Miracle-dz/UniFAR-FTUs huggingface dataset:
Building bridges, not walls: spinal cord regeneration in zebrafish

ABSTRACT Spinal cord injury is a devastating condition in which massive cell death and disruption of neural circuitry lead to long-term chronic functional impairment and paralysis. In mammals, spinal cord tissue has minimal capacity to regenerate after injury. In stark contrast, the regeneration of a completely transected spinal cord and accompanying reversal of paralysis in adult zebrafish is arguably one of the most spectacular biological phenomena in nature. Here, we review reports from the last decade that dissect the mechanisms of spinal cord regeneration in zebrafish. We highlight recent progress as well as areas requiring emphasis in a line of study that has great potential to uncover strategies for human spinal cord repair. Summary: Unlike mammals, teleost fish are capable of efficient, spontaneous recovery after a paralyzing spinal cord injury. Here, we highlight the major events through which laboratory model zebrafish regenerate spinal cord tissue.
Molecular Cloning and Characterization of PEBP2β, the Heterodimeric Partner of a Novel Drosophila runt-Related DNA Binding Protein PEBP2α

Abstract Polyomavirus enhancer binding protein, PEBP2 (PEA2), is a heterodimer of two distinct subunits, α and β, of which the former directly binds to DNA and the latter acts auxiliary to enhance the DNA binding. Recent cloning studies has revealed that the α subunit is homologous to the products of the Drosophila segmentation gene runt and the human AML1 gene, and that it functions as a major regulator for the T cell-specific gene expression. We have currently cloned cDNAs for the β subunit. The isolated cDNAs contain three isoforms that are presumed to arise from alternative RNA splicing and encode polypeptides consisting of 187, 182, and 155 amino acids, respectively. These polypeptides neither show any significant homology with known other proteins including the α subunit nor have any known DNA-binding and dimerization domains. Thus, PEBP2, as the complex of these subunits, is thought to constitute an entirely novel category of heteromeric transcriptional regulator together with the Runt and AML1 proteins. Gel retardation assays of the cDNA-encoded proteins produced in an in vitro translation system or in Escherichia coli demonstrated that the larger two β isoforms, but not the smallest one, can dimerize with the α subunit. Furthermore, this heterodimerization was shown to cause a marked increase in the intrinsic DNA binding affinity of the α subunit.
Translating 'protein foods' from the new Canada's Food Guide to consumers: Knowledge gaps and recommendations.

The revised version of Canada's Food Guide, released in January 2019, issued new guidance by combining meat and alternatives with milk and alternatives into a single group called 'protein foods' and emphasized selecting plant-based foods from this category more often. Though the changes represent a simple depiction of a healthy plate, the new Food Guide has opened knowledge gaps about 'protein foods' and exposed new concerns about the interpretation and implementation of the Food Guide among vulnerable groups, particularly children and the elderly. To address key knowledge and research gaps, nutrition leaders need to reach a consensus on key messages to best inform the development of tools and resources to support practitioners in translating messages to consumers, including foodservice standards. Among consumers, families with young children are a primary target for these resources as they develop their life-long habits to ensure they have the knowledge and skills to select, prepare, and consume nutrient-rich protein foods. The new Food Guide provides an opportunity to address the existing knowledge gaps, develop tools and resources to support health professionals, and design interventions that will help Canadian families choose, prepare, and eat nutrient-rich protein foods. Novelty bullets • An updated Canadian regulatory framework is needed for protein labelling and content/health claims • There are knowledge gaps about protein foods consumption and food literacy needed to optimize nutritional health • Mandatory nutrition policies are needed to safeguard the provision of high-quality 'protein foods' across institutions that serve children and older adults.
The Secondary Chemistry and Complex Morphology of Galls Formed by the Cynipinae (Hymenoptera): Why and How?

