Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying the acoustic repertoire of a population: the vocalizations of free-ranging bottlenose dolphins in Fiordland, New Zealand.

Quantification of the vocal repertoire of a species is critical for subsequent analysis of signal functionality, geographical variation, social relevance, and transmission. While signal repertoires have been documented for numerous animal species, detailed descriptions for the cetaceans are rare. This study describes the vocalizations of free-ranging bottlenose dolphins resident to the waters of Fiordland, New Zealand. The field recordings presented in this paper were made using both audio band and broadband apparatus. Subsequent classification of vocalizations using multivariate parameters enabled a quantification of the entire vocal output of the focal animals. These results were used to propose a meaningful repertoire of signals employed by this species. A total of 12 individual signal types were described, comprising four broad structural classes: "tonal," "single bursts," "click bursts," and "repeat bursts. " The proposed repertoire will allow subsequent investigation into vocal behavior. It appears that the successful description of a species' repertoire is dependent on the use of appropriate recording systems, a high number of representative recordings with good signal-to-noise ratio, and subsequent validation of the original classification system.
Nucleolar colocalization of TAF1 and testis‐specific TAFs during Drosophila spermatogenesis

In Drosophila, testis‐specific TBP‐associated factors (tTAFs) predominantly localize to spermatocyte nucleoli and regulate the transcription of genes necessary for spermatocyte entry into meiosis. tTAFs are paralogs of generally expressed TAF subunits of transcription factor IID (TFIID). Our recent observation that the generally expressed TAF1 isoform TAF1‐2 is greatly enriched in testes prompted us to explore the functional relationship between general TAFs and tTAFs during spermatogenesis. Analysis by immunofluorescence microscopy revealed that among the general TFIID subunits examined (TATA‐box binding protein [TBP], TAF1, TAF4, TAF5, and TAF9), only TAF1 colocalized with the tTAF Mia in spermatocyte nucleoli. Nucleolar localization of TAF1, but not Mia, was disrupted in tTAF mutant flies, and TAF1 dissociated from DNA prior to Mia as spermatocytes entered meiosis. Taken together, our results suggest stepwise assembly of a testis‐specific TFIID complex (tTFIID) whereby a TAF1 isoform, presumably TAF1‐2, is recruited to a core subassembly of tTAFs in spermatocyte nucleoli. Developmental Dynamics 236:2836–2843, 2007. © 2007 Wiley‐Liss, Inc.
Identification of intermediates and enzymes involved in the early steps of artemisinin biosynthesis in Artemisia annua.

An important group of antimalarial drugs consists of the endoperoxide sesquiterpene lactone artemisinin and its derivatives. Only little is known about the biosynthesis of artemisinin in Artemisia annua L. , particularly about the early enzymatic steps between amorpha-4,11-diene and dihydroartemisinic acid. Analyses of the terpenoids from A. annua leaves and gland secretory cells revealed the presence of the oxygenated amorpha-4,11-diene derivatives artemisinic alcohol, dihydroartemisinic alcohol, artemisinic aldehyde, dihydroartemisinic aldehyde and dihydroartemisinic acid. We also demonstrated the presence of a number of biosynthetic enzymes such as the amorpha-4,11-diene synthase and the--so far unknown--amorpha-4,11-diene hydroxylase as well as artemisinic alcohol and dihydroartemisinic aldehyde dehydrogenase activities in both leaves and glandular trichomes. From these results, we hypothesise that the early steps in artemisinin biosynthesis involve amorpha-4,11-diene hydroxylation to artemisinic alcohol, followed by oxidation to artemisinic aldehyde, reduction of the C11-C13 double bond to dihydroartemisinic aldehyde and oxidation to dihydroartemisinic acid.
Lessons from Los Angeles: Self-Study on Teaching University Global Citizenship Education to Challenge Authoritarian Education, Neoliberal Globalization and Nationalist Populism

