Miracle-dz/UniFAR-FTUs huggingface dataset:
Amplification of Citrus tristeza virus from a cDNA clone and infection of citrus trees.

Isolates of the Closterovirus, Citrus tristeza virus (CTV), are populations of disparate genotypes and defective RNAs developed during long periods of vegetative propagation of citrus trees. Because it has not been possible to obtain pure cultures of the virus, it is not known what components of the population are primarily responsible for induction of diseases. We previously developed an infectious cDNA clone from which in vitro-produced RNA transcripts could infect protoplasts (Satyanarayana et al., 1999, Proc. Natl. Acad. Sci. USA 96, 7433-7438). However, neither the RNA transcripts nor virions from transcript-infected protoplasts were competent for infection of citrus trees. Using a green fluorescent protein-marked virus as inoculum, we found that the approximately 20-kb RNA from virions or transcripts of cDNA infected only a small percentage of protoplasts ( approximately 0.01%), but virions could infect more than 80% of the protoplasts. Based on this information, we amplified the virus from the cDNA clone (recombinant virus) by successive passages in protoplasts using virions in crude sap as inoculum. By the third to seventh passages in protoplasts, maximal amounts of recombinant progeny virus were produced, which were used for inoculation of small citrus trees by slashing stems in the presence of virion preparations. A relatively high percentage of plants became infected with the recombinant virus from protoplasts, resulting in the first defined pure culture of CTV in plants. The comparative biology of the pure culture of recombinant CTV with that of the parental population in planta demonstrated that the recombinant virus retained through all of the recombinant DNA manipulations the normal functions of replication, movement, and aphid transmissibility, and had a symptom phenotype indistinguishable from that of the parental population. Additionally, fulfilling Koch's postulates of the first pure culture of CTV in plants suggested that the major genotype of the CTV T36 population is the primary determinant of the symptom phenotype. We could distinguish no biological contributions resulting from the minor genotypes and defective RNAs of the parental population.
The Centrosome in Cells and Organisms

Centrosome Center Stage? The centrosome is a major organizer of the cytoskeleton in animal cells. The precise duplication of this organelle at each cell cycle ensures proper organization of the mitotic apparatus and chromosome segregation. However, centrosomes are dispensable for cell division during some stages of development in mouse and Drosophila. Bornens (p. 422) reviews the role of the centrosome in a variety of organisms and discusses how and why they can be dispensed with on occasion. In this vein, Azimzadeh et al. (p. 461, published online 5 January) now demonstrate that centrosomes in Planarian flatworms, best known for their remarkable regeneration abilities, are completely dispensable for both cell division and development. The centrosome acts as the main microtubule-nucleating organelle in animal cells and plays a critical role in mitotic spindle orientation and in genome stability. Yet, despite its central role in cell biology, the centrosome is not present in all multicellular organisms or in all cells of a given organism. The main outcome of centrosome reproduction is the transmission of polarity to daughter cells and, in most animal species, the sperm-donated centrosome defines embryo polarity. Here I will discuss the role of the centrosome in cell polarity, resulting from its ability to position the nucleus at the cell center, and discuss how centrosome innovation might have been critical during metazoan evolution.
Triage with the SciKnowMine System in the Mouse Genome Informatics ( MGI ) Curation Process

We describe ‘SciKnowMine’: a software-driven platform for delivering document triage functionality in an extensible web-based biocuration system. The system was designed principally to provide an extensible platform that could be instantiated with any machine learning model document triage as needed. At this stage we emphasized the design of the underlying data structures supporting the triage task and the systems-administration functionality needed to build a deployable system. We instantiated this system at the Mouse Genome Informatics group at the Jackson Laboratory through August / September of 2013 and report here the outcomes of this deployment. Relevance and Impact Background MGI has been one of the foremost biomedical informatics groups that actively support the development of text mining systems as part of their biocuration workflow. They provided data for shared task challenges for the TREC community concerned specifically with document triage of biomedical text in 2004-5 (1, 2) and have invested their support in the community actively since then. We regard the fact that MGI does not have any functional text mining tools for use in their everyday curation work as a serious failure for the field as a whole. We therefore focus our efforts on: (a) developing a well-designed base-level application that reuses simple, well-tested classification technology; (c) deploying this system to MGI so that it could be run from within MGI with minimal support from our team. Within the preliminary work described here, we present the SciKnowMine Triage Web Application (SKM-TWA) as an open-source system for consideration by the community (3). At the time of writing, (June 7th 2013), we have just deployed a working first prototype of the system as a robust virtual appliance for use by MGI curators). We present this write-up as a contribution to the BioCreative 4 IAT challenge because the key issues that determine success in our work have been primarily infrastructural, logistical, and engineering-driven rather than a detailed consideration of the algorithmic approach being used. These are not issues being
Experimental justification of a method for low-PMD measurements

