Miracle-dz/UniFAR-FTUs huggingface dataset:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators’ overall experience of a system, regardless of the system’s high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV.
ANTIMICROBIAL ACTIVITIES OF LEAF EXTRACTS OF PISTACIA AND SCHINUS SPECIES AGAINST SOME PLANT PATHOGENIC FUNGI AND BACTERIA

Leaf extracts of Pistacia vera, Pistacia atlantica, Schinus terebenthifolius and Schinus molle were investigated for their antimicrobial effect against Agrobacterium tumefaciens, Pseudomonas savastanoi pv. savastanoi, Fusarium solani and Rhizoctonia solani. Extracts were prepared from dried and powdered leaves with solvents (hexane, ethanol, methanol and water) with different degrees of polarity. Aqueous and methanolic extracts exhibited a high level of antifungal and antibacterial activity. Leaf extracts from P. atlantica showed a high level of antibacterial activity. However, leaf extracts from Schinus terebenthifolius and Schinus molle showed the best antifungal activities. Total polyphenol contents of extracts was positively correlated with the diameter of the inhibition zones suggesting their potential antimicrobial activity. A preliminary phytochemical screening revealed the presence of tannins, flavanoids and alcaloids. These findings suggest that leaves of Pistacia and Schinus spp. are potential sources of antimicrobial compounds.
Cathepsin B, D, and L regulation in cyclosporin A-mediated gingival hyperplasia of a patient with sarcoidosis.

BACKGROUND Cyclosporin A (CsA) is an immunosuppressant with side effects including gingival hyperplasia. Sarcoidosis is a systemic disease characterized by granulomas. Here, we report on a rare case of sarcoidosis with gingival hyperplasia to clarify whether clinical observation corresponds to in vitro results. METHODS Gingival fibroblasts (HGFs) were isolated from healthy gingiva and cultured with CsA. Total RNA was collected and expression of mRNAs examined using semi-quantitative RT-PCR analysis. Cathepsin B, D, and L expression in overgrown gingiva of the patient was examined by immunohistochemistry. RESULTS Cathepsin D, L, and vascular endothelial growth factor (VEGF)165 mRNA were markedly suppressed in CsA-treated HGFs, whereas cathepsin B, matrix metalloproteinase-1 (MMP-1) and tissue inhibitor of metalloproteinase-1 (TIMP-1) mRNA were not reduced. Next, the decrease of cathepsin B and L expression in enlarged gingiva was observed, whereas an increase of cathepsin D expression was observed. Clinically, the enlarged gingival lesions were fully resolved by performing oral infection control. CONCLUSIONS Cathepsins regulation might be an important factor in the development of CsA-mediated gingival hyperplasia.
The Question of Phonology and Reading

of the word is not entirely familiar and requires effortful decoding. First the child says /i . i/, then /iz/, then /land/, then /iz land/, and all of a sudden she gets it right: she correctly reads island aloud. English is notorious for words like island, with spellings that only partly reveal how they are spoken. Nonetheless, the way a word is spelled almost always reveals something of how to say it aloud, something of its phonology. This fact illustrates the alphabetic principle, which has long lead scientists to wonder about the role of phonology in reading. For instance, does a printed word’s phonology play a role in deriving meaning from the word? A central question of reading is whether understanding individual written words always depends upon prior access to their phonology: Do mental representations of phonology mediate the comprehension of written words? This question is based on the idea that reading can be taken apart as the links of a chain of mental events. Think again of the 6-year-old child and the word island. Reading island aloud, the effect, seems to depend on an intermediate representation of island’s phonology, its cause. Presented with the visual stimulus island, the child’s mind first forms a representation of the word’s spelling. The spelling representation will be decoded, or puzzled out, to create a representation of phonology. In turn, the mental representation of island ’s phonology activates the motor program of its pronunciation, and the child says island aloud. The child portrayed as reading island aloud illustrates the classic view of stimulus Æ mediating representations Æ response: the idea of a causal chain between the stimulus word island and its pronunciation. It is from this vantage point that the question of phonology and reading is posed. Both the printed word island and island ’s pronunciation appear in some sense to be outside the child’s head, but she constructs phonology inside her head. Phonology is intermediate, both in the sense of a middle position in time or space and in the sense of a mental causal link between the printed word and its pronunciation (cf. Fodor, 1981; Kihlstrom, 1987; Markman & Dietrich, 2000). 4
Anti‐malarial drug resistance, malnutrition and socio‐economic status

