Miracle-dz/UniFAR-FTUs huggingface dataset:
DeepEddy: A simple deep architecture for mesoscale oceanic eddy detection in SAR images

Automatic detection of mesoscale oceanic eddies is in great demand to monitor their dynamics which play a significant role in ocean current circulation and marine climate change. Traditional methods of eddies detection using remotely sensed data are usually based on physical parameters, geometrics, handcrafted features or expert knowledge, they face a great challenge in accuracy and efficiency due to the high variability of oceanic eddies and our limited understanding of their physical process, especially for rich and large remotely sensed data. In this paper, we propose a simple deep architecture DeepEddy to detect oceanic eddies automatically and be free of expert knowledge. DeepEddy can learn high-level and invariant features of oceanic eddies hierarchically. It is designed with two principal component analysis (PCA) convolutional layers for eddies feature learning, a binary hashing layer for non-linear transformation, a feature pooling layer using block-wise histograms and spatial pyramid pooling to resolve the complicated structures and poses of oceanic eddies, and a classifier for the final eddies identification. We verify the accuracy of the architecture with comprehensive experiments on high spatial resolution Synthetic Aperture Radar (SAR) images. We achieve the state-of-the-art accuracy of 96.68%.
Crypt hyperplastic enteropathy in distal duodenum in Helicobacter pylori infection - report of two cases without evidence of celiac disease.

OBJECTIVES Patients with Helicobacter pylori (HP) infection have been reported to have in addition to duodenitis architectural changes of the duodenal bulb mucosa including villous atrophy and crypt hyperplasia. We here for the first time present two cases of HP-infected adult patients with a crypt hyperplastic enteropathy also in the distal duodenum mimicking celiac disease (CD). METHODS We evaluated separately the morphology of the anatomical bulb and distal duodenal mucosa using validated quantitative morphometric tools, i.e., the villous height (VH) and crypt depth (CrD) and their ratios. The fresh frozen samples were evaluated for the presence of the CD-specific transglutaminase 2-targeted subepithelial IgA deposits. RESULTS Both patients had celiac-type crypt hyperplastic mucosal injury in the distal part of the duodenum in the absence of serum autoantibodies and subepithelial IgA deposits. After two years follow-up, having still a normal gluten-containing diet, none of the patients developed CD. Moreover, in the patient re-biopsied two years later, the CD-type enteropathy had healed after HP eradication. CONCLUSIONS Prospective studies on HP-infected patients are needed in order to confirm our findings.
Cranial muscles in amphibians: development, novelties and the role of cranial neural crest cells

Our research on the evolution of the vertebrate head focuses on understanding the developmental origins of morphological novelties. Using a broad comparative approach in amphibians, and comparisons with the well‐studied quail‐chicken system, we investigate how evolutionarily conserved or variable different aspects of head development are. Here we review research on the often overlooked development of cranial muscles, and on its dependence on cranial cartilage development. In general, cranial muscle cell migration and the spatiotemporal pattern of cranial muscle formation appears to be very conserved among the few species of vertebrates that have been studied. However, fate‐mapping of somites in the Mexican axolotl revealed differences in the specific formation of hypobranchial muscles (tongue muscles) in comparison to the chicken. The proper development of cranial muscles has been shown to be strongly dependent on the mostly neural crest‐derived cartilage elements in the larval head of amphibians. For example, a morpholino‐based knock‐down of the transcription factor FoxN3 in Xenopus laevis has drastic indirect effects on cranial muscle patterning, although the direct function of the gene is mostly connected to neural crest development. Furthermore, extirpation of single migratory streams of cranial neural crest cells in combination with fate‐mapping in a frog shows that individual cranial muscles and their neural crest‐derived connective tissue attachments originate from the same visceral arch, even when the muscles attach to skeletal components that are derived from a different arch. The same pattern has also been found in the chicken embryo, the only other species that has been thoroughly investigated, and thus might be a conserved pattern in vertebrates that reflects the fundamental nature of a mechanism that keeps the segmental order of the head in place despite drastic changes in adult anatomy. There is a need for detailed comparative fate‐mapping of pre‐otic paraxial mesoderm in amphibians, to determine developmental causes underlying the complicated changes in cranial muscle development and architecture within amphibians, and in particular how the novel mouth apparatus in frog tadpoles evolved. This will also form a foundation for further research into the molecular mechanisms that regulate rostral head morphogenesis. Our empirical studies are discussed within a theoretical framework concerned with the evolutionary origin and developmental basis of novel anatomical structures in general. We argue that a common developmental origin is not a fool‐proof guide to homology, and that a view that sees only structures without homologs as novel is too restricted, because novelties must be produced by changes in the same framework of developmental processes. At the level of developmental processes and mechanisms, novel structures are therefore likely to have homologs, and we need to develop a hierarchical concept of novelty that takes this into account.
A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions

