hypothesized that attractants do bias the results of malaise trap research. The project was designed to test this hypothesis. We placed two identical traps in similar areas of the Southwestern Riverside County Multi-Species Reserve near Western Center Academy. All variables were maintained across these traps, except for the type of attractant used (independent variable). Traps were placed three feet apart, both parallel to the prevailing wind in a homogeneously vegetated field. After one week, we counted and identified the insects down to order manually under a microscope and their genomes were sequenced. This process was repeated the following week. The data from the two traps were compared to each other and to a concurrent Mount San Jacinto Junior College study to test our hypothesis. Based on analysis of our data, we found our hypothesis to be supported by the data and there was indeed a bias when using denatured alcohol.
Regional Location Calibration in Asia

Seismic event location for global nuclear explosion monitoring is a multi-faceted problem. This paper presents a spectrum of issues and efforts involved in improving location performance worldwide. Our efforts are largely designed around providing validated, rigorously calibrated travel times, azimuths, and slownesses along with accurate error estimates. To do so entails a significant effort that includes data mining, data integration, database management, developing optimal 1-, 2-, and 3-D Earth models, using the Earth models to predict wave propagation, developing corrections and errors for travel times, azimuths, and slownesses, and validation of all products. Results presented here will focus on Asia. Previous work has shown that non-stationary modified Bayesian kriging of travel-time residuals successfully improves regional seismic event location, and this method is being extended to calculate corrections for azimuth and slowness. The ability to krige over 3-D Earth models is also being implemented. In order to produce the most useful corrections, we require accurate ground truth. For this we are continuing efforts to create a location database consis ting of the best available seismic event locations and the most accurate and precise travel times. Building this database relies on participation from universities, other National Nuclear Security Administration (NNSA) laboratories, and contacts in private industry. Through the kriging procedure we are able to stabilize location algorithms, but the ultimate usefulness of the corrections themselves is directly related to the quality of the ground truth from which the corrections are derived. Indeed, epicentral mislocations from location algorithms (EvLoc) using travel-time correction surfaces are directly proportional to the location errors of the ground truth used to generate the corrections. In aseismic regions, corrections for travel time, azimuth, and slowness are predicted from optimal Earth models using one of the following methods, depending on application: TauP, ray bending, reflectivity, or finite difference. We have developed a model-building tool that can incorporate many different types of data, from surfaces (Moho, bathymetry, topography), to local or regional 1-, 2-, and 3-D models, to reflection profiles, to point data. Numbers of layers are defined within prominent sections of the lithosphere, and interpolation between data points is used to create a smooth, self-consistent 3-D Earth model. 430 24th Seismic Research Review – Nuclear Explosion Monitoring: Innovation and Integration
Transformation of the Herbicides MCPP and Atrazine under Natural Aquifer Conditions

The potential for aerobic biotransformation of the herbicides MCPP [(+/ -)-2-(4-chloro-2-methylphenoxy)propionic acid] and Atrazine [2-chloro-4-ethylamino-6-isopropylamino-s-triazine] under natural aquifer conditions was investigated. A natural gradient experiment was carried out in an aerobic ground-water zone at the Canadian Forces Base Borden, Borden, Ontario, Canada. Over 90 days, a continuous plume was created by weekly injections of the herbicides (average concentrations of 400 jug/1 each), together with a conservative tracer, chloride. The fate of the herbicides was monitored at multilevel piezometers located downgradient from the injection well. In parallel, experiments with in situ testers (Gillham et al., 1990) were set up in the aquifer and microcosms were set up in the laboratory. For MCPP, the natural gradient experiment showed an adaptation period of 42-56 days followed by transformation from 400 to 30 μg/1. As predicted, MCPP was not retarded compared to the conservative tracer. No transformation was observed in the in situ testers over 47 days. In the laboratory experiments no transformation was observed over 74 days. Atrazine was recalcitrant within the experimental period of 96 days in the natural gradient experiment. A retardation factor R = 1.2, within the predicted range, was found for Atrazine in the Borden aquifer. No transformation was observed either in the in situ testers or in the laboratory experiments after a period of 96 and 74 days, respectively. These results suggest that both MCPP and Atrazine are mobile in sand aquifers. Atrazine appears persistent, at least for 96 days, while MCPP undergoes considerable transformation.
H-plane SIW horn antenna with enhanced front-to-back ratio for 5G applications