To investigate the relationship between nutritional status and resistance to chloroquine treatment, we designed a nested case‐control study prospective with respect to the outcome of Plasmodium falciparum‐infected school children aged 5–14 years from Honiara, Solomon Islands. 38 chloroquine‐resistant cases were compared with treatment‐susceptible controls with respect to current nutritional status, behavioural characteristics, medical and demographic data. The overall prevalence of moderate malnutrition was 28%. The incidence rate of chloroquine resistance was 23%. Malnourished children were generally at higher risk for treatment failure than well‐nourished ones (OR: 3.6; 95%CI: 1.6–8.4; P= 0.001). This effect was modified by socio‐economic status. Stratified analysis by logistic regression resulted in an eightfold risk of resistance for malnourished children in the higher socio‐economic category (OR:8.1; 95%CI: 2.4–27.9; P= 0.0001). In children from the lower socio‐economic group, the effect of malnutrition was not significant (OR:1.5; 95%CI:0.4–5.6). Socio‐economic differences may affect the immune status. The treatment response in children of lower socio‐economic status, which are more exposed to malaria, may therefore be less affected by malnutrition.
Application of fuzzy tree on chaotic time series prediction

In this paper, adaptive-tree-structure-based fuzzy model is applied to predict chaotic time series. The fuzzy partition of input data set is adaptive to the pattern of data distribution to optimize the number of the subsets automatically by binary-tree model. A fuzzy area around every discriminant edge is set up by the membership functions corresponding to every subset of input data. A complex nonlinear function is obtained by piecewise linear approximation and smoothing the discontinuous at the discriminant edges of subsets to reduce the error of approximation. The fuzzy tree model is evaluated using prediction of the Mackey-Glass chaotic time series. In comparison with some existing methods, it is shown that the FT is also of less computation and higher accuracy.
Threshold voltage instability in organic TFT with SiO2 and SiO2/parylene-stack dielectrics

We study the charge trapping/detrapping kinetics on pentacene-based organic thin-film-transistors featuring SiO2 and SiO2/parylene C stack gate insulators. The threshold voltage variation is correlated with the gate pulse width and amplitude, and it is due to charge trapping, rather than permanent degradation. The detrapping kinetics is thermally-activated and it is accelerated if the device is illuminated. The additional parylene layer brings benefits by strongly reducing the charge trapping/detrapping, and increasing the hole mobility and the drain current.
Huntingtin Aggregation Kinetics and Their Pathological Role in a Drosophila Huntington’s Disease Model

Huntington’s disease is a neurodegenerative disorder resulting from expansion of a polyglutamine tract in the Huntingtin protein. Mutant Huntingtin forms intracellular aggregates within neurons, although it is unclear whether aggregates or more soluble forms of the protein represent the pathogenic species. To examine the link between aggregation and neurodegeneration, we generated Drosophila melanogaster transgenic strains expressing fluorescently tagged human huntingtin encoding pathogenic (Q138) or nonpathogenic (Q15) proteins, allowing in vivo imaging of Huntingtin expression and aggregation in live animals. Neuronal expression of pathogenic Huntingtin leads to pharate adult lethality, accompanied by formation of large aggregates within the cytoplasm of neuronal cell bodies and neurites. Live imaging and Fluorescence Recovery After Photobleaching (FRAP) analysis of pathogenic Huntingtin demonstrated that new aggregates can form in neurons within 12 hr, while preexisting aggregates rapidly accumulate new Huntingtin protein within minutes. To examine the role of aggregates in pathology, we conducted haplo-insufficiency suppressor screens for Huntingtin-Q138 aggregation or Huntingtin-Q138–induced lethality, using deficiencies covering ∼80% of the Drosophila genome. We identified two classes of interacting suppressors in our screen: those that rescue viability while decreasing Huntingtin expression and aggregation and those that rescue viability without disrupting Huntingtin aggregation. The most robust suppressors reduced both soluble and aggregated Huntingtin levels, suggesting toxicity is likely to be associated with both forms of the mutant protein in Huntington’s disease.
Structural Basis for the Immunomodulatory Function of Cysteine Protease Inhibitor from Human Roundworm Ascaris lumbricoides

