Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrastructural anatomy of nodes of Ranvier in the peripheral nervous system as revealed by STED microscopy

Significance In vertebrates, the action potential travels along myelin-coated electrically isolated axons and is regenerated at the nodes of Ranvier, which lack myelination and are characterized by a tight interaction between the axon and glial cells. Specific sets of proteins are enriched in each region of the nodes. Thanks to its subdiffraction resolution, stimulated emission depletion (STED) microscopy here uncovers the organization of 12 of these proteins at the nanoscale. The superresolved imaging reveals an extremely fine interplay and alignment of the axonal and glial cytoskeleton, with a defined ∼190-nm periodicity. Furthermore, the results point to the importance of the lateral organization of proteins at nodal gaps, an aspect that is yet unexplored. We used stimulated emission depletion (STED) superresolution microscopy to analyze the nanoscale organization of 12 glial and axonal proteins at the nodes of Ranvier of teased sciatic nerve fibers. Cytoskeletal proteins of the axon (betaIV spectrin, ankyrin G) exhibit a high degree of one-dimensional longitudinal order at nodal gaps. In contrast, axonal and glial nodal adhesion molecules [neurofascin-186, neuron glial-related cell adhesion molecule (NrCAM)] can arrange in a more complex, 2D hexagonal-like lattice but still feature a ∼190-nm periodicity. Such a lattice-like organization is also found for glial actin. Sodium and potassium channels exhibit a one-dimensional periodicity, with the Nav channels appearing to have a lower degree of organization. At paranodes, both axonal proteins (betaII spectrin, Caspr) and glial proteins (neurofascin-155, ankyrin B) form periodic quasi–one-dimensional arrangements, with a high degree of interdependence between the position of the axonal and the glial proteins. The results indicate the presence of mechanisms that finely align the cytoskeleton of the axon with the one of the Schwann cells, both at paranodal junctions (with myelin loops) and at nodal gaps (with microvilli). Taken together, our observations reveal the importance of the lateral organization of proteins at the nodes of Ranvier and pave the way for deeper investigations of the molecular ultrastructural mechanisms involved in action potential propagation, the formation of the nodes, axon–glia interactions, and demyelination diseases.
Increased placental growth factor (PlGF) concentrations in children and adolescents with obesity and the metabolic syndrome

OBJECTIVE: Childhood obesity and the Metabolic Syndrome (MetS) are associated with an increased risk for early onset endothelial dysfunction and atherosclerosis. Placental growth factor (PlGF), a member of the vascular endothelial growth factor family, plays an important role in atherosclerosis by stimulating angiogenesis and atherogenic migration of monocytes/macrophages into the arterial wall. The aim of this study was to investigate differences in circulating PlGF concentrations between children with obesity/metabolic syndrome and non-obese children. We have previously shown increased high-sensitivity troponin (hs-TnT) concentrations in children with MetS from the same cohort. DESIGN: Fifty-seven obese (49 without and 8 with MetS) and 25 non-obese children (controls) were assessed at the Childhood Obesity Clinic of our Department. Obesity was defined using the IOTF criteria. MetS was defined based on the IDF criteria. PlGF was measured using electrochemiluminescence methodology. RESULTS: Mean PIGF concentrations of obese children were significantly higher (p=0.048) compared with those of the controls. Analysis of the three groups, the obese (without MetS), the MetS and the control, demonstrated a significant difference in PlGF concentrations (p=0.035). Subgroup analysis revealed increased PlGF concentrations in children with the MetS compared to the controls (p=0.009). Troponin had a significant positive correlation with PlGF overall (p=0.003) and in the obese group (p=0.046). CONCLUSIONS: Increased serum concentrations of PlGF, a biomarker of angiogenesis, are found in obese children with the MetS compared to non-obese controls, whereas PlGF correlated positively with troponin. Longitudinal studies may reveal the prognostic role of this biomarker in the progression of atherosclerosis in obese children with the MetS.
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants1[OPEN]

A computational pipeline generates high-quality and genome-scale sets of metabolic enzymes, pathways, and gene clusters from plant genomes. Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.
Three Techniques on Protein Extraction from Cotton Fibers and Two-dimensional Electrophoreses

A prerequisite for two-dimensional electrophoresis(2-DE) is the high-quality sample preparation.Cotton fibers contain a variety of compounds that interfere with 2-DE,such as cellulose,polyphenols,polysaccharides and so on,which has made the protein extraction and 2DE rather difficult to deal with.Three known methods were employed to extract the protein from cotton fibers.The productivity and purity of the harvested protein were compared,as well as the resolution and profiles of the 2-DE.As a result,the phenol extract showed a better proteome map,comparing with water method and urea method.It is expected that this phenol method could be one of the options for protein extraction from cotton fibers.
Adherence to Oral Therapy for Urgency Urinary Incontinence: Results from the Anticholinergic Versus Botox Comparison (ABC) Trial

