Miracle-dz/UniFAR-FTUs huggingface dataset:
Left Ventricle Segmentation by Circular Shape Constrained Clustering Algorithm

This study presents a novel clustering algorithm for the automatic segmentation of the left ventricle (LV). A circular shape function is incorporated into the dissimilarity measure of the objective function of the well-known fuzzy c-means (FCM) clustering algorithm. In that way, the proposed circular shape constrained FCM (CS-FCM) algorithm integrates both intensity related feature and spatial shape information into the clustering procedure. As a result, pixels having similar intensity information but located in different regions (LV region and non-LV region) can be differentiated. A weighting parameter is introduced to adjust the weight of the spatial distance against the intensity feature, which increases the flexibility of the proposed CS-FCM algorithm. The experimental results on benchmark cardiac magnetic resonance (CMR) images show two obvious advantages of the proposed CS-FCM over the standard clustering algorithms: it successfully distinguishes the LV from other structures which have similar intensity as the LV. Also, it correctly segments the LV even when the papillary muscles are adjacent to or fall inside the LV region.
Influences of superheated steam roasting on changes in sugar , amino acid and flavor active components of cocoa bean ( Theobroma cacao ) Influences of superheated steam roasting of cocoa bean

BACKGROUND: Roasting is one of the important unit operations in the cocoa base industries that develop unique flavor in products. Cocoa beans were subjected to roast at different temperature and time using superheated steam. Influence of roasting temperature (150-250 C) and time (10-50 min) on sugars, free amino acids and volatile flavoring compounds were investigated. This article is protected by copyright. All rights reserved. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jsfa.8302 A cc ep te d A rti cl e RESULTS: The concentration of total reducing sugars was reduced up to 64.61, 77.22 and 82.52 % with increased roasting temperature at 150, 200 and 250 C for 50 min respectively. The hydrophobic amino acids were reduced up to 29.21, 36.41 and 48.87 % with increased roasting temperature at 150, 200 and 250 C for 50 min respectively. A number of Pyrazines, esters, aldehydes, alcohols, ketones, carboxyl acids and hydrocarbons were detected in all the samples at different concentration range. The most flavor active compound Pyrazines formations were the highest concentration (2.96 mg/kg) at 200 C for 10 min. CONCLUSION: The superheated steam roasting method achieves the optimum roasting condition within a short duration Therefore, the quality of cocoa beans can be improved using superheated steam during the roasting process.
Changes in the nutritional quality of five Mangifera species harvested in two-maturity stages Running title : Nutritional quality of five Mangifera species

This article is protected by copyright. All rights reserved. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jsfa.8377 A cc ep te d A rti cl e BACKGROUND: There are 69 species of edible Mangifera recognized in Southeast Asia. Most of these species have not been characterized for nutritional properties. Here we describe the nutritional quality of the pulp of several Mangifera species: Mangifera casturi, Mangifera lalijiwa, Mangifera odorata, Mangifera zeylanica and two cultivars of Mangifera indica ‘Tommy-Kent’ and ‘Tommy Atkins’ at two maturity stages. RESULTS: The results show that nutritional quality varied with the maturity stage and among the species. The immature pulp of all species had higher content of total dietary fiber, vitamin C, vitamin E, total soluble polyphenols and antioxidant capacity. In mature pulp, the protein, ash, fat, soluble carbohydrates and B vitamin values were higher in all species. The species with the best nutritional quality were in order from highest to lowest: Mangifera casturi, Mangifera odorata, M. zeylanica, Mangifera indica cultivars and Mangifera lalijiwa. CONCLUSION: The fruit pulp of three species had higher nutritional quality in two maturity stages, in comparison with Mangifera indica cultivars. These other Mangifera species can be nutritionally important in communities facing food insecurity, and have potential as emerging crops. The decline of these valuable species in their natural habitats is an increasing concern, and their nutritional properties justify greater efforts to protect them.
Burkholderia rhizosphaerae sp . nov . , isolated from forest soil 2 and rhizosphere soil