Immunosuppression associated with infections of nematode parasites has been documented. Cysteine protease inhibitor (CPI) released by the nematode parasites is identified as one of the major modulators of host immune response. In this report, we demonstrated that the recombinant CPI protein of Ascaris lumbricoides (Al-CPI) strongly inhibited the activities of cathepsin L, C, S, and showed weaker effect to cathepsin B. Crystal structure of Al-CPI was determined to 2.1 Å resolution. Two segments of Al-CPI, loop 1 and loop 2, were proposed as the key structure motifs responsible for Al-CPI binding with proteases and its inhibitory activity. Mutations at loop 1 and loop 2 abrogated the protease inhibition activity to various extents. These results provide the molecular insight into the interaction between the nematode parasite and its host and will facilitate the development of anthelmintic agents or design of anti-autoimmune disease drugs.
Neuronal responses support a role for orbitofrontal cortex in cognitive set reconfiguration

We are often faced with the need to abandon no-longer beneficial rules and adopt new ones. This process, known as cognitive set reconfiguration, is a hallmark of executive control. Although cognitive functions like reconfiguration are most often associated with dorsal prefrontal structures, recent evidence suggests that the orbitofrontal cortex (OFC) may play an important role as well. We recorded activity of OFC neurons while rhesus macaques performed a version of the Wisconsin Card Sorting Task that involved a trial-and-error stage. OFC neurons demonstrated two types of switch-related activity, an early (switch-away) signal and a late (switch-to) signal, when the new task set was established. We also found a pattern of match modulation: a significant change in activity for the stimulus that matched the current rule (and would therefore be selected). These results extend our understanding of the executive functions of the OFC. They also allow us to directly compare OFC with complementary datasets we previously collected in ventral (VS) and dorsal (DS) striatum. Although both effects are observed in all three areas, the timing of responses aligns OFC more closely with DS than with VS.
Serial Changes in Complete Blood Counts in Patients with Leptospirosis: Our Experience.

INTRODUCTION Leptospirosis is an infectious disease caused by Leptospira interrogans. It is endemic in many parts of the world. The symptoms vary between milder forms to severe type with organ dysfunction. The disease presents with diagnostic challenge as it clinically mimics acute febrile illness due to other causes. AIM To study serial changes in complete blood counts in patients with leptospirosis. MATERIALS AND METHODS A retrospectively collected data was prospectively studied for clinical and laboratory data of leptospirosis patients proven by raised IgM titres by ELISA on day 2 (counted from day of admission of patient to hospital) of unexplained fever. The changes in complete blood counts from admission upto the discharge of the patient were studied. SPSS version 13 (SPSS Inc. Chicago) was used for data analysis. The collected data was analysed using frequency, percentage, mean, median, standard deviation and Mann-Whitney test. A p-value less than 0.05 were considered significant. RESULTS Mean haemoglobin concentration showed a progressive decline (<12.5 gm/dl) from day 1 to day 7 in both mild and severe disease. Platelet counts were significantly low (p=0.002), (<1,50,000 cells/mm3) in severe disease and showed a declining trend as compared to mild disease. Total leukocyte counts were significantly higher (p=0.001), (>11,000 cells/m3) in patients with severe disease from day 4 to day 5 of the illness. CONCLUSION Complete blood count is a routine test done in the monitoring of patients with leptospirosis. Declining haemoglobin, marked thrombocytopenia and a normal to high total leukocyte count will help in early detection of severe disease and thus preventing mortality by timely management.
AN INVITATION TO MARKET-BASED OPTION PRICING AND ITS APPLICATIONS( the 50th Anniversary of the Operations Research Society of Japan)

This article provides an overview of market-based option pricing and its applications. First, two fundamental approaches for market-based option pricing from the literature are introduced. Then, three important new processes, the deterministic volatility model, the stochastic volatility model, and a model including jump, are discussed. Finally, several empirical analyses on the NIKKEI225 option market are provided as examples.
Health-related quality of life in children with heart failure as perceived by children and parents

Advancements in paediatric heart failure management have resulted in improved survival and a focus on long-term outcomes including health-related quality of life. We compared health-related quality of life in children with heart failure with healthy patients, children with chronic conditions, and children with cardiovascular disease. Families (n=63) and children (n=73) aged 2–20 years with heart failure were enrolled and compared with data previously published for healthy patients (n=5480), those with chronic conditions (n=247), and those with cardiovascular disease (n=347). Patients and parents completed the PedsQL 4.0 and the Cardiac 3.0 Module health-related quality-of-life questionnaires. PedsQL scores including Total, Psychosocial Health Summary, and Physical were compared between groups. In general, patients with heart failure had lower scores than the healthy population (p=0.001), and comparable scores with those with chronic conditions. Parents perceived no difference in physical scores for children with heart failure when compared with healthy children, and perceived higher scores for children with heart failure when compared with those with chronic conditions (p⩽0.003). Furthermore, children with heart failure had decremental health-related quality-of-life scores as the American Heart Association stage of heart failure increased, such that patients with stage C heart failure had scores similar to children with severe cardiovascular disease. Children with heart failure reported significantly impaired health-related quality of life compared with healthy children and similar scores compared with children with chronic conditions. Parental perceptions appear to underestimate these impairments. Children with heart failure appear to have progressive impairment of health-related quality of life with advancing stage of heart failure.
Professional recognition: promoting recognition through the Higher Education Academy in a UK higher education institution

