Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved gap‐repair cloning method that uses oligonucleotides to target cognate sequences

In vivo or gap‐repair cloning in yeast has been widely recognized as one of the most efficient means for error‐free construction of plasmids. A protocol is described here that allows easy and efficient gap‐repair cloning that is based on two major modifications. Instead of subcloning, the targeting plasmids are constructed using oligonucleotides from sequences derived from the upstream and downstream sequences of the fragment to be cloned. These sequences are selected so that they can lead to the generation of recognition sites for restriction enzymes that produce blunt ends. Accordingly, this procedure can be applied to any DNA fragment, regardless of whether these include unique restriction sites to generate the targeting ends. With the strategy described, ∼50 bp upstream and downstream targeting ends are generated that allow efficient cloning. Further, to allow easy identification of the positive clones, the annealed oligonucleotides are cloned in frame with the lacZ fragment present in the plasmid. Accordingly, these plasmids produce blue Escherichia coli colonies on media containing X‐Gal. On the other hand, plasmids rescued from yeast that have acquired the respective cognate sequences produce white colonies. To demonstrate the efficiency of the method, this report includes the cloning of fragments harbouring the CDC28, CAK1, CIN5 and CLB2 genes. We found that 30–100% of the analysed plasmids carried the expected inserts. Copyright © 2009 John Wiley & Sons, Ltd.
Complexity, connections and sense-making : stakeholder experiences of primary English language curriculum change in one province in Vietnam

This thesis sets out to explore the complexity of curriculum reform by examining how different stakeholders, experiencing English language curriculum reform in different ‘layers’ of the education system in one province in Vietnam, make sense of change in relation to their professional roles, practices and behaviours. While there is a plethora of research on curriculum change in TESOL contexts, much of this is focused on the teacher and the practical constraints they might face in implementing a new curriculum. The multi-level interactions and relationships involved in sense-making, and the complexity that such interconnectedness suggests, seems to be a neglected research area. This qualitative case study begins to fill this research gap. Using a complexity perspective, the study investigated the perceptions, understandings and responses to primary English language curriculum change of seven primary English language teachers working in three districts in one province in Vietnam. The study also examined the sense-making of three district specialists and four university INSET trainers who are involved in supporting those teachers in implementing the new curriculum. Data were generated through multiple qualitative interviews, classroom observations and document analysis carried out over two research phases. The research identified a number of control parameters which appeared to be constraining the participants’ practices and behaviours towards a paradigm shuffle rather than a paradigm shift. The findings show how the interconnectedness of the educational culture, perceptions of risk, feelings of being supported and the flow of communication experienced by the different participants seemed to mediate teachers’ emergent classroom practices and behaviours. The research identifies several policy implications for policy makers, curriculum change planners and TESOL practitioners which have emerged from these control parameters, and which are likely to help promote the desired curriculum change outcomes.
Involvement of a Soybean ATP-Binding Cassette-Type Transporter in the Secretion of Genistein, a Signal Flavonoid in Legume-Rhizobium Symbiosis1

Legume plants have an ability to fix atmospheric nitrogen into nutrients via symbiosis with soil microbes. As the initial event of the symbiosis, legume plants secrete flavonoids into the rhizosphere to attract rhizobia. Secretion of flavonoids is indispensable for the establishment of symbiotic nitrogen fixation, but almost nothing is known about the membrane transport mechanism of flavonoid secretion from legume root cells. In this study, we performed biochemical analyses to characterize the transport mechanism of flavonoid secretion using soybean (Glycine max) in which genistein is a signal flavonoid. Plasma membrane vesicles prepared from soybean roots showed clear transport activity of genistein in an ATP-dependent manner. This transport activity was inhibited by sodium orthovanadate, a typical inhibitor of ATP-binding cassette (ABC) transporters, but was hardly affected by various ionophores, such as gramicidin D, nigericin, or valinomycin, suggesting involvement of an ABC transporter in the secretion of flavonoids from soybean roots. The Km and Vmax values of this transport were calculated to be 158 μm and 322 pmol mg protein−1 min−1, respectively. Competition experiments using various flavonoids of both aglycone and glucoside varieties suggested that this ABC-type transporter recognizes genistein and daidzein, another signaling compound in soybean root exudates, as well as other isoflavonoid aglycones as its substrates. Transport activity was constitutive regardless of the availability of nitrogen nutrition. This is, to our knowledge, the first biochemical characterization of the membrane transport of flavonoid secretion from roots.
Discovery and characterization of two novel CB1 receptor splice variants with modified N‐termini in mouse

