Miracle-dz/UniFAR-FTUs huggingface dataset:
Soybean-Nodulating Strains With Low Intrinsic Competitiveness for Nodulation, Good Symbiotic Performance, and Stress-Tolerance Isolated From Soybean-Cropped Soils in Argentina

Soybean is the most important oilseed in the world, cropped in 120–130 million hectares each year. The three most important soybean producers are Argentina, Brazil, and United States, where soybean crops are routinely inoculated with symbiotic N2-fixing Bradyrhizobium spp. This extended inoculation gave rise to soybean-nodulating allochthonous populations (SNAPs) that compete against new inoculant for nodulation, thus impairing yield responses. Competitiveness depends on intrinsic factors contributed by genotype, extrinsic ones determined by growth and environmental conditions, and strain persistence in the soil. To assess these factors in Argentinean SNAPs, we studied 58 isolates from five sites of the main soybean cropping area. BOX-A1R DNA fingerprint distributed these isolates in 10 clades that paralleled the pHs of their original soils. By contrast, reference Bradyrhizobium spp. strains, including those used as soybean-inoculants, were confined to a single clade. More detailed characterization of a subset of 11 SNAP-isolates revealed that five were Bradyrhizobium japonicum, two Bradyrhizobium elkanii, two Rhizobium radiobacter (formerly Agrobacterium tumefaciens), one Bradyrhizobium diazoefficiens, and one Paenibacillus glycanilyticus-which did not nodulate when inoculated alone, and therefore was excluded from further characterization. The remaining subset of 10 SNAP-isolates was used for deeper characterization. All SNAP-isolates were aluminum- and heat-tolerant, and most of them were glyphosate-tolerant. Meanwhile, inoculant strains tested were sensitive to aluminum and glyphosate. In addition, all SNAP-isolates were motile to different degrees. Only three SNAP-isolates were deficient for N2-fixation, and none was intrinsically more competitive than the inoculant strain. These results are in contrast to the general belief that rhizobia from soil populations evolved as intrinsically more competitive for nodulation and less N2-fixing effective than inoculants strains. Shoot:root ratios, both as dry biomass and as total N, were highly correlated with leaf ureide contents, and therefore may be easy indicators of N2-fixing performance, suggesting that highly effective N2-fixing and well-adapted strains may be readily selected from SNAPs. In addition, intrinsic competitiveness of the inoculants strains seems already optimized against SNAP strains, and therefore our efforts to improve nodules occupation by inoculated strains should focus on the optimization of extrinsic competitiveness factors, such as inoculant formulation and inoculation technology.
Chemoarchitecture of the Monotreme Olfactory Bulb

The cyto- and chemoarchitecture of the olfactory bulb of two monotremes (shortbeaked echidna and platypus) was studied to determine if there are any chemoarchitectural differences from therian mammals. Nissl staining in conjunction with enzyme reactivity for NADPH diaphorase, and immunoreactivity for calcium binding proteins (parvalbumin, calbindin and calretinin), neuropeptide Y, tyrosine hydroxylase and non-phosphorylated neurofilament protein (SMI-32 antibody) were applied to the echidna. Material from platypus bulb was Nissl stained, immunoreacted for calretinin, or stained for NADPH diaphorase. In contrast to eutherians, no immunoreactivity for either the SMI-32 antibody or calretinin was found in the mitral or dispersed tufted cells of the monotremes and very few parvalbumin or calbindin immunoreactive neurons were found in the bulb of the echidna. On the other hand, immunoreactivity for tyrosine hydroxylase in the echidna was similar in distribution to that seen in therians, and periglomerular and granule cells showed similar patterns of calretinin immunoreactivity to eutherians. Multipolar neuropeptide Y immunoreactive neurons were confined to the deep granule cell layer and underlying white matter of the echidna bulb and NADPH diaphorase reactivity was found in occasional granule cells, fusiform and multipolar cells of the inner plexiform and granule cell layers, as well as underlying white matter. Unlike eutherians, no NPY immunoreactive or NADPH diaphorase reactive neurons were seen in the glomerular layer. The bulb of the echidna was comparable in volume to prosimians of similar body weight, and its constituent layers were highly folded. In conclusion, the monotreme olfactory bulb does not show any significant chemoarchitectural dissimilarities from eutheria, despite differences in mitral/tufted cell distribution.
Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.
Anti-tumor Efficacy Assessment of the Sigma Receptor Pan Modulator RC-106. A Promising Therapeutic Tool for Pancreatic Cancer

