Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Enhanced Exemplar-Based Clustering for Incomplete EEG Signals

The diagnosis and treatment of epilepsy is a significant direction for both machine learning and brain science. This paper newly proposes a fast enhanced exemplar-based clustering (FEEC) method for incomplete EEG signal. The algorithm first compresses the potential exemplar list and reduces the pairwise similarity matrix. By processing the most complete data in the first stage, FEEC then extends the few incomplete data into the exemplar list. A new compressed similarity matrix will be constructed and the scale of this matrix is greatly reduced. Finally, FEEC optimizes the new target function by the enhanced α-expansion move method. On the other hand, due to the pairwise relationship, FEEC also improves the generalization of this algorithm. In contrast to other exemplar-based models, the performance of the proposed clustering algorithm is comprehensively verified by the experiments on two datasets.
Nitric Oxide Stimulates Acute Pancreatitis Pain via Activating the NF-κB Signaling Pathway and Inhibiting the Kappa Opioid Receptor

Pain is the most important clinical feature of acute pancreatitis (AP); however, its specific mechanism is currently unclear. In this study, we showed that AP caused an increase in nitric oxide (NO) secretion, activated the NF-κB pathway in the dorsal root ganglia (DRGs), and caused pain. We established an AP model in vivo and tested the expression of NO, the kappa opioid receptor (KOR), and pain factors. We showed that NO in AP was significantly elevated and increased the expression of pain factors. Next, by treating DRGs in vitro, it was found that NO activated the NF-κB pathway; conversely, NF-κB had no effect on NO. Moreover, inhibition of NF-κB promoted the KOR, whereas NF-κB did not change after KOR activation. Finally, behavioral experiments showed that a NO donor increased the pain behavior of mice, while a NO scavenger, NF-κB inhibitor, or KOR agonist attenuated the pain response in mice. These results suggest that iNOS/NO/NF-κB/KOR may be a key mechanism of pain in AP, providing a theoretical basis for the use of peripheral-restricted KOR agonists for pain treatment in AP.
Dimorfismo sexual em Siluriformes e Gymnotiformes (Ostariophysi) da Amazônia

The present paper aims to summarize cases of sexual dimorphism in Siluriformes and Gymnotiformes. This summary focuses on Neotropical representatives, with emphasis on Amazonian fish. Fishes from this region exhibit high species-level diversity, although the intraspecific limits of many of these forms are unknown. In Loricariidae (Siluriformes), mapping of dimorphic traits on cladograms has helped to demonstrate that patterns of sex dimorphism are consistent with hypotheses of monophyly, thus reinforcing its role as an important evolutionary phenomenon. In Apteronotidae (Gymnotiformes), mapping of characters on phylogenetic trees suggests that sexual dimorphism (regarding snout size, form, and presence/absence of teeth) has evolved independently in multiple taxa. Recently in Gymnotiformes, detected taxonomic errors are attributed to extreme differences between males and females in their morphology.
The Analysis of PTPN6 for Bladder Cancer: An Exploratory Study Based on TCGA

PTPN6 (protein tyrosine phosphatase nonreceptor type 6), a tyrosine phosphatase, is known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. Previous studies have demonstrated that PTPN6 expression is relatively elevated in several malignancies. However, the role of PTPN6 in bladder cancer (BC) remains unclear. The purpose of this study was to explore the prognostic value of PTPN6 in BC. RNA-seq data from The Cancer Genome Atlas (TCGA) was used to identify the expression level of PTPN6 in BC. The relationship between clinical pathologic features and PTPN6 were analyzed with the Wilcoxon signed-rank test. The prognostic and predictive value of PTPN6 was evaluated by survival analysis and nomogram. Gene Set Enrichment Analysis (GSEA) was conducted to explore the potential molecular mechanisms of PTPN6 in BC. Finally, Tumor Immune Estimation Resource (TIMER) was applied to investigate the relationship between PTPN6 and immune cell infiltration in the tumor microenvironment. Results indicated that PTPN6 was overexpressed in BC tissues compared with normal bladder tissues and was significantly correlated with grade, stage, T, and N. Survival analysis showed that low expression of PTPN6 was significantly related to the poor overall survival (OS) in BC patients. Coexpression analysis showed that PTPN6 and TNFRSF14 (Tumor necrosis factor receptor superfamily member 14) have a close correlation in BC. GSEA showed that multiple cancer-associated signaling pathways are differentially enriched in the PTPN6 high expression phenotype. Moreover, the expression level of PTPN6 was positively associated with the infiltration of B cells, CD4+T cells, dendritic cells, and neutrophils and negatively associated with CD8+ T cells and macrophages in BC. In conclusion, we identified that PTPN6 may be a novel prognostic biomarker in BC based on the TCGA database. Further clinical trials are needed to confirm our observations and mechanisms underlying the prognostic value of PTPN6 in BC also deserve further experimental exploration.
M142. INCREASED VENTRAL STRIATAL FUNCTIONAL CONNECTIVITY IN PATIENTS WITH SCHIZOPHRENIA DURING REWARD ANTICIPATION

