Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellulase and Alkaline Treatment Improve Intestinal Microbial Degradation of Recalcitrant Fibers of Rapeseed Meal in Pigs

The aim of the current study was to investigate whether degradation of rapeseed meal (RSM) by a swine gut microbiota consortium was improved by modifying RSM by treatment with cellulase (CELL), two pectinases (PECT), or alkaline (ALK) compared to untreated RSM and to assess whether microbiota composition and activity changed. The predicted relative abundances of carbohydrate digestion and absorption, glycolysis, pentose phosphate pathway, and pyruvate metabolism were significantly increased upon CELL and ALK feeding, and CELL and ALK also exhibited increased total short-chain fatty acid (SCFA) production compared to CON. Megasphaera, Prevotella, and Desulfovibrio were significantly positively correlated with SCFA production. Findings were validated in ileal cannulated pigs, which showed that CELL and ALK increased fiber degradation of RSM. In conclusion, CELL and ALK rather than PECT1 or PECT2 increased fiber degradation in RSM, and this information could guide feed additive strategies to improve efficiency and productivity in the swine industry.
Biological invasion of the Drew University (New Jersey) forest preserve by Norway maple (Acer platanoides L.).

WEBB, S. L. (Biology Department, Drew University, Madison, NJ 07940 USA) AND C. K. KAUNZINGER. Biological invasion of the Drew University (New Jersey) Forest Preserve by Norway maple (Acer platanoides L.). Bull. Torrey Bot. Club 120: 343-349. 1993. -The invasiveness of nonnative Acer platanoides in an isolated New Jersey Fagus grandifolia-Quercus spp. -Acer saccharum forest preserve was investigated by comparing size and age profiles of the exotic species with those of other tree populations present. Increment cores show that Acer platanoides was present by 1915 and is now plentiful in all younger age classes. Acer platanoides is the second most abundant canopy species (17.2% of stems), outnumbered only by Fagus grandifolia (41%), and more numerous than either Acer saccharum (9.4%) or Quercus spp. (11.7%). Because of its relatively recent arrival, Acer platanoides ranks in dominance (8.2% relative basal area) below Quercus velutina (29.1%), Fagus grandifolia (26.1%), and Quercus alba (12.1%), but above Acer saccharum (1.9%). Acer platanoides seems likely to increase in importance in the future, because its abundant (> 2000/ha) shade-tolerant seedlings and saplings comprise 59% of all small (DBH < 5 cm) woody stems, over twice the amount of Fagus grandifolia reproduction (23.1%) and five times the Acer saccharum reproduction (10.5%). To maintain or restore examples of relatively natural forest communities in this region, it may be necessary to restrict horticultural plantings and remove mature individuals of this popular tree in the vicinity of nature preserves.
Hypertonic saline and mannitol in patients with traumatic brain injury

Abstract Background: To compare the effects of 3% hypertonic saline solution and 20% mannitol solution on intracranial hypertension. Methods: WAN-FANGDATA, CNKI, and CQVIP databases were searched, and relevant literatures of randomized controlled trials comparing 3% hypertonic saline solution with mannitol in reducing intracranial hypertension from 2010 to October 2019 were collected. Meta-analysis was performed using RevMan software. Results : As a result, 10 articles that met the inclusion criteria were finally included. A total of 544 patients were enrolled in the study, 270 in the hypertonic saline group and 274 in the mannitol group. There was no significant difference in the decrease of intracranial pressure and the onset time of drug between the 2 groups after intervention (all P > .05). There was a statistically significant difference between the hypertonic saline group and the mannitol group in terms of duration of effect in reducing intracranial pressure (95% confidence interval: 0.64–1.05, Z = 8.09, P < .00001) and cerebral perfusion pressure after intervention (95% confidence interval: 0.15–0.92, Z = 2.72, P = .007). Conclusion: Both 3% hypertonic saline and mannitol can effectively reduce intracranial pressure, but 3% hypertonic saline has a more sustained effect on intracranial pressure and can effectively increase cerebral perfusion pressure.
Effects of cottonseed meal hydrolysate on growth performance and biochemical indices of Cyprinus carpio var.Jian

