Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement of cerebral perfusion territories using arterial spin labelling

The ability to assess the perfusion territories of major cerebral arteries can be a valuable asset to the diagnosis of a number of cerebrovascular diseases. Recently, several arterial spin labeling (ASL) techniques have been proposed for determining the cerebral perfusion territories of individual arteries by three different approaches: (1) using a dedicated labeling radio frequency (RF) coil; (2) applying selective inversion of spatially confined areas; (3) employing multidimensional RF pulses. Methods that use a separate labeling RF coil have high signal‐to‐noise ratio (SNR), low RF power deposition, and unrestricted three‐dimensional coverage, but are mostly limited to separation of the left and right circulation, and do require extra hardware, which may limit their implementation in clinical systems. Alternatively, methods that utilize selective inversion have higher flexibility of implementation and higher arterial selectivity, but suffer from imaging artifacts resulting from interference between the labeling slab and the volume of interest. The goal of this review is to provide the reader with a critical survey of the different ASL approaches proposed to date for determining cerebral perfusion territories, by discussing the relative advantages and disadvantages of each technique, so as to serve as a guide for future refinement of this promising methodology. Copyright © 2007 John Wiley & Sons, Ltd.
A fast content delivery mechanism using the CCN and enhanced base stations

The Internet was designed to support host-oriented services. However, users are typically interested in the content itself rather than the location of the content. As the usage of the Internet for content retrieval is increasing rapidly, some intelligent methods have to be employed in the base stations to provide faster and seamless content delivery. In this paper, we propose a CCN-based fast content delivery mechanism using an enhanced base station called smart base station (SBS) which incorporates advanced features such as content-oriented communication, a learning module, prediction-based mobility support, and an efficient storage management scheme. Simulation results are also provided to show the feasibility of the proposed mechanism.
A new mouse line for cell ablation by diphtheria toxin subunit A controlled by a Cre‐dependent FLEx switch

Recombinase responsive mouse lines expressing diphtheria toxin subunit A (DTA) are well established tools for targeted ablation of genetically defined cell populations. Here we describe a new knock‐in allele at the Gt(Rosa)26Sor locus that retains the best features of previously described DTA alleles—including a CAG promoter, attenuated mutant DTA cDNA, and ubiquitous EGFP labeling—with the addition of a Cre‐dependent FLEx switch for tight control of expression. The FLEx switch consists of two pairs of antiparallel lox sites requiring Cre‐mediated recombination for inversion of the DTA to the proper orientation for transcription. We demonstrate its utility by Cre‐dependent ablation of both a broad domain in the embryonic nervous system and a discrete population of cells in the fetal gonads. We conclude that this new DTA line is useful for targeted ablation of genetically‐defined cell populations.
Development of a TaqMan assay for the six major genotypes of hepatitis C virus: Comparison with commercial assays

A quantitative real‐time PCR assay was developed that detects genomic RNA from reference strains representing the six major genotypes of hepatitis C virus (HCV) with equal sensitivity and accurately measured HCV RNA in JFH1 HCV‐infected Huh7.5 cells. The method is indirectly calibrated to the first international (WHO 96/790) HCV standard preparation and has a linear dynamic range of 102.6–106.5 IU/ml. In addition, the inter‐ and intra‐assay precision were ∼3% CV and <2% CV, respectively. Comparison with results obtained by commercially available HCV RNA Nucleic Acid Technology kits (Versant HCV RNA 3.0 b‐DNA and Amplicor HCV Monitor), that also employ the WHO standard, allowed validation of the TaqMan assay against all major HCV genotypes. Both commercial methods detected HCV RNA over a wide dynamic range, but showed a consistent difference of about 0.3 log10 when evaluating samples of different HCV genotypes. The genome titers obtained with the three methods correlated with the infectivity titers previously determined for the HCV reference strains. TaqMan assays have become an essential tool to follow viral load in clinical samples and cell culture‐based experiments and this technology offers significant advantages in linear dynamic range, sensitivity and customization. J. Med. Virol. 80:72–79, 2008. © 2007 Wiley‐Liss, Inc.
Differential Influence of the Antiretroviral Pharmacokinetic Enhancers Ritonavir and Cobicistat on Intestinal P-Glycoprotein Transport and the Pharmacokinetic/Pharmacodynamic Disposition of Dabigatran

