Miracle-dz/UniFAR-FTUs huggingface dataset:
Degeneracy in the robust expression of spectral selectivity, subthreshold oscillations, and intrinsic excitability of entorhinal stellate cells

Biological heterogeneities are ubiquitous and play critical roles in the emergence of physiology at multiple scales. Although neurons in layer II (LII) of the medial entorhinal cortex (MEC) express heterogeneities in their channel properties, the impact of such heterogeneities on the robustness of cellular-scale physiology has not been assessed. Here, we performed a 55-parameter stochastic search spanning 9 voltage- or calcium-activated channels to assess the impact of channel heterogeneities on the concomitant emergence of 10 electrophysiological characteristics of LII stellate cells (SCs). We generated 50,000 models and found a heterogeneous subpopulation of 155 valid models to robustly match all electrophysiological signatures. We employed this heterogeneous population to demonstrate the emergence of cellular-scale degeneracy in LII SCs, whereby disparate parametric combinations expressing weak pairwise correlations resulted in similar models. We then assessed the impact of virtually knocking out each channel from all valid models and demonstrate that the mapping between channels and measurements was many-to-many, a critical requirement for the expression of degeneracy. Finally, we quantitatively predict that the spike-triggered average of LII SCs should be endowed with theta-frequency spectral selectivity and coincidence detection capabilities in the fast gamma-band. We postulate this fast gamma-band coincidence detection as an instance of cellular-scale efficient coding, whereby SC response characteristics match the dominant oscillatory signals in LII MEC. The heterogeneous population of valid SC models built here unveils the robust emergence of cellular-scale physiology despite significant channel heterogeneities, and forms an efficacious substrate for evaluating the impact of biological heterogeneities on entorhinal network function. KEY POINTS Stellate cells (SC) in layer II (LII) of the medial entorhinal cortex express cellular-scale degeneracy in the concomitant manifestation of several of their unique physiological signatures. Several disparate parametric combinations expressing weak pairwise correlations resulted in models with very similar physiological characteristics, including robust theta-frequency membrane potential oscillations spanning several levels of subthreshold depolarization. Electrophysiological measurements of LII SCs exhibited differential and variable dependencies on underlying channels, and the mapping between channels and measurements was many-to-many. Quantitative predictions point to theta-frequency spectral selectivity and fast gamma-range coincidence detection capabilities in class II/III spike-triggered average of LII SCs, with the postulate for this to be an instance of cellular-scale efficient coding. A heterogeneous cell population that accounts for both channel and intrinsic heterogeneities in LII SCs, which could be employed by network models of entorhinal function to probe the impact of several biological heterogeneities on spatial navigation circuits.
Impact of Influent Carbon to Phosphorus Ratio on Performance and Phenotypic Dynamics in Enhanced Biological Phosphorus Removal (EBPR) System - Insights into Carbon Distribution, Intracellular Polymer Stoichiometry and Pathways Shifts

This study investigated the impact of influent carbon to phosphorus (P) ratio on the variation in P-removal performance and associated intracellular polymers dynamics in key functionally relevant microbial populations, namely, PAOs and GAOs, at both individual and populations levels, in laboratory scale sequencing batch reactor-EBPR systems. Significant variations and dynamics were evidenced for the formation, utilization and stoichiometry of intracellular polymers, namely polyphosphate, glycogen and Polyhydroxyalkanoates in PAOs and GAOs in the EBPR systems that were operated with influent C/P ranged from 20 to 50, presumably as results of phylogenetic diversity changes and, or metabolic functions shifts in these two populations at different influent C/P ratios. Single cell Raman micro-spectroscopy enabled quantification of differentiated polymer inclusion levels in PAOs and GAOs and, showed that as the influent rbCOD/P ratio increases, the excessive carbon beyond stoichiometric requirement for PAOs would be diverted into GAOs. Our results also evidenced that when condition becomes more P limiting at higher rbCOD/P ratios, both energy and reducing power generation required for acetate uptake and PHB formation might shift from relying on both polyP hydrolysis and glycolysis pathway, to more enhancement and dependence on glycolysis in addition to partial/reverse TCA cycle. These findings provided new insights into the metabolic elasticity of PAOs and GAOs and their population-level parameters for mechanistic EBPR modeling. This study also demonstrated the potential of application of single cell Raman micro-spectroscopy method as a powerful tool for studying phenotypic dynamics in ecological systems such as EBPR.
Genetic diversity and population structure of Brachiaria brizantha (A.Rich.) Stapf accessions from Ethiopia