Numerous studies have been carried out in the mouse model, investigating the role of the cannabinoid receptor type 1 (CB1). However, mouse CB1 (mCB1) receptor differs from human CB1 (hCB1) receptor in 13 amino acid residues. Two splice variants, hCB1a and hCB1b, diverging in their amino‐termini, have been reported to be unique for hCB1 and, via different signaling properties, contribute to CB1 receptor physiology and pathophysiology. We hypothesized that splice variants also exist for the mCB1 receptor and have different signaling properties. On murine hippocampal cDNA, we identified two novel mCB1 receptor splice variants generated by splicing of introns with 117 bp and 186 bp in the N‐terminal domain, corresponding to deletions of 39 or 62 amino acids, respectively. The mRNAs for the splice variants mCB1a and mCB1b are expressed at low levels in different brain regions. Western blot analysis of protein extracts from stably transfected HEK293 cells indicates a strongly reduced glycosylation because of the absence of two glycosylation sites in mCB1b. On‐cell western analysis in these stable lines revealed increased internalization of mCB1a and mCB1b upon stimulation with the agonist WIN55,212‐2 as compared to mCB1. Results also point toward an increased affinity to SR141716 for mCB1a, as well as slightly enhanced inhibition of neurotransmission compared to mCB1. In mCB1b, agonist‐induced MAPK phosphorylation was decreased compared to mCB1 and mCB1a. Identification of mouse CB1 receptor splice variants may help to explain differences found between human and mouse endocannabinoid systems and improve the understanding of CB1 receptor signaling and trafficking in different species.
CD4 Cell Priming and Tolerization Are Differentially Programmed by APCs upon Initial Engagement1

Bone marrow-derived APCs present both parenchymal-self and pathogen-derived Ags in a manner that elicits either T cell tolerization or immunity, respectively. To study the parameters that confer tolerogenic vs immunogenic APC function we used an adoptive transfer system in which naive TCR transgenic hemagglutinin (HA)-specific CD4+ T cells are either tolerized upon encountering HA expressed constitutively as a parenchymal self-Ag (self-HA) or primed to express effector function upon encountering transiently expressed vaccinia-derived HA (viral-HA). When the duration of viral-HA presentation was extended for the period required to elicit tolerization toward self-HA, CD4 cell tolerization to viral-HA did not occur. Furthermore, CD4 cells exhibited both phenotypic as well as functional differences during early stages of tolerization and priming, suggesting that these divergent differentiation processes are programmed soon after the initial APC-CD4 cell interaction. When mice expressing self-HA were infected with an irrelevant vaccinia, CD4 cell tolerization still occurred, indicating that priming vs tolerization cannot be explained by pathogen-induced third parties (i.e., non-APCs) that act directly on CD4 cells. Taken together, these results suggest that CD4 cell tolerization to parenchymal self-Ags and priming to pathogen-derived Ags are initiated by functionally distinct APCs.
Dosimetry of in situ activated dysprosium microspheres