Abstract: Two strains, Y-12T and Y-47T, and a strain, WR43T were isolated from forest soil of a mountain and rhizosphere soil at Daejeon in Korea, respectively. All three strains grew between 10 and 55 °C (optimal growth at 28-30 °C), between pH 3.0 and 8.0 (optimal growth at pH 6.0) and at salinities of 0-4.0 % (w/v) NaCl, growing optimally with 0 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, three strains were found to belong to the genus Burkholderia, showing closest phylogenetic similarity to Burkholderia diazotrophica JPY461T (97.2-97.7 %) and inter-sequence similarities ranged from 98.0 % to 98.7 %. The predominant ubiquinone was Q-8 and the major fatty acids were C16:0 and C17:0 cyclo, and the DNA G + C content of novel isolates were 61.6 64.4 mol%. On the basis of polyphasic analysis from this study, the bacterial strains were distinguished from their phylogenetic neighbours by their chemotaxonomic properties and other biochemical characteristics. DNA-DNA relatedness among three novel strains and the closest neighbour strongly support the proposal that these strains represent novel species within the genus Burkholderia, for which the names Burkholderia humisilvae sp. nov. (type strain, Y-12T = KACC 17601T = NBRC 109933T = NCAIM B 02543T), Burkholderia solisilvae sp. nov. (type strain, Y47T = KACC 17602T = NBRC 109934T = NCAIM B 02539T) and Burkholderia rhizosphaerae sp. nov. (type strain, WR43T = KACC 17603T = NBRC 109935T = NCAIM B 02541T) are proposed.
Development of a carbohydrate-supplemental semidefined medium for the semiselective cultivation of Lactobacillus spp . Running Title : Semidefined medium for lactobacilli

The macronutrient and micronutrient compositions of traditional media used to cultivate Lactic Acid Bacteria are largely undefined, which precludes their use in many metabolic bioassays. In order to address this deficiency, we developed MS: a carbohydrate-supplemental semidefined medium with low-background coloration. MS was designed to support the semiselective cultivation of a wide-range of fastidious species belonging to the Lactobacillus clade of the Lactic Acid Bacteria. When supplemented with 100 mM D-Glucose, the MS medium stimulated the proliferation of 21 strains belonging to the Lactobacillus clade of the Lactic Acid Bacteria, including Pediococcus spp. and Lactobacillus spp. The MS medium supported biomass accumulation comparable to MRS, an undefined medium routinely used for the cultivation of lactobacilli. Interestingly, however, the novel MS medium exhibited greater semiselectivity against non-Lactic Acid Bacteria than MRS. Together, these results suggest that MS is an A cc ep te d A rt ic le This article is protected by copyright. All rights reserved. acceptable alternative to MRS for use in metabolic and phenotypic bioassays that use a colorimetric reporter system or would benefit from a semidefined nutrient composition.
SEXUAL DIMORPHISM IN PSEUDOPUS APODUS (REPTILIA: SAURIA: ANGUIDAE) FROM THE STEPPE CRIMEA

The current paper is focused on sexual dimorphism of a giant glass lizard, or sheltopusik, Pseudopus apodus apodus (Pallas, 1775) from its northernmost populations inhabiting the Crimea. In total, 72 P. apodus individuals (45 males and 27 females) were collected at the Kerch Peninsula during 2013–2017. To estimate the variability, 13 morphometric parameters and 18 indices characterizing the head and body proportions were used. It was found that males and females differed significantly by means of almost all parameters, except the body and tail sizes. Besides that, the differences by 10 ratios characterizing head proportions were revealed as well. However, a reliable determination of the lizard sex using linear sizes and/or ratios values seems to be impossible because of the strong overlap of the variability ranges in both sexes. At the same time, the use of the canonical discriminant analysis by the complex of morphometric parameters and by ratios has shown that the males and females in both datasets are classified correctly basing on the sex with an accuracy approximating 100%. The differences in the allometric growth of males and females partially define the sexual dimorphism of P. apodus on head size and shape. A sex-related differences in the development of at least one pair of parameters (head and snout lengths) were clearly evident, since isometry was established for males, while allometry ‒ for females. Moreover, the systems of correlation between the body and head parts differ in both sexes. Thus, male characterisitics correlate significanly, while the female ones were less toughly connected, and some pairs of parameters did not correlate at all.
Title : Ecology and identification of environmental fungi and metabolic processes involved in the biodeterioration of Brazilian soapstone historical monuments Running title : Brazilian historical monument biodeterioration