: Millimeter-wave (mmWave) antennas are indispensable components in the fifth-generation (5G) wireless communication systems. With the inherent advantages of integration capability, substrate integrated waveguide (SIW) antenna is an excellent choice for applications in the mmWave frequency bands. However, reflection losses occur at dielectric-filled thin apertures of SIW antennas. These reflections can be overcome by impedance matching between the aperture and the free space. In this study, we introduce an mmWave SIW horn antenna having impedance matching transitions (IMTs) across the horn’s aperture width. The designed antenna, operating in the 24–28 GHz band, is simulated with a full-wave analysis tool. The simulation results of the modified SIW horn have been confirmed by the experimental results and shown to be satisfactory. The IMTs result in an enhancement of the front-to-back ratio (FTBR). The modified SIW horn antenna with a novel printed transition achieves sidelobe levels (SLLs) of better than –9 dB at 27 GHz, with an enhanced FTBR above 15 dB. In the 24–28 GHz band, the antenna has a reflection coeﬀicient variation of better than –10 dB.
Testing the plateau: a reexamination of disparity and morphologic constraints in early Paleozoic crinoids

Abstract Studies of crinoid morphology have been pivotal in understanding the constraints on the range of morphology within a clade as well as the patterns of disparity throughout the Phanerozoic. Newly discovered and described faunas and recent study of early Paleozoic crinoid diversity provide an ideal opportunity to reanalyze Ordovician through Early Silurian crinoid disparity with more complete taxonomic coverage and finer stratigraphic resolution. Using the coarse stratigraphic binning of Foote (1999), the updated morphologic data set has a similar disparity pattern to those previously reported for the early Paleozoic. However, with the more resolved stratigraphic binning used by Peters and Ausich (2008), a significant difference exists between the original and current data sets. Both data sets have a pronounced disparity high during the late Middle Ordovician. However, the updated disparity curve has a much higher initial disparity during the Early Ordovician and a pronounced rise in disparity during the Silurian recovery. Examination of differential sampling, proportions of the crinoid orders through time, and methods of coding characters indicate these factors have little effect on the pattern of crinoid disparity. The Silurian morphospace expansion occurs primarily within disparids and coincides with the origination of the myelodactylids. These findings corroborate the rapid expansion of morphospace during the Ordovician. However, crinoid disparity did not remain static and, although less frequent than during the initial radiation, new body plans evolved following the Ordovician Extinction (e.g., the myelodactylids). These results are consistent with the hypothesis of ecology constraining the limits on morphologic disparity at the class level.
Wage Differential between Caste Groups: Are Younger and Older Cohorts Different?

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Fast Point to Mesh Distance by Domain Voxelization

Computing the distance from a point to a triangle mesh is a key computational step in robotics pipelines such as registration and collision detection, with applications to path planning, SLAM, and RGB-D vision. Numerous techniques to accelerate this computation have been developed, many of which use a cheap pre-processing step to construct a hierarchical decomposition of the mesh. If the mesh is fixed and known ahead of time, there is an opportunity to conduct more expensive pre-computations to accelerate the subsequent distance queries. This work presents a voxelization approach, implemented on both CPU and GPU, to compute point to mesh distance that constructs for each voxel a near-minimal set of triangles that is guaranteed to include every triangle that is closest to at least one point in the voxel. Theoretical and numerical comparisons with six alternative distance algorithms demonstrate the speed advantages of the proposed method.
Spatially Complete Surface Albedo Data Sets: Value-Added Products Derived from Terra MODIS Land Products

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. The availability of global albedo data over a large range of spectral channels and at high spatial resolution has dramatically improved with the launch of the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument aboard NASA s Earth Observing System (EOS) Terra spacecraft in December 1999. However, lack of spatial and temporal coverage due to cloud and snow effects can preclude utilization of official products in production and research studies. We report on a technique used to fill incomplete MOD43 albedo data sets with the intention of providing complete value-added maps. The technique is influenced by the phenological concept that within a certain area, a pixel s ecosystem class should exhibit similar growth cycle events over the same time period. The shape of an area s phenological temporal curve can be imposed upon existing pixel-level data to fill missing temporal points. The methodology will be reviewed by showcasing 2001 global and regional results of complete albedo and NDVl data sets.