Humanity and our planet faces a number of growing interconnected problems as well as opportunities exacerbated by globalization(s), which demand new paradigms of teaching and learning. Despite criticisms, global citizenship education (GCE) has been offered as an attempt to assist policy makers and practitioners to address complex global problems through education. Filling a void on empirical research of teaching university GCE in the United States and guided by such questions as what should be the roles and responsibilities of universities in addressing global problems and how should teacher education programs incorporate pedagogies of GCE, the author offers preliminary findings from a qualitative self-study on teaching GCE to undergraduates in Los Angeles.Before exploring critical approaches to GCE, the author examines challenges of authoritarian education, neoliberal globalization and nationalist populism that GCE confronts. Moreover, the author illuminates pedagogical themes of critical GCE that emerged from the research, and considers models of critical GCE and why they deserve more attention throughout US universities, specifically within teacher education programs and schools/departments of education.
The role of total body fat mass and trunk fat mass, combined with other endocrine factors, in menstrual recovery and psychopathology of adolescents with Anorexia Nervosa

Abstract Objective: To determine the threshold of total body and trunk fat mass required for menstrual recovery and to assess the impact of body composition in psychopathology of adolescents with Anorexia Nervosa (AN). Methods: Prospective study of 60 adolescents presented with secondary amenorrhea and diagnosed with AN. Anthropometrics, body composition by dual-energy X-ray absorptiometry, hormonal studies and responses to mental health screens (EAT-26), were obtained at the beginning and at complete weight restoration, in all adolescents, independently of menstrual recovery (Group A) or not (Group B). Results: At weight restoration, Group A total body fat mass, trunk fat mass, and trunk/extremities fat ratio were significantly higher (p < .001) than Group B. Menstruation was expected in 20% of total body fat mass and 20% of trunk fat mass (% of total trunk tissue). At time of menstrual recovery, total body fat mass (%) and trunk fat mass (%) were significantly negatively correlated with EAT-26 (r = −0.363, p = .032) and (r = −0.416, p = .013), respectively, while an increase of 0.40% of trunk fat mass (%) lowers EAT-26 by one unit. Discussion: Trunk fat mass distribution can positively influence psychopathology of adolescents with AN.
Neural network classification of EEG signals using time-frequency representation

This paper addresses the problem of classification of electroencephalogram (EEG) signals obtained from human subjects performing two mental tasks. One task named baseline involves relaxing and thinking of nothing in particular and the other task named multiplication involves mentally multiplying two 2-digit integers. First, the EEG signals are pre-processed using independent component analysis for removal of artifacts. Then, a time-frequency representation of the signals is generated, from which wavelet-based texture features are extracted for classification. The texture features are fed into a three-layer neural network classifier trained by the backpropagation algorithm. A classification rate of 96% is obtained for the dataset examined. The entire classification system has been implemented in the LabVIEW graphical programming environment providing a user-friendly interface to alter and monitor various parameters of the neural network classifier.
Partial 13C and 15N Chemical‐Shift Assignments of the Disulfide‐Bond‐Forming Enzyme DsbB by 3D Magic‐Angle Spinning NMR Spectroscopy

DsbB is a 20 kDa Escherichia coli inner‐membrane protein that catalyzes disulfide‐bond formation in periplasmic proteins. We report highly resolved, multidimensional magic‐angle spinning NMR spectra at 750 MHz 1H frequency, which enable partial 13C and 15N chemical‐shift assignments of the signals. The narrow line widths observed indicate excellent microscopic order of the protein sample, suitable for full structure determination by solid‐state NMR. Experiments were performed exclusively on uniformly 13C,15N‐labeled DsbB. Chemical‐shift‐correlation experiments based on dipolar transfer yielded strong signals in the 3D spectra, many of which have been site‐specifically assigned to the four transmembrane helices of DsbB. Significant numbers of additional residues have been assigned to stretches of amino acids, although not yet placed in the amino acid sequence. We also report the temperature dependence of signal intensities from −50 °C to 0 °C, a range over which samples of DsbB are highly stable. Structural and dynamic information derived from SSNMR studies can give insight into DsbB in a state that so far has not been successfully crystallized.
Preliminary description of biocidal (syringomycin) activity in fluorescent plant pathogenic Pseudomonas species

