Miracle-dz/UniFAR-FTUs huggingface dataset:
cDNA Cloning and Sequence Analysis of a Pathogen-Induced Thaumatin-Like Protein from Rice (Oryza sativa)

Induced resistance in rice (Oryza sativa) against the rice blast fungus Pyricularia o y z a e can be triggered by a prior inoculation with the nonhost pathogen Pseudomonassyringae pv. syringae (Smith and Métraux, 1991). , The onset of this resistance correlates with the activation of putative defense genes. Recently, we described the isolation and characterization of a cDNA encoding a peroxidase that is induced locally but not systemically after infiltration of rice leaves with P. syringae pv. syringae (Reimmann et al., 1992). Here we report the complete sequence of a cDNA encoding a thaumatin-like protein (Table I). The 663-nucleotide long cDNA (without the poly[A] tail) contains an open reading frame of 177 amino acids beginning with an ATG start codon at position 29 and ending with a TAA stop codon at position 560. The first 26 amino acids code for a putative signal peptide, indicating that the protein enters the secretory pathway. Sequence comparison with thaumatin, a sweet-tasting protein from the West African shrub Thaumatococcus daniellii (Edens et al., 1982), reveals 50% identical and 10% conserved amino acids, indicating that the cDNA clone pPIR2 encodes a protein belonging to the large family of thaumatin-like proteins. This family includes some pathogenesis-related proteins, the antifungal permatins, and the osmotin family of proteins that is induced during the adaptation of plants to osmotic stress (Singh et al., 1987; Linthorst, 1991; Vigers et al., 1991). The protein encoded by pPIR2 has a similar size (17,992 D including the signal peptide) as, and shows the strongest homology to, a pathogen-induced thaumatin-like protein from wheat (Rebmann et al., 1991). Similar to the wheat protein, the thaumatin-like protein from rice (as deduced from its cDNA sequence) contains an intemal deletion of about one-fourth of the amino acids compared to the thaumatins and to other thaumatin-like proteins. Northern blot analysis using the cloned insert of pPIR2 as a radiolabeled probe showed a transient increase of a 0.7-kb transcript in rice leaves infiltrated with P. syringae pv. syringae but not in uninoculated control leaves. The transcript was clearly detectable 8 h after the infiltration, reached a maximum after 24 h, and started to decline after 48 h. Although induced resistance in rice has been reported to be systemic (Smith and Métraux, 1991), the increase in the mRNA leve1 of the thaumatin-like protein was observed only locally.
Experimental Identification and Vibration Control of A Non-Collocated Piezoelectric Flexible Manipulator Using Optimal Multi-Poles Placement Control

This paper presents experimental identification and vibration suppression of a flexible manipulator with non-collocated piezoelectric actuators and strain sensors using optimal multipoles placement control. To precisely identify the system model, a reduced order transfer function with relocated zeros is proposed, and a first-order inertia element is added to the model to compensate the non-collocation. Comparisons show the identified model match closely with the experimental results both in the time and frequency domains, and a fit of 97.2% is achieved. Based on the identified model, a full-state multi-poles placement controller is designed, and the optimal locations of the closed loop poles are determined. The feasibility of the proposed controller is validated by simulations. Moreover, the controller is tested for different locations of the closed loop poles, and an excellent performance of the optimal locations of the closed loop poles is shown. Finally, the effectiveness of the proposed controller is demonstrated by experiments. Results show that the vibrations of the expected modes are significantly diminished. Besides, vibrations of the higher modes are also slightly suppressed. Accordingly, multi-mode vibrations of the manipulator are well attenuated, and the tip displacement converges quickly with the proposed method.
Hepcidin – central regulator of iron metabolism