The present study aimed to evaluate the action of organic acids produced by the fungal population associated with the biodeterioration process of the Twelve Prophets of Aleijadinho, a set of soapstone sculptures in Congonhas, state of Minas Gerais, Brazil. For this, samples of fungi were obtained from the surface of each of the twelve outdoor stone sculptures that comprise the set of prophets. Identification of the colonizing filamentous fungi was performed by classical microbiology and molecular methods. Some species of filamentous fungi-dependent cultivation were detected, and the presence of species Aspergillus versicolor, Curvularia lunata, Epicoccum nigrum, Penicillium citrinum, and Pseudocercospora norchiensis indicated a connection with the excretion of organic acids. The acids produced by each of these fungal species were analyzed quantitatively by chromatographic methods, revealing potential biodeterioration by the action of acidic metabolites excreted in the stone. A cc ep te d A rt ic le This article is protected by copyright. All rights reserved.
Author ' s personal copy

The development of bio-electronic prostheses, hybrid human-electronics devices and bionic robots has been the aim of many researchers. Although neurophysiologic processes have been widely investigated and bio-electronics has developed rapidly, the dynamics of a biological neuronal network that receive sensory inputs, store and control information is not yet understood. Toward this end, we have taken an interdisciplinary approach to study the learning and response of biological neural networks to complex stimulation patterns. This paper describes the design, execution, and results of several experiments performed in order to investigate the behavior of complex interconnected structures found in biological neural networks. The experimental design consisted of biological human neurons stimulated by parallel signal patterns intended to simulate complex perceptions. The response patterns were analyzed with an innovative artificial neural network (ANN), called ITSOM (Inductive Tracing Self Organizing Map). This system allowed us to decode the complex neural responses from a mixture of different stimulations and learned memory patterns inherent in the cell colonies. In the experiment described in this work, neurons derived from human neural stem cells were connected to a robotic actuator through the ANN analyzer to demonstrate our ability to produce useful control from simulated perceptions stimulating the cells. Preliminary results showed that in vitro human neuron colonies can learn to reply selectively to different stimulation patterns and that response signals can effectively be decoded to operate a minirobot. Lastly the fascinating performance of the hybrid system is evaluated quantitatively and potential future work is discussed. © 2008 Elsevier Ireland Ltd. All rights reserved.
Title: Epidemiology and outcomes of primary sclerosing cholangitis with and without inflammatory bowel disease in an Australian cohort. Short title: Epidemiology and outcomes of PSC with and without IBD in Australia Authors

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/liv.13328 This article is protected by copyright. All rights reserved. Received Date : 09-Sep-2016 Revised Date : 05-Nov-2016 Accepted Date : 18-Nov-2016 Article type : Original Articles Editor : Espen Melum
Synergistetes bacteria have been detected in high numbers in subgingival plaque from patients with chronic periodontitis and from the root canals of teeth with endodontic infections (