Abstract Background Recent studies have pointed at the ventral striatum as one of the main candidates underlying motivational dysfunctions in schizophrenia. Patients with negative symptoms show decreased BOLD activity in the ventral striatum and this activity strongly correlates with apathy scores during reward anticipation. While in patients with schizophrenia blunted ventral striatal activation during reward anticipation has been widely reported, little is known about abnormal striatal functional connectivity during reward anticipation. In this study, we performed generalized whole-brain psychophysiological interaction (gPPI) analyses using the right and left ventral striatum as seeds in schizophrenia patients with apathy and reduced ventral striatal activation from two published fMRI studies (Kirschner et al., 2016; Stepien et al., 2018). Methods Forty-four healthy controls (18 females, mean age = 31.1) and 40 patients with schizophrenia (10 females, mean age = 32.5) performed a variant of the Monetary Incentive Delay task within an fMRI design. Negative symptoms were assessed with the Brief Negative Symptoms Scale (BNSS). GPPI analyses were done using the PPPI toolbox on SPM 8. To examine potential difference in striatal functional connectivity, we performed two sample t-tests between patients with schizophrenia and healthy controls using the contrast [High Reward Anticipation – No Reward Anticipation]. Results Patients with schizophrenia showed increased functional connectivity between the right ventral striatum and the anterior cingulate cortex, posterior cingulate cortex, cerebellum, motor cortex, parietal cortex, temporo-parietal junction and thalamus compared to controls (cluster-level FDR p<0.05). No higher connectivity was found in controls compared to patients. For the regions with increased functional connectivity, we performed correlations between the patients’ gPPI signal and apathy. We found significant correlations between apathy and functional connectivity between the right ventral striatum and the right posterior cingulate cortex (r=0.40, p<.05) and right parietal cortex (r=0.39, p<.05). Discussion Our preliminary results indicate that physiological changes in the ventral striatum lead to dysfunctional connectivity with a cortex-wide network, affecting both cortico-striatal-thalamic-cortical and cortico-striatal-thalamic-cerebellar pathways. In addition, we show that some of these changes are related to apathy levels. This work provides novel insights in cortico-striatal network dysfunction during reward processing in patients with schizophrenia.
Starch in the Arabidopsis plant

The genetic and genomic resources available for the model plant Arabidopsis have allowed rapid progress in understanding the pathways of leaf starch synthesis and degradation. The pathway of starch synthesis is generally similar to that in other plants, but Arabidopsis research has permitted new insights into the mechanism of granule initiation. The pathway of starch degradation is very different from the ‘textbook’ version, largely derived from research on germinating cereal grains. The starch granule is attacked by β- rather than α-amylases, and this process is strongly dependent on a cycle of phosphorylation and dephosphorylation of the granule surface. The major product of granule degradation is maltose, which is exported to the cytosol where it is metabolised to hexose phosphate and then to sucrose. Cytosolic maltose metabolism requires a glucanotransferase and a glucosyl acceptor which is believed to be a complex heteroglycan. Plant productivity and yield are highly dependent on leaf starch turnover, and starch metabolism is coordinated with other factors and processes that determine growth rate. Research in Arabidopsis provides an important knowledge base for the study of starch metabolism in other, less tractable species.
An Analysis of the Anti-Neuropathic Effects of Qi She Pill Based on Network Pharmacology