ABSTRACT Dabigatran etexilate (DE) is a P-glycoprotein (P-gp) probe substrate, and its active anticoagulant moiety, dabigatran, is a substrate of the multidrug and toxin extrusion protein-1 (MATE-1) transporter. The antiretroviral pharmacokinetic enhancers, ritonavir and cobicistat, inhibit both these transporters. Healthy volunteers received single doses of DE at 150 mg alone, followed by ritonavir at 100 mg or cobicistat at 150 mg daily for 2 weeks. DE was then given 2 h before ritonavir or cobicistat. One week later, DE was given simultaneously with ritonavir or cobicistat. No significant increases in dabigatran pharmacokinetic (PK) exposure or thrombin time (TT) measures were observed with the simultaneous administration of ritonavir. Separated administration of ritonavir resulted in a mean decrease in dabigatran PK exposure of 29% (90% confidence interval [CI], 18 to 40%) but did not significantly change TT measures. However, cobicistat increased dabigatran PK exposure (area under the concentration-versus-time curve from time zero to infinity and maximum plasma concentration) by 127% each (90% CI, 81 to 173% and 59 to 196%, respectively) and increased TT measures (33% for the area-under-the-effect curve from time zero to 24 h [90% CI, 22 to 44%] and 51% for TT at 24 h [90% CI, 22 to 78%]) when given simultaneously with dabigatran. Similar increases were observed when cobicistat was administered separately by 2 h from the administration of dabigatran. In all comparisons, no significant increase in the dabigatran elimination half-life was observed. Therefore, it is likely safe to coadminister ritonavir with DE, while there is a potential need for reduced dosing and prudent clinical monitoring with the coadministration of cobicistat due to the greater net inhibition of intestinal P-gp transport and increased bioavailability. (This study has been registered at ClinicalTrials.gov under identifier NCT01896622.)
American Cancer Society, American Society for Colposcopy and Cervical Pathology, and American Society for Clinical Pathology Screening Guidelines for the Prevention and Early Detection of Cervical Cancer

Abstract An update to the American Cancer Society (ACS) guideline regarding screening for the early detection of cervical precancerous lesions and cancer is presented. The guidelines are based on a systematic evidence review, contributions from six working groups, and a recent symposium co-sponsored by the ACS, American Society for Colposcopy and Cervical Pathology (ASCCP), and American Society for Clinical Pathology (ASCP), which was attended by 25 organizations. The new screening recommendations address age-appropriate screening strategies, including the use of cytology and high-risk human papillomavirus (HPV) testing, follow-up (e.g., management of screen positives and screening interval for screen negatives) of women after screening, age at which to exit screening, future considerations regarding HPV testing alone as a primary screening approach, and screening strategies for women vaccinated against HPV16/18 infections.
Using data mining to predict success in a weight loss trial

BACKGROUND Traditional methods for predicting weight loss success use regression approaches, which make the assumption that the relationships between the independent and dependent (or logit of the dependent) variable are linear. The aim of the present study was to investigate the relationship between common demographic and early weight loss variables to predict weight loss success at 12 months without making this assumption. METHODS Data mining methods (decision trees, generalised additive models and multivariate adaptive regression splines), in addition to logistic regression, were employed to predict: (i) weight loss success (defined as ≥5%) at the end of a 12-month dietary intervention using demographic variables [body mass index (BMI), sex and age]; percentage weight loss at 1 month; and (iii) the difference between actual and predicted weight loss using an energy balance model. The methods were compared by assessing model parsimony and the area under the curve (AUC). RESULTS The decision tree provided the most clinically useful model and had a good accuracy (AUC 0.720 95% confidence interval = 0.600-0.840). Percentage weight loss at 1 month (≥0.75%) was the strongest predictor for successful weight loss. Within those individuals losing ≥0.75%, individuals with a BMI (≥27 kg m-2 ) were more likely to be successful than those with a BMI between 25 and 27 kg m-2 . CONCLUSIONS Data mining methods can provide a more accurate way of assessing relationships when conventional assumptions are not met. In the present study, a decision tree provided the most parsimonious model. Given that early weight loss cannot be predicted before randomisation, incorporating this information into a post randomisation trial design may give better weight loss results.
Hierarchical Interaction Structure of Neural Activities in Cortical Slice Cultures