The clinical manifestation of necrotizing ulcerative gingivitis (NUG) is distinct from that of common gingivitis in that it is characterized by local necrosis of the gingival tissues, rapid onset, pain and extensive bleeding. The phylum Synergistetes is a novel bacterial phylum consisting of Gramnegative anaerobes, with evidence of presence in biofilms associated with periodontal and endodontic infections. To date, the involvement of members of this phylum in NUG has not been investigated. This study aimed to evaluate the presence and levels of known human oral Synergistetes bacterial clusters in dental plaque from patients with NUG and compare them with those found in gingivitis. Marginal dental plaque samples from 21 NUG and 21 gingivitis patients were analysed quantitatively by fluorescent in situ hybridization and microscopy for members of two oral Synergistetes clusters (A and B) and for Jonquetella anthropi. Synergistetes cluster A bacteria were detected in all samples but at higher levels (9.4-fold) and proportions (2.5-fold) in NUG patients than in gingivitis patients. However, with regard to Synergistetes cluster B bacteria, there were no differences between NUG and gingivitis patients. J. anthropi was detected in only half of the samples and at lower levels than the other taxa. In conclusion, these data demonstrate that Synergistetes cluster A bacteria, but not cluster B bacteria or J. anthropi, are more strongly associated with NUG than with gingivitis.
The temporal dimension of visual attention models

This thesis explores methodologies for scanpath prediction on images using deep learning frameworks. As a preliminary step, we analyze the characteristics of the data provided by different datasets. We then explore the use of Convolutional Neural Networks (CNN) and Long-Short-Term-Memory (LSTM) newtworks for scanpath prediction. We observe that these models fail due to the high stochastic nature of the data. With the gained insight, we propose a novel time-aware visual saliency representation named Saliency Volume, that averages scanpaths over multiple observers. Next, we explore the SalNet network and adapt it for saliency volume prediction, and we find several ways of generating scanpaths from saliency volumes. Finally, we fine-tuned our model for scanpaht prediction on 360-degree images and successfully submitted it to the Salient360! Challenge from ICME. The source code and models are publicly available at https://github.com/massens/saliency-360salient-2017.
Aspergillus oryzae Running title : Regulation of CreA degradation in A . oryzae

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/mmi.14072 This article is protected by copyright. All rights reserved. PROF. KATSUYA GOMI (Orcid ID : 0000-0003-3463-8072)
Metabolic Expenditure in Pregnant Women Enrolled in a Randomized Study of Walking

Preeclampsia is a disorder that occurs in 5-8% of pregnancies. What begins as elevated blood pressure and proteinuria can threaten the lives of both mother and fetus in the absence of treatment. Although the specific cause of preeclampsia is unknown, maternal risk factors for developing the condition include obesity, preexisting high blood pressure, diabetes, and endothelial dysfunction, among others (Preeclampsia Foundation, 2013). Interventions that decrease the incidence of preeclampsia and remain appropriate for the physiologic changes in pregnancy and the well-being of the fetus are needed. The purpose of this study was to assess the self-reported physical activity of pregnant women who enrolled in a randomized trial of a walking intervention. Women (n=123) who were enrolled in the study entitled “Exercise Intervention to Reduce Recurrent Preeclampsia” (R01 NR05375) had a history of preeclampsia, were sedentary, and were motivated to enter an intervention to reduce the likelihood of the recurrence of preeclampsia. Informed consent was administered and the participating women were randomized, resulting in 61 women in the attention control group and 62 women in the walking intervention group. Participants were 28.6 ± 5.25 (mean ± SD) years of age and were enrolled in the study at an average gestational age of 15.96 ± 3.02 weeks. The racial distribution of the sample was 19.5% African-American and 79.7% Caucasian. Participants completed the Paffenbarger Physical Activity Questionnaire at three time points during their pregnancy to assess activity. Data were calculated as metabolic equivalents (METs), an expression of energy expenditure. Although both study groups has similar METs per 24 hours at each measurement, participants in the walking intervention did reduce light activity and increase higher levels of activity as compared to women in the attention control group. Key Terms: Preeclampsia, Paffenbarger, Metabolic Equivalents, Exercise, Pregnancy METABOLIC EXPENDITURE IN PREGNANT WOMEN 3
Genome-wide analysis of mechanosensitive channel of small conductance (MscS)-like gene family in common bean