Mechanical signals play a critical role in the regulation of muscle mass, but the molecules that sense mechanical signals and convert this stimulus into the biochemical events that regulate muscle mass remain ill‐defined. Here we report a mass spectrometry‐based workflow to study the changes in protein phosphorylation that occur in mouse skeletal muscle 1 h after a bout of electrically evoked maximal‐intensity contractions (MICs). Our dataset provides the first comprehensive map of the MIC‐regulated phosphoproteome. Using unbiased bioinformatics approaches, we demonstrate that our dataset leads to the identification of many well‐known MIC‐regulated signalling pathways, as well as to a plethora of novel MIC‐regulated events. We expect that our dataset will serve as a fundamentally important resource for muscle biologists, and help to lay the foundation for entirely new hypotheses in the field.
A Collaborative Model of Low-Level and High-Level Descriptors for Semantics-Based Music Information Retrieval

Although technologies of both low-level and high-level descriptors for music information retrieval (MIR) are advancing, there are some essential deficiencies while utilizing them separately. In this paper we propose a model where the low-level and high-level descriptors collaborate to support semantics-based MIR. The ontology of ldquomusic scenerdquo domain is constructed as a demonstration, and a set of domain related low-level and high-level descriptor analyses are introduced. Given the domain ontology and the analysis results as input, an abduction process is adopted to compute the semantics-based interpretations. Evaluations show that the collaborative model does not only give a better recall rate of semantics-based retrieval than separated models, but also maintains a promising precision meanwhile.
Prevalence of Myelin Oligodendrocyte Glycoprotein and Aquaporin-4–IgG in Patients in the Optic Neuritis Treatment Trial

Importance Autoantibodies to aquaporin-4 (AQP4) and myelin oligodendrocyte glycoprotein (MOG) are recently established biomarkers of autoimmune optic neuritis whose frequency and accompanying phenotype, especially for MOG-IgG, are still being characterized. The Optic Neuritis Treatment Trial (ONTT) was a well-known randomized clinical trial in optic neuritis; therefore, knowledge of the serostatus and accompanying phenotype of these patients would be useful to determine the frequency of these antibodies in patients presenting with typical monocular optic neuritis and their outcomes. Objectives To determine the AQP4-IgG and MOG-IgG serostatus of patients within the ONTT and describe the clinical features of seropositive patients. Design, Setting, and Participants In this follow-up study of the randomized clinical trial, ONTT, conducted between July 1, 1988, and June 30, 1991, analysis of serum for AQP4-IgG and MOG-IgG was performed from January 1 to April 30, 2017. A total of 177 patients from the ONTT with acute optic neuritis and serum available for analysis were enrolled from 13 academic referral centers. Interventions Analysis of serum for AQP4-IgG and MOG-IgG was performed at Mayo Clinic Neuroimmunology Laboratory in 2017 with a flow cytometry, live cell, AQP4- and MOG-transfected cell-based assay. Main Outcomes and Measures Aquaporin-4–IgG and MOG-IgG serostatus. Results Of the 177 patients in the study (135 women and 42 men; mean [SD] age, 32.8 [6.9] years), 3 were positive for MOG-IgG (1.7%) and none were positive for AQP4-IgG. All 3 patients positive for MOG-IgG had disc edema at presentation. Two patients later had a single episode of recurrent optic neuritis. All 3 patients had complete recovery of visual acuity, and none were corticosteroid dependent, although peripheral visual field loss persisted in 1 patient. None of the 3 patients positive for MOG-IgG had demyelinating lesions on magnetic resonance imaging scans, and none had developed multiple sclerosis at the 15-year follow-up. Conclusions and Relevance Frequency of MOG-IgG was rare in the ONTT, and AQP4-IgG was not found in patients in the ONTT. Characteristics of patients positive for MOG-IgG in the ONTT support the previously described phenotype of MOG-IgG optic neuritis. Myelin oligodendrocyte glycoprotein–related disease appears to be a different entity than multiple sclerosis. Overall, AQP4-IgG and MOG-IgG may be less common in isolated optic neuritis than previously reported.
Standing waves are not distinctive to conventional angiograms