Introduction: Pancreatic cancer (PC) is one of the most lethal tumor worldwide, with no prognosis improvement over the past 20-years. The silent progressive nature of this neoplasia hampers the early diagnosis, and the surgical resection of the tumor, thus chemotherapy remains the only available therapeutic option. Sigma receptors (SRs) are a class of receptors proposed as new cancer therapeutic targets due to their over-expression in tumor cells and their involvement in cancer biology. The main localization of these receptors strongly suggests their potential role in ER unfolded protein response (ER-UPR), a condition frequently occurring in several pathological settings, including cancer. Our group has recently identified RC-106, a novel pan-SR modulator with good in vitro antiproliferative activities toward a panel of different cancer cell lines. In the present study, we investigated the in vitro properties and pharmacological profile of RC-106 in PC cell lines with the aim to identify a potential lead candidate for the treatment of this tumor. Methods: Pancreatic cancer cell lines Panc-1, Capan-1, and Capan-2 have been used in all experiments. S1R and TMEM97/S2R expression in PC cell lines was quantified by Real-Time qRT-PCR and Western Blot experiments. MTS assay was used to assess the antiproliferative effect of RC-106. The apoptotic properties of RC-106 was evaluated by TUNEL and caspase activation assays. GRP78/BiP, ATF4, and CHOP was quantified to evaluate ER-UPR. Proteasome activity was investigated by a specific fluorescent-based assay. Scratch wound healing assay was used to asses RC-106 effect on cell migration. In addition, we delineated the in vivo pharmacokinetic profile and pancreas distribution of RC-106 in male CD-1 mice. Results: Panc-1, Capan-1, and Capan-2 express both SRs. RC-106 exerts an antiproliferative and pro-apoptotic effect in all examined cell lines. Cells exposure to RC-106 induces the increase of the expression of ER-UPR related proteins, and the inhibition of proteasome activity. Moreover, RC-106 is able to decrease PC cell lines motility. The in vivo results show that RC-106 is more concentrated in pancreas than plasma. Conclusion: Overall, our data evidenced that the pan-SR modulator RC-106 is an optimal candidate for in vivo studies in animal models of PC.
Decision-Making From the Animal Perspective: Bridging Ecology and Subjective Cognition

To succeed organisms must trade priority across various needs, such as growth, survival, and reproduction. In naturally complex environments this incurs high computational costs. Models exist for several types of decisions, e.g. optimal foraging or life history theory. However, most models ignore proximate complexities and infer simple rules specific to each context. They try to deduce what the organism must do, but do not provide a mechanistic explanation of how it implements decisions. We posit that the underlying cognitive machinery cannot be ignored. From the point of view of the animal, the fundamental problems are what are the best contexts to choose and which stimuli require a response to achieve a specific goal (e.g., homeostasis, survival, reproduction). This requires a cognitive machinery enabling the organism to make predictions about the future and behave autonomously. Our simulation framework includes three essential aspects: (a) the focus on the autonomous individual, (b) the need to limit and integrate information from the environment, and (c) the importance of goal-directed rather than purely stimulus-driven cognitive and behavioral control. The resulting models integrate cognition, decision-making, and behavior in the whole phenotype that may include the genome, physiology, hormonal system, perception, emotions, motivation and cognition. We conclude that the fundamental state is the global organismic state that includes both physiology and the animal’s subjective “mind”. The approach provides an avenue for evolutionary understanding of subjective phenomena and self-awareness as evolved mechanisms for adaptive decision-making in natural environments.
Adaptation of a Mice Doppler Echocardiography Platform to Measure Cardiac Flow Velocities for Embryonic Chicken and Adult Zebrafish

