Miracle-dz/UniFAR-FTUs huggingface dataset:
A masquerade-like serine proteinase homologue is necessary for phenoloxidase activity in the coleopteran insect, Holotrichia diomphalia larvae.

Previously, we reported the molecular cloning of cDNA for the prophenoloxidase activating factor-I (PPAF-I) that encoded a member of the serine proteinase group with a disulfide-knotted motif at the N-terminus and a trypsin-like catalytic domain at the C-terminus [Lee, S.Y. , Cho, M.Y. , Hyun, J.H. , Lee, K.M. , Homma, K.I. , Natori, S. , Kawabata, S.I. , Iwanaga, S. & Lee, B.L. (1998) Eur. J. Biochem. 257, 615-621]. PPAF-I is directly involved in the activation of pro-phenoloxidase (pro-PO) by limited proteolysis and the overall structure is highly similar to that of Drosophila easter serine protease, an essential serine protease zymogen for pattern formation in normal embryonic development. Here, we report purification and molecular cloning of cDNA for another 45-kDa novel PPAF from the hemocyte lysate of Holotrichia diomphalia larvae. The gene encodes a serine proteinase homologue consisting of 415 amino-acid residues with a molecular mass of 45 256 Da. The overall structure of the 45-kDa protein is similar to that of masquerade, a serine proteinase homologue expressed during embryogenesis, larval, and pupal development in Drosophila melanogaster. The 45-kDa protein contained a trypsin-like serine proteinase domain at the C-terminus, except for the substitution of Ser of the active site triad to Gly and had a disulfide-knotted domain at the N-terminus. A highly similar 45-kDa serine proteinase homologue was also cloned from the larval cDNA library of another coleopteran, Tenebrio molitor. By in vitro reconstitution experiments, we found that the purified 45-kDa serine proteinase homologue, the purified active PPAF-I and the purified pro-PO were necessary for expressing phenoloxidase activity in the Holotrichia pro-PO system. However, incubation of pro-PO with either PPAF-I or 45-kDa protein, no phenoloxidase activity was observed. Interestingly, when the 45-kDa protein was incubated with PPAF-I and pro-PO in the absence, but not in the presence of Ca2+, the 45-kDa protein was cleaved to a 35-kDa protein. RNA blot hybridization revealed that expression of the 45-kDa protein was increased in the Holotrichia hemolymph after Escherichia coli challenge.
Delayed onset of progressive dystonia following subacute 3‐nitropropionic acid treatment in Cebus apella monkeys

Delayed abnormal movements can be observed in patients with acute neurologic insult after a prolonged period of apparent neurologic stability. To reproduce such a secondary neurologic manifestation in primates, the present experiment investigated whether systemic administration of subacute 3‐nitropropionic acid (3NP), a mitochondrial toxin, could induce abnormal movements that were delayed and progressive over time. Four Cebus apella monkeys received systemic 3NP injections until acute neurologic signs manifested. The monkeys were regularly video‐recorded and rated for abnormal movements for up to 15 weeks after the cessation of 3NP treatment. Five to 6 weeks after the 3NP treatment, monkeys displayed a significant increase in dyskinesias compared with pretreatment conditions. Over time the chorea attenuated, whereas the dystonic movements increased in intensity and severity which was characterized by a delayed decrease of peak tangential velocity. The intensity of abnormal movements and extent of affected body regions observed in each monkey were consistent with the size of basal ganglia hypersignal as documented by T2 sequence on magnetic resonance imaging. Thus, more severe motor impairments were associated with large magnetic resonance image abnormalities. This novel primate model may be particularly useful for studying the structural changes underlying delayed and progressive manifestations of abnormal movements with the ultimate goal of facilitating the evaluation of novel therapeutic strategies.
Translation of disease associated gene signatures across tissues

It has recently been shown that disease associated gene signatures can be identified by profiling tissue other than the disease related tissue. In this paper, we investigate gene signatures for Irritable Bowel Syndrome (IBS) using gene expression profiling of both disease related tissue (colon) and surrogate tissue (rectum). Gene specific joint ANOVA models were used to investigate differentially expressed genes between the IBS patients and the healthy controls taken into account both intra and inter tissue dependencies among expression levels of the same gene. Classification algorithms in combination with feature selection methods were used to investigate the predictive power of gene expression levels from the surrogate and the target tissues. We conclude based on the analyses that expression profiles of the colon and the rectum tissue could result in better predictive accuracy if the disease associated genes are known.
Carcinoma of the esophagus and esophagogastric junction: sensitivity of radiographic diagnosis.