We report two cases in which the characteristic patterns of standing waves were noted on computed tomography angiogram (CTA). Standing waves have often been reported in conventional arteriography; however, it is rarely ever documented in CTA. Case 1: An 18-year-old male presented with sensorymotor deficits in the bilateral upper and lower extremities after a motor vehicle accident. A CTA of the head and neck showed a cervical vertebral fracture (C3–C4). The CTA also revealed a regular beaded contour of the bilateral internal carotid arteries consistent with standing waves (Panel A and B (arrows): coronal view and sagittal view of the bilateral internal carotid artery). Case 2: A 35-year-old female with systemic lupus erythematosus and fibromyalgia was admitted with pleuritic chest pain, acute respiratory failure and a sudden drop in hemoglobin from 10 g/dL to 6.9 g/dL. CTA of the chest, abdomen, and pelvis displayed a regular beaded appearance of the superior mesenteric artery, again consistent with standing waves (Panel C (arrow): sagittal view of the abdominal aorta and superior mesenteric artery).
Improving titer while maintaining quality of final formulated drug substance via optimization of CHO cell culture conditions in low-iron chemically defined media

ABSTRACT During biopharmaceutical process development, it is important to improve titer to reduce drug manufacturing costs and to deliver comparable quality attributes of therapeutic proteins, which helps to ensure patient safety and efficacy. We previously reported that relative high-iron concentrations in media increased titer, but caused unacceptable coloration of a fusion protein during early-phase process development. Ultimately, the fusion protein with acceptable color was manufactured using low-iron media, but the titer decreased significantly in the low-iron process. Here, long-term passaging in low-iron media is shown to significantly improve titer while maintaining acceptable coloration during late-phase process development. However, the long-term passaging also caused a change in the protein charge variant profile by significantly increasing basic variants. Thus, we systematically studied the effect of media components, seed culture conditions, and downstream processing on productivity and quality attributes. We found that removing β-glycerol phosphate (BGP) from basal media reduced basic variants without affecting titer. Our goals for late-phase process development, improving titer and matching quality attributes to the early-phase process, were thus achieved by prolonging seed culture age and removing BGP. This process was also successfully scaled up in 500-L bioreactors. In addition, we demonstrated that higher concentrations of reactive oxygen species were present in the high-iron Chinese hamster ovary cell cultures compared to that in the low-iron cultures, suggesting a possible mechanism for the drug substance coloration caused by high-iron media. Finally, hypotheses for the mechanisms of titer improvement by both high-iron and long-term culture are discussed.
National Patterns of Commonly Prescribed Psychotropic Medications to Young People.

OBJECTIVE To describe national annual prescribing patterns of stimulant, antidepressant, and antipsychotic medications to young people. METHODS Prescriptions for three commonly prescribed psychotropic classes (stimulants, antidepressants, and antipsychotics) to young people aged 3-24 years were analyzed from the IMS LifeLink LRx National Longitudinal Prescription database (n = 6,351,482). Denominators were adjusted to generalize estimates to the U.S. POPULATION Comparisons are presented of percentages filling ≥1 prescription of each medication class during the study year stratified by patient sex, age, and prescriber specialty. RESULTS The total annual percentage of prescriptions filled by youth for any of the three medication classes was by age 3-5 years (0.8%), 6-12 years (5.4%), 13-18 years (7.7%), and 19-24 years (6.0%). Stimulant use was highest for older children (age 11 = 5.7%). Antidepressant use tended to increase with age and was highest for young adults (age 24 = 4.8%). Annual antipsychotic prescription percentages were lower than antidepressant or stimulant percentages for all age groups, with a peak in adolescence (age 16 = 1.3%). Annual stimulant and antipsychotic percentages for males were higher than corresponding percentages for females, but converged for young adults. Psychiatrists and child psychiatrists accounted for most of the prescriptions of antidepressants (22.2%-53.2%) and antipsychotics (51.7%-70%), but fewer of the stimulant prescriptions (30.4%-36.2%). CONCLUSIONS The age and sex distribution of stimulants and antidepressants among young people is broadly consistent with known epidemiologic patterns of their established indications for attention-deficit/hyperactivity disorder, anxiety, and depression. The pattern of antipsychotics may reflect the heterogeneity of disorders and conditions treated with this medication class.
Polyethylene glycol intestinal lavage in addition to usual antibiotic treatment for severe Clostridium difficile colitis: a randomised controlled pilot study