Strains representing the fluorescent plant pathogenic Pseudomonas spp. , Ps. agarici, Ps. asplenii, Ps. avellanae, Ps. beteli, Ps. caricapapayae, Ps. cichorii, Ps. corrugata, Ps. ficuserectae, Ps. flectens, Ps. fuscovaginae, Ps. marginalis, Ps. meliae, Ps. savastanoi, Ps. syringae, Ps. tolaasii and Ps. viridiflava were tested for biocidal activity using Aspergillus niger as assay organism. Inhibitory behaviour was found in strains of Ps. asplenii, Ps. blatchfordae, Ps. cichorii, Ps. corrugata, Ps. fuscovaginae, Ps. marginalis, Ps. marginalis pv. pastinacea, Ps. syringae pv. syringae, Ps. syringae pv. aptata, Ps. syringae pv. atrofaciens, Ps. syringae pv. lapsa, Ps. tolaasii, and strains of a Pseudomonas sp. pathogenic to Actinidia, in the Ps. savastanoi genomic sp. Antifungal activity could be identified with the production of members of the syringomycin family of toxins by strains in Ps. syringae, Ps. asplenii and Ps. fuscovaginae. These toxin reactions support suggestions made elsewhere of the synonymy of the latter two species. In a preliminary characterization using tests for stability to heat, protease, acid and alkaline treatments, unknown toxins consistent with syringomycin‐like toxins the strains from Actinidia speciesColour RGB 0,0,128. The toxins from Ps. cichorii and from Ps. corrugata differed in their reactions from all other agents. Pseudomonas tolaasii produces the antifungal compound tolaasin. The white line reaction with ‘Ps. reactans’, a test for tolaasin production by strains of Ps. tolaasii, was confirmed as specific for this compound. Some of these low molecular weight toxins may be produced by some of these plant pathogenic strains.
The significance of overweight and obesity for individual health behaviour: An economic analysis based on the Swedish surveys of living conditions 1980—81, 1988—89, and 1996—97

Aims: The aim of the study was to examine whether being overweight (25≤BMI<30) or obese (BMI≥30) affect subsequent individual health behaviour, applying the framework of the individual-as-producer-of-health model. Methods: A set of panel data for 3,693 individuals interviewed repeatedly in 1980—81, 1988—89, and 1996—97 was created from the Swedish population-based biannual survey of living conditions. Self-assessed health was chosen as indicator of individual health capital and physical exercise as indicator of individual health investment. Results: (a) Men and women who suffered from obesity invested significantly less in their health in terms of physical exercise and reported significantly lower self-assessed health than the general male and female population, respectively. (b) Men who suffered from overweight invested less in their health and reported significantly lower self-assessed health than the general population, whereas women who were overweight — but not obese — did not differ from the general population. (c) Men and women who went from being obese to being overweight reported self-assessed health levels that did not differ from the general male and female population, respectively, but exercised less than men and women in general. Conclusions: The results imply (a) that the individual weight history must be taken into account in studies of the effect of obesity and overweight on health and health-related behaviour and (b) that men and women differ concerning the impact of obesity and overweight on health and health investments.
Bayesian meta‐analysis and meta‐regression for gene–disease associations and deviations from Hardy–Weinberg equilibrium

