Miracle-dz/UniFAR-FTUs huggingface dataset:
Error Analysis for Visual Odometry on Indoor, Wheeled Mobile Robots With 3-D Sensors

The objective of this paper is to improve the visual odometry performance through the analysis of the sensor noise and the propagation of an error through the entire visual odometry system. The visual odometry algorithm is implemented on an indoor, wheeled mobile robot (WMR) constrained to planar motion, and uses an integrated color-depth (RGB-D) camera, and a one-point (1-pt), 3 degree-of-freedom inverse kinematic solution, enabling a closed-form bound on the propagated error. There are three main contributions of this paper. First, feature location errors for the RGB-D camera are quantified. Second, these feature location errors are propagated through the entire visual odometry algorithm. Third, the visual odometry performance is improved by using the predicted error to weight individual 1-pt solutions. The error bounds and the improved visual odometry scheme are experimentally verified on a WMR. Using the error-weighting scheme, the proposed visual odometry algorithm achieves the performance of approximately 1.5% error, without the use of iterative, outlier-rejection tools.
Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins

Despite decades of investigations, the principal mechanisms responsible for the high affinity and specificity of proteins for key physiological cations K+, Na+, and Ca2+ remain a hotly debated topic. At the core of the debate is an apparent need (or lack thereof) for an accurate description of the electrostatic response of the charge distribution in a protein to the binding of an ion. These effects range from partial electronic polarization of the directly ligating atoms to long-range effects related to partial charge transfer and electronic delocalization effects. While accurate modeling of cation recognition by metalloproteins warrants the use of quantum-mechanics (QM) calculations, the most popular approximations used in major biomolecular simulation packages rely on the implicit modeling of electronic polarization effects. That is, high-level QM computations for ion binding to proteins are desirable, but they are often unfeasible, because of the large size of the reactive-site models and the need to sample conformational space exhaustively at finite temperature. Several solutions to this challenge have been proposed in the field, ranging from the recently developed Drude polarizable force-field for simulations of metalloproteins to approximate tight-binding density functional theory (DFTB). To delineate the usefulness of different approximations, we examined the accuracy of three recent and commonly used theoretical models and numerical algorithms, namely, CHARMM C36, the latest developed Drude polarizable force fields, and DFTB3 with the latest 3OB parameters. We performed MD simulations for 30 cation-selective proteins with high-resolution X-ray structures to create ensembles of structures for analysis with different levels of theory, e.g., additive and polarizable force fields, DFTB3, and DFT. The results from DFT computations were used to benchmark CHARMM C36, Drude, and DFTB3 performance. The explicit modeling of quantum effects unveils the key electrostatic properties of the protein sites and the importance of specific ion-protein interactions. One of the most interesting findings is that secondary coordination shells of proteins are noticeably perturbed in a cation-dependent manner, showing significant delocalization and long-range effects of charge transfer and polarization upon binding Ca2+.
Estimating the prevalence of Positive Tuberculin Skin Test Reactions in General Population and High-risk Groups: A Meta-analysis

Results of tuberculin skin test (TST) surveys among different populations have been reported in many studies as a method for detecting primary Mycobacterium tuberculosis infection. Combining these results provides reliable estimates of primary latent tuberculosis (TB) infection for health policymakers. This study aims to estimate the prevalence of latent TB infection in general and high-risk populations in Iran. National and international databanks were searched using specific keywords. After restricting the search strategy, duplicates exclusion, reviewing titles, abstracts and full texts, and quality assessment, eligible papers were selected. The heterogeneity between the results was assessed according to Cochrane and I-squared indices. The prevalence of positive TST reactions was estimated using fixed and random effect models. Totally, 33 papers were entered into the meta-analysis reporting the TST results in 12693 people aged over 18. The prevalence (95% confidence intervals) of positive TST reactions in all groups, general population, health staff, medical students, household close contacts, patients with TB, immunocompromised patients, HIV/AIDS patients, and those with risky behaviors was 26.2% (19.6–32.8), 25.4% (4.8–46.1), 38.9% (27.4–50.9), 13.4% (9.9–16.7), 35.9% (16.4–55.5), 13.7% (8.4–18.9), 29.4% (21.2–37.7), and 14.6% (3.9–25.3), respectively. Our study showed great varieties of positive TST results among different Iranian subpopulations. Furthermore, the prevalence of latent TB infection among health professionals and family members of TB patients was considerably different from that of the other subgroup. Since TB control programs such as active case finding are routinely conducted among household close contacts and HIV/AIDS cases, other high-risk groups including health-care workers and immunocompromised patients should be taken into consideration in these preventive programs.
Dynamical Behaviors of Stochastic Hopfield Neural Networks with Both Time-Varying and Continuously Distributed Delays