Ultrasonography is the most widely used imaging technique in cardiovascular medicine. In this technique, a piezoelectric crystal produces, sends, and receives high frequency ultrasound waves to the body to create an image of internal organs. It enables practical real time visualization in a non-invasive manner, making the modality especially useful to image dynamic cardiac structures. In the last few decades, echocardiography has been applied to in vivo cardiac disease models, mainly to rodents. While clinical echocardiography platforms can be used for relatively large animals such as pigs and rats, specialized systems are needed for smaller species. Theoretically, as the size of the imaged sample decreases, the frequency of the ultrasound transducer needed to image the sample increases. There are multiple modes of echocardiography imaging. In Doppler mode, erythrocytes blood flow velocities are measured from the frequency shift of the sent ultrasound waves compared to received echoes. Recorded data are then used to calculate cardiac function parameters such as cardiac output, as well as the hemodynamic shear stress levels in the heart and blood vessels. The multi-mode (i.e., b-mode, m-mode, Pulsed Doppler, Tissue Doppler, etc.) small animal ultrasound systems in the market can be used for most in vivo cardiac disease models including mice, embryonic chick and zebrafish. These systems are also associated with significant costs. Alternatively, there are more economical single-mode echocardiography platforms. However, these are originally built for mice studies and they need to be tested and evaluated for smaller experimental models. We recently adapted a mice Doppler echocardiography system to measure cardiac flow velocities for adult zebrafish and embryonic chicken. We successfully assessed cardiac function and hemodynamic shear stress for normal as well as for diseased embryonic chicken and zebrafish. In this paper, we will present our detailed protocols for Doppler flow measurements and further cardiac function analysis on these models using the setup. The protocols will involve detailed steps for animal stabilization, probe orientation for specific measurements, data acquisition, and data analysis. We believe this information will help cardiac researchers to establish similar echocardiography platforms in their labs in a practical and economical manner.
Effect of wall-mediated hydrodynamic fluctuations on the kinetics of a Brownian nanoparticle

The reactive flux formalism (Chandler 1978 J. Chem. Phys. 68, 2959–2970. (doi:10.1063/1.436049)) and the subsequent development of methods such as transition path sampling have laid the foundation for explicitly quantifying the rate process in terms of microscopic simulations. However, explicit methods to account for how the hydrodynamic correlations impact the transient reaction rate are missing in the colloidal literature. We show that the composite generalized Langevin equation (Yu et al. 2015 Phys. Rev. E 91, 052303. (doi:10.1103/PhysRevE.91.052303)) makes a significant step towards solving the coupled processes of molecular reactions and hydrodynamic relaxation by examining how the wall-mediated hydrodynamic memory impacts the two-stage temporal relaxation of the reaction rate for a nanoparticle transition between two bound states in the bulk, near-wall and lubrication regimes.
An Efficient Model Based on Smoothed ℓ0 Norm for Sparse Signal Reconstruction

Compressed sensing (CS) is a new theory. With regard to the sparse signal, an exact reconstruction can be obtained with sufficient CS measurements. Nevertheless, in practical applications, the transform coefficients of many signals usually have weak sparsity and suffer from a variety of noise disturbances. What's worse, most existing classical algorithms are not able to effectively solve this issue. So we proposed an efficient algorithm based on smoothed ℓ 0 norm for sparse signal reconstruction. The direct ℓ 0 norm problem is NP hard, but it is unrealistic to directly solve the ℓ 0 norm problem for the reconstruction of the sparse signal. To select a suitable sequence of smoothed function and solve the ℓ 0 norm optimization problem effectively, we come up with a generalized approximate function model as the objective function to calculate the original signal. The proposed model preserves sharper edges, which is better than any other existing norm based algorithm. As a result, following this model, extensive simulations show that the proposed algorithm is superior to the similar algorithms used for solving the same problem.
Reducing the Cost of Authenticity with Leakages: a CIML2-Secure AE Scheme with One Call to a Strongly Protected Tweakable Block Cipher

This paper presents CONCRETE (Commit−Encrypt−Send− the−Key) a new Authenticated Encryption mode that offers CIML2 security, that is, ciphertext integrity in the presence of nonce misuse and side-channel leakages in both encryption and decryption. CONCRETE improves on a recent line of works aiming at leveled implementations, which mix a strongly protected and energy demanding implementation of a single component, and other weakly protected and much cheaper components. Here, these components all implement a tweakable block cipher TBC. CONCRETE requires the use of the strongly protected TBC only once while supporting the leakage of the full state of the weakly protected components – it achieves CIML2 security in the so-called unbounded leakage model. All previous works need to use the strongly protected implementation at least twice. As a result, for short messages whose encryption and decryption energy costs are dominated by the strongly protected component, we halve the cost of a leakage-resilient implementation. CONCRETE additionally provides security when unverified plaintexts are released, and confidentiality in the presence of simulatable leakages in encryption and decryption.
An evaluation of pseudoperipheral vertex finders for the Reverse Cuthill-McKee method for bandwidth and profile reductions of symmetric matrices