Violation of Hardy–Weinberg equilibrium (HWE) can raise doubts about the validity of the conclusions from genetic association studies. However, for most currently performed gene–disease association studies, the available tests have low power to detect deviations from HWE. We consider this issue from a meta‐analysis perspective, and suggest an approach to estimate the deviation and investigate its relationship with the observed genetic effects. Different degrees of deviation from HWE have previously been proposed as a potential source of heterogeneity across studies. We present a hierarchical meta‐regression model that can be applied to test this assumption, using the concept of the fixation coefficient. We re‐analyse seven meta‐analyses to illustrate these methods. The uncertainty in the genetic effect estimate tended to increase once the fixation coefficient was taken into account. Dependence of the genetic effect size on the deviation from HWE was found in one meta‐analysis, while in the other six examples, deviations from HWE did not clearly explain between‐study heterogeneity in the genetic effects. The proposed hierarchical models allow the synthesis of data across gene–disease association studies with appropriate consideration of HWE issues. Copyright © 2006 John Wiley & Sons, Ltd.
Hybrid neural network topology (HNNT) for line outage contingency ranking

The line outage contingency was identified as one of the contributors to voltage instability problem. This event has led to significant financial losses in power system resulted from the failure in power operation and energy delivery. This paper presents a hybrid neural network topology (HNNT) for line outage contingency ranking. HNNT is a combination of artificial neural network (ANN) with a loading classifier and fundamental expert system modules. The post-outage severity was predicted by an ANN module trained using the Levenberg-Marquardt modified backpropagation. A line-based voltage stability index termed as fast voltage stability index (FVSI) was utilized as the indicator. Loading classifier distributed the post-outage severity into their respective loading condition. The contingency severities were consequently ranked into four categories using a rule-based module (RBM) that acts as the fundamental expert system. Validation was performed on the IEEE Reliability Test System (RTS) and results indicated that the proposed HNNT can be applied practically.
Fact or fiction? A longitudinal study of play and the development of reflective functioning.

In Fonagy and Target's (1996, 2000) developmental model of mentalization, play is theorized as a precursor of later mentalization and reflective function (RF); however, the relationship between play and later mentalization and RF has yet to be empirically tested. These processes are particularly important in the context of trauma, but an empirical model of the relationships among mentalization, play, and trauma is currently lacking. The aim of this longitudinal study was to examine whether children's capacity to engage in pretend play, to symbolize, and to make play narratives was associated with later RF in those children. Thirty-nine sexually abused children and 21 nonabused children (aged 3 to 8) participated in the study. The Children's Play Therapy Instrument was used to assess children's free play. Three years after the play assessment, children's RF was assessed using the Child Attachment Interview, coded with the Child and Adolescent Reflective Functioning Scale. Pretend play completion was associated with later other-understanding. Play was also found to mediate the relationship between sexual abuse and children's later mentalization regarding others. These findings are consistent with Fonagy and Target's emphasis on the role of pretend play in the development of a nuanced sense of the qualities of the mind and reality. In sum, the findings lend support to Fonagy and Target's account of playing with reality, and the development of mentalization suggests that it may be more than "fiction. " Furthermore, these results suggest that children's ability to create meaningful and coherent play sequences after sexual abuse is associated with the development of a better understanding of their relationships with others. Clinical implications and future directions are discussed.
Who is Paying the Bills? Health Care Costs for Musculoskeletal Back Disorders, Washington State Union Carpenters, 1989–2003

Objective: Factors associated with private health insurance payment rates for musculoskeletal back disorders were examined among a 15-year cohort of union carpenters. Payment patterns were contrasted with work-related back injury rates over time. Methods: Negative binomial regression was used to assess payment rates; generalized estimated equations accounted for multiple observations per person and cost correlation within subjects. Results: Payment rates increased after work-related injury and with the number of injuries. Increasing private payments and deductibles (inflation-adjusted and discounted) were observed in contrast with a marked decline in reported work-related injuries. Conclusions: Private insurance payments do not appear to be independent of work-related back injury. Findings suggest cost-shifting from workers’ compensation to the union-provided health insurance and to the worker; they also provide a warning regarding reliance on workers’ compensation statistics for surveillance of work-related disorders or disease.
Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue.