Brachiaria is a tropical, warm-season grass native to Africa. It is an extensively cultivated forage in the tropics with proven benefits on livestock productivity. Brachiaria is well-known for high biomass production, animal nutrition, carbon sequestration, biological nitrification inhibition, soil conservation, and adaptation to drought and low fertility soils. However, the use of Brachiaria grass for fodder production in Africa has been little explored largely due to lack of cultivars suitable to different production environments. The exploration and use of natural diversity is fundamental for an efficient Brachiaria breeding program. We analysed genetic diversity and population structure of 112 Ethiopian Brachiaria brizantha accessions using 23 microsatellite markers. A total of 459 alleles were detected with an average polymorphic information content of 0.75 suggesting high discriminating ability of these markers. The molecular variance analysis showed a high contribution (86%) of within-cluster differences to the total variation. Three allelic pools revealed by STRUCTURE analysis in 112 accessions were in agreement with the clustering patterns seen in neighbor-joining tree and principal coordinates analyses. A core collection of 39 B. brizantha accessions was constituted. This study concludes a high genetic diversity of Ethiopian B. brizantha accessions and their importance in Brachiaria breeding programs.
Super Potent Bispecific Llama VHH Antibodies Neutralize HIV via a Combination of gp41 and gp120 Epitopes

Broad and potent neutralizing llama single domain antibodies (VHH) against HIV-1 targeting the CD4 binding site (CD4bs) have previously been isolated upon llama immunization. Here we describe the epitopes of three additional VHH groups selected from phage libraries. The 2E7 group binds to a new linear epitope in the first heptad repeat of gp41 that is only exposed in the fusion-intermediate conformation. The 1B5 group competes with co-receptor binding and the 1F10 group interacts with the crown of the gp120 V3 loop, occluded in native Env. We present biophysical and structural details on the 2E7 interaction with gp41. In order to further increase breadth and potency, we constructed bi-specific VHH. The combination of CD4bs VHH (J3/3E3) with 2E7 group VHH enhanced strain-specific neutralization with potencies up to 1400-fold higher than the mixture of the individual VHHs. Thus, these new bivalent VHH are potent new tools to develop therapeutic approaches or microbicide intervention.
Categorizing Professional Discourse

Rhetorical categories can and should be developed by scholars of professional writing to identify how values held within professions constrain the ways discourse is interpreted in organizational settings. Empirical research (conducted by the author and others), discourse theory, and pedagogical practice in professional writing strongly suggest that at least three categories of professional writing exist: engineering, administrative, and technical/professional writing. The author demonstrates this claim and distinguishes the characteristics of these three categories. Engineering writing is shown to respond to professional values of scientific objectivity and professional judgment as well as to corporate interests. Administrative writing reflects the locus of decision-making authority and promotes institutional identity. Technical/professional writing aims to accommodate audience needs through complying with professional readability standards. Future research should focus on defining the characteristics of these varieties more precisely. Articulated definitions of these three varieties of professional writing can help scholars and practitioners better understand how discourse is framed and interpreted in organizational settings.
Enhanced epigenetic inheritance in Arabidopsis thaliana

Plants are sessile organisms and as such are frequently exposed to a wide range of environmental stress conditions. Exposure to such stresses, can affect plant growth and survival. Therefore plants have developed strategies to rapidly adapt to fluctuating environmental conditions which, in some cases, these adaptive responses can be passed on to the offspring. One mechanism implicated in this transgenerational “stress memory” involves changes in DNA methylation that are directed by external stress. However, it has previously found that this so-called “stress memory” is temporary, as in the absence of stress these epigenetic changes are rapidly erased. In this study, a new methodology was established to enhance the transmission of epigenetic changes directed by stress by exposed the stress during somatic embryogenesis by using overexpression of AtRWP-RKD4 in Arabidopsis thaliana. The data show that the introduction of abiotic stress during somatic embryogenesis leads to partly heritable adaptation phenotype in the non-stress progenies. The phenotypical changes are followed by the changes in transcriptome and methylome in which these molecular changes are observed in tissue-specific manners. Based on these findings, this new methodology can be applied to develop stable stress-adaptation phenotypic in plants.
Time-varying feedback control for nonholonomic mobile robots forming group formations

Presents an approach to control for multiple nonholonomic wheeled mobile robots of the Hilare-type to form group formations. To control the formation, each robot has its own coordinate system and it controls its relative positions to its neighboring robots. Particularly, it has a vector called a formation vector, and the formation is controllable by the vectors. Since the robots have nonholonomic constraints, it is not possible for them to directly move in omni-directions, which means that such nonholonomic vehicles cannot be asymptotically stabilized by smooth static-state feedback control laws. We introduce a smooth time-varying feedback control law whose asymptotic stability is guaranteed in a mathematical framework, averaging theory. The validity of this law is verified by computer simulations.
Video anomaly detection and localisation based on the sparsity and reconstruction error of auto-encoder

