Miracle-dz/UniFAR-FTUs huggingface dataset:
Substitution of manure for chemical fertilizer affects soil microbial community diversity, structure and function in greenhouse vegetable production systems

Soil microbial communities and enzyme activities together affect various ecosystem functions of soils. Fertilization, an important agricultural management practice, is known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research was to make a comparative study of the effects of different nitrogen (N) fertilizer rates and types (organic and inorganic) on soil physicochemical properties, enzyme activities and microbial attributes in a greenhouse vegetable production (GVP) system of Tianjin, China. Results showed that manure substitution of chemical fertilizer, especially at a higher substitution rate, improved soil physicochemical properties (higher soil organic C (SOC) and nutrient (available N and P) contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure application induced a higher fungi/bacteria ratio due to a lower response in bacterial than fungal growth. Also, manure application greatly increased bacterial stress indices, as well as microbial communities and functional diversity. The principal component analysis showed that the impact of manure on microbial communities and enzyme activities were more significant than those of chemical fertilizer. Furthermore, redundancy analysis indicated that SOC and total N strongly influenced the microbial composition, while SOC and ammonium-N strongly influenced the microbial activity. In conclusion, manure substitution of inorganic fertilizer, especially at a higher substitution rate, was more efficient for improving soil quality and biological functions.
TUBB Variants Underlying Different Phenotypes Result in Altered Vesicle Trafficking and Microtubule Dynamics

Tubulinopathies are rare neurological disorders caused by alterations in tubulin structure and function, giving rise to a wide range of brain abnormalities involving neuronal proliferation, migration, differentiation and axon guidance. TUBB is one of the ten β-tubulin encoding genes present in the human genome and is broadly expressed in the developing central nervous system and the skin. Mutations in TUBB are responsible for two distinct pathological conditions: the first is characterized by microcephaly and complex structural brain malformations and the second, also known as “circumferential skin creases Kunze type” (CSC-KT), is associated to neurological features, excess skin folding and growth retardation. We used a combination of immunocytochemical and cellular approaches to explore, on patients’ derived fibroblasts, the functional consequences of two TUBB variants: the novel mutation (p.N52S), associated with basal ganglia and cerebellar dysgenesis, and the previously reported variant (p.M73T), linked to microcephaly, corpus callosum agenesis and CSC-KT skin phenotype. Our results demonstrate that these variants impair microtubule (MT) function and dynamics. Most importantly, our studies show an altered epidermal growth factor (EGF) and transferrin (Tf) intracellular vesicle trafficking in both patients’ fibroblasts, suggesting a specific role of TUBB in MT-dependent vesicular transport.
Energy Efficiency of Electro-Driven Brackish Water Desalination: Electrodialysis Significantly Outperforms Membrane Capacitive Deionization.

Electro-driven technologies are viewed as a potential alternative to the current state-of-the-art technology, reverse osmosis, for the desalination of brackish waters. Capacitive deionization (CDI), based on the principle of electrosorption, has been intensively researched under the premise of being energy efficient. However, electrodialysis (ED), despite being a more mature electro-driven technology, has yet to be extensively compared to CDI in terms of energetic performance. In this study, we utilize Nernst-Planck based models for continuous flow ED and constant-current membrane capacitive deionization (MCDI) to systematically evaluate the energy consumption of the two processes. By ensuring equivalently sized ED and MCDI systems - in addition to using the same feed salinity, salt removal, water recovery, and productivity across the two technologies - energy consumption is appropriately compared. We find that ED consumes less energy (has higher energy efficiency) than MCDI for all investigated conditions. Notably, our results indicate that the performance gap between ED and MCDI is substantial for typical brackish water desalination conditions (e.g., 3 g L-1 feed salinity, 0.5 g L-1 product water, 80% water recovery, and 15 L m-2 h-1 productivity), with the energy efficiency of ED often exceeding 30% and being nearly an order of magnitude greater than MCDI. We provide further insights into the inherent limitations of each technology by comparing their respective components of energy consumption, and explain why MCDI is unable to attain the performance of ED, even with ideal and optimized operation.
Integrated analysis of miRNA and mRNA expression profiles in the brains of BTBR mice