OBJECTIVE The purpose of this study was to determine the sensitivity of barium studies in revealing carcinoma of the esophagus and esophagogastric junction. MATERIALS AND METHODS We retrospectively reviewed 50 cases of squamous cell carcinoma of the esophagus (n = 25) and adenocarcinoma of the esophagus (n = 14) or esophagogastric junction (n = 11) in which double-contrast (n = 46) or single-contrast (n = 4) barium studies had been done. The original radiology reports were reviewed to determine whether the lesions had been seen on barium studies and whether cancer had been diagnosed. Records were also reviewed to determine the number of patients who underwent esophageal endoscopy because of findings suggestive of cancer on barium studies at some point from January 1992 through December 1992. Pathology records were then reviewed to determine the number of true- and false-positive barium studies during this same period. RESULTS Lesions were shown on barium studies in 49 (98%) of 50 patients, and carcinoma of the esophagus or esophagogastric junction was diagnosed or suspected in 48 patients (96%). In a separate part of the study, we found that endoscopy had been recommended to rule out malignant tumor in only 26 (1%) of 2484 patients who underwent barium studies at some point from January 1992 through December 1992. Endoscopy revealed cancer in 11 of those 26 patients; the remaining 15 were assumed to have false-positive radiologic examinations. Barium studies therefore had a positive predictive value of 42%. CONCLUSION The double-contrast barium study is a sensitive technique for the diagnosis of carcinoma of the esophagus and esophagogastric junction. This high sensitivity can be achieved while recommending endoscopy in only about 1% of all patients who undergo barium studies.
Assessing the Performance of Prediction Models: A Framework for Traditional and Novel Measures

The performance of prediction models can be assessed using a variety of methods and metrics. Traditional measures for binary and survival outcomes include the Brier score to indicate overall model performance, the concordance (or c) statistic for discriminative ability (or area under the receiver operating characteristic [ROC] curve), and goodness-of-fit statistics for calibration. Several new measures have recently been proposed that can be seen as refinements of discrimination measures, including variants of the c statistic for survival, reclassification tables, net reclassification improvement (NRI), and integrated discrimination improvement (IDI). Moreover, decision–analytic measures have been proposed, including decision curves to plot the net benefit achieved by making decisions based on model predictions. We aimed to define the role of these relatively novel approaches in the evaluation of the performance of prediction models. For illustration, we present a case study of predicting the presence of residual tumor versus benign tissue in patients with testicular cancer (n = 544 for model development, n = 273 for external validation). We suggest that reporting discrimination and calibration will always be important for a prediction model. Decision-analytic measures should be reported if the predictive model is to be used for clinical decisions. Other measures of performance may be warranted in specific applications, such as reclassification metrics to gain insight into the value of adding a novel predictor to an established model.
How drought affects the financial characteristics of Australian farm businesses

The financial performance of 240 farms in a drought‐affected agricultural region of Australia is analysed. The decadal study period included some years of widespread drought, as well as years with only subregional droughts or no drought. Some droughts created larger adverse financial impacts than others. Mostly, the more droughts farms experienced, the worse was their financial performance relative to farms within the same quantile of farm performance. Despite the incidence of drought, by the end of the decade, almost all the farm businesses were wealthier from increasing their farm size and becoming more crop dominant. Unexpectedly, consecutive years of drought had a significant positive effect on the operating profit per hectare and retained profit per hectare of farms in a majority of their respective quantiles. Many farms that experienced consecutive drought were forced to make structural changes, shifting away from livestock production towards additional cropping. These structural changes boosted farm performance over the decade. The incidence of drought affected some measures of farm performance differently whilst others were affected similarly. Understanding these metrics of farm performance and the structural changes underway in an agricultural region helps form a more complete view of drought impacts.
The citrulline biosynthetic operon, argC‐F, and a ribose transport operon, rbs, from Bacillus subtilis are negatively regulated by Spo0A

A method Is described here that can be used to identify operons whose expression Is controlled by any particular regulator protein. This method was used to Identify operons whose expression is negatively regulated by Spo0A in Bacillus subtilis. Twenty‐eight strains were identified, each of which contains an operon‐lacZ transcriptional fusion, negatively regulated, either directly or Indirectly, by Spo0A. In one of these strains (CSA8), the lacZ gene is fused to the argC‐F operon positioned at 100° on the B. subtilis chromosome. The regulated expression of this operon by Spo0A ∼ P is mediated indirectly through the transition state regulator AbrB and is manifest only during growth on solid medium. In a second strain (CSA15), the lacZ gene is fused to an operon encoding a transport system which displays features characteristic of the ABC group of transporters, and which has a very high level of identity to the ribose transport system from Escherichia coli Expression of the ribose transport operon is directed by a single SigA‐type promoter. Transcription from this promoter is repressed by the phosphorylated form of Spo0A during the late‐exponential/transition phase of the growth cycle and this control is not mediated through the transition‐state regulator, AbrB.
The development of a conceptual framework for spirituality in the South African employee assistance programme context

