Deep Learning Predicts Rapid Over-softening and Shelf Life in Persimmon Fruits

In contrast to the progress in the research on physiological disorders relating to shelf life in fruit crops, it has been difficult to non-destructively predict their occurrence. Recent high-tech instruments have gradually enabled non-destructive predictions for various disorders in some crops, while there are still issues in terms of efficiency and costs. Here, we propose application of a deep neural network (or simply deep learning) to simple RGB images to predict a severe fruit disorder in persimmon, rapid over-softening. With 1,080 RGB images of ‘Soshu’ persimmon fruits, three convolutional neural networks (CNN) were examined to predict rapid over-softened fruits with a binary classification and the date to fruit softening. All of the examined CNN models worked successfully for binary classification of the rapid over-softened fruits and the controls with > 80% accuracy using multiple criteria. Furthermore, the prediction values (or confidence) in the binary classification were correlated to the date to fruit softening. Although the features for classification by deep learning have been thought to be in a black box by conventional standards, recent feature visualization methods (or “explainable” deep learning) has allowed identification of the relevant regions in the original images. We applied Grad-CAM, Guided backpropagation, and layer-wise relevance propagation (LRP), to find early symptoms for CNNs classification of rapid over-softened fruits. The focus on the relevant regions tended to be on color unevenness on the surface of the fruit, especially in the peripheral regions. These results suggest that deep learning frameworks could potentially provide new insights into early physiological symptoms of which researchers are unaware

How to Perform Reproducible Experiments in the ELLIOT Recommendation Framework: Data Processing, Model Selection, and Performance Evaluation

Recommender Systems have shown to be an efective way to alleviate the over-choice problem and provide accurate and tailored recommendations. However, the impressive number of proposed recommendation algorithms, splitting strategies, evaluation protocols, metrics, and tasks, has made rigorous experimental evaluation particularly challenging. ELLIOT is a comprehensive recommendation framework that aims to run and reproduce an entire experimental pipeline by processing a simple confguration fle. The framework loads, flters, and splits the data considering a vast set of strategies. Then, it optimizes hyperparameters for several recommendation algorithms, selects the best models, compares them with the baselines, computes metrics spanning from accuracy to beyond-accuracy, bias, and fairness, and conducts statistical analysis. The aim is to provide researchers a tool to ease all the experimental evaluation phases (and make them reproducible), from data reading to results collection. ELLIOT is freely available on GitHub at https://github.com/sisinflab/ellio

Immunoregulatory gene polymorphisms in women with preeclampsia

The costimulatory molecules CD28, cytotoxic T-lymphocyte antigen-4 (CTLA-4) (cytotoxic T-lymphocyte-associated antigen-4) and inducible costimulator (ICOS) are believed to have a critical modulatory role in the immune response. However, few studies have been performed on the role of these immune regulatory molecules and their polymorphisms in women with preeclampsia (PE). the aim of our study was to evaluate the CTLA4 (+49 A/G) (rs 231775), CD28 (+17 T/C) (rs 3116496) and ICOS (-1564 T/C) (rs 4675378) gene polymorphisms in Brazilian women with PE. This case-control study included 130 patients with PE and 261 control women without any obstetric or systemic disorders. Genomic DNA was extracted from peripheral blood, and the polymorphism genotyping was performed by digesting the PCR products with the restriction endonucleases BbvI (CTLA-4), Afel (CD28) and AluI (ICOS). Data were analyzed by X(2) or Fisher's exact test; a P-value of < 0.05 was considered as significant. There were significant differences in the ICOS genotype and allelic frequencies between the PE and control groups (P=0.01 and P=0.01, respectively). We found a significantly lower frequency of the ICOS (-1564) T allele in women with mild PE compared with the controls. There were no differences in the CTLA-4 (+49 A/G) and CD28 (+17 T/C) genotypes and allelic frequencies between the PE patients and controls. Our data suggest that PE is associated with ICOS, but is not associated with the CTLA-4 or CD28 gene polymorphisms. Hypertension Research (2011) 34, 384-388; doi:10.1038/hr.2010.247; published online 16 December 2010Fundacao de Amparo a PesquisaCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Federal de São Paulo, Dept Obstet, BR-01415002 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Obstet, BR-01415002 São Paulo, BrazilFundacao de Amparo a Pesquisa: 07/57446-0Web of Scienc