Recent advances in the analysis of neuronal activities suggest that the instantaneous activity patterns can be mostly explained by considering only first-order and pairwise interactions between recorded elements, i.e., action potentials or local field potentials (LFP), and do not require higher-than-pairwise-order interactions. If generally applicable, this pairwise approach greatly simplifies the description of network interactions. However, an important question remains: are the recorded elements the units of interaction that best describe neuronal activity patterns? To explore this, we recorded spontaneous LFP peak activities in cortical organotypic cultures using planar, integrated 60-microelectrode arrays. We compared predictions obtained using a pairwise approach with those using a hierarchical approach that uses two different spatial units for describing the activity interactions: single electrodes and electrode clusters. In this hierarchical model, short-range interactions within each cluster were modeled by pairwise interactions of electrode activities and long-range interactions were modeled by pairwise interactions of cluster activities. Despite the relatively low number of parameters used, the hierarchical model provided a more accurate description of the activity patterns than the pairwise model when applied to ensembles of 10 electrodes. Furthermore, the hierarchical model was successfully applied to a larger-scale data of ∼60 electrodes. Electrode activities within clusters were highly correlated and spatially contiguous. In contrast, long-range interactions were diffuse, suggesting the presence of higher-than-pairwise-order interactions involved in the LFP peak activities. Thus, the identification of appropriate units of interaction may allow for the successful characterization of neuronal activities in large-scale networks.
Catalytic and chaperone-like functions in an intrinsically disordered protein associated with desiccation tolerance

Intrinsically disordered proteins (IDPs) lack well-defined structure but are widely represented in eukaryotic proteomes. Although the functions of most IDPs are not understood, some have been shown to have molecular recognition and/or regulatory roles where their disordered nature might be advantageous. Anhydrin is an uncharacterized IDP induced by dehydration in an anhydrobiotic nematode, Aphelenchus avenae. We show here that anhydrin is a moonlighting protein with two novel, independent functions relating to desiccation tolerance. First, it has a chaperone-like activity that can reduce desiccation-induced enzyme aggregation and inactivation in vitro. When expressed in a human cell line, anhydrin localizes to the nucleus and reduces the propensity of a polyalanine expansion protein associated with oculopharyngeal muscular dystrophy to form aggregates. This in vivo activity is distinguished by a loose association of anhydrin with its client protein, consistent with a role as a molecular shield. In addition, anhydrin exhibits a second function as an endonuclease whose substrates include supercoiled, linear, and chromatin linker DNA. This nuclease activity could be involved in either repair of desiccation-induced DNA damage incurred during anhydrobiosis or in apoptotic or necrotic processes, for example, but it is particularly unexpected for anhydrin because IDP functions defined to date anticorrelate with enzyme activity. Enzymes usually require precise three-dimensional positioning of residues at the active site, but our results suggest this need not be the case. Anhydrin therefore extends the range of IDP functional categories to include catalysis and highlights the potential for the discovery of new functions in disordered proteomes.
CDK13, a New Potential Human Immunodeficiency Virus Type 1 Inhibitory Factor Regulating Viral mRNA Splicing

