Miracle-dz/UniFAR-FTUs huggingface dataset:
An Umbraviral Protein, Involved in Long-Distance RNA Movement, Binds Viral RNA and Forms Unique, Protective Ribonucleoprotein Complexes

ABSTRACT Umbraviruses are different from most other viruses in that they do not encode a conventional capsid protein (CP); therefore, no recognizable virus particles are formed in infected plants. Their lack of a CP is compensated for by the ORF3 protein, which fulfils functions that are provided by the CPs of other viruses, such as protection and long-distance movement of viral RNA. When the Groundnut rosette virus (GRV) ORF3 protein was expressed from Tobacco mosaic virus (TMV) in place of the TMV CP [ΤMV(ORF3)], in infected cells it interacted with the TMV RNA to form filamentous ribonucleoprotein (RNP) particles that had elements of helical structure but were not as uniform as classical virions. These RNP particles were observed in amorphous inclusions in the cytoplasm, where they were embedded within an electron-dense matrix material. The inclusions were detected in all types of cells and were abundant in phloem-associated cells, in particular companion cells and immature sieve elements. RNP-containing complexes similar in appearance to the inclusions were isolated from plants infected with ΤMV(ORF3) or with GRV itself. In vitro, the ORF3 protein formed oligomers and bound RNA in a manner consistent with its role in the formation of RNP complexes. It is suggested that the cytoplasmic RNP complexes formed by the ORF3 protein serve to protect viral RNA and may be the form in which it moves through the phloem. Thus, the RNP particles detected here represent a novel structure which may be used by umbraviruses as an alternative to classical virions.
A User-Oriented Approach to Designing FIR Deconvolution Filters

Based on learning in input-output signal domain and controlling noise amplification by varying sampling rate, a pragmatic approach is developed for designing FIR deconvolution filters with the desired noise gains producing accurate as possible output time-domain waveforms for filter support intervals defined by a user. As an example, FIR linear phase digital differentiator is designed by the developed methodology for socalled logarithmic derivative technique and its performance is compared with that of the appropriate equiripple minimax and maximally linear differentiators. Key-Words: FIR Deconvolution Filters, Design by Learning, Regularization by Choosing Sampling Rate
Health Literacy and Its Determinants in Adult Patients Referred to Dental Clinics: A Cross Sectional Study in Mashhad, Iran

Background: Health literacy is the capacity of individuals to obtain, understand, and interpret basic health information that is necessary to make appropriate health-related decisions. Objectives: This study aimed to investigate the association between oral health literacy and the decayed, missing, and filled teeth (DMFT) index, which was conducted in Mashhad dental clinics in 2016. Methods: In this cross-sectional study, 380 patients referred to private and public clinics in Mashhad filled out the oral health literacy adult’s questionnaire (OHL-AQ). The questionnaire contained 4 sections: reading, numeracy, listening, and decision making. Each correct answer was assigned a score of 1 and incorrect or no response were assigned with zero score. The DMFT index was evaluated based on decayed, missing, and filling teeth. Data analysis was performed using chi-square and linear regression tests. Results: The mean score for oral health literacy was 10.6±3.4. Among patients 46.8 had favorable oral health literacy level, 19.7 were with relatively favorable, and 33.4 were with unfavorable health literacy levels. The average of the DMFT index in the studied group was 8.3±4.9 and was higher among males than females. A significant correlation between the health literacy level and the DMFT index was observed; however, the correlation was negative and weak (R= - 0.127). Conclusions: The average of oral health literacy level for the entire study population was relatively appropriate, and the majority of the subjects (46.8) represented a good oral health literacy level. Furthermore, education, economic status, and collecting information from different sources of oral health are important factors affecting the level of oral health literacy. © 2019, Author(s). © 2019, Author(s).
Ranibizumab for the treatment of degenerative ocular conditions