Background Qi She Pill (QSP) is a traditional prescription for the treatment of neuropathic pain (NP) that is widely used in China. However, no network pharmacology studies of QSP in the treatment of NP have been conducted to date. Objective To verify the potential pharmacological effects of QSP on NP, its components were analyzed via target docking and network analysis, and network pharmacology methods were used to study the interactions of its components. Materials and Methods Information on pharmaceutically active compounds in QSP and gene information related to NP were obtained from public databases, and a compound-target network and protein-protein interaction network were constructed to study the mechanism of action of QSP in the treatment of NP. The mechanism of action of QSP in the treatment of NP was analyzed via Gene Ontology (GO) biological process annotation and Kyoto Gene and Genomics Encyclopedia (KEGG) pathway enrichment, and the drug-like component-target-pathway network was constructed. Results The compound-target network contained 60 compounds and 444 corresponding targets. The key active compounds included quercetin and beta-sitosterol. Key targets included PTGS2 and PTGS1. The protein-protein interaction network of the active ingredients of QSP in the treatment of NP featured 48 proteins, including DRD2, CHRM, β2-adrenergic receptor, HTR2A, and calcitonin gene-related peptide. In total, 53 GO entries, including 35 biological process items, 7 molecular function items, and 11 cell related items, were identified. In addition, eight relevant (KEGG) pathways were identified, including calcium, neuroactive ligand-receptor interaction, and cAMP signaling pathways. Conclusion Network pharmacology can help clarify the role and mechanism of QSP in the treatment of NP and provide a foundation for further research.
Immunohistochemical Studies of Insulin-Like Growth Factor-I in Corpora Lutea of Cycling and Pregnant Mice, Rats, Hamsters, Guinea Pigs and Cattle

Immunohistochemical staining of insulin-like growth factor-I (IGF-I) in the corpora lutea (CL) during estrous cycle and pregnancy was compared among mice, rats, hamsters, guinea pigs and cattle. During the estrous cycle, while clear staining was not detected in the hamster CL, the CL of the mouse, rat and guinea pig showed modest staining except for the mouse CL 1 day after ovulation which showed very weak staining. In contrast, immunoreactive IGF-I in the bovine CL showed distinct changes. While very weak staining was noted during the follicular and early luteal phases, the intensity increased markedly thereafter, peaking at the late luteal phase. During preg-nancy, the mouse and rat CL showed positive staining, and the intensity increased at late preg-nancy, especially in the rat CL intense focal staining was noted. In the hamster CL, clear positive staining was detected only at late pregnancy. In contrast, in the guinea-pig and bovine CL, al-though intense staining was detected during mid-pregnancy, the staining decreased at late preg-nancy. The results revealed species differences in the accumulation of immunoreactive IGF-I in CL.
Water management as a future necessity in sheep feedlots

Improving water management in rural towns such as Wagin, Western Australia, will decrease infrastructure damage caused by water and salinity and produce a ‘new water’ resource. The aim of this paper is to predict feedlot water demand using a bioeconomic model, H20Sheep, to determine if using such a ‘new water’ resource could be a viable option for this production system. Wagin (–33.3075 S, 117.3403 E), a township south-east of Perth, was chosen as the specific location for a sheep feedlot producing prime lambs. In this paper, the H20Sheep model was used to show how feedlot returns are influenced by the price of water, different feeding regimens and climate change. This was done by integrating feed and water intake of lambs, general feedlot water use and waste disposal. To show relative sensitivity of changing other model parameters that are not directly connected with water, changes in the purchase and sale price of lambs were also investigated. As might be expected, H20Sheep shows that returns from a sheep feedlot enterprise can be extremely sensitive to changes in lamb purchase (just over 7% increase will result in negative returns) and sale prices (a 4% decrease will generate a negative outcome). With respect to water, the findings indicate that, while increases in water use in the feedlot and price have to be greater than the increase in relative price of sheep, monitoring the biological parameters associated with water as well as water prices is still important both from a management and an economic perspective. Hence, if towns involved in the Rural Towns – Liquid Assets project, such as Wagin, decide to sell their water, the relevant policy makers should ensure that the sale price enables an effective water management system for the town and is also attractive to end-users such as feedlots.
Review of the Biocatalysis/Biodegradation Database (UM-BBD)