The experiment was conducted to investigate the effects of dietary protein resources replaced by cottonseed meal hydrolysate on growth performance,serum biochemical indices and intestinal digestive enzyme activities of Cyprinus carpio var.Jian(48.56±1.39) g.Fish were divided into 3 groups and fed with different diets.Group Ⅰ was fed with basal diet,group Ⅱ with the basal diet in which 2% fish meal was replaced by equivalent cottonseed meal hydrolysate,and group Ⅲ with the basal diet in which 2% plant protein resources(1%soybean meal+0.5%rapeseed meal+0.5% cottonseed meal) was replaced by equivalent cottonseed meal hydrolysate.The result showed that weight gain ratios and specific growth rates of group Ⅱ and Ⅲ were significantly higher than that of group Ⅰ(P0.05). Feed conversion ratios of group Ⅱ and Ⅲ were significantly lower than that of group Ⅰ(P0.05). Viscera somatic index and hepato somatic index of group Ⅱ and Ⅲ were lower than that of group Ⅰ. Protein contents of whole fish of group Ⅱ and Ⅲ were significantly higher than that of group Ⅰ(P0.05). Activities of Lysozyme,Alkaline phosphatase in serum and protease in intestine of group Ⅱ and Ⅲ were higher than that of group Ⅰ.
The cocrystal of 3-((4-(3-isocyanobenzyl) piperazine-1-yl) methyl) benzonitrile with 5-hydroxy isophthalic acid prevents protofibril formation of serum albumin

Abstract The formation of amyloid-like fibrils is a central problem in biophysical chemistry and medicine. Fibril formation and their deposition in various tissues and organs are associated with many human diseases. Searching for molecules able to prevent the formation of fibrils is, therefore, necessary. In this work, we examined the potential of a cocrystal (SS3) of 3-((4-(3-isocyanobenzyl) piperazine-1-yl) methy) benzonitrile with 5-hydroxy isophthalic acid, to prevent fibrillation of human serum albumin. We found that the cocrystal strongly bound to human serum albumin (HSA) with association constant (K a) of 5.8 ± 0.7 × 105 M−1. The SS3 binding was found to cause small alterations in both secondary and tertiary structure of the protein. Transmission electron microscopy showed that the cocrystal completely prevented the formation of worm-like protofibrils by HSA at SS3/HSA molar ratio of 1:1. The molecule was found to prevent the aggregation in a concentration dependent manner. It was also observed that most of protein in the presence of SS3 remained in soluble state and the secondary structure contained native-like α-helical structure. Therefore, we conclude that the cocrystal effectively prevented conversion of HSA into worm-like protofibril. These finding suggest that combination of molecules in the form of cocrystal or other stable combination could pave a way for the development of drugs against amyloidosis. Communicated by Ramaswamy H. Sarma
GeoNet++: Iterative Geometric Neural Network with Edge-Aware Refinement for Joint Depth and Surface Normal Estimation

In this paper, we propose a geometric neural network with edge-aware refinement (GeoNet++) to jointly predict both depth and surface normal maps from a single image. Building on top of two-stream CNNs, GeoNet++ captures the geometric relationships between depth and surface normals with the proposed depth-to-normal and normal-to-depth modules. In particular, the “depth-to-normal” module exploits the least square solution of estimating surface normals from depth to improve their quality, while the “normal-to-depth” module refines the depth map based on the constraints on surface normals through kernel regression. Boundary information is exploited via an edge-aware refinement module. GeoNet++ effectively predicts depth and surface normals with high 3D consistency and sharp boundaries resulting in better reconstructed 3D scenes. Note that GeoNet++ is generic and can be used in other depth/normal prediction frameworks to improve 3D reconstruction quality and pixel-wise accuracy of depth and surface normals. Furthermore, we propose a new 3D geometric metric (3DGM) for evaluating depth prediction in 3D. In contrast to current metrics that focus on evaluating pixel-wise error/accuracy, 3DGM measures whether the predicted depth can reconstruct high quality 3D surface normals. This is a more natural metric for many 3D application domains. Our experiments on NYUD-V2 [1] and KITTI [2] datasets verify that GeoNet++ produces fine boundary details and the predicted depth can be used to reconstruct high quality 3D surfaces.
Application of SRAP on Analysis of Genetic Diversity in Tobacco Germplasms

