Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic and genotypic characteristics of cowpea rhizobia from soils of Ethiopia

Phenotypic and genotypic characteristics of cowpea rhizobia indigenous to soils of Ethiopia are unknown. Forty indigenous cowpea rhizobial isolates were collected from cowpea-growing areas of the country and were characterized for their growth and genetic properties. Based on their cultural characteristics, the isolates were categorized into fast (FG), slow (SG), and extraslow-growings (ESG). The FG, SG, and ESG isolates had mean generation time (h)/colony diameter (mm)/date of turbidity formation (d) in the range of 2.5-7.5/2-4/2-3, 7.5-30/0.5-3.5/3-5, and 30-50/0.5-1/5-7, respectively. Thirty two and sixteen percentages of the isolates were FG and ESG, respectively. Most of the isolates (87%) could grow on culture medium of pH 4.5, but were intolerant of pH 8. The intrinsic antibiotics resistance (IAR) pattern was FG>SG>ESG for ampicillin, ciprofloxacin, chloramphenicol, erythromycin, neomycin sulfate and penicillin, whereas the pattern was FG SG>ESG for dextrin, dextrose, glucose, starch and sucrose whereas it was FG 7.5 h were grouped together at 70% of similarity. Partial sequence analysis of 16S rRNA gene showed the existence of isolates most similar to rhizobial species of Bradyrhizobium species, Bradyrhizobium japonicum, Bradyrhizobium elkanii, Rhizobium rubi, and Mesorhizobium species. In general, cowpea rhizobial isolates from soils of Ethiopia in this study were mainly SG and sensitive to stress in vitro conditions, but versatile in utilization of varieties of C and N substrates. Such studies are important in Ethiopia to identify rhizobial isolates that could be amendable for use as inoculants to improve cowpea production. Key words: Phylogeny, diversity, isolates, growth categories, cluster analysis.
Crushed crambe from biodiesel production as replacement for soybean meal in the supplement of steers grazing

Abstract To evaluate the substitution of soybean meal by crushed crambe as a source of protein, five crossbred steers rumen cannulated weighting 426 ± 25 kg BW were distributed in a 5 × 5 Latin square design. The steers were allocated in different levels of crushed crambe groups (0, 25, 50, 100 and 150 g/kg in concentrate supplement). Dry matter intake (DMI), rumen fluid pH, nitrogen (N) urinary excretion, propionate and isovalerate ruminal concentrations increased linearly (p < .05) with the replacement of soybean meal by crushed crambe. Crude protein (CP) intake, butyrate and valerate concentrations, and N retention and balance (g/d) showed linear decreases by the inclusion of crushed crambe. There was a quadratic decrease (p < .05) for neutral detergent fibre (NDF) intake and valerate concentration. Total short-chain fatty acids (SCFAs) increased quadratically (p < .05) with the inclusion of crushed crambe. The supplement and total DMI, digestibility of DM, CP and NDF, N–NH3, acetate, isobutyrate concentrations and intake, excretion faecal and total of N, microbial protein synthesis, urinary excretion and blood concentration of urea and creatinine were not affected (p > .05) by the crushed crambe inclusion in the diet. It is recommended that 100 g/kg of the crushed crambe inclusion replacing soybean meal supplements to grazing steers because improved supplement DMI and total SCFAs, reducing ruminal fermentation and nitrogen excretion, without affecting digestibility and microbial protein synthesis. Highlights DM intake and digestibility were not affected in steers fed crushed crambe. Urinary N excretion increased with crushed crambe replacing soybean meal.
A Gain Design Method for a Linear Extended State Observers to Improve Robustness of Deadbeat Control