The BTBR T+ Itpr3tf (BTBR) mouse has developmental disorders in brain and many aberrant neuroanatomical structures and brain dysfunction. However, identification of the pathological mechanisms underlying abnormal brain development in the brains of BTBR mice is still lacking. Increasingly evidence showed that epigenetics plays an important role in the processes of brain development. In this study, we analyzed microRNA (miRNA) and mRNA expression profiles in the cortical brain tissue from BTBR mice, using RNA sequencing. As compared to C57BL/6J (B6) mice, 1,271 differentially expressed genes (DEGs) and 36 known differentially expressed miRNAs (DEMs) were found in the brain from BTBR mice. The functional annotation and categories of DEGs and DEMs were analyzed. Integration analysis identified 103 known miRNA–mRNA interaction pairs. We further verified selected several genes and miRNAs which may be associated with brain development using quantitative RT‐PCR (qRT‐PCR). Finally, we speculate that reduced myelin‐associated oligodendrocytic basic protein and transmembrane proteins 260 may be linked with abnormal brain development in BTBR mice.
Occlusion-Aware Region-Based 3D Pose Tracking of Objects With Temporally Consistent Polar-Based Local Partitioning

Region-based methods have become the state-of-art solution for monocular 6-DOF object pose tracking in recent years. However, two main challenges still remain: the robustness to heterogeneous configurations (both foreground and background), and the robustness to partial occlusions. In this paper, we propose a novel region-based monocular 3D object pose tracking method to tackle these problems. Firstly, we design a new strategy to define local regions, which is simple yet efficient in constructing discriminative local color histograms. Contrary to previous methods which define multiple circular regions around the object contour, we propose to define multiple overlapped, fan-shaped regions according to polar coordinates. This local region partitioning strategy produces much less number of local regions that need to be maintained and updated, while still being temporally consistent. Secondly, we propose to detect occluded pixels using edge distance and color cues. The proposed occlusion detection strategy is seamlessly integrated into the region-based pose optimization pipeline via a pixel-wise weight function, which significantly alleviates the interferences caused by partial occlusions. We demonstrate the effectiveness of the proposed two new strategies with a careful ablation study. Furthermore, we compare the performance of our method with the most recent state-of-art region-based methods in a recently released large dataset, in which the proposed method achieves competitive results with a higher average tracking success rate. Evaluations on two real-world datasets also show that our method is capable of handling realistic tracking scenarios.
The Relationships Between Stress, Mental Disorders, and Epigenetic Regulation of BDNF

Brain-derived neurotrophic factor (BDNF), a critical member of the neurotrophic family, plays an important role in multiple stress-related mental disorders. Although alterations in BDNF in multiple brain regions of individuals experiencing stress have been demonstrated in previous studies, it appears that a set of elements are involved in the complex regulation. In this review, we summarize the specific brain regions with altered BDNF expression during stress exposure. How various environmental factors, including both physical and psychological stress, affect the expression of BDNF in specific brain regions are further summarized. Moreover, epigenetic regulation of BDNF, including DNA methylation, histone modification, and noncoding RNA, in response to diverse types of stress, as well as sex differences in the sensitivity of BDNF to the stress response, is also summarized. Clarification of the underlying role of BDNF in the stress process will promote our understanding of the pathology of stress-linked mental disorders and provide a potent target for the future treatment of stress-related illness.
ORMDL3 but not neighboring 17q21 gene LRRC3C is expressed in human lungs and lung cells of asthmatics

CONFLIC TS OF INTERE S T Dr Till reports grants from ASIT Biotech and consultancy fees from Aimmune during the conduct of the study; Dr Stage reports he was employed by ALK during the conduct of the study. Dr Skypala has nothing to disclose; Dr Biedermann reports he gave advice to or got an honorarium for talks or received a research grant from: ALK, Mylan, Novartis, Sanofi-Regeneron, Phadia Thermo-Fisher and Celgene during the conduct of the study.
Solar-induced chlorophyll fluorescence and short-term photosynthetic response to drought.