To investigate the genetic diversity of tobacco germplasms,46 common cultivated tobacco varieties/lines,including 30 cultivars of Nicotiana tabacum L.and 16 N.rustica L.varieties,were amplified by 15 SRAP(sequence-related amplified polymorphism) primers selected from 160 primers.The results showed that a total of 3036 SRAP bands were obtained with 15 informative primer combinations,of which 636 bands were polymorphic and the average for per-primer was 42 bands.The UPGMA cluster based on SRAP indicated that 46 samples could be clustered into two groups,the same type tobacco varieties could be approximately clustered together,which indicated that SRAP is useful in revealing the genetic diversity among tobacco germplasms.
Rapid reconstruction of highly undersampled, non‐Cartesian real‐time cine k‐space data using a perceptual complex neural network (PCNN)

Highly accelerated real‐time cine MRI using compressed sensing (CS) is a promising approach to achieve high spatio‐temporal resolution and clinically acceptable image quality in patients with arrhythmia and/or dyspnea. However, its lengthy image reconstruction time may hinder its clinical translation. The purpose of this study was to develop a neural network for reconstruction of non‐Cartesian real‐time cine MRI k‐space data faster (<1 min per slice with 80 frames) than graphics processing unit (GPU)‐accelerated CS reconstruction, without significant loss in image quality or accuracy in left ventricular (LV) functional parameters. We introduce a perceptual complex neural network (PCNN) that trains on complex‐valued MRI signal and incorporates a perceptual loss term to suppress incoherent image details. This PCNN was trained and tested with multi‐slice, multi‐phase, cine images from 40 patients (20 for training, 20 for testing), where the zero‐filled images were used as input and the corresponding CS reconstructed images were used as practical ground truth. The resulting images were compared using quantitative metrics (structural similarity index (SSIM) and normalized root mean square error (NRMSE)) and visual scores (conspicuity, temporal fidelity, artifacts, and noise scores), individually graded on a five‐point scale (1, worst; 3, acceptable; 5, best), and LV ejection fraction (LVEF). The mean processing time per slice with 80 frames for PCNN was 23.7 ± 1.9 s for pre‐processing (Step 1, same as CS) and 0.822 ± 0.004 s for dealiasing (Step 2, 166 times faster than CS). Our PCNN produced higher data fidelity metrics (SSIM = 0.88 ± 0.02, NRMSE = 0.014 ± 0.004) compared with CS. While all the visual scores were significantly different (P < 0.05), the median scores were all 4.0 or higher for both CS and PCNN. LVEFs measured from CS and PCNN were strongly correlated (R2 = 0.92) and in good agreement (mean difference = −1.4% [2.3% of mean]; limit of agreement = 10.6% [17.6% of mean]). The proposed PCNN is capable of rapid reconstruction (25 s per slice with 80 frames) of non‐Cartesian real‐time cine MRI k‐space data, without significant loss in image quality or accuracy in LV functional parameters.
Investigation on the Interaction between Cellulosic Paper and Organic Acids Based on Molecular Dynamics

Organic acid is an important factor that accelerates the aging of cellulosic insulation materials. In this study, the interactions between cellulose and five acids, representative of what may be found in an aging transformer, were studied using molecular dynamics. The adsorption process of the five acids onto the surface of crystalline cellulose shows that the three low molecular acids are more readily adsorbed onto cellulose than the two high molecular acids. The deformation and adsorption energies of the acids all increase with an increase in molecular weight when they are stably interacting with cellulose. However, the differences between adsorption energies and deformation energies are positive for the three low molecular acids, whereas they are negative for the two high molecular acids. This indicates that the attachments onto cellulose of low molecular acids are considerably more stabilized than those of the high molecular acids. This is consistent with the experimental results. Furthermore, based on the calculated solubility parameters of acids, the experimental result that the three low molecular acids are to a large degree absorbed onto the cellulose, whereas the two high molecular acids remain in the oil, was theoretically elucidated using the theory of similarity and intermiscibility.
Resource plasticity-driven carbon-nitrogen budgeting enables specialization and division of labor in a clonal community