Degenerative ocular conditions, such as age-related macular degeneration, diabetic retinopathy, retinal vein occlusions, and myopic degeneration, have become a major public health problem and a leading cause of blindness in developed countries. Anti-vascular endothelial growth factor (VEGF) drugs seem to be an effective and safe treatment for these conditions. Ranibizumab, a humanized monoclonal antibody antigen-binding fragment, which inhibits all biologically active isoforms of VEGF-A, is still the gold standard treatment for the majority of these pathological entities. In this review, we present the results of the most important clinical trials concerning the efficacy and safety of ranibizumab for the treatment of degenerative ocular conditions.
Effects of Eight Weeks of Bicycle Ergometer Sprint Training on Human Muscle Buffer Capacity

This investigation was undertaken to determine whether human skeletal muscle buffer capacity (BCm) is affected by training. Eight untrained males participated in 8 weeks of sprint training on bicycle ergometers. Muscle biopsy samples were taken from the vastus lateralis before and at several times following an incremental bicycle ergometer test (0 min, 5 min, 15 min). These subjects were tested before (PRE) and following (POST) the training period. Seven endurance-trained cyclists (ET) were also tested for the purpose of comparing the BCm of ET to that of PRE and POST. Biopsy samples were quick-frozen in liquid nitrogen and later analyzed for lactate concentration (HLam), homogenate pH (pHm), and creatine phosphate concentration. BCm was calculated from the change in HLam and pHm observed from rest to exhaustion and was expressed as mmol X kg-1 X pH-1 (Slykes). There was no significant difference in resting HLam or resting pHm among the groups. There was a significant difference in HLam at exhaustion between PRE (21.41 +/- 1.65 mmol X kg-1), POST (25.61 +/- 2.38 mmol X kg-1), and ET (11.16 +/- 0.31 mmol X kg-1) but no significant difference in pHm at exhaustion between PRE (6.65 +/- 0.03 pH units) and POST (6.69 +/- 0.06 pH units). pHm at exhaustion for the ET group was significantly higher than the others at 6.91 +/- 0.02 pH units. A significant difference between PRE and POST BCm was found (PRE: 44.68 +/- 3.03 S1; POST: 61.04 +/- 4.11 S1) while ET BCm (47.21 +/- 7.26 S1) was not significantly different from PRE. These data indicate that muscle buffer capacity is increased with highly intense sprint training but provide no evidence to suggest that muscle buffer capacity is affected by endurance training.
Robust Low-tubal-rank Tensor Completion

Real multi-way data may suffer from missing entries, noise and outliers simultaneously. The recently proposed tubal nuclear norm (TNN) has shown its superiority in tensor completion. However, statistical analysis of TNN based models is still deficient. This paper aims to robustly recover a polluted incomplete tensor with rigorous statistical guarantee. Specifically, an estimator based on a weighed variant of TNN is proposed to complete a low-tubal-rank tensor corrupted by element sparse errors or slice sparse sample outliers from partial noisy observations. Non-asymptotic upper bounds on the estimation error are established and further proved to be minimax optimal up to a log factor. Sharpness of the upper bounds is verified on synthetic datasets and superiority of the proposed estimator is demonstrated through robust video inpainting.
LONG-TERM SAFETY OF BIOSIMILAR MEDICINAL PRODUCTS – KEY FOR ADMINISTRATION?

The emergence of therapeutically effective biological agents has been a major breakthrough for the management of a wide range of chronic diseases with problematic, delayed or even lack of response to standard therapies, from psoriasis to atopic dermatitis, chronic urticaria, inflammatory bowel disease and rheumatoid arthritis. Biosimilar drugs are biological products as well, marketed as alternatives to the original biological medicine, whose safety and efficacy profile are very similar but not identical to the innovative biological medicinal product, which has already been authorised and placed on the market for 10 years or longer. In this review, we discuss complex issues such as the development of the biosimilar products, regulation aspects, safety and efficacy of biosimilar products as well as their use in clinical practice. Some extended reports are also addressed. By changing the context and providing a new option for mitigating increasing healthcare cost and improving the quality of life for more and more patients, biosimilar drugs are at the forefront of contemporary medicine.
A Changing Number of Alternative States in the Boreal Biome: Reproducibility Risks of Replacing Remote Sensing Products