Objectives Medication adherence with urgency urinary incontinence (UUI) treatment is challenging and the best assessment methodology is uncertain. We sought to describe adherence with anticholinergic (AC) versus placebo (P) by comparing pill counts and MEMSCAP event data and to identify factors associated with adherence. Methods The randomized controlled AC versus Botox Comparison trial of women with moderate to severe idiopathic UUI included 126 participants initiating AC plus P bladder injection and 121 receiving P pills plus Botox injection. Adherence data on 243 participants (124 AC and 119 P) were calculated by pill count and MEMSCAP data for each 2-month interval during the 6-month study that allowed for dose escalation/drug change. Overall composite adherence estimates were calculated using the average of both methods and weighted by the duration of each 2-month interval. Results Treatment groups had no significant differences in dosing duration (P = 0.76) or mean adherence (AC, 83.3% [16.8] vs P, 84.8% [13.8]). Only 53% of women met the dichotomous outcome of more than 80% adherence during all intervals. Correlation between adherence by pill counts versus MEMSCAP decreased over time with pill counts demonstrating higher adherence than MEMSCAP (r = 0.53, 0.50, and 0.36 for each 2-month interval). Lower adherence was associated with higher baseline incontinence severity and better UUI quality of life for the AC group and with current smoking status in both groups. Conclusions Adherence using pill counts and MEMSCAP was reasonably correlated and similar in both the AC and P groups. In the AC group, higher baseline incontinence severity and better UUI Quality of Life were associated with decreased adherence. Smokers were less adherent.
The In vitro/vivo Evaluation of Prepared Gastric Floating Tablets of Berberine Hydrochloride

Currently available antiulcer drugs suffered from serious side effects which limited their uses and prompted the need for a safe and efficient new antiulcer agent. The objective of this project work was to retain the drug in the stomach for better antiulcer activity and less side effects. Hence, the aim of our present work was to prepare a gastric floating tablet of Berberine hydrochloride (Ber) with suitable in vitro/vivo properties. In this study, different Ber gastric floating tablets were prepared by simple direct compression using various amounts of HPMCK15M and Carbopol 971PNF combined with other tablet excipients. The properties of the tablets including hardness, buoyancy, swelling ability, in vitro drug release, and in vivo pharmacokinetic study were evaluated. The obtained results disclosed that hardness, floating, swelling, and in vitro drug release of the Ber tablets depended mainly on the ratio of polymer combinations. Moreover, among six formulations, F3 exhibited desirable floating, swelling, and extended drug release. In addition, in vivo pharmacokinetic study suggested that prepared gastric floating tablets had significantly sustained-releasing effects compared with market tablets. Therefore, the developed gastric floating tablets of Ber could be an alternative dosage form for treatment of gastrointestinal disease.
Spatial Attention Improves Object Localization: A Biologically Plausible Neuro-Computational Model for Use in Virtual Reality

Visual attention is a smart mechanism performed by the brain to avoid unnecessary processing and to focus on the most relevant part of the visual scene. It can result in a remarkable reduction in the computational complexity of scene understanding. Two major kinds of top-down visual attention signals are spatial and feature-based attention. The former deals with the places in scene which are worth to attend, while the latter is more involved with the basic features of objects e.g. color, intensity, edges. In principle, there are two known sources of generating a spatial attention signal: Frontal Eye Field (FEF) in the prefrontal cortex and Lateral Intraparietal Cortex (LIP) in the parietal cortex. In this paper, first, a combined neuro-computational model of ventral and dorsal stream is introduced and then, it is shown in Virtual Reality (VR) that the spatial attention, provided by LIP, acts as a transsaccadic memory pointer which accelerates object localization.
Effects of daytime versus night‐time cesarean deliveries on Stage II lactogenesis

The circadian timing system has a rhythm and one of the roles of this system is the mediation of hormonal and metabolic adaptations to lactation. This study was conducted to determine whether the time to stage II lactogenesis differed in women who underwent cesarean section (CS) in the daytime (DT) or night‐time (NT).
High fishery catches through trophic cascades in China