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) Tat is a 14-kDa viral protein that acts as a potent transactivator by binding to the transactivation-responsive region, a structured RNA element located at the 5′ end of all HIV-1 transcripts. Tat transactivates viral gene expression by inducing the phosphorylation of the C-terminal domain of RNA polymerase II through several Tat-activated kinases and by recruiting chromatin-remodeling complexes and histone-modifying enzymes to the HIV-1 long terminal repeat. Histone acetyltransferases, including p300 and hGCN5, not only acetylate histones but also acetylate Tat at lysine positions 50 and 51 in the arginine-rich motif. Acetylated Tat at positions 50 and 51 interacts with a specialized protein module, the bromodomain, and recruits novel factors having this particular domain, such as P/CAF and SWI/SNF. In addition to having its effect on transcription, Tat has been shown to be involved in splicing. In this study, we demonstrate that Tat interacts with cyclin-dependent kinase 13 (CDK13) both in vivo and in vitro. We also found that CDK13 increases HIV-1 mRNA splicing and favors the production of the doubly spliced protein Nef. In addition, we demonstrate that CDK13 acts as a possible restriction factor, in that its overexpression decreases the production of the viral proteins Gag and Env and subsequently suppresses virus production. Using small interfering RNA against CDK13, we show that silencing of CDK13 leads to a significant increase in virus production. Finally, we demonstrate that CDK13 mediates its effect on splicing through the phosphorylation of ASF/SF2.
Areas of high conservation value at risk by plant invaders in Georgia under climate change

Abstract Invasive alien plants (IAP) are a threat to biodiversity worldwide. Understanding and anticipating invasions allow for more efficient management. In this regard, predicting potential invasion risks by IAPs is essential to support conservation planning into areas of high conservation value (AHCV) such as sites exhibiting exceptional botanical richness, assemblage of rare, and threatened and/or endemic plant species. Here, we identified AHCV in Georgia, a country showing high plant richness, and assessed the susceptibility of these areas to colonization by IAPs under present and future climatic conditions. We used actual protected areas and areas of high plant endemism (identified using occurrences of 114 Georgian endemic plant species) as proxies for AHCV. Then, we assessed present and future potential distribution of 27 IAPs using species distribution models under four climate change scenarios and stacked single‐species potential distribution into a consensus map representing IAPs richness. We evaluated present and future invasion risks in AHCV using IAPs richness as a metric of susceptibility. We show that the actual protected areas cover only 9.4% of the areas of high plant endemism in Georgia. IAPs are presently located at lower elevations around the large urban centers and in western Georgia. We predict a shift of IAPs toward eastern Georgia and higher altitudes and an increased susceptibility of AHCV to IAPs under future climate change. Our study provides a good baseline for decision makers and stakeholders on where and how resources should be invested in the most efficient way to protect Georgia's high plant richness from IAPs.
Genetic, Psychological, and Personal Network Factors Associated With Changes in Binge Drinking Over 2 Years Among Mexican Heritage Adolescents in the USA.

Background Despite prevalent binge drinking and alcohol-dependent symptoms among Hispanics, few studies have examined how multidimensional factors influence Hispanic adolescents' binge drinking. Purpose This study examines the effects of genetic, psychological, and social network factors on binge drinking over time among Mexican heritage adolescents in the USA and whether there are correlations among genetic variants that are associated with binge drinking and psychological and network characteristics. Methods Mexican heritage adolescents (n = 731) participated in a longitudinal study, which included genetic testing at baseline, alcohol use assessments at first and second follow-ups, and questionnaires on sensation seeking, impulsivity, and peer and family network characteristics at second follow-up. Logistic regression and Spearman correlation analyses were performed. Results After adjusting for demographic characteristics, underlying genetic clustering, and binge drinking at first follow-up, two genetic variants on tryptophan hydroxylase 2 (TPH2; rs17110451, rs7963717), sensation seeking and impulsivity, and having a greater fraction of peers who drink or encourage drinking alcohol were associated with greater risk whereas another genetic variant on TPH2 (rs11178999) and having a greater fraction of close family relationships were associated with reduced risk for binge drinking at second follow-up. Genetic variants in TPH1 (rs591556) were associated with sensation seeking and impulsivity, while genetic variants in TPH2 (rs17110451) were associated with the fraction of drinkers in family. Conclusions Results reveal that genetic variants in the serotonin pathway, behavioral disinhibition traits, and social networks exert joint influences on binge drinking in Mexican heritage adolescents in the USA.
DETECTION OF INSECTS IN BULK WHEAT SAMPLES WITH MACHINE VISION