Previously, we found that in glucose-limited Saccharomyces cerevisiae colonies, metabolic constraints drive cells into groups exhibiting gluconeogenic or glycolytic states. In that study, threshold amounts of trehalose - a limiting, produced carbon-resource, controls the emergence and self-organization of cells exhibiting the glycolytic state, serving as a carbon source that fuels glycolysis (Varahan et al., 2019). We now discover that the plasticity of use of a non-limiting resource, aspartate, controls both resource production and the emergence of heterogeneous cell states, based on differential metabolic budgeting. In gluconeogenic cells, aspartate is a carbon source for trehalose production, while in glycolytic cells using trehalose for carbon, aspartate is predominantly a nitrogen source for nucleotide synthesis. This metabolic plasticity of aspartate enables carbon-nitrogen budgeting, thereby driving the biochemical self-organization of distinct cell states. Through this organization, cells in each state exhibit true division of labor, providing growth/survival advantages for the whole community.
Sequence of Alzheimer disease biomarker changes in cognitively normal adults

Objective To determine the ordering of changes in Alzheimer disease (AD) biomarkers among cognitively normal individuals. Methods Cross-sectional data, including CSF analytes, molecular imaging of cerebral fibrillar β-amyloid (Aβ) with PET using the [11C] benzothiazole tracer Pittsburgh compound B (PiB), MRI-based brain structures, and clinical/cognitive outcomes harmonized from 8 studies, collectively involving 3,284 cognitively normal individuals 18 to 101 years of age, were analyzed. The age at which each marker exhibited an accelerated change (called the change point) was estimated and compared across the markers. Results Accelerated changes in CSF Aβ1-42 (Aβ42) occurred at 48.28 years of age and in Aβ42/Aβ40 ratio at 46.02 years, followed by PiB mean cortical standardized uptake value ratio (SUVR) with a change point at 54.47 years. CSF total tau (Tau) and tau phosphorylated at threonine 181 (Ptau) had a change point at ≈60 years, similar to those for MRI hippocampal volume and cortical thickness. The change point for a cognitive composite occurred at 62.41 years. The change points for CSF Aβ42 and Aβ42/Aβ40 ratio, albeit not significantly different from that for PiB SUVR, occurred significantly earlier than that for CSF Tau, Ptau, MRI markers, and the cognitive composite. Adjusted analyses confirmed that accelerated changes in CSF Tau, Ptau, MRI markers, and the cognitive composite occurred at ages not significantly different from each other. Conclusions Our findings support the hypothesized early changes of amyloid in preclinical AD and suggest that changes in neuronal injury and neurodegeneration markers occur close in time to cognitive decline.
NUCKS1 promotes RAD54 activity in homologous recombination DNA repair

Maranon et al. have identified the NUCKS1 protein as a new regulator of the spatiotemporal events in homologous recombination DNA repair. NUCKS1 prevents RAD54–RAD51AP1 association during RAD51 filament formation and synergizes with RAD54 activity in displacement loop formation.
Isolation of three members of the multigene family encoding ACC oxidases in Hevea brasiliensis and investigation of their responses to ethylene stimulation and wounding

Ethylene is a major stimulating factor for natural rubber production in Hevea brasiliensis and is often applied in the form of Ethephon, an ethylene releaser. In a positive feedback type mechanism, the application of ethylene leads to the enhanced expression of genes involved in ethylene biosynthesis such as ACC oxidases, which are also responsive to wounding. We studied the regulation of ethylene biosynthesis in rubber trees through the characterisation of the ACC oxidase multigene family and the responses of individual genes to ethylene and wounding. Three full-length cDNAs, HbACO1, HbACO2 and HbACO3, were isolated. The HbACOs were 1115, 1174 and 1074 bp long, respectively, with open reading frames encoding polypeptides of 312, 318 and 318 amino acids, respectively. The genomic sequences of HbACO1 and HbACO2 were also characterised, revealing divergent gene structures: HbACO1 (1456 bp) possesses three introns and four exons, while HbACO2 (1418 bp) consists of two introns and three exons. All of the HbACO genes were expressed at all stages of development studied, from in vitro callus to the exploited plant, but with different expression profiles. Nevertheless, no expression was detected in latex. In the bark of the shoot of the first flush of budded plants, HbACO1 was expressed at a higher level than the other genes, and was down-regulated by ethylene and wounding in both leaf and bark tissues. In contrast, HbACO2 and HbACO3 were transiently induced in response to ethylene and wounding. Treatment with 1-MCP, an ethylene action inhibitor, abolished the ethylene induction of HbACO2 gene, showing that this gene was under positive feedback regulation. The expression of HbACO3 gene was also induced by ethylene treatment and wounding, again with an antagonistic effect of 1-MCP. In conclusion, HbACO1 appears to be responsible for basal levels of ethylene production while HbACO2 and HbACO3 are up-regulated in response to external factors. (Resume d'auteur)
A comparison of clinical, laboratory and chest CT findings of laboratory-confirmed and clinically diagnosed COVID-19 patients at first admission.