The University of Minnesota Biocatalysis/Biodegradation Database (Ellis et al., 2001) is an online compilation of microbial catabolic enzymes, reactions, and pathways for primarily synthetic organic chemical compounds. This database can be accessed free of charge at http:// umbbd.ahc. umn.edu/. As of January 2002, the database encompassed over 113 pathways containing 774 reactions, 696 compounds, and 476 enzymes present in over 306 microorganisms. This information is directly applicable toward enhancing the understanding of biocatalysis leading to specialty chemical manufacture and the biodegradation of environmental pollutants (Ellis et al., 1999). Catabolic routes for compounds having any of the 50 functional groups shown in Table 1 are provided. Unlike pathway databases such as EcoCyc (Karp et al., 2002a), MetaCyc (Karp et al., 2002b), and Kegg (Kanehisa et al., 2002), which focus primarily on intermediary metabolism, the UM-BBD is a key resource for biodegradation pathway information and is recently evolving to include the prediction of specialized catabolic routes for new compounds (Ellis et al., 2000).
Cecidogenetic Behavior of some gall-inducing thrips, psyllids, coccids, and gall midges, and morphogenesis of their galls

Abstract Several plant species, belonging to diverse and unrelated families of Angiospemae respond to insect action by developing a gall. Development of a gall is a complex phenomenon that involves subtle alterations initiated at critical and specific points of time during plant differentiation. Galls are truly modified plant tissues; however, galls arise as a sequel to insect attack only, ensuring a suite of adaptations to the inducing insect. Natural selection seems to favor those insects that are able to introduce a perturbation in the plant's growth and developmental process. Unlike the free-living insects, gall-inducing insects display an imperative demand of a particular plant species to complete their life-cycles; such a relationship includes specialized feeding and reproductive behaviors, high levels of specificity to host plants, and contribution to the dynamics of the evolution of the gall-inducing guild. Against this background, this review summarizes and analyzes morphogenesis of some galls induced by thrips, psyllids, coccids, and gall midges in the context of the behavior of the inducing agents, studied mostly from subtropical peninsular India. The review concludes with a comparative synthesis of the available information on insect-induced galls in general, and in the particular context of galls induced by thrips, psyllids, coccids, and gall midges from other biogeographical regions, and the biologies of those insects.
Comparison Between Two Different Levels of Replacement of Free-range Rearing by an Oleic Acid and-tocopherol Enriched Diet on the Quality of Fresh Meat from Iberian Duroc (50%) Pigs

The aim of this work was to study the effect of two types of pig feeding systems (known as recebo) on fatty acid composition, tocopherols contents and susceptibility to lipid oxidation in muscle. A total of 26 Iberian Duroc (50%) barrows were divided into two groups (named as short replacement (SR) and long replacement (LR) groups) according to length of replacement of free-range rearing (based on acorn and pasture) by an oleic acid and B-tocopherol (200 mg/kg) enriched concentrate feed (SR group: 67 days in free-range rearing and finished during 20 days with concentrate diet; LR: 55 days in free-range rearing, finished 50 days with concentrate). No differences were found in chemical composition and colour of Gluteo biceps muscle between the two management systems, except for B-tocopherol content, which showed higher content (p 0.001) in LR pigs than in SR pigs. The fatty acid composition of subcutaneous fat was slightly affected by feeding system. Total intramuscular and neutral lipids from Gluteo biceps muscle presented a higher proportion of C18: 1 n 9 (p 0.05) in SR than in LR pigs; however, no differences were found in total saturated (SFA), monounsaturated (MUFA) and polyunsaturated fatty acids (PUFA). Composition of polar lipids revealed a higher proportion of MUFA and lower of total n 3 fatty acids in LR than in SR pigs. Feeding regime significantly affected susceptibility of muscle to iron-ascorbate-induced peroxidation. Muscles from pigs reared on SR system showing higher levels (p 0.05) of MDA after 50 and 100 min of incubation. These results indicate that the content of oleic acid and tocopherol in muscle depends on the levels of both provided by dietary means, more than the practised handling.
Early development of Xenopus laevis : a laboratory manual