Digital imaging techniques were used to identify insects and body parts (adult lesser grain borer) of Rhyzopertha dominica beetles in bulk wheat samples. The samples contained dockage (weed seeds and damaged wheat kernels), which made the identification of insects more difficult. Multispectral analysis (Red, Green, Blue) was used in combination with pattern recognition techniques. Insect identification experiments were done with subimages of 8 × 8 pixels. Statistical multivariate analysis and structural patterns were used for finding insects. The position of the insect (ventral, dorsal, side) and particles clinging to the insect affected recognition success. Recognition success of R. Dominica adults, some grass seeds, and other non-wheat components was higher than 90%.
The influence of tissue microenvironment on stem cell–based cartilage repair

Mesenchymal stem/progenitor cells and induced pluripotent stem cells have become viable cell sources for prospective cell‐based cartilage engineering and tissue repair. The development and function of stem cells are influenced by the tissue microenvironment. Specifically, the local tissue microenvironment can dictate how stem cells integrate into the existing tissue matrix and how successfully they can restore function to the damaged area in question. This review focuses on the microenvironmental features of articular cartilage and how they influence stem cell–based cartilage tissue repair. Also discussed are current tissue‐engineering strategies used in combination with cell‐based therapies, all of which are designed to mimic the natural properties of cartilage tissue in order to achieve a better healing response.
The relationship between family dining practices, parenting style and family functioning and child learning

Abstract Background: This study examined the association between family dining practices, parenting style and family functioning with child learning among Chinese families with preschool children. Methods: Participants included 663 parent-child dyads recruited from Hong Kong preschools. Child learning was measured through individual assessment of children on preschool concepts, parent and teacher report of child learning. Parents completed questionnaires on parenting style, family functioning, frequency of parents/grandparents dining with target children, mealtime television viewing and feeding practice. Results: Child attainment of preschool concepts was associated with child sex and frequency of father eating with child. Parent report of child learning was associated with child sex, parenting style, family functioning and family feeding practice. Teacher report of child learning was associated with child sex. Conclusion: Child learning could potentially be influenced by family practice including family dining practices, parenting style and family functioning.
Analysis of Regulating Variables in the Changes of Different People's Exercises—Based on the Test of the Integrated Model of HAPTA and TPB

Based on the integrated model of HAPA and TPB as well as on questionnaire and data analysis,this paper tries to make a study of the city young adults(n=152),college students(n=204)and healthy city adults(n=97)in China,aiming at promoting the prediction and the effect of interference on their exercises.The result shows that 1)the integrated model of HAPA and TPB caters more to the prediction and interference of healthy adults' exercises,with the theoretical model closer to the practical model(with 35% of the non-successive model respectively),while college students and young adults take a lower percentage.2)The interactions among action intention,action plan and exercises vary in accordance to the different groups of people.The route coefficient of the three factors among Chinese healthy adults is conspicuous(Y=0.47,P0.05;Y=0.48,P0.05),while college students and young adults show a rather different state.3)The cause variables of action intention vary greatly among different groups of people,with young adults and college students showing more direct route rather than indirect route in terms of exercises.At the same time,the study shows that his father's exercises produce a more conspicuous impact on the young adult(β=0.47,P0.05). The study reaches the conclusion that this model suits better the interference and prediction of the different stages of exercises on the part of Chinese healthy adults;it fits only a small part of the interference and prediction of young adults and college students,and many cause variables prepare more conspicuously direct routes(such as social support,subjective regulation,etc.)rather than features of a phase.It asserts that the interference strategies should be implemented according to the features of different variables among the different groups of people so that a better effect can be achieved.