This article proposes an extended state observer to broaden the stability range of conventional deadbeat controller. The proposed observer is constructed through the model of permanent magnet synchronous machine (PMSM) which considers the parameters mismatch and unmodeled nonlinear elements. For the high bandwidth of current loop, the closed-loop stability is not ensured through the stability of observer. Therefore, the effect on the closed-loop performance which is caused by the observer is analyzed through the closed-loop transfer function and proved that the deadbeat performance can be kept when the parameters are precise. Furthermore, the system robustness performance is improved through adjusting the observer gain properly when parameters mismatch exists. To ensure the closed-loop stability, H∞ norm of the transfer function is chosen as an index to determine the two gain factors of observer. The effectiveness of the proposed algorithm is verified by Simulation and experimental results.
Effect of Trichoderma spp on Plant Height of Local Rice Varieties in the Early Phase of Growth

Shoots are important organs in plant growth, because the process of photosynthesis occurs in shoots, especially in plant leaves. Application Trichoderma as a bio fertilizer can increase the growth of shoots of various plants including superior varieties of rice plants. On the other hand, local rice varieties characterized by relatively slow growth Local varieties have not received sufficient attention of researchers to increase their growth. This has an unfavorable impact on preserving that variety in the field. This study aims to evaluate the response of local rice varieties to the application of Trichoderma spp in the seedbed and after transplanting. Two-factor factorial experiment was designed with a completely randomized design. Factor A consisted of 5 local rice varieties and Factor B consisted of 8 isolates and one control. Local variety was obtained from the West Sumtera region and the Trichoderma isolate came from the rhizosphere of lowland rice plants in Solok Regency and upland rice in West Pasaman. Application of Trichoderma spp is done by soaking the seeds with Trichoderma spp isolate. Response of plant height growth to isolates was observed when in the nursery at 2 weeks old and 2 weeks after transplanting. Data were processed by analysis of variance and Duncan's follow-up test at a significance of 5%. The results showed that plant height is influenced by variety when in the seedbed, but was not affected by the application of Trichoderma spp. Although there was no interaction, plant height after transplanting was influenced by varieties and isolates. The best isolate to increase plant height is KRT with an average height of 86.1 cm compared to a control of only 81.5 cm.
Utility of Immunohistochemistry and Western Blot in Profiling Clinically Suspected Cases of Congenital Muscular Dystrophy

Objective: Immunocharacterization of congenital muscular dystrophy (CMD) to determine the frequency of various subtypes in a large Indian Cohort. Materials and Methods: This retrospective (2014-2017) study was carried on muscle biopsies of clinically suspected cases of CMD with histological evidence of dystrophy/myopathic features. Immunohistochemistry (IHC) to antibodies against laminin (α2, α5,β1,γ1), Collagen-VI (A1,2,3), and Western blot (WB) for α-dystroglycan and POMT1 was performed. Results: The study included 57 cases, of which 15 cases (26.3%) had mean age at presentation of 3.5 years, M: F = 1.5:1, elevated creatinine kinase (CK) (mean 1657 U/L), global developmental delay, multiple contractures, abnormal facies, white matter hyperintensities and showed laminin-α2 deficiency (Merosin deficient CMD). In addition, secondary reduction in laminin-β1, over-expression of laminin-α5, and preserved laminin-γ1 was noted. Ullrich CMD constituted 11/57 cases (19.2%) with mean age at presentation of 5.3 years, M: F = 1.2:1 and normal CK. They presented with proximal muscle weakness, soft velvety palms and soles, contractures, and joint hyperextensibility. Collagen-VI (A1,2,3) showed either complete (n = 3) or sarcolemmal specific (n = 8) loss of staining. Out of the remaining 31 cases, WB for α-dystroglycan was performed in 17 cases which showed deficiency in seven (12.3%). Three of these in addition revealed secondary partial loss of laminin-α2. WB for POMT1 showed deficiency in a single case clinically diagnosed Walker–Warburg syndrome, who presented with seizures and classical features of pachygyria, lissencephaly, and cerebellar cyst on MRI. Twenty-four cases (42.2%) remained uncharacterized and need genetic evaluation. Conclusion: The study helped in characterizing 57.8% of the proband. Immunotyping helps to direct mutational analysis for targeted genes and offers a potential route for prenatal diagnosis.
Comparative analysis of epidemiological and clinical characteristics of appendicitis among children and adults.