When measuring very low differential group delay (DGD), standard techniques are affected by rather high uncertainties. This problem is usually solved by repeating many times the DGD measurements while randomly perturbing the fiber. Such an approach is founded on the basic assumption that polarization scrambling induces the DGD's decorrelation. Nevertheless, it has not been proved yet that the measured DGDs belong to an homogeneous statistical ensemble. We experimentally validate this approach by means of polarization-sensitive reflectometric measurements
Post-Processing Techniques for Improving Predictions of Multilabel Learning Approaches

In Multilabel Learning (MLL) each training instance is associated with a set of labels and the task is to learn a function that maps an unseen instance to its corresponding label set. In this paper, we present a suite of – MLL algorithm independent – post-processing techniques that utilize the conditional and directional label-dependences in order to make the predictions from any MLL approach more coherent and precise. We solve constraint optimization problem over the output produced by any MLL approach and the result is a refined version of the input predicted label set. Using proposed techniques, we show absolute improvement of 3% on English News and 10% on Chinese E-commerce datasets for P@K metric.
Best practices for the use of itraconazole as a replacement for ketoconazole in drug–drug interaction studies

Ketoconazole has been widely used as a strong cytochrome P450 (CYP) 3A (CYP3A) inhibitor in drug–drug interaction (DDI) studies. However, the US Food and Drug Administration has recommended limiting the use of ketoconazole to cases in which no alternative therapies exist, and the European Medicines Agency has recommended the suspension of its marketing authorizations because of the potential for serious safety concerns. In this review, the Innovation and Quality in Pharmaceutical Development's Clinical Pharmacology Leadership Group (CPLG) provides a compelling rationale for the use of itraconazole as a replacement for ketoconazole in clinical DDI studies and provides recommendations on the best practices for the use of itraconazole in such studies. Various factors considered in the recommendations include the choice of itraconazole dosage form, administration in the fasted or fed state, the dose and duration of itraconazole administration, the timing of substrate and itraconazole coadministration, and measurement of itraconazole and metabolite plasma concentrations, among others. The CPLG's recommendations are based on careful review of available literature and internal industry experiences.
Single-Frequency and Single-Polarization DFB Fiber Laser Based on Tapered FBG and Self-Injection Locking

A stable single-polarization narrow linewidth single-frequency distributed feedback (DFB) fiber laser is proposed and demonstrated. For the first time, to our knowledge, the tapered FBG written in the photosensitive large-mode-area (LMA) high-concentration erbium-doped fiber (EDF) is applied in the DFB fiber laser. Self-injection locking is used to make the proposed DFB fiber laser operate in the stable single-polarization state and reduce the linewidth of the DFB fiber laser. The LMA high-concentration EDF is fabricated by the modified chemical vapor deposition technique. The tapered FBG can be seen as the equivalent phase shift FBG, and the equivalent π phase shift is produced by tapering the uniform FBG directly. The threshold of the DFB fiber laser is about 145 mW, and the maximum output power is 43.55 mW at 450-mW pump power. The measured and modified slope efficiencies of the DFB fiber laser are approximately 14.27% and 15.82%, and the optical signal-to-noise ratio (OSNR) of the laser is over 55 dB. The stable single-polarization and single-frequency operation of the fiber laser is realized, and the measured 20-dB linewidth of DFB fiber laser with self-injection locking and without self-injection locking are approximately 10.3 and 52.3 kHz, respectively.
On the condition for fast neural computation