A fast and accurate video anomaly detection and localisation method is presented. The speed and localisation accuracy are two ongoing challenges in real-world anomaly detection. We introduce two novel cubic-patch-based anomaly detector where one works based on power of an auto-encoder (AE) on reconstituting an input video patch and another one is based on the power of sparse representation of an input video patch. It is found that if an AE is efficiently trained on all normal patches, the anomaly patch in testing phase has a more reconstruction error than a normal patch. Also if a sparse AE is learned based on normal training patches, we expect that the given patch to AE is represented sparsely. If the representation is not enough sparse it is considered as a good candidate to be anomaly. For being more fast, these two detectors are combined as a cascade classifier. First, all small patches on test video frame are scanned, those which have not enough sparse representation are resized and sent to next detector for more careful evaluation. The experiment results show that the method mentioned here has a better performance especially in run-time measure than state-of-the-art methods on two UMN and UCSD benchmarks.
A real-time recurrent error propagation network word recognition system

A hybrid system using a connectionist model and a Markov model for the DARPA Resource Management task of large-vocabulary multiple-speaker continuous speech recognition is presented. The connectionist model uses internal feedback for context modeling and provides phone state occupancy probabilities for a simple context independent Markov model. The system has been implemented in real-time on a workstation supported by a DSP board. The use of context-independent phone models leads to the possibility of time-domain pruning and computationally efficient durational modeling, both of which are reported. <<ETX>>
Evolution of the latitudinal diversity gradient in the hyperdiverse ant genusPheidole

AIM: The latitudinal diversity gradient is the dominant pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyper-rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (>1100 species) ant radiation, Pheidole , and evaluate the roles of three general explanations for the latitudinal gradient: variation in diversification rate, tropical conservatism, and ecological regulation. LOCATION: Global. TIME PERIOD: The past 35 million years. MAJOR TAXA STUDIED: The hyperdiverse ant genus Pheidole Westwood. METHODS: We assembled geographic data for 1499 species and morphospecies, and inferred a dated phylogeny of Pheidole of 449 species, including 150 species newly sequenced for this study. We tested correlations between diversification rate and latitude with BAMM, HiSSE, GeoSSE, and FiSSE, and examined patterns of diversification as Pheidole spread around the globe. RESULTS: We found that Pheidole diversification occurred in series of bursts when new continents were colonized, followed by a slowdown in each region. There was no evidence of systematic variation of net diversification rates with latitude across any of the methods. Additionally, we found latitudinal affinity is moderately conserved with a Neotropical ancestor and phylogenetic inertia alone is sufficient to produce the gradient pattern. MAIN CONCLUSIONS: Overall our results are consistent with tropical conservatism explaining the diversity gradient, while providing no evidence that diversification rate varies systematically with latitude. There is evidence of ecological regulation on continental scales through the pattern of diversification after colonization. These results shed light on the mechanisms underlying the diversity gradient, while contributing toward a much-needed invertebrate perspective on global biodiversity dynamics.
Fault Diagnosis and Logic Debugging

Recent advances in Boolean satisfiability have made it an attractive engine for solving many digital very-large-scale- integration design problems. Although useful in many stages of the design cycle, fault diagnosis and logic debugging have not been addressed within a satisfiability-based framework. This work proposes a novel Boolean satisfiability-based method for multiple-fault diagnosis and multiple-design-error diagnosis in combinational and sequential circuits. A number of heuristics are presented that keep the method memory and run-time efficient. An extensive suite of experiments on large circuits corrupted with different types of faults and errors confirm its robustness and practicality. They also suggest that satisfiability captures signif- icant characteristics of the problem of diagnosis and encourage novel research in satisfiability-based diagnosis as a complementary process to design verification.
Latitudinal effects of anthropogenic factors driving raptor species richness across the American continent

Geographic gradients in species richness have been traditionally attributed to variation in environmental conditions. However, untangling the importance of human activities in explaining spatial patterns in raptor species richness, still remains a challenge. We evaluated the relative importance of how human impacts and ecogeographical conditions shape the latitudinal patterns of resident (n = 140) and migratory (n = 35) raptor species richness in the American continent, and analysed whether these factors differ between the Nearctic and the Neotropical regions.
A Proposal of Interactive Disease-Search System using HK Graph