Oak galls formed by cynipine wasps are extremely complex and diverse structurally, histologically and chemically. Evidence suggests that the need for enemyfree space provides the major selective force molding this rich diversity, which in turn allows many species to co-occur locally in spite of highly successful attacks by natural enemies. It is proposed that the Cynipinae form mutualisms with virus or virus-like particles which work in concert with larval salivary secretions to produce galls. This ecological alliance may have engendered the adaptive shift to gall-forming from the seed-eating habit of secondarily phytophagous Hymenoptera. The role of mutualism as a driving force in evolutionary innovation may be considerable.
Cytoplasmic streaming drifts the polarity cue and enables posteriorization of the Caenorhabditis elegans zygote at the side opposite of sperm entry

Cell polarization is required to define body axes during development. The position of spatial cues for polarization is critical to direct the body axes. In Caenorhabditis elegans zygotes, the sperm-derived pronucleus/centrosome complex (SPCC) serves as the spatial cue to specify the anterior-posterior axis. Approximately 30 min after fertilization, the contractility of the cell cortex is relaxed near the SPCC, which is the earliest sign of polarization and called symmetry breaking (SB). It is unclear how the position of SPCC at SB is determined after fertilization. Here, we show that SPCC drifts dynamically through the cell-wide flow of the cytoplasm, called meiotic cytoplasmic streaming. This flow occasionally brings SPCC to the opposite side of the sperm entry site before SB. Our results demonstrate that cytoplasmic flow determines stochastically the position of the spatial cue of the body axis, even in an organism like C. elegans for which development is stereotyped.
The Correlation of Aesthetic Plastic Surgery With Sexual, Social, and Romantic Life in Cyprus

During the 21st century, the interest in cosmetic surgery has dramatically increased. Aesthetic plastic surgery can improve self-esteem and self-confidence, enhancing appearance, social relations, and sexual life. This study aimed to investigate the correlation of aesthetic plastic surgery with sexual, social, and romantic lives in Cyprus. Questionnaire data from 128 cosmetic surgery patients, from a plastic surgery clinic in Nicosia, were obtained approximately 1 week before and 3 months after surgery. The questionnaire was developed by the authors for the purpose of this study and consisted of measures on body image, social life, relationships, and sexuality. Pre- and postoperative values were compared. The majority of participants were women (81.9%), and respondents' mean age was 35.35 years. One of 2 participants reporting had undergone breast augmentation (47.6%). One of 2 participants reported feeling self-confidence after treatment, and the majority of respondents reported a positive influence in all 3 realms: sex life (54.7%), social life (64.4%), and romantic relationship (49.5%). Those who underwent breast augmentation were 4 times more likely to report that their sex life had been positively affected than those who did not undergo breast augmentation. The study provides evidence of improvement in an individual's satisfaction with his or her body image and self-confidence after cosmetic surgery. The study demonstrates the positive impact of cosmetic surgery to social life and relationships, especially breast augmentation surgery to sexuality.
Sepsis is underreported in Swedish intensive care units: A retrospective observational multicentre study

Sepsis is a common indication for admission to the intensive care unit (ICU). Since definitions vary across studies, comparisons of prevalence and outcomes have been challenging. We aimed to compare sepsis according to ICU discharge codes with sepsis according to Sepsis‐3 criteria and to investigate the epidemiology of sepsis in the ICU. We hypothesized that sepsis using discharge codes is underreported.
Resveratrol Ameliorates the Malignant Progression of Pancreatic Cancer by Inhibiting Hypoxia-induced Pancreatic Stellate Cell Activation