The knowledge about mammalian iron metabolism has advanced dramatically over the past decades. Studies of genetics, biochemistry and molecular biology allowed us the identification and characterization of many of the molecules involved in regulation of iron homeostasis. Important progresses were made after the discovery in 2000 of a small peptide – hepcidin – that has been proved to play a central role in orchestration on iron metabolism also providing a link between iron metabolism and inflammation and innate immunity. Hepcidin directly interacts with ferroportin (FPN), the only known mammalian iron exporter, which is expressed by enterocytes, macrophages and hepatocytes. The direct hepcidin–FPN interaction allows an adaptative response from the body in situations that alter normal iron homeostasis (hypoxia, anemia, iron deficiency, iron overload, and inflammation).
Bayesian Priors from Loss Matching

Cet article discute le problème de la construction de lois de probabilité a priori dans un contexte où les opinions ou les informations reflétées par ces lois portent uniquement sur les quantités observables du problème. Nous apportons une attention particulière au cas où le paramètre est caractérisé par la minimisation d'une mesure de divergence, et examinons l'application de la règle de Bayes dans cette perspective. Notre point de vue est fondamentalement non paramétrique, et repose sur le “matching” de deux fonctions de perte, l'une liée au modèle, l'autre à l'a priori.
A distributed assignment algorithm with position-dependent benefit function

This paper considers the assignment problem of mobile robots with a special form of time-attenuating and position-dependent benefit function. We propose a distributed algorithm to solve the assignment problem which ensures to convergence in finite time and results in a solution within nε of being optimal. Moreover, we show by simulation that the convergence time of the algorithm is sensitive to the attenuation factor with distance but insensitive to the velocity of the agents.
The Draft Genome of Globodera ellingtonae

Abstract Globodera ellingtonae is a newly described potato cyst nematode (PCN) found in Idaho, Oregon, and Argentina. Here, we present a genome assembly for G. ellingtonae, a relative of the quarantine nematodes G. pallida and G. rostochiensis, produced using data from Illumina and Pacific Biosciences DNA sequencing technologies.
Insights from the examination of verbal and spatial memory errors in relation to clinical symptoms of patients with recent-onset schizophrenia

Introduction. Memory deficits in patients with schizophrenia (SZ) are considered as a key feature of the clinical manifestations of the disease. In order to further examine the role and nature of memory deficits in SZ, the pattern of errors in verbal and spatial serial recall tasks committed by SZ patients was compared to that of healthy controls. We also tested the relationship between these memory errors and clinical symptoms. Methods. Twenty-seven outpatients with recent-onset SZ and 27 age and gender matched healthy controls had to remember sequences of items (digits or localisations) in a serial recall task. Clinical symptoms were assessed with the PANSS and the SAPS. Results. The results indicate that the number of omissions, intrusions, and transpositions can differentiate patients with SZ from healthy controls. Intrusions and transpositions committed in the verbal domain were associated with the negative subscale of the PANSS. Transposition errors were associated with delusions whether the to-be-remembered information was verbal or spatial. Conclusion. The examination of the pattern of errors, in particular that of transpositions, is a more informative cognitive index than the mere analysis of overall performance, and provides a promising target for treatment.
ITU-R Standardization Activities on Cognitive Radio

Cognitive radio is an emerging technology to further improve the efficiency of spectrum use. Due to the nature of the technology, it has many facets, including its enabling technologies, its implementation issues and its regulatory implications. In ITU-R (International Telecommunications Union — Radiocommunication sector), cognitive radio systems are currently being studied so that ITU-R can have a clear picture on this new technology and its potential regulatory implications, from a viewpoint of global spectrum management. This paper introduces the recent results of the ITU-R studies on cognitive radio on both regulatory and technical aspects. This paper represents a personal opinion of the author, but not an official view of the ITU-R.
From wire-frames to furry animals

This paper describes an approximate method for rapidly generating reflectance functions for highly anisotropic materials. This is applied to the rendering of images of burnished metal. A method is then developed for rendering wire-frame drawings which have a wire-like appearance. Such wire-like elements are "grown" or created on the surface of parametric patches and the results resemble furry animals. This procedural modelling technique is extended to include the generation of
Randomised controlled trial of paper, online and SMS diaries for collecting sexual behaviour information from young people