This paper investigates dynamical behaviors of stochastic Hopfield neural networks with both time-varying and continuously distributed delays. By employing the Lyapunov functional theory and linear matrix inequality, some novel criteria on asymptotic stability, ultimate boundedness, and weak attractor are derived. Finally, an example is given to illustrate the correctness and effectiveness of our theoretical results.
mRNA Decay during Herpes Simplex Virus (HSV) Infections: Protein-Protein Interactions Involving the HSV Virion Host Shutoff Protein and Translation Factors eIF4H and eIF4A

ABSTRACT During lytic infections, the virion host shutoff (Vhs) protein of herpes simplex virus accelerates the degradation of both host and viral mRNAs. In so doing, it helps redirect the cell from host to viral protein synthesis and facilitates the sequential expression of different viral genes. Vhs interacts with the cellular translation initiation factor eIF4H, and several point mutations that abolish its mRNA degradative activity also abrogate its ability to bind eIF4H. In addition, a complex containing bacterially expressed Vhs and a glutathione S-transferase (GST)-eIF4H fusion protein has RNase activity. eIF4H shares a region of sequence homology with eIF4B, and it appears to be functionally similar in that both stimulate the RNA helicase activity of eIF4A, a component of the mRNA cap-binding complex eIF4F. We show that eIF4H interacts physically with eIF4A in the yeast two-hybrid system and in GST pull-down assays and that the two proteins can be coimmunoprecipitated from mammalian cells. Vhs also interacts with eIF4A in GST pull-down and coimmunoprecipitation assays. Site-directed mutagenesis of Vhs and eIF4H revealed residues of each that are important for their mutual interaction, but not for their interaction with eIF4A. Thus, Vhs, eIF4H, and eIF4A comprise a group of proteins, each of which is able to interact directly with the other two. Whether they interact simultaneously as a tripartite complex or sequentially is unclear. The data suggest a mechanism for linking the degradation of an mRNA to its translation and for targeting Vhs to mRNAs and to regions of translation initiation.
Review Article: High-Content Screening: A Decade of Evolution

In the past decade, high-content screening has become a highly developed approach to obtaining richly descriptive quantitative phenotypic data using automated microscopy. From early use in drug screening, the technique has evolved to embrace a diverse range of applications in both academic and industrial sectors and is now widely recognized as providing an efficient and effective approach to large-scale programs investigating cell biology in situ and in context.
The SMAP level 4 carbon product for monitoring terrestrial ecosystem-atmosphere CO2 exchange

The NASA Soil Moisture Active Passive (SMAP) mission Level 4 Carbon (L4_C) product provides model estimates of Net Ecosystem CO2 exchange (NEE) incorporating SMAP soil moisture information as a primary driver. The L4_C product provides NEE, computed as total respiration less gross photosynthesis, at a daily time step and approximate 14-day latency posted to a 9-km global grid summarized by plant functional type. The L4_C product includes component carbon fluxes, surface soil organic carbon stocks, underlying environmental constraints, and detailed uncertainty metrics. The L4_C model is driven by the SMAP Level 4 Soil Moisture (L4_SM) data assimilation product, with additional inputs from the Goddard Earth Observing System, Version 5 (GEOS-5) weather analysis and Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data. The L4_C data record extends from March 2015 to present with ongoing production. Initial comparisons against global CO2 eddy flux tower measurements, satellite Solar Induced Canopy Florescence (SIF) and other independent observation benchmarks show favorable L4_C performance and accuracy, capturing the dynamic biosphere response to recent weather anomalies and demonstrating the value of SMAP observations for monitoring of global terrestrial water and carbon cycle linkages.
Electrochemical control of redox potential affects methanogenesis of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus

To investigate the precise effect of the redox potential on the methanogenesis of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus by using an electrochemical redox controlling system without adding oxidizing or reducing agents. A bioelectrochemical system was applied to control the redox conditions in culture and to measure the methane‐producing activity of M. thermautotrophicus at a constant potential from +0·2 to −0·8 V (vs Ag/AgCl). Methane production and growth of M. thermautotrophicus were 1·6 and 3·5 times increased at −0·8 V, compared with control experiments without electrolysis, respectively, while methanogenesis was suppressed between +0·2 and −0·2 V. A clear relationship between an electrochemically regulated redox potential and methanogenesis was revealed.
PC12 and neuro 2a cells have different susceptibilities to acetylcholinesterase–amyloid complexes, amyloid25–35 fragment, glutamate, and hydrogen peroxide

This work addresses the differential effects of several oxidative insults on two neuronal cell lines, PC12 and Neuro 2a cells, extensively used as neuronal models in vitro. We measured cellular damage using the cytotoxic assays for MTT reduction and LDH release and found that acetylcholinesterase (AChE)–amyloid–β‐peptide (Aβ) complexes, Aβ25–35 fragment, glutamate and H2O2 were over 200‐fold more toxic to PC12 than to Neuro 2a cells. 17α and 17β estradiol were able to protect both cell types from damage caused by H2O2 or glutamate. By contrast, other insults not related to oxidative stress, such as those caused by the nonionic detergent Triton X‐100 and serum deprivation, induced a similar level of damage in both PC12 and Neuro 2a cells. Considering that the Aβ peptide, H2O2 and glutamate are cellular insults that cause an increase in reactive oxygen species (ROS), the intracellular levels of the antioxidant compound, glutathione were verified. Neuro 2a cells were found to have 4‐ to 5‐fold more glutathione than PC12 cells. Our results suggest that Neuro 2a cells are less susceptible to exposure to AChE–Aβ complexes, Aβ25–35 fragment, glutamate and H2O2 than PC12 cells, due to higher intracellular levels of antioxidant defense factors. J. Neurosci. Res. 56:620–631, 1999. © 1999 Wiley‐Liss, Inc.
Productivity and profitability of different crop sequences in semi-arid condition.

A field study was conducted at farmer’s field during 2002-05 in Soda village of Malpura tehsil of Tonk district (Rajasthan, India) with seven crop sequences to find out a suitable cropping sequence based on productivity and profitability. Groundnut-wheat crop sequence recorded maximum pearmillet equivalent yield (PEY) (10.34 t ha -1 ) which was 7.17, 15.67, 25.73 and 26.89 per cent higher than the greengram-wheat (9.60 t ha -1 ), greengram-barley (8.72 t ha -1 ), groundnut-mustard (7.68 t ha -1 ) and pearlmillet-wheat (7.56 t ha -1 ) crop sequences respectively. Similarly, maximum land-use efficiency (LUE) was observed in groundnut-wheat system (72.60%) followed by pearlmillet-wheat system (69.77%) and both were statistically at par, whereas the lowest LUE was recorded in greengram-barley (56.16%) cropping sequence. Groundnut-wheat sequence also recorded the highest net returns (Rs 36580 ha -1 ) and benefit cost ratio (Rs 2.22), whereas sorghum-chickpea showed the lowest net returns (Rs 2710 ha -1 ) and benefit cost ratio (Rs 1.12). Further, Groundnut
Partisan Sorting and Niche Parties in Europe