Polymorphism analysis of the CTLA-4 gene in paracoccidioidomycosis patients

The CTLA-4 protein is expressed in activated T cells and plays an essential role in the immune response through its regulatory effect on T cell activation. Polymorphisms of the CTLA-4 gene have been correlated with autoimmune, neoplastic and infectious illnesses. This work aimed to verify possible associations between single nucleotide polymorphisms (SNPs) in CTLA-4, -318C/T in the promoter and +49A/G in exon 1 and paracoccidioidomycosis (PCM) caused by Paracoccidioides brasiliensis. For this purpose, 66 chronic form PCM patients and 76 healthy controls had their allele, genotype and haplotype frequencies determined. The genetic admixture structure of the patients and controls was evaluated to eliminate ancestral bias. The comparison of frequencies indicated no significant differences between patients and controls that could link the SNPs to PCM. Groups were admixture matched with no difference observed in population ancestry inference, indicating that the absence of association between CTLA-4 polymorphisms and PCM could not be attributed to ancestral bias. This study showed that there was no association between the CTLA-4 SNPs -318 and +49 and the resistance or susceptibility to PCM

Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways

BACKGROUND: SCA28 is an autosomal dominant ataxia associated with AFG3L2 gene mutations. We performed a whole genome expression profiling using lymphoblastoid cell lines (LCLs) from four SCA28 patients and six unrelated healthy controls matched for sex and age. METHODS: Gene expression was evaluated with the Affymetrix GeneChip Human Genome U133A 2.0 Arrays and data were validated by real-time PCR. RESULTS: We found 66 genes whose expression was statistically different in SCA28 LCLs, 35 of which were up-regulated and 31 down-regulated. The differentially expressed genes were clustered in five functional categories: (1) regulation of cell proliferation; (2) regulation of programmed cell death; (3) response to oxidative stress; (4) cell adhesion, and (5) chemical homeostasis. To validate these data, we performed functional experiments that proved an impaired SCA28 LCLs growth compared to controls (p\u2009<\u20090.005), an increased number of cells in the G0/G1 phase (p\u2009<\u20090.001), and an increased mortality because of apoptosis (p\u2009<\u20090.05). We also showed that respiratory chain activity and reactive oxygen species levels was not altered, although lipid peroxidation in SCA28 LCLs was increased in basal conditions (p\u2009<\u20090.05). We did not detect mitochondrial DNA large deletions. An increase of TFAM, a crucial protein for mtDNA maintenance, and of DRP1, a key regulator of mitochondrial dynamic mechanism, suggested an alteration of fission/fusion pathways. CONCLUSIONS: Whole genome expression profiling, performed on SCA28 LCLs, allowed us to identify five altered functional categories that characterize the SCA28 LCLs phenotype, the first reported in human cells to our knowledge. \ua9 2013 Mancini et al.; licensee BioMed Central Ltd

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase&nbsp;1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation&nbsp;disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age&nbsp; 6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score&nbsp; 652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc&nbsp;= 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N&nbsp;= 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in&nbsp;Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in&nbsp;Asia&nbsp;and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Endoscopic and histopathologic changes of the oesophagus in cats with chronic gingivostomatitis: clinical study of 58 cases