Background Diaries are used in sexual behaviour research to reduce recall bias. Diary collection via mobile phone text messaging (SMS) has not been trialled previously in sexual behaviour research. This randomised controlled trial compared SMS, paper and online diaries on response rate, timeliness, completeness of data and acceptability. The correlation between behaviour reported in all three types of diaries and data collected in a retrospective questionnaire was also determined. Methods Participants were recruited by telephone and randomised into one of three groups. They completed weekly sexual behaviour diaries for 3 months by SMS, online or paper (by post). An online survey was conducted at the end of 3 months to compare retrospective reports to the diaries and assess opinions on the diary collection method. Results 72 participants were enrolled in the study, 24 in each group. Online diaries were more likely to be submitted late than SMS diaries (p<0.001). 3.9% of SMS diaries, 3.1% of paper diaries and 0.5% of online diaries were incomplete (p=0.001). Online data collection was the preferred mode for 51%. 65 participants completed the end point retrospective questionnaire. The correlation between the diary and questionnaire on sexual risk classification was substantial (κ=0.74) regardless of diary mode. Conclusions SMS is a convenient and timely method of collecting brief behavioural data, but online data collection was preferable to most participants and more likely to be complete. Data collected in retrospective sexual behaviour questionnaires were found to agree substantially with data collected through weekly self-reported diaries.
Validity and Reliability of Mothers' Reports of Language Development in 1-Year-Old Children in a Large-Scale Survey in Bangladesh

Background In developing countries, it is often important to have measures of development in children under 3 years of age in large-scale surveys or evaluations of nutrition and stimulation programs. However, there is a lack of suitable instruments with established validity. Objective To develop a language test for children aged 12 to 18 months based on mothers' report, suitable for use in large-scale surveys, and examine its concurrent and predictive validity. To determine whether the test is sensitive to home stimulation and nutritional status and compare the test with the Bayley Scales of Infant Development (BSID). Methods A subsample of participants in a large, prospective cohort study in rural Bangladesh (MINIMat) was selected for a study of child development (n = 2,852). A total of 2,418 participants were interviewed concerning their children's expressive and receptive vocabulary, and children were tested using the BSID. Results The language test had reasonable short- and long-term reliability between 12 and 18 months (r = 0.50) and concurrent validity with the Bayley Mental Development Index (MDI) (r = 0.32 language comprehension to 0.41 language expression). Its predictive validity with IQ at age 5 years was similar to that of the Bayley MDI (r = 0.37 to 0.41 for language and r = 0.37 for MDI). Child language was independently associated with postnatal growth, stimulation in the home, gestational age, and socioeconomic status, and a similar set of variables predicted the Bayley MDI. Conclusions The language test was reliable, had acceptable concurrent and predictive validity, and was sensitive to environmental and child characteristics. Mothers' reports of language could be useful in large-scale programs.
Molecular Pathways: Regulation and Targeting of Kinetochore–Microtubule Attachment in Cancer

Kinetochores are large protein structures assembled on centromeric DNA during mitosis that bind to microtubules of the mitotic spindle to orchestrate and power chromosome movements. Deregulation of kinetochore–microtubule (KT–MT) attachments has been implicated in driving chromosome instability and cancer evolution; however, the nature and source of KT–MT attachment defects in cancer cells remain largely unknown. Here, we highlight recent findings suggesting that oncogene-driven changes in kinetochore regulation occur in glioblastoma multiforme (GBM) and possibly other cancers exhibiting chromosome instability, giving rise to novel therapeutic opportunities. In particular, we consider the GLE2p-binding sequence domains of BubR1 and the newly discovered BuGZ, two kinetochore-associated proteins, as candidate therapeutic targets for GBM. Clin Cancer Res; 21(2); 233–9. ©2014 AACR.
Factors Affecting Fenestration of the Footplate in Stapes Surgery: Effectiveness of Fisch’s Reversal Steps Stapedotomy