Mechanosensitive (MS) ion channels are transmembrane proteins that open and close in response to mechanical forces produced by osmotic pressure, sound, touch and gravity. In plants, MS have an important role in different biological processes like gravity detection, maintenance of plastid shape and size, lateral root emergence, growth of pollen tube, and plant-pathogen interactions. In this study, homologous mechanosensitive channel of small conductance (MscS)-like gene family in common bean was identified. Nine Phaseolus vulgaris MscS-like (PvMSL) genes were found to be distributed on five chromosomes. A complete overview of PvMSL genes in common bean is presented, including gene structures, chromosome locations, phylogeny, protein motifs and expression pattern. Subcellular localization predictions of PvMSL family revealed their location to plasma and chloroplast membrane. Phylogenetic analysis of nine PvMSL proteins resulted in two main classes. The predicted gene structure, conserved motif, domain and presence of transmembrane regions in each PvMSL strongly supported their identity as members of MscS-like gene family. Four duplicate events of PvMSL genes were discovered in P. vulgaris chromosomes, and tandem and segmental duplication may cause the expansion of PvMSL genes. Furthermore, PvMSL genes displayed differential expression patterns in tissues and organs. This is the first step towards genome-wide analyses of MSL genes in common bean. Thus, the data obtained in this study provide resources to select candidate genes for future functional analyses that will help understand plant growth, development, and function of MSL gene family in P. vulgaris . Key words : Mechanosensitive, phylogenetic analysis, gene duplication, plant, in silico.
Comparison of acoustical and optical zooplankton measurements using an acoustic scattering model: A case study from the Arctic frontal zone

High−frequency acoustic measurements supplemented by a modern optical method, Laser Optical Plankton Counter (LOPC), allowed us to perform a comparative analysis through the application of a mathematical model. We have studied the correspon− dence between measured and modelled echoes from zooplankton aggregations consisted mainly of two Calanus species. Data were collected from the upper 50 m water layer within the hydrographical frontal zone on the West Spitsbergen Shelf. The application of a “high− −pass” model of sound scattering by fluid−like particles to the distribution of zooplankton sizes measured by LOPC resulted mostly in very good agreement between the measured (420 kHz BioSonics) and modelled values, except for cases with very low zooplankton abundance or with occurrence of stronger scatterers (e.g. macrozooplankton, fish). An acoustic model validated for the elastic parameters of zooplankton confirmed that particles smaller than 1 mm in diameter, although highly abundant, did not contribute significantly to the sound scattering process at a frequency of 420 kHz. The implementation of diverse com− plementary methods has great potential to obtain high spatial and temporal resolution in zooplankton distribution studies; however, their compatibility has to be tested first.
Dissolved zinc in the subarctic North Pacific and Bering Sea: Its distribution, speciation, and importance to primary producers

The eastern subarctic North Pacific, an area of high nutrients and low chlorophyll, has been studied with respect to the potential for iron to control primary production. The geochemistry of zinc, a critical micronutrient for diatoms, is less well characterized. Total zinc concentrations and zinc speciation were measured in near‐surface waters on transects across the subarctic North Pacific and across the Bering Sea. Total dissolved zinc concentrations in the near‐surface ranged from 0.10 nmol L−1 to 1.15 nmol L−1 with lowest concentrations in the eastern portions of both the North Pacific and Bering Sea. Dissolved zinc speciation was dominated by complexation to strong organic ligands whose concentration ranged from 1.1 to 3.6 nmol L−1 with conditional stability constants (K′ZnL/Zn′) ranging from 109.3 to 1011.0. The importance of zinc to primary producers was evaluated by comparison to phytoplankton pigment concentrations and by performing a shipboard incubation. Zinc concentrations were positively correlated with two pigments that are characteristic of diatoms. At one station in the North Pacific, the addition of 0.75 nmol L−1 zinc resulted in a doubling of chlorophyll after 4 days.