This paper presents the results of a study aimed at investigating the dosimetry of stable dysprosium microspheres activated, in situ, by a linac generated photon beam. In phantom measurements of the neutron flux within an 18 MV photon beam were performed using CR-39 detectors and gold activation. The results were used in conjunction with a Monte Carlo computer simulation to investigate the dose distribution resulting from the activation of dysprosium (Dy) microspheres using an 18 MV photon beam. Different depths, lesion volumes and volume concentrations of microspheres are investigated. The linac lower collimator jaws are assumed completely closed to shield the tumour volume from the photon dose. Using a single AP field with 0 × 0 cm2 field size (closed jaws), a photon dose rate of 600 MU min−1 and 80 cm SSD for 10 min, an average dose exceeding 1 Gy can be delivered to spherical lesions of 0.5 cm and higher diameter. The variation of the average dose with the size of the lesion reaches saturation for tumour volumes exceeding 1 cm in diameter. This report shows that the photon beam of a high-energy linac can be used to activate Dy microspheres in situ and, as a result, deliver a significant dose of beta radiation. Non-radioactive Dy microspheres do not have the toxicity and imaging problems associated with commercially available yttrium-90 based products.
Hospice Enrollment, Local Hospice Utilization Patterns, and Rehospitalization in Medicare Patients.

BACKGROUND Rehospitalizations are prevalent and associated with decreased quality of life. Although hospice has been advocated to reduce rehospitalizations, it is not known how area-level hospice utilization patterns affect rehospitalization risk. OBJECTIVES The study objective was to examine the association between hospice enrollment, local hospice utilization patterns, and 30-day rehospitalization in Medicare patients. METHODS With a retrospective cohort design, 1,997,506 hospitalizations were assessed between 2005 and 2009 from a 5% national sample of Medicare beneficiaries. Local hospice utilization was defined using tertiles representing the percentage of all deaths occurring in hospice within each Hospital Service Area (HSA). Cox proportional hazard models were used to assess the relationship between 30-day rehospitalization, hospice enrollment, and local hospice utilization, adjusting for patient sociodemographics, medical history, and hospital characteristics. RESULTS Rates of patients dying in hospice were 27% in the lowest hospice utilization tertile, 41% in the middle tertile, and 53% in the highest tertile. Patients enrolled in hospice had lower rates of 30-day rehospitalization than those not enrolled (2.2% versus 18.8%; adjusted hazard ratio [HR], 0.12; 95% confidence interval [CI], 0.118-0.131). Patients residing in areas of low hospice utilization were at greater rehospitalization risk than those residing in areas of high utilization (19.1% versus 17.5%; HR, 1.05; 95% CI, 1.04-1.06), which persisted beyond that accounted for by individual hospice enrollment. CONCLUSIONS Area-level hospice utilization is inversely proportional to rehospitalization rates. This relationship is not fully explained by direct hospice enrollment, and may reflect a spillover effect of the benefits of hospice extending to nonenrollees.
Functional Mapping of Quantitative Trait Loci Underlying Growth Trajectories Using a Transform‐Both‐Sides Logistic Model

Summary The incorporation of developmental control mechanisms of growth has proven to be a powerful tool in mapping quantitative trait loci (QTL) underlying growth trajectories. A theoretical framework for implementing a QTL mapping strategy with growth laws has been established. This framework can be generalized to an arbitrary number of time points, where growth is measured, and becomes computationally more tractable, when the assumption of variance stationarity is made. In practice, however, this assumption is likely to be violated for age‐specific growth traits due to a scale effect. In this article, we present a new statistical model for mapping growth QTL, which also addresses the problem of variance stationarity, by using a transform‐both‐sides (TBS) model advocated by Carroll and Ruppert (1984, Journal of the American Statistical Association79, 321–328). The TBS‐based model for mapping growth QTL cannot only maintain the original biological properties of a growth model, but also can increase the accuracy and precision of parameter estimation and the power to detect a QTL responsible for growth differentiation. Using the TBS‐based model, we successfully map a QTL governing growth trajectories to a linkage group in an example of forest trees. The statistical and biological properties of the estimates of this growth QTL position and effect are investigated using Monte Carlo simulation studies. The implications of our model for understanding the genetic architecture of growth are discussed.
An in vitro model of mesenchymal stem cell targeting using magnetic particle labelling