Objective To analyze the factors affecting the fenestration of the footplate in stapes surgery and to evaluate the effectiveness of Fisch’s reversal steps stapedotomy. Study Design Retrospective study. Patients A total of 191 patients with otosclerosis in whom 230 primary stapes surgeries were performed by 1 surgeon in 3 tertiary hospitals. Main Outcome Measure Evaluation of factors affecting the fenestration of the footplate in stapes surgery by logistic regression analysis. Results Stapedotomy (small hole in stapes footplate) was performed in 148 ears (64.3%). Partial stapedectomy (half removal of stapes footplate) was performed in 65 ears (28.3%). Total stapedectomy (total removal of stapes footplate) was performed in 17 ears (7.4%). Stapedotomy could be performed in 72.1% of cases (75/104) in which the stapes suprastructure was removed after insertion of the prosthesis and in 57.9% of cases (73/126) in which the stapes suprastructure was removed before the insertion. Stapedotomy could be performed in 65.4% of cases (117/179) in which a 0.6-mm-thick Schuknecht-type Teflon wire piston was used and in 60.8% (31/51) in which a whole Teflon piston was used. Multivariate analysis of factors affect stapedotomy using logistic regression analysis showed that the surgical order of the removal of the stapes suprastructure and insertion of the prosthesis were the most important 2 factors. Conclusion Fisch’s reversal steps technique was useful in performing stapedotomy in all otosclerosis patients. Manipulation of the prosthesis when crimping it to the incus is also important. The prosthesis should be crimped onto the incus and inserted in the footplate opening gently and atraumatically.
GABA‐like immunoreactivity in the cat retina: Light microscopy

Semithin sections of the cat retina were stained with antibodies against GABA conjugated to bovine serum albumin with glutaraldehyde. Labelled cells were visualized by means of the peroxidase‐antiperoxidase method. In the outer plexiform layer both A‐ and B‐type horizontal cells and the B‐type axon terminal system expressed GABA‐like immunoreactivity. Approximately 25–30% of all amacrine cells and the whole inner plexiform layer were heavily labelled. Two types of putative GABA‐ergic interplexiform cells could be distinguished. One of them also expressed tyrosine‐hydroxylase‐like immunoreactivity. A few bipolar cells were also GABA‐immunolabelled. GABA‐like immunoreactivity and 3H‐muscimol uptake were colocalized in 90% of the amacrine cells labelled. However, horizontal cells did not accumulate 3H‐muscimol.
Cognitive deficits early in the course of rheumatoid arthritis

ABSTRACT Objective: The aim was to examine the severity and prevalence of cognitive difficulties in persons with rheumatoid arthritis (RA) within the first three years of diagnosis. Method: One hundred consecutive RA patients aged 28–67 years (90% women) were administered a battery of 6 neuropsychological tests yielding 14 cognitive indices. Self-reported measures of trait anxiety, depression, impact of disease on daily activities, and pain severity were also obtained along with physician-rated disease severity. Results: Twenty percent of RA patients were classified as cognitively impaired, defined as age- and education-adjusted scores at least 1.5 standard deviations below the population mean on 3 or more cognitive indices. Impaired performance, controlling for age, education, and premorbid cognitive capacity, was detected primarily on measures of short-term memory, immediate and delayed episodic recall, and phonemic fluency. There were modest negative associations between cognitive indices and measures of perceived disease severity (pain level, impact of disease on daily functionality, and overall health quality). Conclusions: Cognitive deficits on several domains are frequently encountered in relatively young RA patients during the first few years of the disease and may need to be taken into account as important correlates of disease severity and progression.
MRI of Creutzfeldt-Jakob disease: imaging features and recommended MRI protocol.