Earlier research has concluded that European citizens do not update their Left–Right policy preferences or their party attachments in response to the content of parties’ election manifestos – i.e. partisan sorting is not observed in the mass public in response to shifts in the Left–Right tone of these manifestos. Here we extend this research to analyse whether we observe partisan sorting patterns that correspond with political experts’ perceptions of parties’ Left–Right policy shifts. Given that these experts plausibly consider all pertinent information when estimating parties’ Left–Right orientations – including party elites’ speeches, elite interviews, coalition behaviour, and legislative voting patterns – such a finding would imply that citizens do weigh the wider informational environment when updating their Left–Right orientations and their party support, even if they do not attach great weight to the parties’ policy manifestos. Our analyses provide support for this hypothesis with respect to niche parties, i.e. green, communist, and radical right parties, but not for mainstream parties.
An EWMA control chart for monitoring the mean of skewed populations using weighted variance

This paper discusses the use of weighted variance (WV) in setting up the limits of the exponentially weighted moving average (EWMA) chart for the monitoring of the mean of a process from a skewed population. This chart, called the WV-EWMA chart hereafter, reduces to the standard EWMA chart when the underlying distribution is symmetric. The Type-I and Type-II errors of the WV-EWMA chart are compared with that of the existing charts for skewed populations. Simulation results show that the new method gives a considerable improvement over the existing methods when the underlying distribution is skewed.
Complete mitochondrial genome and phylogenetic analysis of stripe-throated yuhina (Yuhina gularis)

Abstract In China, the stripe-throated yuhina is mainly distributed in southwestern and the population is not abundant. In this study, we sequenced and characterized its complete mitochondrial genome. The complete mitochondrial of stripe-throated yuhina is 17,843 bp in length and contained 13 protein-coding genes, 2rRNA genes, 22 tRNA genes, and 2 control regions. The overall base composition of the mitogenome was 30.6% A, 14.1% G, 23.99% T, 31.31% C. All the genes in the stripe-throated yuhina mitogenome were encoded on the H-strand, except for the ND6 and eight tRNA genes that were transcribed from the L-strand.
High resolution nanomechanical characterization of multi‐domain model membranes by fast Force Volume

Plasma membrane is a complex structure, mainly composed by lipids and proteins, which plays a pivotal role in cell metabolism by regulating its selective permeability to ions and molecules. According to the “raft hypothesis”, lipids in the bilayer are not forming a structurally passive solvent, but are rather organized in specific domains, which present different structural and functional characteristics. The mechanical properties of the lipid part of plasma membrane have been recently characterized through Atomic Force Microscopy, by analyzing the features of force vs distance curves collected on supported lipid bilayers (SLBs). In case of lipid domains sizing from tens to hundreds of nanometers, which mimic in a good way the lateral organization of real membranes, a high lateral resolution and a large number of curves are often required for properly expressing the complexity of the system, with a consequent exponential growth of acquisition and processing time. In this paper we propose a method, based on a recently developed high speed Force Volume technique and on home‐built data processing software, for the mechanical characterization of nanostructured SLBs. With our software we have been able to process data set composed by tens of thousands of curves, collected with a spatial resolution ranging from 8 to 40 nm/pixel. Multiparametric maps and distribution histograms produced by our analysis allowed identifying a specific behavior for each lipid phase in the investigated model membranes, even in presence of nanosized features. Copyright © 2015 John Wiley & Sons, Ltd.
Debt, diplomacy and dreadnoughts: the National Bank of Turkey, 1909–1919

ABSTRACT The National Bank of Turkey (NBT) (1909) was an attempt by the new Young Turk regime to assert economic sovereignty: creating a multinational bank able to provide financing free of the diplomatic conditions previously attached to loans by French banks. NBT's role financing naval rearmament and oil development has attracted a good deal of attention from historians. Using the archives of the bank's founders and Ottoman ministers alongside familiar diplomatic sources, this article is the first to combine Ottoman and European perspectives on NBT, challenging the traditional narrative which presents the Ottoman Empire as the helpless ‘victim’ of the fiscal imperialism of France, Britain and Germany in the years before 1914.
Virus–host interactions: insights from the replication cycle of the large Paramecium bursaria chlorella virus