Publicly available remote sensing products have boosted science in many ways. The openness of these data sources suggests high reproducibility. However, as we show here, results may be specific to versions of the data products that can become unavailable as new versions are posted. We focus on remotely-sensed tree cover. Recent studies have used this public resource to detect multi-modality in tree cover in the tropical and boreal biomes. Such patterns suggest alternative stable states separated by critical tipping points. This has important implications for the potential response of these ecosystems to global climate change. For the boreal region, four distinct ecosystem states (i.e., treeless, sparse and dense woodland, and boreal forest) were previously identified by using the Collection 3 data of MODIS Vegetation Continuous Fields (VCF). Since then, the MODIS VCF product has been updated to Collection 5; and a Landsat VCF product of global tree cover at a fine spatial resolution of 30 meters has been developed. Here we compare these different remote-sensing products of tree cover to show that identification of alternative stable states in the boreal biome partly depends on the data source used. The updated MODIS data and the newer Landsat data consistently demonstrate three distinct modes around similar tree-cover values. Our analysis suggests that the boreal region has three modes: one sparsely vegetated state (treeless), one distinct ‘savanna-like’ state and one forest state, which could be alternative stable states. Our analysis illustrates that qualitative outcomes of studies may change fundamentally as new versions of remote sensing products are used. Scientific reproducibility thus requires that old versions remain publicly available.
Emricasan Ameliorates Portal Hypertension and Liver Fibrosis in Cirrhotic Rats Through a Hepatocyte‐Mediated Paracrine Mechanism

In cirrhosis, liver microvascular dysfunction is a key factor increasing hepatic vascular resistance to portal blood flow, which leads to portal hypertension. De‐regulated inflammatory and pro‐apoptotic processes due to chronic injury play important roles in the dysfunction of liver sinusoidal cells. The present study aimed at characterizing the effects of the pan‐caspase inhibitor emricasan on systemic and hepatic hemodynamics, hepatic cells phenotype, and underlying mechanisms in preclinical models of advanced chronic liver disease. We investigated the effects of 7‐day emricasan on hepatic and systemic hemodynamics, liver function, hepatic microcirculatory function, inflammation, fibrosis, hepatic cells phenotype, and paracrine interactions in rats with advanced cirrhosis due to chronic CCl4 administration. The hepato‐protective effects of emricasan were additionally investigated in cells isolated from human cirrhotic livers. Cirrhotic rats receiving emricasan showed significantly lower portal pressure than vehicle‐treated animals with no changes in portal blood flow, indicating improved vascular resistance. Hemodynamic improvement was associated with significantly better liver function, reduced hepatic inflammation, improved phenotype of hepatocytes, liver sinusoidal endothelial cells, hepatic stellate cells and macrophages, and reduced fibrosis. In vitro experiments demonstrated that emricasan exerted its benefits directly improving hepatocytes’ expression of specific markers and synthetic capacity, and ameliorated nonparenchymal cells through a paracrine mechanism mediated by small extracellular vesicles released by hepatocytes. Conclusion: This study demonstrates that emricasan improves liver sinusoidal microvascular dysfunction in cirrhosis, which leads to marked amelioration in fibrosis, portal hypertension and liver function, and therefore encourages its clinical evaluation in the treatment of advanced chronic liver disease.
Riemannian trust-region methods for H2 optimal model reduction

In this paper, the Riemannian trust-region method for the H2 optimal model reduction problem is proposed. The problem is regarded as optimization problems on the Stiefel and Grassmann manifolds and several geometric quantities of the problems are discussed to develop the Riemannian trust-region method. Numerical experiments show that the proposed methods can solve the H2 optimal model reduction problem effectively.
Binaural cue coding-Part I: psychoacoustic fundamentals and design principles

Binaural Cue Coding (BCC) is a method for multichannel spatial rendering based on one down-mixed audio channel and BCC side information. The BCC side information has a low data rate and it is derived from the multichannel encoder input signal. A natural application of BCC is multichannel audio data rate reduction since only a single down-mixed audio channel needs to be transmitted. An alternative BCC scheme for efficient joint transmission of independent source signals supports flexible spatial rendering at the decoder. This paper (Part I) discusses the most relevant binaural perception phenomena exploited by BCC. Based on that, it presents a psychoacoustically motivated approach for designing a BCC analyzer and synthesizer. This leads to a reference implementation for analysis and synthesis of stereophonic audio signals based on a Cochlear Filter Bank. BCC synthesizer implementations based on the FFT are presented as low-complexity alternatives. A subjective audio quality assessment of these implementations shows the robust performance of BCC for critical speech and audio material. Moreover, the results suggest that the performance given by the reference synthesizer is not significantly compromised when using a low-complexity FFT-based synthesizer. The companion paper (Part II) generalizes BCC analysis and synthesis for multichannel audio and proposes complete BCC schemes including quantization and coding. Part II also describes an alternative BCC scheme with flexible rendering capability at the decoder and proposes several applications for both BCC schemes.
An RFID Reader Based on the Atmel AT91SAM7S64 Micro-Controller