Pancreatic cancer is characterized by a hypoxic tumor microenvironment, which is primarily caused by massive fibrosis with pancreatic stellate cells (PSCs) as a main component. Our previous studies have shown that resveratrol can significantly inhibit pancreatic cancer. However, whether resveratrol can inhibit hypoxia-induced cancer development remains unclear. The objective of this study was to explore whether PSCs and hypoxia synergistically mediate aggressiveness in pancreatic cancer and detect the potential pleiotropic protective effects of resveratrol on hypoxia-induced pancreatic cancer progression. Human PSCs were treated with vehicle or resveratrol under normoxic or hypoxic conditions (3% O2), and PSC activation was assessed by immunofluorescence staining. SiRNA was used to silence hypoxia-inducible factor 1 (HIF-1) expression. The invasive capacity of Panc-1 and Mia Paca-2 cells cocultured with conditioned medium from PSCs was assessed by Transwell assays. To examine tumor formation kinetics, KPC (LSL-KrasG12D/+, Trp53fl/+, and Pdx1-Cre) mice were sacrificed at different time points. To investigate the antitumor effects of resveratrol in vivo, 8-wk-old KPC mice were divided into two groups and treated daily with or without 50 mg/kg resveratrol. Our data indicate that hypoxia induces PSC activation via HIF-1 and that the interleukin 6, vascular endothelial growth factor A, and stromal cell-derived factor 1 derived from activated PSCs promote both invasion and the epithelial–mesenchymal transition and inhibit apoptosis in pancreatic cancer cells. However, resveratrol inhibits hypoxia-induced PSC activation, blocks the interplay between PSCs and pancreatic cancer cells, and suppresses the malignant progression of pancreatic cancer and stromal desmoplasia in a KPC mouse model. Our data highlight that activated PSCs and intratumoral hypoxia are essential targets for novel strategies to prevent tumor–microenvironment interactions. Furthermore, the polyphenolic compound resveratrol effectively ameliorates the malignant progression of pancreatic ductal adenocarcinoma.
MELATONIN INHIBITS CYCLIC AMP PRODUCTION IN CULTURED OVINE PARS TUBERALIS CELLS

On utilise des cultures primaires de cellules de pars tuberalis ovine de la glande pituitaire pour etudier le mode d'action de melatonine. On demontre que la melatonine inhibe la production des AMP cycliques a travers un recepteur lie a une proteine G
An Irregular Metal Trace Inpainting Network for X-ray CT Metal Artifact Reduction.

PURPOSE Metal implants in the patient body can generate severe metal artifacts in X- ray computed tomography (CT) images. These artifacts may cover the tissues around the metal implants in CT images and even corrupt the tissue regions, thus affecting disease diagnosis using these images. Previous deep learning metal trace inpainting methods used both valid pixels of uncorrupted areas and invalid pixels of corrupted areas to patch metal trace (i.e., the holes of removed metal corrupted regions). Such methods cannot recover fine details well and often suffer information mismatch due to interference of invalid pixels, thus incurring considerable secondary artifacts. In this paper, we develop a new irregular metal trace inpainting network for reducing metal artifacts. METHODS We develop a new deep learning network to patch irregular metal trace in metal corrupted sinograms to reduce metal artifacts for isometric fan-beam CT. Our new method patches irregular metal trace in CT sinograms using only valid pixels, avoiding interference from invalid pixels. Further, to enable the inpainting network to recover as many details as possible, we design an auxiliary inpainting network to suppress the probable secondary artifacts in CT images to assist fine detail restoration. The image produced by the auxiliary network is then projected onto a sinogram via a forward projection (FP) algorithm and is fused with the sinogram predicted by the inpainting network in order to predict the final recovered sinogram. Our entire network is trained end-to-end to extract cross-domain information between the sonogram domain and CT image domain. RESULTS We compare our proposed method with two traditional and four deep learning based metal trace inpainting methods, and with an iterative reconstruction method on four datasets: dental fillings (panoramic and local perspectives), hip prostheses, and spine fixations. We use both quantitative and qualitative indices to evaluate our method, and the analyses suggest that our method reduces the most metal artifacts and produces the best quality CT images. Additionally, our proposed method takes 0.1512 seconds on average to process a CT slice, which meets the clinical requirement. CONCLUSIONS This paper proposes a new deep learning network to patch irregular metal trace in corrupted sinograms to reduce metal artifacts. Our method restores more fine details in irregular metal trace and has a superior capability on metal arti-fact reduction compared with state-of-the-art methods.
A clone resource of Magnaporthe oryzae effectors that share sequence and structural similarities across host-specific lineages.

The blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae) is a destructive plant pathogen that can infect about 50 species of both wild and cultivated grasses, including important crops such as rice and wheat. M. oryzae is composed of genetically differentiated lineages that tend to infect specific host genera. To date, most studies of M. oryzae effectors have focused on the rice-infecting lineage. We describe a clone resource of 195 effectors of M. oryzae predicted from all the major host-specific lineages. These clones are freely available as Golden Gate compatible entry plasmids. Our aim is to provide the community with an open source effector clone library to be used in a variety of functional studies. We hope that this resource will encourage studies of M. oryzae effectors on diverse host species.
A practical method for predicting patient‐specific collision in radiotherapy

Abstract Purpose To develop a practical method for predicting patient‐specific collision during the treatment planning process. Materials and method Based on geometry information of the accelerator gantry and the location of plan isocenter, the collision‐free space region could be determined. In this study, collision‐free space region was simplified as a cylinder. Radius of cylinder was equal to the distance from isocenter to the collimator cover. The collision‐free space was converted and imported into treatment planning system (TPS) in the form of region of interest (ROI) which was named as ROISS. Collision was viewed and evaluated on the fusion images of patient's CT and ROIs in TPS. If any points of patient's body or couch fell beyond the safety space, collision would occur. This method was implemented in the Pinnacle TPS. The impact of safety margin on accuracy was also discussed. Sixty‐five plans of clinical patients were chosen for the clinical validation. Results When the angle of couch is zero, the ROISS displays as a series of circles on the cross section of the patient's CT. When the couch angle is not zero, ROISS is a series of ellipses in the transverse view of patient's CT. The ROISS can be generated quickly within five seconds after a single mouse click in TPS. Adding safety margin is an effective measure in preventing collisions from being undetected. Safety margin could increase negative predictive value (NPV) of test cases. Accuracy obtained was 96.3% with the 3 cm safety margin with 100% true positive collision detection. Conclusion This study provides a reliable, accurate, and fast collision prediction during the treatment planning process. Potential collisions can be discovered and prevented early before delivering. This method can integrate with the current clinical workflow without any additional required resources, and contribute to improvement in the safety and efficiency of the clinic.
Selective feeding of the oystercrassostrea gigas fed on a natural microphytobenthos assemblage

In estuarine ecosystems, microphytobenthos resuspended by tidal currents often represents a large part of the food supply available to bivalves which feed selectively. This study investigated the feeding behavior of the Pacific oysterCrassostrea gigas (Thunberg) relative to a natural microphytobenthic assemblage and the effect on the structure of this assemblage. Oysters were fed only benthic microalgae collected on the intertidal mud flats of Bourgneuf Bay (France) at a suspended particulate matter concentration above the threshold of pseudofeces production. All species in the assemblage were endemic diatoms characteritic of tidal mud flat environments. Four dominant ones, which were all solitary cells with spear-shaped frustules [Navicula ammophila (Grunow),Navicula rostellata (Kützing),Plagiotropis lepidoptera (Kuntze), andStaurophora amphioxys (Mann)] represented more than 95% of the 16 species involved. Analysis of feeding processes showed that the retention of the four main diatoms was not significantly different, but that two species, the smallest (N. ammophila [22×4 μm]) and the largest (P. lepidoptera [60×15 μm]), were preferentially ingested. The study of post-ingestive selection revealed that these two species were also preferentially digeted, i.e., preferentially directed into the digestive diverticulum, when they passed through the gut ofC. gigas. Cell size and shape did not appear to account for pre-ingestive and post-ingestive selection. The composition of the assemblage was significantly modified by oyster filtration, although the retention rates of the four main species were not significantly different. The composition of microalgae in pseudofeces and feces as a result of pre-ingestive and post-ingestive selection differed from that in seawater.
Care of Patients with Non-small-cell Lung Cancer Stage III – The Central European Real-world Experience