Creutzfeldt-Jakob Disease (CJD) is a rare, progressive and invariably fatal neurodegenerative disease characterized by specific histopathological features. Of the four subtypes of CJD described, the commonest is sporadic CJD (sCJD). More recently, a new clinically distinct form of the disease affecting younger patients, known as variant CJD (vCJD), has been identified, and this has been causally linked to the bovine spongiform encephalopathy (BSE) agent in cattle. Characteristic appearances on magnetic resonance imaging (MRI) have been identified in several forms of CJD; sCJD may be associated with high signal changes in the putamen and caudate head and vCJD is usually associated with hyperintensity of the pulvinar (posterior nuclei) of the thalamus. These appearances and other imaging features are described in this article. Using appropriate clinical and radiological criteria and tailored imaging protocols, MRI plays an important part in the in vivodiagnosis of this disease.
2.14/3.5 GHz novel dual-band negative group delay circuit design based on composite right/left handed transmission line

This paper proposes a novel design and implementation of a dual-band negative group delay circuit (NGDC) using composite right/left handed (CRLH) transmission line. CRLH λ/4 short stubs and a broadband 3dB 90° hybrid coupler are employed to obtain simultaneously the negative group delay (NGD) condition at two separate bands. The proposed design methodology was used to design a dual-band negative group delay circuit for the frequency bands at 2.14 and 3.5 GHz. Measured group delays were about −7.2 and −6.5 ns at two operational frequencies.
Application of whole-ecosystem 15N tracer approaches to investigate the fate of nitrate in wetlands: Pilot experiments and met

As the impacts of anthropogenic nitrogen (N) pollution of the biosphere become increasingly evident, the fate of excess N in landscapes is recognized as one of the most pressing environmental research needs. Most of this N disappears somewhere in route from the sites of application (mainly on land) to coastal and offshore marine waters; however the precise regions and mechanisms of removal remains elusive. Wetlands along landscape hydrologic flow paths are likely to be important sites for removal of this nitrogen. Consequently, future wetland management, restoration and establishment decisions will likely be heavily impacted by understanding the role of wetlands as nitrogen sinks. The research proposed here involves the development and testing of new techniques for whole-ecosystem stable-isotope (N) tracer studies in wetlands. This venture grant was only partially spent when we obtained a CWS Postdoctoral Grant to further pursue similar research, and therefore the remaining funds were rolled into the new grant. The proposed experiments are designed to work out methods in a small groundwater discharge wetland and then apply the refined methods in a larger stream/beaver pond system. These kinds of experiments elucidate N cycle processes that transform and remove N in these complex ecosystems. This work builds on our extensive experience with such studies in streams, particularly through the LINX project, and dovetails with more in-depth research that we have recently initiated on the microbial processes responsible for N removal in aquatic sediments. This project is enabling us to establish a strong foundation with which to seek funding for a larger project to systematically examine the role of wetlands as N transformers and sinks.
Topological Analysis and Gaussian Decision Tree: Effective Representation and Classification of Biosignals of Small Sample Size.

GOAL Bucking the trend of big data, in microdevice engineering, small sample size is common, especially when the device is still at the proof-of-concept stage. The small sample size, small inter-class variation, and large intra-class variation, have brought biosignal analysis new challenges. Novel representation and classification approaches need to be developed to effectively recognize targets of interests with the absence of a large training set. METHODS Moving away from the traditional signal analysis in the spatiotemporal domain, we exploit the biosignal representation in the topological domain that would reveal the intrinsic structure of point clouds generated from the biosignal. Additionally, we propose a Gaussian-based decision tree (GDT), which can efficiently classify the biosignals even when the sample size is extremely small. RESULTS This study is motivated by the application of mastitis detection using low-voltage alternating current electrokinetics (ACEK) where five categories of bisignals need to be recognized with only 2 samples in each class. Experimental results demonstrate the robustness of the topological features as well as the advantage of GDT over some conventional classifiers in handling small dataset. CONCLUSION Our method reduces the voltage of ACEK to a safe level and still yields high-fidelity results with a short assay time. SIGNIFICANCE This paper makes two distinctive contributions to the field of biosignal analysis, including performing signal processing in the topological domain and handling extremely small dataset. Currently, there have been no related works that can efficiently tackle the dilemma between avoiding electrochemical reaction and accelerating assay process using ACEK.