Retrieving data from transponders that are located at the same time inside a certain area is one of the RFID applications that the gaming industry is interested in. The RFID reader currently produced by Gaming Partners International is aimed at such application. An international cooperation project funded by the named corporation had as target the development of a reader intended to upgrade the existing one. We explain in the following why the decision to use the AT91SAM7S64 microcontroller for the new design translated into benefits in terms of reliability, speed, higher integration and easier development and maintenance
Paraneoplastic Neurological Syndromes and Glutamic Acid Decarboxylase Antibodies.

IMPORTANCE Little is known of glutamic acid decarboxylase antibodies (GAD-abs) in the paraneoplastic context. Clinical recognition of such cases will lead to prompt tumor diagnosis and appropriate treatment. OBJECTIVE To report the clinical and immunological features of patients with paraneoplastic neurological syndromes (PNS) and GAD-abs. DESIGN, SETTING, AND PARTICIPANTS Retrospective case series study and immunological investigations conducted in February 2014 in a center for autoimmune neurological disorders. Fifteen cases with GAD65-abs evaluated between 1995 and 2013 who fulfilled criteria of definite or possible PNS without concomitant onconeural antibodies were included in this study. MAIN OUTCOMES AND MEASURES Analysis of the clinical records of 15 patients and review of 19 previously reported cases. Indirect immunofluorescence with rat hippocampal neuronal cultures and cell-based assays with known neuronal cell-surface antigens were used. One hundred six patients with GAD65-abs and no cancer served as control individuals. RESULTS Eight of the 15 patients with cancer presented as classic paraneoplastic syndromes (5 limbic encephalitis, 1 paraneoplastic encephalomyelitis, 1 paraneoplastic cerebellar degeneration, and 1 opsoclonus-myoclonus syndrome). When compared with the 106 non-PNS cases, those with PNS were older (median age, 60 years vs 48 years; P = .03), more frequently male (60% vs 13%; P < .001), and had more often coexisting neuronal cell-surface antibodies, mainly against γ-aminobutyric acid receptors (53% vs 11%; P < .001). The tumors more frequently involved were lung (n = 6) and thymic neoplasms (n = 4). The risk for an underlying tumor was higher if the presentation was a classic PNS, if it was different from stiff-person syndrome or cerebellar ataxia (odds ratio, 10.5; 95% CI, 3.2-34.5), or if the patient had coexisting neuronal cell-surface antibodies (odds ratio, 6.8; 95% CI, 1.1-40.5). Compared with the current series, the 19 previously reported cases had more frequent stiff-person syndrome (74% vs 13%; P = .001) and better responses to treatment (79% vs 27%; P = .005). Predictors of improvement in the 34 patients (current and previously reported) included presentation with stiff-person syndrome and the presence of a thymic tumor. CONCLUSIONS AND RELEVANCE Patients with GAD-abs must be screened for an underlying cancer if they have clinical presentations different from those typically associated with this autoimmunity or develop classic PNS. The risk for cancer increases with age, male sex, and the presence of coexisting neuronal cell-surface antibodies.
Androgenic suppression of spreading depression in familial hemiplegic migraine type 1 mutant mice