PURPOSE This study aims to identify chest computed tomography (CT) characteristics of coronavirus disease 2019 (COVID-19), investigate the association between CT findings and laboratory or demographic findings, and compare the accuracy of chest CT with reverse transcription-polymerase chain reaction (RT-PCR). METHODS Overall, 120 of 159 consecutive cases isolated due to suspected COVID-19 at our hospital between 17 and 25 March 2020 were included in this retrospective study. All patients underwent both chest CT and RT-PCR at first admission. The patients were divided into two groups: laboratory-confirmed COVID-19 and clinically diagnosed COVID-19. Clinical findings, laboratory findings, radiologic features and CT severity index (CT-SI) of the patients were noted. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of chest CT were calculated for the diagnosis of COVID-19, using RT-PCR as reference. RESULTS The laboratory-confirmed and clinically diagnosed COVID-19 groups consisted of 69 (M/F 43/26, mean age 50.9±14.0 years) and 51 patients (M/F 24/27, mean age 50.9±18.8 years), respectively. Dry cough (62.3% vs. 52.9%), fever (30.4% vs. 25.5%) and dyspnea (23.2% vs. 27.5%) were the most common admission symptoms in the laboratory-confirmed and clinically diagnosed COVID-19 groups, respectively. Bilateral multilobe involvement (83.1% vs. 57.5%), peripheral distribution (96.9% vs. 97.5%), patchy shape (75.4% vs. 70.0%), ground-glass opacities (GGO) (96.9% vs. 100.0%), vascular enlargement (56.9% vs. 50.0%), intralobular reticular density (40.0% vs. 40.0%) and bronchial wall thickening (27.7% vs. 45.0%) were the most common CT findings in the laboratory-confirmed and clinically diagnosed COVID-19 subgroups, respectively. Except for the bilateral involvement and white blood cell (WBC) count, no difference was found between the clinical, laboratory, and parenchymal findings of the two groups. Positive correlation was found between CT-SI and, lactate dehydrogenase (LDH) and C-reactive protein (CRP) values in the laboratory-confirmed COVID-19 subgroup. Chest CT and RT-PCR positivity rates among patients with suspected COVID-19 were 87.5% (105/120) and 57.5% (69/120), respectively. The sensitivity, specificity, PPV, NPV and accuracy rates of chest CT were determined as 94.2% (95% confidence interval [CI], 85.8-98.4), 21.57% (95% CI, 11.3-35.3), 61.90% (95% CI, 58.2-65.5), 73.3% (95% CI, 48.2-89.1) and 63.3% (95% CI, 54.1-71.9), respectively. CONCLUSION Chest CT has high sensitivity and low specificity in the diagnosis of COVID-19. The clinical, laboratory, and CT findings of laboratory-confirmed and clinically diagnosed COVID-19 patients are similar.
Rheology by Design: A Regulatory Tutorial for Analytical Method Validation

The increasing demand for product and process understanding as an active pursuit in the quality guideline Q8 and, more recently, on the draft guideline on quality and equivalence of topical products, has unveiled the tremendous potential of rheology methods as a tool for microstructure characterization of topical semisolid dosage forms. Accordingly, procedure standardization is a dire need. This work aimed at developing and validating a methodology tutorial for rheology analysis. A 1% hydrocortisone cream was used as model cream formulation. Through a risk assessment analysis, the impact of selected critical method variables (geometry, temperature and application mode) was estimated in a broad range of rheological critical analytical attributes—zero-shear viscosity, upper-shear thinning viscosity, lower-shear thinning viscosity, infinite-shear viscosity, rotational yield point, thixotropic relative area, linear viscoelastic region, oscillatory yield point, storage modulus, loss modulus, and loss tangent. The proposed validation of the approach included the rheometer qualification, followed by the validation of numerous operational critical parameters regarding a rheology profile acquisition. The thixotropic relative area, oscillatory yield point, flow point and viscosity related endpoints proved to be highly sensitive and discriminatory parameters. This rationale provided a standard framework for the development of a reliable and robust rheology profile acquisition.