Recently, public interest in health is growing. In addition, the rapid development of information technology gives us much medical information, that places increased demands on the medical support systems using the information. The aim of this study is to develop a medical support system by using Hierarchical Keyword Graph (HK Graph). This system infers and shows the candidates of the name of disease with graph structure after a user inputs his/her symptoms. Then it shows appropriate hospitals considering the disease, specialty of each hospital, the distance from home, and so on. This paper focuses on the part of the inference of disease from inputted symptoms. It proposes interactive disease-search system using HK Graph which can visualize the relationship among words with network structure based on the co-occurrence information.
Live tracking of Moving samples in confocal microscopy for vertically grown roots tips

Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker - a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.
A booster configuration with adaptive reduction of transmitter-receiver antenna coupling for pager systems

This paper discusses a design method and experimental results of a booster which is designed for use in pager systems. In order to reduce the coupling between the transmitter and receiver antennas this booster employs an adaptive canceling scheme that is a type of signal regeneration relay. A blind algorithm for canceling is derived using the minimum output power criterion. This paper proposes two stage canceling processed in the RF-band and baseband. An experimental equipment demonstrates that it can operate well under fluctuating coupling conditions. A field research, finally, verifies its effectiveness.
Modeling spatiotemporal distribution of Dipterocarpus turbinatus Gaertn. F in Bangladesh under climate change scenarios

ABSTRACT Climate change affects plant phenology, spatial distribution, and even extinction of vulnerable species. Dipterocarpus turbinatus, locally known as garjan, is a valuable but vulnerable native tree species of Bangladesh whose spatial distribution under future climate change scenarios is not fully understood. The aim of this study was to examine the effects of present and future climatic scenarios on spatiotemporal distribution of D. turbinatus. We used maximum entropy species distribution modeling to perform the present and future habitat suitability of garjan under different climate scenarios. The representative concentration pathways (RCP) 2.6 and 8.5 were considered for bioclimatic variables from the Global Climate Model – Hadley Global Environment Model 2 Atmosphere-Ocean. The predictive accuracy of the model was more than 97% in both the training and test data. The prediction results suggest that compared to present areas (7624 km2) under moderate habitat class it will be 2755 km2 and 1239 km2, respectively, in 2050 and 2070 under RCP2.6 scenario and decreases more rapidly under RCP8.5 scenario. Besides, the prediction also indicates that the habitat of the species will shift toward the high altitudinal south-eastern corner of the country whereas local extinction might occur in the north-eastern part during 2070.
Implementation of ML Using Naïve Bayes Algorithm for Identifying Disease-Treatment Relation in Bio-Science Text

In recent years many successful machine learning applications have been developed, ranging from data- mining programs to information-filtering systems that learn users' reading preferences. At the same time, there have been important advances in the theory and algorithms that can be used identify the diseases and treatment relations in a Bio-Science text. Imagine a computer learns from medical records which treatments are most effective for new diseases. Having the machine learning concept behind we have proposed a Machine Learning (ML) approach based on Naive Bayes (NB) algorithm to improve the automatic disease identification in the medical field. And also we have improved text classification by using an integrated model.
Automated 3D Mapping of Submarine Tunnels

Advances in embedded computer architecture, digital signal processing, guidance and navigation, and digital sensing have made it possible to develop relatively compact instruments that can be used to create highly accurate three dimensional maps of channelized aquifers (flooded spring tunnels), bypass tunnels for dams, storm runoff networks, freshwater delivery tunnels, and other submarine features. One such implementation was recently designed and built for a National Geographic Society expedition to Wakulla Springs, Florida and was used to create the first three dimensional cave map. The Wakulla Digital Wall Mapper (DWM) consisted of a series of bulkhead-isolated cylinders measuring 324 mm diameter by 1122 mm in length and weighing 82 kg. The DWM contained five integrated subsystems including an onboard guidance and navigation system, a customdesigned sonar array, a digital user interface, a pitch/yaw control system, and a master integration and data management system. In all, eight onboard computers control the instrument. Drift in the Inertial Measurement Unit (IMU) was the major design concern since it directly affected the accuracy of the maps generated. A high-accuracy reference network of induction radio beacons was used to provide the necessary control. It was found that a time-based drift compensation algorithm, working between radio control points, provided a useful and simple approach to positional error reduction.
Migratory flights and local wintering movements of Greylag Geese Anser anser in western Europe

ABSTRACT The local and migratory movements of Greylag Geese Anser anser wintering in southwest and northwest Europe were revealed with global positioning system tracking. Geese in the southwest had smaller home ranges than those from the northwest, and birds also moved large distances over wintering grounds and showed flexibility in the annual choice of wintering sites.