A fundamental question in theoretical neuro-science is to answer why neural systems can process information extremely fast. Here we investigate the effect of noise and neuronal collaborative activity on speeding up population decoding. We consider a one-dimensional stimulus encoded by a number of integrate-and-fire neurons. We find that 1) when noise is Poissionian, i.e., its variance is proportional to the mean, and 2) when a neural ensemble is at its stochastic equilibrium state, noise has the ‘best’ effect of accelerating computation, in the sense that the strength of external inputs is linearly encoded by the number of neurons firing in a short-time window, and that the neural system can use a simple strategy to decode the input rapidly and accurately. Interestingly, we also observe that under this noisy environment, the accuracy of neural decoding in short-time window is insensitive to the noise strength.
The Rational of Catalytic Activity of Herpes Simplex Virus Thymidine Kinase

Most antiherpes therapies exploit the large substrate acceptance of herpes simplex virus type 1 thymidine kinase (TKHSV1) relative to the human isoenzyme. The enzyme selectively phosphorylates nucleoside analogs that can either inhibit viral DNA polymerase or cause toxic effects when incorporated into viral DNA. To relate structural properties of TKHSV1ligands to their chemical reactivity we have carried out ab initio quantum chemistry calculations within the density functional theory framework in combination with biochemical studies. Calculations have focused on a set of ligands carrying a representative set of the large spectrum of sugar-mimicking moieties and for which structural information of the TKHSV1-ligand complex is available. The k cat values of these ligands have been measured under the same experimental conditions using an UV spectrophotometric assay. The calculations point to the crucial role of electric dipole moment of ligands and its interaction with the negatively charged residue Glu225. A striking correlation is found between the energetics associated with this interaction and the k cat values measured under homogeneous conditions. This finding uncovers a fundamental aspect of the mechanism governing substrate diversity and catalytic turnover and thus represents a significant step toward the rational design of novel and powerful prodrugs for antiviral and TKHSV1-linked suicide gene therapies.
ABCDE--an evolving concept in the early detection of melanoma.

T HE PUBLIC HEALTH IMPACT OF MALIGNANT melanoma continues to increase. It has been estimated that 59 580 newly diagnosed cases of invasive melanoma and an additional 46 170 cases of in situ melanoma will occur in the United States in 2005. Currently, 1 in 62 people in the United States will develop invasive melanoma during their lifetime (up from 1 in 1500 in 1930), and should the current rate of increase in incidence continue, by 2010 the lifetime risk will increase to 1 in 50 (Figure 1). If in situ cases are included, the lifetime risk of a US patient developing melanoma is 1 in 34. The annual cost of treating skin cancer in the Medicare population alone in the United States is now estimated at $1 billion, with 90% of treatment costs associated with therapy for advanced disease.
Pituitary gland and blood lymphocytes

It has been shown that injection of adrenocorticotrophic hormone (A.C.T.H.) in mice, rats and rabbits produces a temporary fall in the absolute number of blood lymphocytes (Dougherty & White, 1943, 1944). This response would appear to be mediated by the adrenal cortex, for injection of extracts of the adrenal cortex produce a similar lymphopenia, whereas injection of A.C. T.H. into adrenalectomized animals has no effect (Dougherty & White, 1944). These results have been confirmed by other workers. For details and discussion see recent reviews by Valentine, Craddock & Lawrence (1948), and White (1949). It thus seemed possible that the production of a temporary lymphopenia might be used as an indicator of the secretion of A.C. T.H. by the anterior pituitary gland. In preliminary experiments electrical stimulation of various regions of the hypothalamus and pituitary gland was performed by the remote control method in unanaesthetized rabbits to see whether a lymphopenia might be so produced. For this method of stimulation (Harris, 1948 a) it was necessary to immobilize the rabbits in clamps for periods up to 2 hr. These experiments were stopped, however, when it was found that the emotional stress involved by immobilizing the animals in clamps (without electrical stimulation) was sufficient to produce the lymphopenic response. This paper deals with the part played by the pituitary gland in this reaction to emotional stress. The effects of electrical stimulation of the hypothalamus and hypophysis by a technique that does not require immobilization of the animal form a further report.
Detection of neonatal EEG seizure using multichannel matching pursuit