Feline chronic gingivostomatitis (FCG) is a painful, debilitating disease that affects animals of both sexes, all breeds and all ages. Affected animals exhibit dysphagia, pain, salivation occasionally accompanied by bleeding, altered behavior, loss of weight, dull hair coat and aggressiveness. Anorexia is rarely noticed in cats with FCG.Gastroesophageal reflux disease is commonly encountered in human medicine, but is rarely reported in cats. Metaplasia (Barrett’s oesophagus) is also common among human patients with oesophagitis. Oesophageal diseases, including oesophagitis, are unusual among feline patients and oesophageal metaplasia is ever rarer.Oesophagitis was noticed in 98 % of the endoscopically examined cats with FCG. Microscopic inflammation was recorded in some specimens of macroscopically normal-appearing oesophageal mucosa. Interestingly, 5 oesophageal specimens obtained from these cats exhibited metaplasia. The intensity of the oesophageal inflammation did not correlate with the severity of oral inflammation, even though there was a tendency for more severe inflammation of the distal part of the oesophagus in chronicities larger than 6 months. Interestingly, none of the cats exhibited clinical signs of oesophageal disease regardless of the severity of oesophagitis. However, it is possible that signs of oesophagitis such as salivation could have been masked by the signs of FCG. Endoscopic re-examination of the oesophagus after FCG treatment revealed macroscopic healing of the mucosa in 2 cases. On the contrary, FCG relapse showed deterioration of oesopahgitis in one case which was endoscopically re-examined. It seems that oesophagitis in cats with FCG contributes to morbidity and potentially could predispose to neoplasia. Cats with FCG have a high incidence of asymptomatic oesophagitis, especially in the proximal and distal parts of the oesophagus.Fifty-seven FCG cats and 25 controls were tested for FCV. The majority of cats both with FCG (96,4 %) and controls (88 %), were found to be infected with FCV. It seems that the commonly used vaccines do not provide adequate protection against the virus. The viral load did not correlate with the severity of the oral inflammation. Improvement of the clinical signs of the disease coincided with a dramatic decline in the viral load, even though no specific antiviral therapy was undertaken. However, all cats remained chronic carriers. It seems that FCV does not play part in the pathophysiology of the disease, even though it might worsen the inflammation of the oral cavity.Concerning the blood parameters, FCG might be responsible for lower hematocrit in the affected cats. Additionally, animals with higher scores of oral inflammation tended to have lower ALB concentrations in their serum. Finally, when chronicity exceeded 6 months, higher Eos counts were noticed.Η Χρόνια Ουλοστοματίτιδα της Γάτας (ΧΟΓ) αποτελεί μια εμμένουσα και ιδιαίτερα επώδυνη πάθηση, η οποία χαρακτηρίζεται από φλεγμονή αποκλειστικά των μαλακών ιστών της στοματικής κοιλότητας. Η νόσος αφορά όλες τις ηλικίες, όλες τις φυλές και τα 2 φύλα. Οι προσβεβλημένες γάτες εκδηλώνουν έντονη δυσφαγία και πόνο, σιελόρροια συχνά συνοδευόμενη από αιμορραγία, αλλαγή της συμπεριφοράς τους, απώλεια σωματικού βάρους, κακή όψη τριχώματος και επιθετικότητα. Αληθής ανορεξία σπάνια παρατηρείται εξαιτίας της στοματίτιδας.Η οισοφαγίτιδα από παλινδρόμηση προσβάλλει μεγάλο ποσοστό ανθρώπων, ενώ δεν είναι λίγα τα περιστατικά που εξελίσσονται σε μεταπλασία (οισοφάγος Barrett). Οι παθήσεις του οισοφάγου έχουν επίπτωση στην ποιότητα ζωής των ασθενών και αυξάνουν τη θνησιμότητα στις περιπτώσεις που εξελίσσονται σε νεοπλασία. Στην κτηνιατρική βιβλιογραφία, δεν υπάρχουν εκτεταμένες αναφορές σχετικά με τις παθήσεις του οισοφάγου στη γάτα και ειδικότερα για την οισοφαγίτιδα, ενώ ακόμα λιγότερες περιγράφουν περιστατικά μεταπλασίας του οργάνου.Στην παρούσα διατριβή διαπιστώθηκε ότι το 98 % των γατών με ΧΟΓ εκδήλωναν οισοφαγίτιδα σε τουλάχιστον 1 από τα τριτημόρια του οισοφάγου. Κατά την μικροσκοπική εξέταση των ιστοτεμαχίων που λήφθηκαν από τον οισοφαγικό βλεννογόνο, διαπιστώθηκε διήθηση από φλεγμονικά κύτταρα σε ορισμένα ιστοτεμάχια με φυσιολογική μακροσκοπική εικόνα. Επιπλέον, από τη μελέτη των ιστοτεμαχίων που εξετάστηκαν, διαπιστώθηκε μεταπλασία σε 5 δείγματα. Η ένταση της οισοφαγίτιδας δε συσχετίστηκε με τη σοβαρότητα της φλεγμονής του στόματος, όμως, παρατηρήθηκε τάση για εντονότερη φλεγμονή στο οπίσθιο τριτημόριο του οισοφάγου, στα περιστατικά με χρονιότητα μεγαλύτερη από 6 μήνες. Επίσης, δεν παρατηρήθηκαν χαρακτηριστικά κλινικά συμπτώματα οισοφαγίτιδας, ακόμα και στα περιστατικά με σοβαρότερη φλεγμονή του οισοφάγου. Ωστόσο, είναι πιθανό ορισμένα από τα συμπτώματα της οισοφαγίτιδας όπως η σιελόρροια, να καλύπτονταν από τα κλινικά συμπτώματα της ΧΟΓ. Ιδιαίτερα ενδιαφέρον εύρημα της διατριβής, αποτελεί το γεγονός πως σε ένα περιστατικό με ΧΟΓ που υποτροπίασε, παρατηρήθηκε και υποτροπή της οισοφαγίτιδας. Αντίστοιχα, σε δύο περιστατικά στα οποία διαπιστώθηκε βελτίωση της κλινικής εικόνας της ΧΟΓ, διαπιστώθηκε και ενδοσκοπικά ότι δεν εμφανίζονταν αλλοιώσεις οισοφαγίτιδας. Η οισοφαγίτιδα ενδέχεται να επιδεινώνει την κλινική εικόνα των γατών με ΧΟΓ και να υποβαθμίζει το βιοτικό τους επίπεδο. Οι γάτες με ΧΟΓ έχουν αυξημένες πιθανότητες να πάσχουν από οισοφαγίτιδα στο πρόσθιο ή/και στο οπίσθιο τριτημόριο του οισοφάγου.Παράλληλα, 57 από τις γάτες με ΧΟΓ και 25 μάρτυρες ελέγχθηκαν για πιθανή μόλυνσή τους από τον FCV. To 96,4 % των γατών με ΧΟΓ και το 88 % των μαρτύρων διαπιστώθηκε ότι ήταν προσβεβλημένες από τον ιό. Τα ποσοστά προσβολής των γατών ήταν ιδιαίτερα υψηλά, ανεξαρτήτως ηλικίας, φυλής, φύλου και στοματικής υγείας. Ακόμη, η βαρύτητα της φλεγμονής των μαλακών ιστών της στοματικής κοιλότητας, δε συσχετίστηκε με το φορτίο του ιού. Σε μικρό αριθμό ζώων που επανεξετάστηκαν, η θεραπεία της ΧΟΓ (χωρίς να εμπεριέχεται σε αυτή κάποια αντιική θεραπεία) οδήγησε σε σημαντική μείωση του φορτίου του ιού στη στοματική κοιλότητα, όμως τα ζώα παρέμειναν χρόνιοι φορείς. Από τα ευρήματα συμπεραίνεται ότι, κατά πάσα πιθανότητα, ο ιός δεν ευθύνεται για την πρόκληση της ΧΟΓ, όμως, είναι πιθανό να επιβαρύνει τη φλεγμονή της στοματικής κοιλότητας.Όσον αφορά ορισμένες από τις παραμέτρους των αιματολογικών εξετάσεων, υπάρχουν ενδείξεις ότι η ΧΟΓ είναι πιθανό να συσχετίζεται με κάποιου βαθμού μείωση του αιματοκρίτη στις γάτες που πάσχουν. Επιπλέον, οι προσβεβλημένες γάτες με σοβαρότερη φλεγμονή στη στοματική κοιλότητα παρουσιάζουν τάση για χαμηλότερες τιμές λευκωματινών στον ορό του αίματος. Τέλος, στα περιστατικά με χρονιότητα μεγαλύτερη από 6 μήνες παρουσιάζεται τάση για αυξημένο αριθμό εωσινόφιλων στο περιφερικό αίμα