This study is on how one higher education institution included the United Kingdom Professional Standards Framework, developed by the Higher Education Academy, as a strategic benchmark for teaching and learning. The article outlines the strategies used to engage all academic (and academic-related) staff in achieving relevant professional recognition under the framework and highlights the need for such a project to be driven by visible and consistent commitment from senior management. A survey of participants highlights the benefits to be gained by entrants to the profession from participation in an accredited course, and by more established professionals from the individual entry route. While a significant proportion of participants expressed scepticism about the benefits of work towards recognition, findings indicate a significant degree of peer development underpinning activities which enhanced individual and group confidence, supported developing practice on an ongoing basis and were believed to be relevant to students and other stakeholders.
Sequential release of cytokines, lipid mediators and nitric oxide in experimental colitis

The object of this study was to establish whether different pro- and anti-inflammatory mediators were formed in colonic tissue from experimental colitis depending on the course of the disease. Concentrations of mediators of inflammation were examined in colonic tissue in dextran induced colitis in mice. Initial inflammation was produced by 5 days treatment of 10% dextran sodium sulfate (DSS) in drinking water, followed by a further 9 day period of 2% DSS in an attempt to produce a milder chronic inflammation. The degree of inflammation was scored by a standardized macroscopic and histological examination. Initially, a 60% maximum inflammation score was observed at day 4. At this time inflammation was associated with the release of interleukin-lβ (IL-1β) and tumour necrosis factor-α (TNFα), whereas both prostaglandins 6kPGF1α and PGE2 and nitric oxide (NO) markedly decreased. Then a 25% inflammation score was reached which coincided with an increased production of platelet-activating factor (PAF). No significant changes were observed in leukotriene B4 and C4 formation. In conclusion, pro-inflammatory cytokines IL-1β and TNFα are considered to be primary mediators, whereas PAF, eicosanoids and NO may reflect secondary mediators in experimental colitis.
Parenthood and Productivity of Highly Skilled Labor: Evidence from the Groves of Academe

We examine the effect of parenthood on the research productivity of academic economists. Combining the survey responses of nearly 10,000 economists with their publication records as documented in their RePEc accounts, we do not find that motherhood is associated with low research productivity. Nor do we find a statistically significant unconditional effect of a first child on research productivity. Conditional difference-in-differences estimates, however, suggest that the effect of parenthood on research productivity is negative for unmarried women and positive for untenured men. Moreover, becoming a mother before 30 years of age appears to have a detrimental effect on research productivity.
Daily expression of two circadian clock genes in compound eyes of Helicoverpa armigera: evidence for peripheral tissue circadian timing

Circadian clock genes in peripheral tissues usually play an important role in regulating the circadian rhythms. Light is the most important environmental signal for synchronizing endogenous rhythms with the daily light‐dark cycle, and compound eyes are known as the principal circadian photoreceptor for photic entrainment in most moths. However, there is little evidence for circadian timing in compound eyes. In the current study, we isolated the timeless gene, designated Ha‐tim (GenBank accession number: KM233162), from the cotton bollworm Helicoverpa armigera. Ha‐tim and period (Ha‐per) showed low messenger RNA levels in the compound eyes compared to the other tested adult organs. Ha‐tim and Ha‐per transcript levels were dependent on an endogenous rhythm that fluctuated over a daily cycle in the compound eyes and heads. The cycles of Ha‐tim and Ha‐per transcript levels followed similar time courses, and identical expression patterns of the two genes were observed in the compound eyes and heads. Ha‐tim and Ha‐per were down‐regulated in the compound eyes after light exposure, copulation and starvation. These results indicated that Ha‐tim and Ha‐per transcript levels were regulated by endogenous and exogenous factors. Our study helped to improve our understanding of the circadian clock machinery in compound eyes and other peripheral tissues.