It is unusual for a newborn to have the classic “tonic-clonic” seizure experienced by adults and older children. Signs of seizure in newborns are either subtle or may become clinically silent. Therefore, the electroencephalogram (EEG) is becoming the most reliable tool for detecting neonatal seizure. Being non-stationary and multicomponent, EEG signals are suitably analyzed using time-frequency (TF) based methods. In this paper, we present a seizure detection method using a new measure based on the matching pursuit (MP) decomposition of EEG data. Signals are represented in the TF domain where seizure structural characteristics are extracted to form a new coherent TF dictionary to be used in the MP decomposition. A new approach to set data-dependent thresholds, used in the seizure detection process, is proposed. To enhance the performance of the detector, the concept of areas of incidence is utilized to determine the geometrical correlation between EEG recording channels.
Fall Detection Based on Tilt Angle and Acceleration Variations

Fall accidents cause serious injury to the elderly. In an aging society, there may be no person to take care of an elder anytime. Therefore, an automatic fall detection system becomes important. Although a fall can be more accurately detected by mounting several sensors on a human body, there have uncomfortable and inconvenient problems. It becomes a research trend to directly use a smartphone to help to detect and deal with fall accidents. In this paper, the acceleration sensor of a smartphone is applied to observe the change of angles and acceleration when a person carrying a mobile phone falls down. The corresponding detection application is then developed on a smartphone.
TRAF1: Lord Without A RING

Tumor necrosis factor (TNF) receptor-associated factors (TRAFs) constitute a family of adaptor proteins that associate with the cytosolic tail of particular TNF-family receptors (TNFR) and regulate cytokine signaling by linking TNFRs with downstream protein kinases, ubiquitin ligases, and other effector proteins. A total of six members of this family (TRAF1-6) have been identified in mammals. TRAF1 is unique among TRAFs because it lacks a RING finger domain present in TRAF2-6 that has been shown to be required for TRAF2- and TRAF6-mediated activities. TRAF1 also has the most restricted expression among TRAFs, and is found almost exclusively in activated lymphocytes, dendritic cells, and certain epithelia. Recent evidence obtained from TRAF1-/- mice shows that TRAF1-deficient T cells are hyper-responsive to TNF-α, having increased T cell receptor (TCR)-dependent T cell proliferation rates in vitro. Also, these TRAF1-/- mice had increased sensitivity to TNF-α-induced skin necrosis in vivo. These results support a role for TRAF1 as a negative regulator of signaling by certain TNF-family receptors. This review summarizes current knowledge about TRAF1, focusing on the new information provided by these TRAF1-deficient mice. Also, the pros and cons of TRAFs as potential targets for drug discovery are discussed.
The Early Symptoms of Schizophrenia

Since Bleuler introduced his concept of schizophrenia in 1911, there has been a steady growth of clinical and experimental data relating to this disease. However, the literature dealing with early diagnosis is sparse and as yet there is no general agreement as to what symptomatology constitutes the early clinical picture. Older texts (Kraepelin, 1919; Bleuler, 1911) do not elaborate early diagnosis, dwelling more on distinguishing schizophrenia from other disease entities. Likewise, more recent texts tend to refer to the early stages very briefly in rather vague terms, signifying the development of the disease over the first few years from its onset. Although practice varies, the diagnosis of schizophrenia is often reserved until Bleuler's primary symptoms of disordered volition, thinking and affect appear overtly, by which time there may be also some evidence of deterioration. It is recognized, however, that these symptoms may take years to appear (Gillies, 1949) so that early diagnosis cannot readily be made by using these criteria.
Regulation of transepithelial ion transport and intracellular calcium by extracellular ATP in human normal and cystic fibrosis airway epithelium