Introduction Clostridium difficile infections (CDI) are common, costly and potentially life threatening. Most CDI will respond to antibiotic therapy, but 3%–10% of all patients with CDI will progress to a severe, life-threatening course. Complete removal of the large bowel is indicated for severe CDI. However, the 30-day mortality following surgical intervention for severe CDI ranges from 20% to 70%. A less invasive approach using surgical faecal diversion and direct colonic lavage with polyethylene glycol (PEG) and vancomycin has demonstrated a relative mortality reduction of approximately 50%. As an alternative to these operative approaches, we propose to treat patients with bedside intestinal lavage with PEG and vancomycin instillation via nasojejunal tube, in addition to usual antibiotic management. Preliminary data collected by our research group are encouraging. Methods and analysis We will conduct a 1-year, single-centre, pilot randomised controlled trial to study this new treatment strategy for patients with severe CDI and additional risk factors for fulminant or complicated infection. After informed consent, patients with severe-complicated CDI without immediate indication for surgery will be randomised to either usual antibiotic treatment or usual antibiotic treatment with the addition of 8 L of PEG lavage via nasojejunal tube. This pilot trial will evaluate our eligibility and enrolment rate, protocol compliance and adverse event rates and provide further data to inform a more robust sample size calculation and protocol modifications for a definitive multicentre trial design. Based on historical data, we anticipate enrolling approximately 24 patients during the 1-year pilot study period. As a pilot study, data will be reported in aggregate. Between-group differences will be assessed in a blinded fashion for evidence of harm, and to further refine our sample size calculation. Ethics and dissemination This study protocol has been reviewed and approved by our local institutional review board. Results of the pilot trial and subsequent main trial will be submitted for publication in a peer-reviewed journal. Trial registration number NCT02466698; Pre-results.
Evaluation of high-density, multi-contact nerve cuffs for activation of grasp muscles in monkeys

Objective. The objective of this work was to evaluate whether nerve cuffs can selectively activate hand muscles for functional electrical stimulation (FES). FES typically involves identifying and implanting electrodes in many individual muscles, but nerve cuffs only require implantation at a single site around the nerve. This method is surgically more attractive. Nerve cuffs may also more effectively stimulate intrinsic hand muscles, which are difficult to implant and stimulate without spillover to adjacent muscles. Approach. To evaluate its ability to selectively activate muscles, we implanted and tested the flat interface nerve electrode (FINE), which is designed to selectively stimulate peripheral nerves that innervate multiple muscles (Tyler and Durand 2002 IEEE Trans. Neural Syst. Rehabil. Eng. 10 294–303). We implanted FINEs on the nerves and bipolar intramuscular wires for recording compound muscle action potentials (CMAPs) from up to 20 muscles in each arm of six monkeys. We then collected recruitment curves while the animals were anesthetized. Main result. A single FINE implanted on an upper extremity nerve in the monkey can selectively activate muscles or small groups of muscles to produce multiple, independent hand functions. Significance. FINE cuffs can serve as a viable supplement to intramuscular electrodes in FES systems, where they can better activate intrinsic and extrinsic muscles with lower currents and less extensive surgery.
TAR DNA-binding protein 43 (TDP-43) liquid–liquid phase separation is mediated by just a few aromatic residues

Eukaryotic cells contain distinct organelles, but not all of these compartments are enclosed by membranes. Some intrinsically disordered proteins mediate membraneless organelle formation through liquid–liquid phase separation (LLPS). LLPS facilitates many biological functions such as regulating RNA stability and ribonucleoprotein assembly, and disruption of LLPS pathways has been implicated in several diseases. Proteins exhibiting LLPS typically have low sequence complexity and specific repeat motifs. These motifs promote multivalent connections with other molecules and the formation of higher-order oligomers, and their removal usually prevents LLPS. The intrinsically disordered C-terminal domain of TAR DNA-binding protein 43 (TDP-43), a protein involved in motor neuron disease and dementia lacks a dominant LLPS motif, however, and how this domain forms condensates is unclear. Using extensive mutagenesis of TDP-43, we demonstrate here that three tryptophan residues and, to a lesser extent, four other aromatic residues are most important for TDP-43 to undergo LLPS. Our results also suggested that only a few residues may be required for TDP-43 LLPS because the α-helical segment (spanning ∼20 residues) in the middle part of the C-terminal domain tends to self-assemble, reducing the number of motifs required for forming a multivalent connection. Our results indicating that a self-associating α-helical element with a few key residues regulates condensate formation highlight a different type of LLPS involving intrinsically disordered regions. The C-terminal domain of TDP-43 contains ∼50 disease-related mutations, with no clear physicochemical link between them. We propose that they may disrupt LLPS indirectly by interfering with the key residues identified here.
Study of Strain-Softening Stage in Structurally Inhomogeneous Materials

The paper considers – in terms of modeling and experimental testing – the softening stage manifested in structurally inhomogeneous materials under quasi-static and cyclic load. The method which is used to build the theoretical basis is typical for mechanics. It starts with defining a new material property – strain-softening phase. The stage is realized in the form of a descending branch of the curve on computer diagrams recorded during simple tension or torsion tests on non-reusable specimens in a reasonably rigid testing machine. The type of such a diagram is determined by the structural inhomogeneity of a material, which is defined by distribution law for strength and plasticity properties of structural elements. Complete stress-strain curves or diagrams (CSSD) with a branch descending to zero have been plotted for materials of various classes. Degradation of parameters of a descending branch on a computer diagram recorded for trained specimens provides a new angle on the subject of relation between static and cyclic material properties. The experiments and modeling which were carried out provide basic understanding of softening in terms of deformation.