Significance Fishing marine ecosystems indiscriminately and intensely can have negative impacts on biodiversity, but it may increase the biomass of fish available for capture in the system. We explore the possibility that China’s high fishery catches are a result of predator removal using an ecosystem model of the East China Sea (ECS). We show that China’s high fishery catches can be explained by the removal of larger predatory fish and consequent increases in the production of smaller fish. We project that single-species management would decrease catches in the ECS by reversing these ecosystem effects. Fisheries similar to those in China produce a large fraction of global catch; management reform in these areas must consider the entire ecosystem, rather than individual species. Indiscriminate and intense fishing has occurred in many marine ecosystems around the world. Although this practice may have negative effects on biodiversity and populations of individual species, it may also increase total fishery productivity by removing predatory fish. We examine the potential for this phenomenon to explain the high reported wild catches in the East China Sea—one of the most productive ecosystems in the world that has also had its catch reporting accuracy and fishery management questioned. We show that reported catches can be approximated using an ecosystem model that allows for trophic cascades (i.e., the depletion of predators and consequent increases in production of their prey). This would be the world’s largest known example of marine ecosystem “engineering” and suggests that trade-offs between conservation and food production exist. We project that fishing practices could be modified to increase total catches, revenue, and biomass in the East China Sea, but single-species management would decrease both catches and revenue by reversing the trophic cascades. Our results suggest that implementing single-species management in currently lightly managed and highly exploited multispecies fisheries (which account for a large fraction of global fish catch) may result in decreases in global catch. Efforts to reform management in these fisheries will need to consider system wide impacts of changes in management, rather than focusing only on individual species.
Synthesis, bioactivity, 3D-QSAR studies of novel dibenzofuran derivatives as PTP-MEG2 inhibitors

PTP-MEG2 plays a critical role in the diverse cell signalling processes, so targeting PTP-MEG2 is a promising strategy for various human diseases treatments. In this study, a series of novel dibenzofuran derivatives was synthesized and assayed for their PTP-MEG2 inhibitory activities. 10a with highest inhibitory activity (320 nM) exhibited significant selectivity for PTP-MEG2 over its close homolog SHP2, CDC25 (IC50 > 50 μM). By means of the powerful “HipHop” technique, a 3D-QSAR study was carried out to explore structure activity relationship of these molecules. The generated pharmacophore model revealed that the one RA, three Hyd, and two HBA features play an important role in binding to the active site of the target protein-PTP-MEG2. Docking simulation study indicated that 10a achieved its potency and specificity for PTP-MEG2 by targeting unique nearby peripheral binding pockets and the active site. The absorption, distribution, metabolism and excretion (ADME) predictions showed that the 11 compounds hold high potential to be novel lead compounds for targeting PTP-MEG2. Our findings here can provide a new strategy or useful insights for designing the effective PTP-MEG2 inhibitors.
Detecting and Visualizing Profile Correlation in Subspace

In this paper, we propose a novel method for detecting and visualizing profile correlation in subspace. The proposed method is able to (1) detect shifting-and-scaling correlated profiles in subspace, where the correlation can be either positive or negative, (2) summarize and visualize the shifting-and-scaling correlation in subspace, and (3) allow users to explore interested correlation subspace interactively. Initially, shifting and scaling were regarded as two different correlation patterns, in which profiles in subspace can overlap by a single shifting and scaling respectively. In later work, a much more generous correlation, shifting-and-scaling correlation, was studied, compared to which, shifting correlation and scaling correlation are just two special cases. Shifting-and-scaling correlation ensures subspace profile coherence not only in tendency as those tendency-based methods do, but also in value change proportion in subspace. However, no work has been focused on visualization of subspace shifting-and-scaling correlation yet. Our work is the first one to enable interactive exploration and visualization of subspace shifting-and-scaling correlation.
Monitoring of Human Uterus Transplantation With Cervical Biopsies: A Provisional Scoring System for Rejection

Until now, absolute uterine factor infertility has been the major untreatable form of female infertility. Uterus transplantation has recently proven to be the first successful treatment for absolute uterine factor infertility, with demonstration of live births. In this study, live donation uterus transplantation was performed in nine women. In total, 163 cervical biopsies (149 protocol, 14 follow‐up) were taken to detect histopathological signs of rejection. Based on experience from animal experiments, we used a three‐grade scoring system to evaluate biopsies systematically. Nine episodes of rejection were diagnosed in five patients: grade 1 in six episodes, grade 2 in two episodes, and grade 3 in one episode. Treatment decisions were based on histopathology, and all rejection episodes were reversed after treatment. The biopsies were reviewed retrospectively, and immunohistochemistry was performed to characterize the inflammatory infiltrates. A borderline category was introduced to avoid overtreatment of patients. Based on our review of all biopsies, we put forward a simple grading system for monitoring of rejection and to guide immunosuppressive treatment in uterus transplantation.
Reliable Isometric Point Correspondence from Depth