1 The role of extracellular nucleotides in regulation of ion transport activities (short circuit current, Isc) of human respiratory epithelia was studied. 2 Application of nucleotides to the apical or basolateral membrane of human nasal epithelium induced a concentration‐dependent increase in Isc. 3 The rank order of potency of purine‐ or pyrimidine‐induced changes in Isc of normal human nasal epithelium when applied to the apical membrane (UTP ≥ ATP > ATPγS > 2MeSATP > ADPβS ≫ βγMeATP ≥ βγMeATP) or basolateral membrane (2MeSATP > UTP > ATP > ATPγS > αβMeATP > βγMeATP) is consistent with involvement of a P2 purinoceptor. A similar rank order of potencies was observed for nucleotide effects on intracellular calcium measured by Fura‐2 fluorescence using microspectrofluorimetry. 4 Similar nucleotide potency in the regulation of ion transport and intracellular calcium in cystic fibrosis (CF) airway epithelium (UTP ≥ ATP) was observed, suggesting purinoceptors might be used to stimulate ion transport processes that would promote hydration of airway secretions and facilitate their clearance from CF lungs. 5 These data provide evidence for the regulation of ion transport by P2 purinoceptors in normal and cystic fibrosis human airway epithelium.
Influence of excessive lysine and/or methionine supplementation on growth performance and carcass traits in broiler chicks

Cette etude a ete realisee sur des poulets de chair qui ont recu une ration comportant de la lysine (Lys) et/ou de la methionine (Met) en exces, pendant la periode de demarrage (0 a 21 j) afin d'evaluer leurs performances de croissance, les caracteristiques de leur carcasse, le poids relatif de certains de leurs organes et de doser certains parametres sanguins. Un total de 304 poulets mâles âges de 1 jour ont ete aleatoirement repartis en 4 groupes (n=76) chacun comportant 4 lots de 19 oiseaux. Les poulets ont recu 4 regimes "demarrage" contenant differents niveaux de Lys et Met. : (I) 13.67 g/kg Lys (124% de CNR) et 6.28 g/kg Met (126% de CNR); (II) 22.07 g/kg Lys (200% de CNR) et 6.28 g/kg Met (126% de CNR); (III) 13.67 g/kg Lys (124% de CNR) et 10.08 g/kg Met (200% de CNR); (IV) 22.07 g/kg Lys (200% de CNR) et 10.08 g/kg Met (200% de CNR). Les resultats indiquerent que le poids vif (PV) et le gain de PV des groupes recevant plus de Lys (Rations Il et IV) etaient significativement plus faibles que ceux des poussins appartenant aux deux autres groupes experimentaux. La quantite d'aliments ingeres, l'indice de conversion alimentaire, les rendements de carcasse, de cuisse, de brechet et les poids relatifs du coeur, de la rate, de la bourse de Fabricus n'ont pas ete affectes par un apport excessif en Lys et/ou en Met. Neanmoins,le developpement de la cuisse a ete significativement plus important dans les groupes recevant les rations contenant de la Lys en exces (ration II et IV), et parmi les tous les groupes experimentaux, la ration IV presentait la valeur la plus elevee. Les donnees ont montre que la ration de base des poulets etait desequilibree en acides amines. Une addition excessive de Lys dans la ration a diminue le PV et le le gain de PV entre 0 et 21 j d'âge, independamment de l'addition de Met. D'autre part, l'apport en exces de Lys, separement ou combine avec un apport excessif de Met, a augmente le rendement de la cuisse.
Dietary Cholesterol and Plasma Lipoproteins

Although dietary cholesterol undoubtedly affects the plasma cholesterol level, the magnitude of this effect depends on several factors: 1. the amount of cholesterol ingested; 2. the amount of dietary fat; 3. the type of dietary fat; 4. the efficiency of metabolic compensatory mechanisms; 5. interactions with other dietary factors. Some of these are not sufficiently well recognized and account for considerable confusion. For instance, studies in which the addition of a single egg (250mg cholesterol) to a daily diet already rich in cholesterol, carried out in outpatients in whom other dietary constituents are surmised but not established, cannot be interpreted. The apparent absence of a clear relationship between dietary cholesterol and coronary disease within a single affluent society (in contrast to studies between populations) is similarly clouded, although such a relationship has recently been shown in the Chicago Western Electric Study (1).