An Alternative to Carbon Additives : The Fabrication of Conductive Layers Enabled by Soluble Conducting Polymer Precursors – A Case Study for Organic Batteries

Utilizing organic redox-active materials as electrodes is a promising strategy to enable innovative battery designs with low environmental footprint during production, which can be hard to achieve with traditional inorganic materials. Most electrode compositions, organic or inorganic, require binders for adhesion and conducting additives to enable charge transfer through the electrode, in addition to the redox-active material. Depending on the redox-active material, many types and combinations of binders and conducting additives have been considered. We designed a conducting polymer (CP), with a soluble, trimeric unit based on 3,4-ethylenedioxythiophene (E) and 3,4-propylenedioxythiophene (P) as the repeat unit, acting as a combined binder and conducting additive. While CPs as additives have been explored earlier, in the current work, the use of a trimeric precursor enables solution processing together with the organic redox-active material. To evaluate this concept, the CP was blended with a redox polymer (RP), which contained a naphthoquinone (NQ) redox group at different ratios. The highest capacity for the total weight of the CP/RP electrode was 77 mAh/g at 1 C in the case of 30% EPE and 70% naphthoquinone-substituted poly(allylamine) (PNQ), which is 70% of the theoretical capacity given by the RP in the electrode. We further used this electrode in an aqueous battery, with a MnSO4 cathode. The battery displayed a voltage of 0.95 V, retaining 93% of the initial capacity even after 500 cycles at 1 C. The strategy of using a solution-processable CP precursor opens up for new organic battery designs and facile evaluation of RPs in such