We propose a new iterative isometric point correspondence method that relies on diffusion distance to handle challenges posed by commodity depth sensors, which usually provide incomplete and noisy surface data exhibiting holes and gaps. We formulate the correspondence problem as finding an optimal partial mapping between two given point sets, that minimizes deviation from isometry. Our algorithm starts with an initial rough correspondence between keypoints, obtained via a standard descriptor matching technique. This initial correspondence is then pruned and updated by iterating a perfect matching algorithm until convergence to find as many reliable correspondences as possible. For shapes with intrinsic symmetries such as human models, we additionally provide a symmetry aware extension to improve our formulation. The experiments show that our method provides state of the art performance over depth frames exhibiting occlusions, large deformations and topological noise.
WILD BIRDS AS A POTENTIAL SOURCE OF KNOWN AND NOVEL MULTILOCUS SEQUENCE TYPES OF ANTIBIOTIC-RESISTANT ENTEROCOCCUS FAECALIS

Abstract: We assessed the antibiotic resistance and genetic diversity of 27 Enterococcus faecalis isolates from 25 wild bird species in Poland. Resistance to lincomycin (100%) was most common followed by tetracycline (48%), erythromycin (44%), and ciprofloxacin (22%). High-level resistance to streptomycin and kanamycin was observed in 19% and 15% of isolates, respectively. One isolate (4%) exhibited low-level resistance to penicillin and vancomycin, and all isolates were susceptible to gentamicin and chloramphenicol. Antibiotic resistance was linked to the tet(M), tet(L), erm(A), erm(B), msr(A/B), ant(6)-Ia, and aph(3′)-IIIa genes. None of the tested van (vanA, vanB, vanC1, vanC2/C3, vanD, vanE, vanG) genes were found in the vancomycin-resistant isolate. Based on pulsed-field gel electrophoresis and multilocus sequence typing analysis, the E. faecalis population from wild birds revealed high genetic diversity. All isolates were divided into 22 pulsotypes and 18 sequence types (STs), among which seven STs were newly assigned (ST748-ST753 and ST764). The most-prevalent STs were ST290 and ST374 followed by ST287 and ST34. The coexistence of strains assigned to the same STs in wild birds and in nonwildlife populations strongly indicated that many wild bird species could constitute a source of E. faecalis for infections in humans, pets, and farm animals.
FABRICATION OF NANO-POROUS STRUCTURED POLYLACTIDE (PLLA) FIBERS THROUGH ELECTROSPINNING

PLLA ultrafine fibers with mesopores of 30 ～ 150 nm were prepared by electrospinning.Their surface morphology was studied using scanning electron microscopy(SEM). The fiber diameter and morphology could be controlled by adjusting the composition ratio of the dichloromethane(DCM)/N,N-dimethylformamide(DMF) solvent mixture,PLLA concentration and electric filed.Accordingly,fibers with varied surface structure such as smooth surface,shallow pits,or deep pores were obtained.Under optimal electrospinning conditions of DCM/DMF 4 ∶ 1,PLLA concentration of 9 wt%,electric field 1 kV/cm and relative humidity of 52%,dense mesoporous PLLA ultrafine fibers with mean pore diameter of 150 nm were fabricated.Moreover,it showed 3-dimensional inter-connected pore-structure throughout PLLA ultrafine fibers.Most pores were elongated along the fiber axis due to the stretching in the process of electrospinning.The characteristic porous PLLA fiber was formed by a combination of thermal induced phase separation(TIPs) with water assisted breath figure mechanisms,because of the sharp temperature drop caused by the quick solvent evaporation in the electrospinning process.The PLLA fibers with shallow pits or pores of 80 nm in diameter showed water contact angle of 104°,whereas the fibers with deep pores of 150 nm in diameter were highly hydrophobic with water contact angle up to 146.6°. The hydrophobic fibrous mats could quickly absorb oil,90 g/g in 90 s and 145 g/g in 25 min.Their maintaining capacity of oil absorption was 90%.
CD19 negative precursor B acute lymphoblastic leukemia (B‐ALL)—Immunophenotypic challenges in diagnosis and monitoring: A study of three cases

CD19 is a B‐cell specific marker, expressed on all stages of B‐lymphocytes including plasma cells. It is widely used in the flow cytometric immunophenotyping (FCI) of B‐cell and plasma cell malignancies. The analysis approach of FCI for the diagnosis and monitoring of B‐cell acute lymphoblastic leukemia (B‐ALL) is totally based on the CD19‐based primary gating strategy and it would be challenging to study B‐ALL without CD19 expression. Since CD19 negative B‐ALL are extremely rare, we report three cases of B‐ALL with negative expression of CD19 and discussed its implication in the diagnosis, residual disease monitoring and future targeted therapy.