Drought is among the most damaging climate extremes, potentially causing significant decline in ecosystem functioning and services at the regional to global scale, thus monitoring of drought events is critically important. Solar-induced chlorophyll fluorescence (SIF) has been found to strongly correlate with Gross Primary Production on the global scale. Recent advances in the remote sensing of SIF allow for large-scale, real-time estimation of photosynthesis using this relationship. However, several studies have used SIF to quantify the impact of drought with mixed results, and the leaf-level mechanisms linking SIF and photosynthesis are unclear, particularly how the relationship may change under drought. We conducted a drought experiment with 2-yr old Populus deltoides. We measured leaf-level gas exchange, SIF, and Pulse-Amplitude-Modulated (PAM) fluorescence before and during the one-month drought. We found clear responses of net photosynthesis and stomatal conductance to water stress, however, SIF showed a smaller response to drought. Net photosynthesis (Anet ) and conductance dropped 94% and 95% on average over the drought, while SIF values only decreased slightly (21%). Electron transport rate dropped 64% when compared to the control over the last week of drought, but the electron transport chain did not completely shut down as Anet approached zero. Additionally, SIF yield (SIFy ) was positively correlated with steady-state fluorescence (Fs ) and negatively correlated with non-photochemical quenching (NPQ) (R2 =0.77). Both Fs and SIFy , after normalization by the minimum fluorescence from a dark-adapted sample (Fo ), showed a more pronounced drought response, although the results suggest the response is complicated by several factors. Leaf-level experiments can elucidate mechanisms behind large-scale remote sensing observations of ecosystem functioning. The value of SIF as an accurate estimator of photosynthesis may decrease during mild stress events of short duration, especially when the response is primarily stomatal and not fully coupled with the light reactions of photosynthesis. We discuss potential factors affecting the weak SIF response to drought, including upregulation of NPQ, change in internal leaf structure and chlorophyll concentration, and photorespiration. The results suggest that SIF is mainly controlled by the light reactions of photosynthesis, which operate on different timescales than the stomatal response.
Oligoclonal IgG antibodies in multiple sclerosis target patient-specific peptides

IgG oligoclonal bands (OCBs) are present in the cerebrospinal fluid (CSF) of more than 95% of patients with multiple sclerosis (MS), and are considered to be the immunological hallmark of disease. However, the target specificities of the IgG in MS OCBs have remained undiscovered. Nevertheless, evidence that OCBs are associated with increased levels of disease activity and disability support their probable pathological role in MS. We investigated the antigen specificity of individual MS CSF IgG from 20 OCB-positive patients and identified 40 unique peptides by panning phage-displayed random peptide libraries. Utilizing our unique techniques of phage-mediated real-time Immuno-PCR and phage-probed isoelectric focusing immunoblots, we demonstrated that these peptides were targeted by intrathecal oligoclonal IgG antibodies of IgG1 and IgG3 subclasses. In addition, we showed that these peptides represent epitopes sharing sequence homologies with proteins of viral origin, and proteins involved in cell stress, apoptosis, and inflammatory processes. Although homologous peptides were found within individual patients, no shared peptide sequences were found among any of the 42 MS and 13 inflammatory CSF control specimens. The distinct sets of oligoclonal IgG-reactive peptides identified by individual MS CSF suggest that the elevated intrathecal antibodies may target patient-specific antigens.
Correlation of Aqueous, Vitreous, and Plasma Cytokine Levels in Patients With Proliferative Diabetic Retinopathy

Purpose To investigate the relationship between proangiogenic and inflammatory cytokines in concurrent vitreous, aqueous, and plasma samples from patients with proliferative diabetic retinopathy (PDR). Methods Vitreous, aqueous, and plasma samples were analyzed using multiplex immunoassay for 10 PDR-related cytokines (IL-6, IL-8, TNF-α, monocyte chemoattractant protein-1 [MCP-1], macrophage inflammatory protein-1β [MIP-1β], VEGF receptor 1 [Flt-1], placental growth factor [PlGF], VEGF-A, VEGF-C, VEGF-D). A total of 17 patients with PDR and 7 controls were included. The primary outcome was correlation of cytokines in vitreous, aqueous, and plasma. The secondary outcome was the comparison of cytokine levels in controls and diabetics with and without recent anti-VEGF injection. Results The following factors were elevated in diabetics compared with controls: vitreous IL-6, IL-8, TNF-α, MCP-1, MIP-1β, PlGF, and VEGF-A; and aqueous IL-6, IL-8, PlGF, and VEGF-C (all P < 0.05). Vitreous and aqueous IL-8, PlGF, and VEGF-A were significantly correlated in patients with PDR (all P < 0.05). Plasma cytokines were not correlated with those in vitreous and aqueous (all P > 0.05). Vitreous and aqueous IL-6, IL-8, TNF-α, PlGF, and VEGF-A differed among controls and diabetics with and without recent anti-VEGF injection (all P < 0.05). In one-to-one comparisons, aqueous VEGF-A levels were lower in diabetic patients who had recent anti-VEGF injection compared with those who did not (P = 0.01). Conclusions In this proof-of-concept study, IL-8, VEGF-A, and PlGF demonstrated a strong correlation in vitreous and aqueous of patients with PDR. The aqueous may serve as a proxy for vitreous for some cytokines involved in PDR. Recent anti-VEGF injections decreased VEGF-A levels in aqueous, but did not significantly affect other cytokines, suggesting a role for other targeted therapies in PDR management.
The association between etiology of hepatocellular carcinoma and race‐ethnicity in Florida