The specific targeting of cells to sites of tissue damage in vivo is a major challenge precluding the success of stem cell‐based therapies. Magnetic particle‐based targeting may provide a solution. Our aim was to provide a model system to study the trapping and potential targeting of human mesenchymal stem cells (MSCs) during in vitro fluid flow, which ultimately will inform cell targeting in vivo. In this system magnet arrays were used to trap superparamagnetic iron oxide particle‐doped MSCs. The in vitro experiments demonstrated successful cell trapping, where the volume of cells trapped increased with magnetic particle concentration and decreased with increasing flow rate. Analysis of gene expression revealed significant increases in COL1A2 and SOX9. Using principles established in vitro, a proof‐of‐concept in vivo experiment demonstrated that magnetic particle‐doped, luciferase‐expressing MSCs were trapped by an implanted magnet in a subcutaneous wound model in nude mice. Our results demonstrate the effectiveness of using an in vitro model for testing superparamagnetic iron oxide particles to develop successful MSC targeting strategies during fluid flow, which ultimately can be translated to in vivo targeted delivery of cells via the circulation in a variety of tissue‐repair models. Copyright © 2012 John Wiley & Sons, Ltd.
Testing the Efficiency of the Art Market Using Quantile‐Based Unit Root Tests with Sharp and Smooth Breaks

This paper examines the efficiency market hypothesis for the art market using a novel nonlinear quantile-based unit root test while accounting for sharp shifts and smooth breaks in the data. We use quarterly data which covers 1998:1 and 2015:1. Our analysis is based on 15 art price indices: Contemporary, Drawings, France, Global index (Euro), Global index (USD), Modern art, Nineteenth century, Old Masters, Paintings, Photographies, Postwar, Prints, Sculptures, UK and US. We find evidence of structural shifts and nonlinearity in the art indices. We cannot reject the null of unit root and/or stationarity in the art series based on the conventional linear unit root tests and quantile-based test that did not account for structural breaks. However, when we use the same methods but accounting for sharp shifts and smooth breaks, we are able to reject the unit root null for each of the art indices. Further we find evidence of asymmetric behaviour in some of the indices: two global indices, Paintings, Prints, Sculptures, Modern art and Postwar, where unit root exist at some quantiles but not at others. Overall, our result suggest that the art market is inefficient. We provide some practical and policy implications of our findings.
Learning Convolutional Domain-Robust Representations for Cross-View Face Recognition

This paper proposes to obtain high-level, domain-robust representations for cross-view face recognition. Specially, we introduce Convolutional Deep Belief Networks (CDBN) as the feature learning model, and an CDBN based interpolating path between the source and target views is built to model the correlation of cross-view data. The promising results outperform other state-of-the-art methods.
Deficits in short-term memory in posttraumatic stress disorder.

OBJECTIVE The purpose of this study was to compare the memory function of patients with posttraumatic stress disorder (PTSD) to that of matched comparison subjects. METHOD Vietnam veterans with combat-related PTSD (N = 26) were compared to physically healthy comparison subjects (N = 15) matched for age, race, sex, years of education, handedness, socioeconomic status, and alcohol abuse. Memory and intelligence were assessed with a battery of neuropsychological tests, including the Russell revision of the Wechsler Memory Scale, the Selective Reminding Test, and subtests of the Wechsler Adult Intelligence Scale-Revised (WAIS-R). RESULTS The PTSD patients scored significantly lower than the comparison subjects on the Wechsler Memory Scale logical memory measures for immediate recall (mean = 11.6, SD = 3.3 versus mean = 20.9, SD = 6.6) and delayed recall (mean = 8.0, SD = 3.3 versus mean = 17.8, SD = 6.4). The PTSD patients also scored significantly lower on the total recall, long-term storage, long-term retrieval, and delayed recall measures for the verbal component of the Selective Reminding Test and on the recall, long-term storage, long-term retrieval, and continuous long-term retrieval measures for the visual component of the Selective Reminding Test. There was no significant difference between the PTSD patients and comparison subjects in prorated full-scale IQ as measured by the WAIS-R. CONCLUSIONS Patients with PTSD may have deficits in short-term memory. Counseling and rehabilitation that address these deficits may be of value for PTSD patients.
Study on Evaluation System of Common Physical Education Class Teaching Quality in Colleges