Previous publications have reviewed the main algorithms for the identification of pseudoperipheral vertices in graphs. Based on this experience, this paper evaluates seven promising methods for solving the problem of finding a proper pseudoperipheral vertex in a graph. This paper analyzes these seven pseudoperipheral vertex finders along with a new variant of Kaveh’s B algorithm. This paper evaluates these algorithms with the purpose of identifying proper starting vertices for the Reverse Cuthill-McKee method. Extensive experiments among these pseudoperipheral vertex finders show that the George-Liu algorithm remains in the state of the practice to provide pseudoperipheral vertices to the Reverse Cuthill-McKee method when applied to matrices with symmetric sparsity patterns.
SoK: On DFA Vulnerabilities of Substitution-Permutation Networks

Recently, the NIST launched a competition for lightweight cryptography and a large number of ciphers are expected to be studied and analyzed under this competition. Apart from the classical security, the candidates are desired to be analyzed against physical attacks. Differential Fault Analysis (DFA) is an invasive physical attack method for recovering key information from cipher implementations. Up to date, almost all the block ciphers have been shown to be vulnerable against DFA, while following similar attack patterns. However, so far researchers mostly focused on particular ciphers rather than cipher families, resulting in works that reuse the same idea for different ciphers. In this article, we aim at bridging this gap, by providing a generic DFA attack method targeting Substitution-Permutation Network (SPN) based families of symmetric block ciphers. We provide the overview of the state-of-the-art of the fault attacks on SPNs, followed by generalized conditions that hold on all the ciphers of this design family. We show that for any SPN, as long as the fault mask injected before a non-linear layer in the last round follows a non-uniform distribution, the key search space can always be reduced. This shows that it is not possible to design an SPN-based cipher that is completely secure against DFA, without randomization. Furthermore, we propose a novel approach to find good fault masks that can leak the key with a small number of instances. We then developed a tool, called Joint Difference Distribution Table (JDDT) for pre-computing the solutions for the fault equations, which allows us to recover the last round key with a very small number of pairs of faulty and non-faulty ciphertexts. We evaluate our methodology on various block ciphers, including PRESENT-80, PRESENT-128, GIFT-64, GIFT-128, AES-128, LED-64, LED-128, Skinny, Pride and Prince. The developed technique would allow automated DFA analysis of several candidates in the NIST competitio
Geopostors: a real-time geometry/impostor crowd rendering system

The simulation of large crowds of humans is important in many fields of computer graphics, including real-time applications such as games, as they can breathe life into otherwise static scenes and enhance believability. Although many new games are released each year, it is very unusual to find large-scale crowds populating the environments depicted. Such applications need to deal with having limited resources available at each frame. With many hundreds or thousands of potential virtual humans in a crowd, traditional techniques rapidly become overwhelmed and are not able to sustain an interactive frame-rate. Therefore, simpler approaches to the rendering, animation and behaviour control of the crowds are needed. Additionally, these new approaches must provide for variety, as environments inhabited by carbon-copy clones can be disconcerting and unrealistic.
An ultra-low-voltage active rectifier for energy harvesting applications

This paper presents an ultra-low-voltage active rectifier for micro energy harvesting. A two stage concept is used including a first passive stage and an active diode as second stage. A bulk-input comparator design is used which is well suited for low voltage applications. The power consumption is 200 nW and the minimum operation voltage is 350 mV using a 0.35 µm low VTh CMOS technology. The voltage drop over the rectifier is some tens of millivolt which results in voltage and power efficiencies of over 90 %. Input voltages with frequencies in the range of mHz to low kHz can be rectified.
Improved Belief Propagation by Employing the Positive Effects of the Feedback Messages

In this paper, a modification to belief propagation (BP) decoding algorithm is proposed, which is based on extracting the prior messages of each variable node to help the BP decoding, and is particularly effective for low-density parity-check (LDPC) codes with short cycles, where the existence of cycles makes the original BP algorithm perform suboptimal. The proposed algorithm, referred to as “employing the positive effects of the feedback messages (EPEFM)”, extracts the positive effects of the feedback messages and then makes use of them as prior messages to assist the decoding of the BP algorithm. Simulation results confirm the effectiveness of our proposed algorithm, which improves the performance in high signal-to-noise-ratio (SNR) region without loss in low SNR region.
Split phase induction motor operation from PWM voltage source inverter

An examination is made of the operation of split-phase induction motors from pulse width modulated (PWM) voltage source inverters. Splitting the phase windings leads to reduced voltage ratings for the inverter switches. The inverters are operated with space phasor based PWM. It is well known that with this technique, a three phase inverter can give a maximum peak fundamental of 0.577 V/sub DC/ for the motor phase voltage (with a circular trajectory for the voltage space phasor), as against 0.5 V/sub DC/ with sine triangle modulation. <<ETX>>