The incidence of hepatocellular carcinoma (HCC) has risen considerably in the US since 1980. The main causes include metabolic disorders (NAFLD, diabetes, obesity, metabolic syndrome), alcohol‐related disease (ALD) and hepatitis C and B virus infections (HCV, HBV). Etiology‐specific HCC incidence rates by detailed race‐ethnicity are needed to improve HCC control and prevention efforts.
Consequences of epigenetic derepression in facioscapulohumeral muscular dystrophy

Facioscapulohumeral muscular dystrophy (FSHD), a common hereditary myopathy, is caused either by the contraction of the D4Z4 macrosatellite repeat at the distal end of chromosome 4q to a size of 1 to 10 repeat units (FSHD1) or by mutations in D4Z4 chromatin modifiers such as Structural Maintenance of Chromosomes Hinge Domain Containing 1 (FSHD2). These two genotypes share a phenotype characterized by progressive and often asymmetric muscle weakening and atrophy, and common epigenetic alterations of the D4Z4 repeat. All together, these epigenetic changes converge the two genetic forms into one disease and explain the derepression of the DUX4 gene, which is otherwise kept epigenetically silent in skeletal muscle. DUX4 is consistently transcriptionally upregulated in FSHD1 and FSHD2 skeletal muscle cells where it is believed to exercise a toxic effect. Here we provide a review of the recent literature describing the progress in understanding the complex genetic and epigenetic architecture of FSHD, with a focus on one of the consequences that these epigenetic changes inflict, the DUX4‐induced immune deregulation cascade. Moreover, we review the latest therapeutic strategies, with particular attention to the potential of epigenetic correction of the FSHD locus.
Genetic Characterization of Piroplasms in Donkeys and Horses from Nigeria

Simple Summary Theileria equi and Babesia caballi are blood-parasites of horses and donkeys that are transmitted by ticks and may cause severe clinical illness. Many infected animals are carriers of parasites without showing signs of disease and, thus, pose a risk of transmission. Nigeria is a major passageway in animal import, export and transport within Africa. This movement of animals may play a key role in the spread of parasites. The aim of this study was to characterize these parasites that infect both horses and donkeys in Nigeria. Blood was collected from horses and draught-donkeys at two separately-owned farms in northern Nigeria. Infection with T. equi was detected in both donkeys and horses, with four of the five known genotypes present in Africa. Infection with a single genotype of B. caballi was detected in donkeys. Our results suggest that donkeys may be an important reservoir of these parasites. The high diversity of T. equi supports the hypothesis that animal transport through Nigeria may contribute to the spread of parasites to and from other countries in the region. Abstract Equine piroplasmosis (EP) is a tick-borne disease of equids, caused by the two haemoprotozoal parasites: Theileria equi and Babesia caballi. Nigeria constitutes a major crossroads of animal transport in West Africa and may serve as a factor in EP dissemination in the region. The study aim was to characterize EP parasites in donkeys and horses in northern Nigeria using a molecular approach. Blood was collected from 57 donkeys and 47 horses. EP infection was detected and characterized by polymerase chain reaction (PCR). Twenty five donkeys (43.8%) were infected with T. equi, five (8.8%) with B. caballi, three (5.3%) with dual infections. Four horses (8.5%) were infected by T. equi and none by B. caballi. Four of the five known T. equi 18S rRNA genotypes (A, B, C and D) were identified. Theileria equi ema-1 and ema-2 genes were amplified in only 2 and 10 samples, respectively, showing no genetic variation. All B. caballi isolates were classified as rap-1 genotype A1. Twenty-two (42.3%) of the donkeys were positive for anti-T. equi antibodies and 29 (55.8%) were positive for anti-B. caballi antibodies, using immunofluorescence antibody test (IFAT). The study results demonstrate high genetic variation within T. equi parasites, suggesting that donkeys may be reservoirs of EP parasites in West Africa.
Combined treatments with metformin and phosphodiesterase inhibitors alleviate non-alcoholic fatty liver disease in high-fat diet-fed rats: A comparative study.