The traditional common physical education class teaching evaluation in college is normally provided by the school leaders or the organization wardens from Educational Administration.Due to neglect the particularity of physical education teaching,evaluation is often used the same standards and mode with other courses to evaluate the quality of physical education teaching.Scientific evaluation on college Physical Education teaching should not only rely on the school administration,even more dependent on the students and colleagues,quantitative analysis combined with quantitative statistics can be an objective,comprehensive,true reflection of the quality of Physical Education teaching.
Cytochrome P450 Regulation by α-Tocopherol in Pxr-Null and PXR-Humanized Mice

The pregnane X receptor (PXR) has been postulated to play a role in the metabolism of α-tocopherol owing to the up-regulation of hepatic cytochrome P450 (P450) 3A in human cell lines and murine models after α-tocopherol treatment. However, in vivo studies confirming the role of PXR in α-tocopherol metabolism in humans presents significant difficulties and has not been performed. PXR-humanized (hPXR), wild-type, and Pxr-null mouse models were used to determine whether α-tocopherol metabolism is influenced by species-specific differences in PXR function in vivo. No significant difference in the concentration of the major α-tocopherol metabolites was observed among the hPXR, wild-type, and Pxr-null mice through mass spectrometry-based metabolomics. Gene expression analysis revealed significantly increased expression of Cyp3a11 as well as several other P450s only in wild-type mice, suggesting species-specificity for α-tocopherol activation of PXR. Luciferase reporter assay confirmed activation of mouse PXR by α-tocopherol. Analysis of the Cyp2c family of genes revealed increased expression of Cyp2c29, Cyp2c37, and Cyp2c55 in wild-type, hPXR, and Pxr-null mice, which suggests PXR-independent induction of Cyp2c gene expression. This study revealed that α-tocopherol is a partial agonist of PXR and that PXR is necessary for Cyp3a induction by α-tocopherol. The implications of a novel role for α-tocopherol in Cyp2c gene regulation are also discussed.
Self-Tuning Virtual Synchronous Machine: A Control Strategy for Energy Storage Systems to Support Dynamic Frequency Control

This paper investigates the use of a virtual synchronous machine (VSM) to support dynamic frequency control in a diesel-hybrid autonomous power system. The proposed VSM entails controlling the grid-interface converter of an energy storage system (ESS) to emulate the inertial response and the damping power of a synchronous generator. In addition, self-tuning algorithms are used to continuously search for optimal parameters during the operation of the VSM in order to minimize the amplitude and rate of change of the frequency variations and the power flow through the ESS. The performances of the proposed self-tuning (ST)-VSM and the constant parameters (CP)-VSM were evaluated by comparing their inertial responses and their damping powers for different scenarios of load variations. For the simulated cases, the ST-VSM achieved a similar performance to that of the CP-VSM, while reducing the power flow through the ESS in up to 58%. Moreover, in all the simulated scenarios, the ST-VSM was found to be more efficient than the CP-VSM in attenuating frequency variations, i.e., it used less energy per Hertz reduced.
Rayleigh backscattering of four-wave mixing in bidirectional optical communication systems

The Rayleigh backscatter properties of four-wave-mix light (FWM) are theoretically and experimentally investigated for the first time. The experimental results agree well with the theoretical predictions. It was found that the Rayleigh backscattering of FWM light may cause severe crosstalk problems in bidirectional multichannel systems.
Class 1 Integrons Increase Trimethoprim-Sulfamethoxazole MICs against Epidemiologically Unrelated Stenotrophomonas maltophilia Isolates

ABSTRACT Twenty-five plasmid-specified antimicrobial resistance determinants common to gram-negative bacilli from nosocomial infection were investigated from 31 Stenotrophomonas maltophilia isolates. Twenty-four clones were identified by pulsed-field gel electrophoresis, and in three clones that exhibited an increased trimethoprim-sulfamethoxazole MIC, the sul1 determinant was found. These results support not only the higher spread of class 1 integrons compared to other mechanisms but also the potential limitation of using trimethoprim-sulfamethoxazole for therapy of severe S. maltophilia infections.