Abstract Background Management of non-small-cell lung cancer (NSCLC) is affected by regional specificities. The present study aimed at determining diagnostic and therapeutic procedures including outcome of patients with NSCLC stage III in the real-world setting in Central European countries to define areas for improvements. Patients and methods This multicentre, prospective and non-interventional study collected data of patients with NSCLC stage III in a web-based registry and analysed them centrally. Results Between March 2014 and March 2017, patients (n=583) with the following characteristics were entered: 32% females, 7% never-smokers; ECOG performance status (PS) 0, 1, 2 and 3 in 25%, 58%, 12% and 5%, respectively; 21% prior weight loss; 53% squamous carcinoma, 38% adenocarcinoma; 10% EGFR mutations. Staging procedures included chest X-ray (97% of patients), chest CT (96%), PET-CT (27%), brain imaging (20%), bronchoscopy (89%), endobronchial ultrasound (EBUS) (13%) and CT-guided biopsy (9%). Stages IIIA/IIIB were diagnosed in 55%/45% of patients, respectively. N2/N3 nodes were diagnosed in 60%/23% and pathologically confirmed in 29% of patients. Most patients (56%) were treated by combined modalities. Surgery plus chemotherapy was administered to 20%, definitive chemoradiotherapy to 34%, chemotherapy only to 26%, radiotherapy only to 12% and best supportive care (BSC) to 5% of patients. Median survival and progression-free survival times were 16.8 (15.3;18.5) and 11.2 (10.2;12.2) months, respectively. Stage IIIA, female gender, no weight loss, pathological mediastinal lymph node verification, surgery and combined modality therapy were associated with longer survival. Conclusions The real-world study demonstrated a broad heterogeneity in the management o f stage III NSCLC in Central European countries and suggested to increase the rates of PET-CT imaging, brain imaging and invasive mediastinal staging.
Coinfection with SARS‐CoV‐2 and other respiratory pathogens in patients with COVID‐19 in Guangzhou, China

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously provisionally named 2019 novel coronavirus or 2019-nCoV) disease (COVID-19) in China at the end of 2019 has caused a global pandemic and remains as a major public health issue This article is protected by copyright. All rights reserved.
Correlation of 4Pi and Electron Microscopy to Study Transport Through Single Golgi Stacks in Living Cells with Super Resolution

Two problems have hampered the use of light microscopy for structural studies of cellular organelles for a long time: the limited resolution and the difficulty of obtaining true structural boundaries from complex intensity curves. The advent of modern high‐resolution light microscopy techniques and their combination with objective image segmentation now provide us with the means to bridge the gap between light and electron microscopy in cell biology applications. In this study, we provide the first comparative correlative analysis of three‐dimensional structures obtained by 4Pi microscopy and segmented by a zero‐crossing procedure with those of transmission electron microscopy (TEM). The distribution within the cisternae of isolated Golgi stacks of the cargo protein procollagen 3 was mapped by both 4Pi microscopy and TEM for a detailed comparative analysis of their imaging capabilities. A high correlation was seen for the structures, indicating the particular accuracy of the 4Pi microscopy. Furthermore, for the first time, transport of a cargo molecule (vesicular stomatitis virus G protein‐pEGFP) through individual Golgi stacks (labeled by galactosyl transferase‐venusYFP) was visualized by 4Pi microscopy. Following the procedures validated by the correlative analysis, our transport experiments show that (i) VSVG‐pEGFP rapidly enter/exit individual Golgi stacks, (ii) VSVG‐pEGFP never fills the GalT‐venusYFP compartments completely and (iii) the GalT‐venusYFP compartment volume increases upon VSVG‐pEGFP arrival. This morphological evidence supports some previous TEM‐based observations of intra‐Golgi transport of VSVG‐pEGFP and provides new insights toward a better understanding of protein progression across Golgi stacks. Our study thus demonstrates the general applicability of super‐resolution fluorescence microscopy, coupled with the zero‐crossing segmentation procedure, for structural studies of suborganelle protein distributions under living cell conditions.
A Revision of the Lari (Aves, Charadriiformes) from the Early Miocene of Saint-Gérand-Le-Puy (Allier, France)

ABSTRACT Three species of gull-like birds were described by Milne-Edwards in the 19th century from the early Miocene of Saint-Gérand-le-Puy, France, two of which have been since then moved to the genus Laricola. These fossils are redescribed and revised in the present study. We further describe two new species of the taxon Laricola, L. intermedia, sp. nov., and L. robusta, sp. nov., as well as two species of a new taxon Sternalara, S. minuta and S. milneedwardsi, thus substantially increasing the number of charadriiform taxa known from this locality. To find out how Laricola relates to modern taxa, we performed a phylogenetic analysis of 41 osteological characters, which resulted in Laricola being placed outside of Lariidae, as early representatives of the newly designated group Laromorphae, which encompasses terns, gulls, and skimmers. The results of our analysis have additionally enabled us to evaluate relationships between extant taxa of the Laromorphae.