Nonalcoholic fatty liver disease (NAFLD) is an excessive accumulation of fats in the liver resulted in hepatic inflammation and fibrous tissue formation along with insulin resistance. This study was designed to investigate the possible protective effects of metformin alone and in combination with different phosphodiesterase inhibitors (PDEIs). Rats were fed a high-fat diet (HFD) for sixteen weeks to induce NAFLD. Starting from week 12, rats received metformin alone or in combination with pentoxifylline, cilostazol or sildenafil. HFD administration resulted in hepatic steatosis and inflammation in rats. In addition, liver index, body composition index, activities of liver enzymes, and serum lipids deviated from normal. Further, significant elevations were recorded compared to control in terms of serum glucose, insulin and HOMA-IR, oxidative stress parameters, hepatic TNF-α and NF-кB gene expression and iNOS protein expression. Rats treated with metformin showed a significant improvement in the aforementioned parameters. However, the addition of pentoxifylline to metformin treatment synergized its action and produced a fortified effect against HFD-induced NAFLD better than other PDEIs. Data from this study indicated that combined treatment of metformin and pentoxifylline had the most remarkable ameliorated effects against HFD-induced NAFLD; further clinical investigations are in-need to approve PDEIs for NAFLD treatment.
CB1 Receptor-Dependent and Independent Induction of Lipolysis in Primary Rat Adipocytes by the Inverse Agonist Rimonabant (SR141716A)

(1) Background: Acute administration of the cannabinoid receptor 1 (CB1R) inverse agonist Rimonabant (SR141716A) to fed Wistar rats was shown to elicit a rapid and short-lasting elevation of serum free fatty acids. (2) Methods: The effect of Rimonabant on lipolysis in isolated primary rat adipocytes was studied to raise the possibility for direct mechanisms not involving the (hypothalamic) CB1R. (3) Results: Incubation of these cells with Rimonabant-stimulated lipolysis to up to 25% of the maximal isoproterenol effect, which was based on both CB1R-dependent and independent mechanisms. The CB1R-dependent one was already effective at Rimonabant concentrations of less than 1 µM and after short-term incubation, partially additive to β-adrenergic agonists and blocked by insulin and, in part, by adenosine deaminase, but not by propranolol. It was accompanied by protein kinase A (PKA)-mediated association of hormone-sensitive lipase (HSL) with lipid droplets (LD) and dissociation of perilipin-1 from LD. The CB1R-independent stimulation of lipolysis was observed only at Rimonabant concentrations above 1 µM and after long-term incubation and was not affected by insulin. It was recapitulated by a cell-free system reconstituted with rat adipocyte LD and HSL. Rimonabant-induced cell-free lipolysis was not affected by PKA-mediated phosphorylation of LD and HSL, but abrogated by phospholipase digestion or emulsification of the LD. Furthermore, LD isolated from adipocytes and then treated with Rimonabant (>1 µM) were more efficient substrates for exogenously added HSL compared to control LD. The CB1R-independent lipolysis was also demonstrated in primary adipocytes from fed rats which had been treated with a single dose of Rimonabant (30 mg/kg). (4) Conclusions: These data argue for interaction of Rimonabant (at high concentrations) with both the LD surface and the CB1R of primary rat adipocytes, each leading to increased access of HSL to LD in phosphorylation-independent and dependent fashion, respectively. Both mechanisms may lead to direct and acute stimulation of lipolysis at peripheral tissues upon Rimonabant administration and represent targets for future obesity therapy which do not encompass the hypothalamic CB1R.