To answer the research question of “What would a conceptual framework for spirituality in an employee assistance (EAP) context entail? ” an exploratorydescriptive approach was followed. A literature study was conducted to understand the construct of spirituality and the importance thereof in human functioning. Further, spirituality in practical contexts was explored, both in the workplace and in the EAP contexts. The researcher concluded that spirituality is better situated in the EAP that in the workplace setting in general. To further explore spirituality in the EAP context, a quantitative approach was followed and a survey in the form of web-based questionnaire was distributed to a list of EAP practitioners and professionals, which was obtained form EAPA-SA. Survey links were distributed to 232 (valid) email addresses of the members on the EAPA-SA list, and an additional 25 survey links were distributed to other respondents using snowball sampling. Out of the total of 257 valid survey links distributed, a total of 57 completed responses were received, a response rate of 22%. The survey aimed to explore the knowledge, attitudes and practices in respect of spirituality in their respective employee assistance practices. The respondents rated spirituality quite highly in both their own and in their clients’ lives, indicating strong positive attitudes towards spirituality and that they frequently deal with spiritual matters in practice. However, respondents indicated uncertainty regarding their own knowledge levels and the training they received to enable them to deal with these matters in practice. Incorporating the results of the literature and empirical studies, a conceptual framework and recommendations for spiritual interventions in EAP practice are proposed.
A harmonic constrained minimum energy controller for a single-phase grid-tied inverter using model predictive control

This paper presents a decoupled power control method for a single-phase grid-tied inverter that uses model predictive control (MPC) to minimize the number of switch state changes required to control the output bridge while simultaneously constraining the output current harmonics. On one hand, minimizing the number of switch state changes in the output bridge of the inverter results in minimizing switching losses. On the other hand, lower switching frequencies typically result in larger harmonic currents. The proposed controller evaluates a cost function with an adjustable weight factor. Total harmonic distortion (THD) of grid side current is the constraint of the controller which seeks to minimize switch state changes to lower switching losses while meeting the THD constraint. Thus the MPC performs constrained multi-objective optimization. Because the controller is harmonic-constrained, the single-phase inverter has robust operation under pulsating dc-link voltage, which allows a smaller dc-link capacitor and higher bus ripple voltage. The weight factor can be chosen from an engineering tradeoff between the output current THD and the switching frequency. The simulation results are verified experimentally by implementing the controller using DS1007 platform by dSPACE.
Electrocardiogram Based Identification using a New Effective Intelligent Selection of Fused Features

Over the years, the feasibility of using Electrocardiogram (ECG) signal for human identification issue has been investigated, and some methods have been suggested. In this research, a new effective intelligent feature selection method from ECG signals has been proposed. This method is developed in such a way that it is able to select important features that are necessary for identification using analysis of the ECG signals. For this purpose, after ECG signal preprocessing, its characterizing features were extracted and then compressed using the cosine transform. The more effective features in the identification, among the characterizing features, are selected using a combination of the genetic algorithm and artificial neural networks. The proposed method was tested on three public ECG databases, namely, MIT-BIH Arrhythmias Database, MITBIH Normal Sinus Rhythm Database and The European ST-T Database, in order to evaluate the proposed subject identification method on normal ECG signals as well as ECG signals with arrhythmias. Identification rates of 99.89% and 99.84% and 99.99% are obtained for these databases respectively. The proposed algorithm exhibits remarkable identification accuracies not only with normal ECG signals, but also in the presence of various arrhythmias. Simulation results showed that the proposed method despite the low number of selected features has a high performance in identification task.
The casein kinase I family: roles in morphogenesis.

Wnt signals play important roles in development and oncogenesis and are transduced through at least two pathways: a canonical beta-catenin-dependent and a beta-catenin-independent cascade. Casein kinase I (CKI) is required in both invertebrates and vertebrates to transduce canonical Wnt signals. However, its role in the beta-catenin-independent pathway was unknown. During vertebrate embryogenesis, the beta-catenin-independent cascade is thought to control cell movements and has been postulated to be analogous to the Drosophila planar cell polarity pathway, which signals through the JNK cascade. Here, we report that blocking CKI function inhibits embryonic morphogenesis and activates JNK in cell lines. These studies suggest that CKI might also act in the beta-catenin-independent pathway and indicate a role for CKI during convergence extension in early vertebrate development.
Computational exploration of the activated pathways associated with DNA damage response in breast cancer