Familial hemiplegic migraine type 1 (FHM1), a severe migraine with aura variant, is caused by mutations in the CACNA1A gene. Mutant mice carrying the FHM1 R192Q mutation exhibit increased propensity for cortical spreading depression (CSD), a propagating wave of neuroglial depolarization implicated in migraine aura. The CSD phenotype is stronger in female R192Q mutants and diminishes after ovariectomy. Here, we show that orchiectomy reciprocally increases CSD susceptibility in R192Q mutant mice. Chronic testosterone replacement restores CSD susceptibility by an androgen receptor‐dependent mechanism. Hence, androgens modulate genetically‐enhanced CSD susceptibility and may provide a novel prophylactic target for migraine. Ann Neurol 2009;66:564–568
Epidemiology of Functional Gastrointestinal Disorders in Japan and in the World

Functional gastrointestinal disorders (FGIDs), represented by functional dyspepsia (FD) and irritable bowel syndrome (IBS), are a group of disorders that include variable combinations of chronic or recurrent gastrointestinal symptoms not explained by structural or biochemical abnormalities. FGIDs account for a significant percentage of patients seen in primary care settings with abdominal symptoms. Although the definition of FGIDs can easily affect the prevalence, the prevalences of dyspepsia/FD and IBS diagnosed by the Rome III criteria in the general population are 5.3–20.4% and 1.1–29.2%, respectively. Recent reports of FD and IBS defined by the Rome III criteria indicated a female predominance. Regarding the subtype prevalence of FD, postprandial distress syndrome was more prevalent than epigastric pain syndrome (5.6–13.9% vs 0.9–9.5%). The subtype prevalence of IBS is characterized by male predominance for IBS with diarrhea and female predominance for IBS with constipation. Factors affecting the development of FGIDs such as epidemiological factors including genetic and environmental factors, are important. Gene polymorphisms are involved in the development of FGIDs. The prevalence differs among races and geographic areas. Foods may affect the development of FGIDs, but the causal relationships between food and FGIDs are not conclusive. The symptoms often regress and appear in the course of these entities. Building a favorable patient-doctor relationship is effective for controlling symptoms of FGIDs. Physicians should explain that FGIDs are highly prevalent conditions, impair the patients’ quality of life even without evident underlying organic causes and are not life-threatening conditions to ensure patients’ understanding.
Hypothyroidism in patients with Bipolar I Disorder treated primarily with lithium

SUMMARY Aims – This study evaluated the frequency and clinical significance of abnormal Thyroid Stimulating Hormone (TSH) and Free Thyroxine Index (FTI) in patients with bipolar I disorder treated primarily with lithium. Method – We evaluated the medical records of 143 participants in the Pittsburgh study of Maintenance Therapies in Bipolar Disorder who did not have a thyroid abnormality at entry. Results – Thirty-six percent of the 143 patients developed abnormal TSH and/or FTI values. Thirty-eight percent of the 135 patients who received lithium developed abnormal TSH and/or FTI, spent significantly longer time in the acute treatment phase (t = -3.6, df = 133, p = .0004), and had significantly higher mean Hamilton Scale for Depression scores over the course of the maintenance phase (t = -2.3, df = 71.6, p = .03). Time on lithium and development of abnormal TSH and/or FTI were positively correlated (r = .25, p = .004). Conclusions – Thyroid dysfunction can be frequent in patients exposed to lithium treatment for bipolar I disorder; it also appears to be correlated with a slower response to acute treatment, and may be related to poorer quality of long-term remission. A prospective study is needed to confirm our findings and determine whether more aggressive thyroid replacement can optimize thyroid function to facilitate clinical recovery. Declaration of Interest: Supported in part by National Institute of Mental Health Grants MH 029618 (Drs. Frank and Fagiolini) and MH 030915 (Drs. Kupfer and Fagiolini), and the Bosin Memorial Fund of The Pittsburgh Foundation (Drs. Fagiolini, Kupfer, Cook, Scott, Novick and Frank). Dr. Fagiolini is on the advisory board and a consultant to Pfizer Inc, and Bristol Myers Squibb, and is on the speaker bureau of Bristol Myers Squibb, Eli Lilly Italy, Pfizer Inc, and Shire. Dr. Frank is on the advisory board of Pfizer Inc. and Eli Lilly & Company, and is a consultant to Pfizer Italia and Sender Amerique. Dr. Kupfer is on the advisory board of Pfizer, Inc., Forest Pharmaceuticals, Inc., and Solvay-Wyeth Pharmaceuticals, and is a consultant to Servier Amerique.