Preface Acknowledgements Chapter 1: Introduction Chapter 2: Morphology of Xenopus Embryos and Adults Chapter 3: Manipulating Gene Expression in Xenopus Chapter 4: Equipment for Embryo Experiments Chapter 5: Obtaining Embryos Chapter 6: Preparing Embryos for Manipulation Chapter 7: Embryo Perturbations Chapter 8: Microinjection Chapter 9: Fate Mapping and Lineage Labeling Chapter 10: Microdissection Chapter 11: Transgenesis in Xenopus Embryos Chapter 12: Immunocytochemistry Chapter 13: Whole-mount In situ Hybridization Chapter 14: Histology Appendix 1: Culture Media and Solutions Appendix 2: Timing of Development of Xenopus laevis Embryos and Temperature Dependence Appendix 3: Nucleic Acid Methods Appendix 4: Cautions Appendix 5: Suppliers Appendix 6: Trademarks Index
Island Loss for Improving the Classification of Facial Attributes with Transfer Learning on Deep Convolutional Neural Network

—Classification task on the human facial attribute is hard because of the similarities in between classes. For example, emotion classification and age estimation are two important applications. There are very little changes between the different emotions of a person and a different person has a different way of expressing the same emotion. Same for age classification. There is little difference between consecutive ages. Another problem is the image resolution. Small images contain less information and large image requires a large model and lots of data to train properly. To solve both of these problems this work proposes using transfer learning on a pre-trained model combining a custom loss function called Island Loss to reduce the intra-class variation and increase the inter-class variation. The experiments have shown impressive results on both of the application with this method and achieved higher accuracies compared to previous methods on several benchmark datasets.
Antioxidant and Angiotensin-Converting Enzyme Inhibitory Activities of Protein Hydrolysates Prepared from Threadfin Bream (Nemipterus spp.) Surimi By-products

Solid wastes from threadfin bream (Nemipterus spp.) surimi production composed of head and frame were hydrolyzed by various commercial proteases (Alcalase, Flavourzyme, Neutrase, Protamex, papain, and pepsin) to produce protein hydrolysates with bioactive properties. An Alcalase-hydrolyzed sample at 24.4% degree of hydrolysis (DH) displayed the highest antioxidant activity based on 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, ferric reducing antioxidant power (FRAP) assay, and potassium ferricyanide method. In addition, it showed an inhibitory activity toward angiotensin-converting enzyme (ACE) of 25.5%. Antioxidant activity of threadfin bream by-product hydrolysates increased with hydrolysis time and reached the highest DPPH activity after 6 h, while that hydrolyzed for 3 h showed the highest reducing power based on FRAP and potassium ferricyanide assays. In addition, ACE inhibitory activity was found to be at an optimum after 3 h of hydrolysis. The hydrolysates (1 mg/mL) also retarded oxidation of a linoleic acid emulsion system to a similar extent as 0.1 mg/mL 3-tert-butyl-4-hydroxy anisole (BHA), indicating a potential use in the food system. Protein hydrolysates from threadfin bream surimi by-products could be tailor-made to possess both antioxidant and ACE inhibitory activity through controlling DH of Alcalase-catalyzed reactions.
Sexual preferences of female zebra finches: imprinting on beak colour

Sexual preferences of adult zebra finches are influenced by early learning of parental characteristics. We studied how imprinting affects the preference of female zebra finches for male beak colour. The beaks of male and female parents were painted, 2-3 days before hatch and thereafter until the young were fledged, as follows: male red, female orange (R-O group); male orange, female red (O-R group); both male and female red (R-R group); or both male and female orange (O-O group). Females were raised by painted parents until 35 days, then visually isolated from other birds until test at 100 days. In 4-way choice tests using red- and orange-painted stimulus males, females from Groups O-R and R-O chose males with beaks painted the same colour as their father's beak, whereas females from Groups R-R and O-O did not. We conclude that preference for male beak colour was acquired only by females reared by parents with unlike, discriminative, beak colours. The results suggest an associative learning basis for sexual imprinting.