BACKGROUND This study aimed to investigate whether there are some differences between pediatric and adult patients with appendicitis. METHODS We retrospectively reviewed the records of 279 pediatric and 275 adult patients with respect to demographics, past medical history, duration of symptoms, laboratory and radiological findings, operation notes, pathological reports, length of hospital stay and post-operative outcomes. RESULTS No significant differences were found with respect to gender, rates of perforation and negative appendectomy, laboratory findings, and overall outcomes between children and adults. However, our study suggests that the diagnosis is more difficult in children, the most preferred radiologic diagnostic methods are abdominal ultrasound and plain X-ray in children vs. computed tomography in adults, air-fluid levels and right-sided scoliosis are more commonly detected on X-ray in children, appendiceal perforation is more common at both extreme of ages, the appendix is perforated earlier and length of hospital stay is longer in children, and misdiagnosis at first admission in children and advanced age in adults were the risk factors associated with the complications. CONCLUSION The present study found some important differences between childhood and adulthood appendicitis. If these differences are considered when evaluating the patients, more desired outcomes can be achieved for both clinicians and patients.
Seismic hazard assessment of the Shillong Plateau using a probabilistic approach

Abstract Seismotectonic processes of the Shillong Plateau (SP) have been influenced by the Himalayan orogeny, the India-Burmese subduction, and the Bengal Basin evolution leading to high seismic activity in the region. With a goal of assessing seismic hazards in the SP and providing a scientific information to engineering and disaster risk management communities, a probabilistic seismic hazard analysis is employed to determine hazard in highly-populated districts of SP and particularly in Shillong, Nongpoh, and Tura cities, located within the districts. This analysis is based on the use of historical and instrumentally recorded regional earthquakes since 1411 and deals with uncertainties related to earthquake magnitudes, rupture locations, and the frequency of ground motion exceedance. Individual hazard curves indicate that the Barapani fault possesses the highest frequency of seismic hazard for Shillong city and Nongpoh, and the Eocene hinge zone and Dauki faults are responsible for the highest frequency of seismic hazard at Tura. The results of the hazard assessment together with those obtained earlier using a scenario-based approach demonstrate that although the Oldham fault located near Tura can produce a great, but rare earthquake, few other nearby faults are capable of producing smaller magnitude events with a higher probability of occurrence.
Community Detection in Social Networks: Multilayer Networks and Pairwise Covariates

Community Detection in Social Networks: Multilayer Networks and Pairwise Covariates Sihan Huang Community detection is one of the most fundamental problems in network study. The stochastic block model (SBM) is arguably the most studied model for network data with different estimation methods developed with their community detection consistency results unveiled. Due to its stringent assumptions, SBM may not be suitable for many real-world problems. In this thesis, we present two approaches that incorporate extra information compared with vanilla SBM to help improve community detection performance and be suitable for applications. One approach is to stack multilayer networks that are composed of multiple single-layer networks with common community structure. Numerous methods have been proposed based on spectral clustering, but most rely on optimizing an objective function while the associated theoretical properties remain to be largely unexplored. We focus on the ‘early fusion’ method [114], of which the target is to minimize the spectral clustering error of the weighted adjacency matrix (WAM). We derive the optimal weights by studying the asymptotic behavior of eigenvalues and eigenvectors of the WAM. We show that the eigenvector of WAM converges to a normal distribution as in [129], and the clustering error is monotonically decreasing with the eigenvalue gap. This fact reveals the intrinsic link between eigenvalues and eigenvectors, and thus the algorithm will minimize the clustering error by maximizing the eigenvalue gap. The numerical study shows that our algorithm outperforms other state-of-art methods significantly, especially when signal-to-noise ratios of layers vary widely. Our algorithm also yields higher accuracy result for S&P 1500 stocks dataset than competing models. The other approach we propose is to consider heterogeneous connection probabilities to remove the strong assumption that all nodes in the same community are stochastically equivalent, which may not be suitable for practical applications. We introduce a pairwise covariates-adjusted stochastic block model (PCABM), a generalization of SBM that incorporates pairwise covariates information. We study the maximum likelihood estimates of the coefficients for the covariates as well as the community assignments. It is shown that both the coefficient estimates of the covariates and the community assignments are consistent under suitable sparsity conditions. Spectral clustering with adjustment (SCWA) is introduced to fit PCABM efficiently. Under certain conditions, we derive the error bound of community estimation under SCWA and show that it is community detection consistent. PCABM compares favorably with the SBM or degree-corrected stochastic block model under a wide range of simulated and real networks when covariate information is accessible.
Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells

The nuclear envelope (NE) is an endoplasmic reticulum (ER) subdomain that contains characteristic components dedicated to nuclear functions. These include nuclear pore complexes (NPCs) – the channels for nucleocytoplasmic transport, and the nuclear lamina (NL) – a scaffold for NE and chromatin organization at the nuclear periphery. Since numerous human diseases associated with NE/NL proteins occur in mesenchyme-derived cells, a more comprehensive characterization of proteins concentrated at the NE in these cell types is warranted. Accordingly, we used proteomics to analyze NE and other subcellular fractions isolated from mesenchymal stem cells and from differentiated adipocytes and myocytes. We evaluated the proteomics datasets to calculate relative protein enrichment in the NE fraction, using a spectral abundance-based scoring system that accurately described most benchmark proteins. We then examined five high-scoring transmembrane proteins expressed in all three cell types that were not previously known to be enriched at the NE. Using quantitative immunofluorescence microscopy to track ectopically expressed proteins, we validated that all five of these components are substantially concentrated at the NE of multiple cell types. One (Itprip) is exposed to the outer nuclear membrane, a second (Smpd4) is enriched at the NPC, and the three others (Mfsd10, Tmx4, and Arl6ip6) are suggested to reside in the inner nuclear membrane. Considering their sequences and other features, these proteins provide new focal points for studying the functions and membrane dynamics of the NE. Our datasets should be useful for identifying additional NE-concentrated proteins, and for evaluating candidates that are identified in screening.
Dental homologies and evolutionary transformations in Caviomorpha (Hystricognathi, Rodentia): new data from the Paleogene of Peruvian Amazonia

ABSTRACT Dental homologies and evolutionary transformations within caviomorph rodents have long been disputed. Here, we participate in these debates in providing new insights from the dental morphology of Paleogene caviomorphs from Peruvian Amazonia (Contamana and Shapaja). Their analyses and comparisons with many hystricognaths allow (1) to generalize some hypotheses previously proposed about occlusal morphology of caviomorph cheek teeth, and (2) to propose new ones. In caviomorphs, the third crest of upper teeth would correspond either to a mesoloph or to a mesolophule or to a combination of both. The transformation from a pentalophodont pattern to a tetralophodont pattern would be explained by the disappearance of the metaloph. Likewise, the transformation from a tetralophodont pattern to a trilophodont pattern is observed by the loss of the third crest. A direct transformation from a pentalophodont pattern to a trilophodont pattern is also observed. Concerning lower teeth, discrepancies of homologies are centered on the mesial cristids, which can be notably distinguished depending on their compositions and connections with other structures. The ancestral patterns of caviomorph lower molars and dp4s were likely tetralophodont and pentalophodont, respectively. However, schemes with five and four (even three) transverse cristids cannot be ruled out for the two loci, respectively.
CONDITIONAL DAMPED RANDOM SURFACE VELOCITY MODEL OF TURBULENT JET BREAKUP

A turbulent jet breakup model is derived using concepts from probability theory. Velocity ﬂuctu-ations at the free surface are hypothesized to be the cause of turbulent jet breakup. This idea is formalized by treating the ﬂuctuations as random variables, subject to damping from the free surface. In contrast to previous theories, this theory uses a conditional ensemble average to determine quantities of interest because not all ﬂuctuations produce droplets. An energy balance and a closure model are used to determine the Sauter mean diameter. Similar approaches are used to determine the breakup onset location, breakup length, and spray angle. To validate the model, data from previous experimental studies using long pipe nozzles was compiled. Data for rough pipes was used to include turbulence intensity in the study.
Genetic inheritance of traits relating to seedling and size in ornamental pepper