The increasing interest in cytoplasmic factories generated by eukaryotic‐infecting viruses stems from the realization that these highly ordered assemblies may contribute fundamental novel insights to the functional significance of order in cellular biology. Here, we report the formation process and structural features of the cytoplasmic factories of the large dsDNA virus Paramecium bursaria chlorella virus 1 (PBCV‐1). By combining diverse imaging techniques, including scanning transmission electron microscopy tomography and focused ion beam technologies, we show that the architecture and mode of formation of PBCV‐1 factories are significantly different from those generated by their evolutionary relatives Vaccinia and Mimivirus. Specifically, PBCV‐1 factories consist of a network of single membrane bilayers acting as capsid templates in the central region, and viral genomes spread throughout the host cytoplasm but excluded from the membrane‐containing sites. In sharp contrast, factories generated by Mimivirus have viral genomes in their core, with membrane biogenesis region located at their periphery. Yet, all viral factories appear to share structural features that are essential for their function. In addition, our studies support the notion that PBCV‐1 infection, which was recently reported to result in significant pathological outcomes in humans and mice, proceeds through a bacteriophage‐like infection pathway.
Importance and Physiological Effects of Hemolymphagy in Triatomines (Hemiptera: Reduviidae)

ABSTRACT Triatomines are hematophagous insects and the vectors for Trypanosoma cruzi in the Americas. Although their preferred meal is blood from vertebrate hosts, unfed triatomine nymphs are often seen feeding on different arthropod species. Triatomine saliva has a wide range of activities that aid the hematophagic process. However, nothing is known about its role during hemolymphagy. In the current study, we reproduced hemolymphagy under laboratory conditions and evaluated the influence of hemolymphagy on the survival of Triatoma infestans nymphs. The effects of saliva on the activation of the prophenoloxidase cascade in the invertebrate host and the influence of the saliva on the motility of the bugs and contractions of the dorsal vessels were assessed. Hemolymphagy prolonged the survival rate of T. infestans first instars from 60 to >120 d compared with unfed nymphs. The saliva from T. infestans caused a 50% reduction in the amplitude and frequency of the dorsal vessel contractions of adult Rhodnius prolixus and induced paralysis for >10 min when the saliva was injected into second instars. T. infestans saliva was able to inhibit the activation of the prophenoloxidase cascade from a R. prolixus hemolymph, but had no effect on the phenoloxidase activity after the cascade was activated. The paralyzing molecule in the saliva was <5 kDa and probably had no proteic or lipidie characteristics. These results suggest that triatomine saliva may play an important role during hemolymphagy by inducing paralysis and suppressing immune responses in the invertebrate host. The importance of hemolymphagy for the survival of nymphs in periods when vertebrate blood is scarce is also discussed.
A Supervised Hybrid Classifier for Brain Tissues and White Matter Lesions on Multispectral MRI

Accurate quantification of brain tissues is a very challenging problem in neuroimaging, such as quantification of gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF), and white matter lesions (WMLs). However, on many cases brain tissues and white matter lesions cannot be segmented and separated simultaneously by current techniques. Recently, a TRIO algorithm (TRIOA) is proposed to integrate three algorithms, Independent Component Analysis (ICA), Support Vector Machine (SVM) and Fisher's Linear Discriminant Analysis (FLDA) (ICA+SVM+IFLDA) which can effectively classify GM, WM and CSF by considering MR images as multispectral images in the native coordinate space. This paper further extends TRIOA in conjunction with Band Expansion Process (BEP), called Extended TRIOA (ETRIOA), to classify brain tissues as well as WMLs simultaneously. The accuracy assessment of the ETRIOA was evaluated by using the similarity index. The conducted experimental results demonstrate the clinical applicability of ETRIOA in simultaneous classification of GM, WM, CSF and WMLs.