PURPOSE Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples. PATIENTS AND METHODS A gene signature was developed from a balanced set of 73 patients with recurrent disease (high risk) and 142 patients with no recurrence (low risk) within 5 years of surgery. RESULTS The 634-probe set signature identified high-risk patients with a hazard ratio (HR) of 2.62 (P < .001) during cross validation of the training set. In an independent validation set of 144 samples, the signature identified high-risk patients with an HR of 2.53 (P < .001) for recurrence and an HR of 2.21 (P = .0084) for cancer-related death. Additionally, the signature was shown to perform independently from known prognostic factors (P < .001). CONCLUSION This gene signature represents a novel prognostic biomarker for patients with stage II colon cancer that can be applied to FFPE tumor samples.
Prospective Investigation of Poultry and Fish Intake in Relation to Cancer Risk

Dietary guidelines advise consumers to limit intake of red meat and choose lean protein sources, such as poultry and fish. Poultry consumption has been steadily increasing in the United States, but the effect on cancer risk remains unclear. In a large U.S. cohort, we prospectively investigated poultry and fish intake and cancer risk across a range of malignancies in men and women. Diet was assessed at baseline (1995–1996) with a food frequency questionnaire in 492,186 participants of the NIH-AARP Diet and Health Study. Over a mean follow-up of 9 years, we identified 74,418 incident cancer cases. In multivariable Cox proportional hazards regression models, we estimated the substitution and addition effects of white meat (poultry and fish) intake in relation to cancer risk. In substitution models with total meat intake held constant, a 10-g (per 1,000 kcal) increase in white meat intake offset by an equal decrease in red meat intake was associated with a statistically significant reduced (3%–20%) risk of cancers of the esophagus, liver, colon, rectum, anus, lung, and pleura. In addition models with red meat intake held constant, poultry intake remained inversely associated with esophageal squamous cell carcinoma, liver cancer, and lung cancer, but we observed mixed findings for fish intake. As the dietary recommendations intend, the inverse association observed between white meat intake and cancer risk may be largely due to the substitution of red meat. Simply increasing fish or poultry intake, without reducing red meat intake, may be less beneficial for cancer prevention. Cancer Prev Res; 4(11); 1903–11. ©2011 AACR.
Supraspinal factors in human muscle fatigue: evidence for suboptimal output from the motor cortex.

1. Voluntary activation of elbow flexor muscles can be optimal during brief maximal voluntary contractions (MVCs), although central fatigue, a progressive decline in the ability to drive the muscle maximally, develops during sustained or repeated efforts. We stimulated the motor cortex and motor point in human subjects to investigate motor output during fatigue. 2. The increment in force (relative to the voluntary force) produced by stimulation of the motor point of biceps brachii increased during sustained isometric MVCs of the elbow flexors. Motoneuronal output became suboptimal during the contraction, i.e. central fatigue developed and accounted for a small but significant loss of maximal voluntary force. During 3 min MVCs, voluntary activation of biceps fell to an average of 90.7% from an average of > 99%. 3. The increment in force (relative to the voluntary force) produced by magnetic cortical stimulation was initially small (1.0%) but also increased during sustained MVCs to 9.8% (with a 2 min MVC). Thus, cortical output was not optimal at the time of stimulation nor were sites distal to the motor cortex already acting maximally. 4. A sphygmomanometer cuff around the upper arm blocked blood supply to brachioradialis near the end of a sustained MVC and throughout subsequent brief MVCs. Neither maximal voluntary force nor voluntary activation recovered during ischaemia after the sustained MVC. However, fatigue‐induced changes in EMG responses to magnetic cortical stimulation recovered rapidly despite maintained ischaemia. 5. In conclusion, during sustained MVCs, voluntary activation becomes less than optimal so that force can be increased by stimulation of the motor cortex or the motor nerve. Complex changes in excitability of the motor cortex also occur with fatigue, but can be dissociated from the impairment of voluntary activation. We argue that inadequate neural drive effectively ‘upstream’ of the motor cortex must be one site involved in the genesis of central fatigue.