Pepper exhibits genetic diversity and versatility in use. Knowledge of the genetic control of traits in peppers is of great importance to breeding programs given the variety of types, sizes, colors and flavors. The aim of the present study was to examine the inheritance of seedling and plant traits in ornamental pepper (Capsicum annuum). The experiment was conducted in a greenhouse in the plant biotechnology section of the Agricultural Sciences Center, Federal University of Paraiba. Seven ornamental pepper accessions (Capsicum annuum L.) belonging to CCA-UFPB's Germplasm Bank were used: UFPB001, UFPB004, UFPB77.3, UFPB099, UFPB134, UFPB137 and UFPB390. Morphoagronomic characterization was performed based on Capsicum descriptors (IPGRI, 1995), and twelve quantitative traits were evaluated regarding seedling and plant. The data were previously subjected to variance analysis and subsequent diallel analysis performed according to Hayman's (1954) method. The t statistic was used to test the adequacy of the additive-dominance model. Seedling height, hypocotyl diameter, cotyledon leaf length, plant height, first fork height, leaf length and width and chlorophyll a and b represent traits that conformed to the additive-dominant model. Genetic gains in regard to plant traits (plant height, first fork height, crown diameter and leaf length and width) in ornamental peppers are possible using breeding programs. Partial dominance of all plant traits is noted, and overdominance of the traits seedling height and cotyledon leaf length and width were observed. The parents UFPB001 and UFPB134 exhibited the highest concentration of favorable alleles for size traits and are indicated for selection for continued improvement programs.
Toward Secure and Privacy-Preserving Distributed Deep Learning in Fog-Cloud Computing

Fog-cloud computing promises many new vertical service areas beyond simple data communication, storing, and processing. Among them, distributed deep learning (DDL) across fog-cloud computing environment is one of the most popular applications due to its high efficiency and scalability. Compared with the centralized deep learning, DDL can provide better privacy protection with training only on sharing parameters. Nevertheless, when DDL meets fog-cloud computing, it still faces two major security challenges: 1) how to protect users’ privacy from being leaked to other internal participants in the training process and 2) how to guarantee users’ identities from being forged by external adversaries. To combat them, several approaches have been proposed via various technologies. Nevertheless, those approaches suffer from drawbacks in terms of security, efficiency, and functionality, and cannot guarantee the legitimacy of participants’ identities during training. In this article, we propose a secure and privacy-preserving DDL (SPDDL) for fog-cloud computing. Compared with the state-of-the-art works, our proposal achieves a better tradeoff between security, efficiency, and functionality. In addition, our SPDDL can guarantee the unforgeability of users’ identities against external adversaries. Extensive experimental results indicate the practical feasibility and high efficiency of our SPDDL.
Neural Correlates of Interobserver Visual Congruency in Free-Viewing Condition

Dynamic visual scenes lead to varying consistency of observers’ eye movements, reflecting one intrinsic characteristic of visual scenes, termed interobserver visual congruency (IOVC). However, the neural correlates underlying IOVC are largely unknown especially in the free-viewing condition. In this study, we explored the neural correlates of IOVC using functional magnetic resonance imaging (fMRI) and eye-tracking data acquired in a naturalistic paradigm. Specifically, we estimated IOVC of movie shots from eye-tracking data and then conducted two statistical analyses for functional inference, including a hypothesis-driven analyses [general linear model (GLM)] and a data-driven approach [intersubject correlation (ISC)]. The GLM analysis demonstrated that IOVC recruited two distinctive streams of neural systems. Specifically, neural activities in superior temporal gyrus, default mode network, and hippocampus were positively correlated with IOVC, whereas those in the primary and secondary visual cortices, as well as the dorsal attention network exhibited negative correlations. Further ISC analysis revealed that movie shots with higher IOVC evoked more synchronous brain activities in the primary auditory cortex, primary visual cortex, and superior parietal lobule compared to those shots with lower IOVC. This study provides some novel evidence of visual processing in the human brain in the free-viewing condition.