Molecular signaling events regulate cellular activity. Cancer stimulating signals trigger cellular responses that evade the regulatory control of cell development. To understand the mechanism of signaling regulation in cancer, it is necessary to identify the activated pathways in cancer. We have developed RepairPATH, a computational algorithm that explores the activated signaling pathways in cancer. The RepairPATH integrates RepairNET, an assembled protein interaction network associated with DNA damage response, with the gene expression profiles derived from the microarray data. Based on the observation that cofunctional proteins often exhibit correlated gene expression profiles, it identifies the activated signaling pathways in cancer by systematically searching the RepairNET for proteins with significantly correlated gene expression profiles. Analyzing the gene expression profiles of breast cancer, we found distinct similarities and differences in the activated signaling pathways between the samples from the patients who developed metastases and the samples from the patients who were disease free within 5 years. The cellular pathways associated with the various DNA repair mechanisms and the cell‐cycle checkpoint controls are found to be activated in both sample groups. One of the most intriguing findings is that the pathways associated with different cellular processes are functionally coordinated through BRCA1 in the disease‐free sample group, whereas such functional coordination is absent in the samples from patients who developed metastases. Our analysis revealed the potential cellular pathways that regulate the signaling events in breast cancer. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Annular Arrangement and Collaborative Actions of Four Domains of Protein-disulfide Isomerase

We presented for the first time a small angle x-ray scattering study of intact protein-disulfide isomerase (PDI) in solution. The restored model revealed that PDI is a short and roughly elliptical cylinder with a molecular mass of 69 kDa and dimensions of 105 × 65 × 40 Å, and the four thioredoxin-fold domains in the order a-b-b′-a′ are arranged in an annular fashion. Atomic force microscope imaging also supported the finding that PDI appears as an approximately flat elliptical cylinder. A PDI species with apparent molecular mass of 116 kDa measured by using size-exclusion chromatography, previously assumed to be a dimer, was determined to exist mainly as a monomer by using analytical ultracentrifugation. The C-terminal fragment 441–491 contributed to the anomalous molecular mass determination of PDI by size-exclusion chromatography. The annular model of PDI accounted for the cooperative properties of the four domains in both the isomerase and chaperone functions of PDI.
Do antioxidant supplements interfere with skeletal muscle adaptation to exercise training?

A popular belief is that reactive oxygen species (ROS) and reactive nitrogen species (RNS) produced during exercise by the mitochondria and other subcellular compartments ubiquitously cause skeletal muscle damage, fatigue and impair recovery. However, the importance of ROS and RNS as signals in the cellular adaptation process to stress is now evident. In an effort to combat the perceived deleterious effects of ROS and RNS it has become common practice for active individuals to ingest supplements with antioxidant properties, but interfering with ROS/RNS signalling in skeletal muscle during acute exercise may blunt favourable adaptation. There is building evidence that antioxidant supplementation can attenuate endurance training‐induced and ROS/RNS‐mediated enhancements in antioxidant capacity, mitochondrial biogenesis, cellular defence mechanisms and insulin sensitivity. However, this is not a universal finding, potentially indicating that there is redundancy in the mechanisms controlling skeletal muscle adaptation to exercise, meaning that in some circumstances the negative impact of antioxidants on acute exercise response can be overcome by training. Antioxidant supplementation has been more consistently reported to have deleterious effects on the response to overload stress and high‐intensity training, suggesting that remodelling of skeletal muscle following resistance and high‐intensity exercise is more dependent on ROS/RNS signalling. Importantly there is no convincing evidence to suggest that antioxidant supplementation enhances exercise‐training adaptions. Overall, ROS/RNS are likely to exhibit a non‐linear (hormetic) pattern on exercise adaptations, where physiological doses are beneficial and high exposure (which would seldom be achieved during normal exercise training) may be detrimental.
Sequence of the malK gene in E.coli K12.

We present the sequence of gene malK which encodes a component of the system for maltose transport in E.coli K12. We also determined the position of deletion (S50) which fuses malK to the following gene lamB; the malK-lamB protein hybrid contains all of the malK protein. The mRNA corresponding to the last two thirds of gene malK could form stable stem and loop structures. The malK protein, as deduced from the gene sequence, would include 370 residues and correspond to a molecular weight of 40700. The sequence as well as sequence comparisons with the ndh protein of E.coli are discussed in terms of the location and function of the malK protein.
Apply Pedestrian Dead Reckoning to indoor Wi-Fi positioning based on fingerprinting

Fingerprinting-based Wi-Fi positioning has been of great interest in recent years due to the wide deployment of Wi-Fi infrastructures. However, it is costly and low efficient to generate radio map for fingerprinting. Several methods have been proposed to address this issue. Most of them need Global Positioning System (GPS) to provide real time location, thus only work well in outdoor environments. In this paper, Pedestrian Dead Reckoning (PDR) is utilized to improve the efficiency of generating radio map and the positioning accuracy for indoor Wi-Fi localization system. In particular, an improved PDR is presented to provide real time positioning for generating radio map, then apply this PDR to positioning phase to improve the positioning accuracy, and finally validate the applicability of the proposed method by experiment. The experiment results show that the radio map constructed by improved PDR has similar performance as the radio map constructed by true locations, and the positioning accuracy can be improved by 7.03% compared to conventional localization methods.