Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple sequences and factors are involved in stability/degradation of Awnt‐1, Awnt‐5A and Awnt‐5B mRNAs during axolotl development

Following fertilization in amphibian, early cleavage stages are maternally controlled at a post‐transcriptional level before initiation of zygotic transcriptions at the mid blastula transition (MBT). We document the expression levels of the axolotl Awnt‐1, Awnt‐5A and Awnt‐5B genes as well as the adenylation states of their corresponding mRNAs from the end of oogenesis until the tailbud stages. Awnt‐1/‐5A RNAs are stable until MBT then degraded before gastrulation. Awnt‐5B RNAs are degraded at fertilization and zygotically expressed after MBT with high level expression from gastrulation. Estimation of the poly(A) tail lengths reveals no direct link between deadenylation and degradation periods for each Awnt transcript. To investigate the molecular mechanisms involved in Awnt‐1/‐5A/‐5B RNAs stability, synthetic full‐length or 3′ untranslated region (UTR) Awnt RNAs progressively deleted from their 3′ end were microinjected in axolotl oocytes, unfertilized and fertilized eggs. We identified degrading and stabilizing sequences in the 3′UTR whose activities depend on the cellular context and are also modulated by the 5′UTR and coding sequence within each RNA. Using axolotl nuclear extracts from stage VI oocytes, we further produced evidence of destabilizing factors targeting the Awnt‐5B RNAs. Altogether, these results show that oocyte maturation and late cleavages following MBT are two important periods when axolotl Wnt RNAs are highly regulated.
Relating Environmental Variation to Selection on Reaction Norms: An Experimental Test

Theoretical models predict that selection on reaction norms should depend on the relative frequency of environmental states experienced by a population. We report a laboratory experimental test of this prediction for thermal performance curves of larval growth rate in Pieris rapae in relation to their thermal environment. We measured short‐term relative growth rate (RGR) for each individual at a series of five temperatures, and then we assigned individuals randomly to warm or cool selection treatments, which differ in the frequency distributions of environmental temperatures. Selection gradient analyses of two independent experiments demonstrated significant positive selection for increasing RGR, primarily through its effects on survival to adulthood and on development rate. In both the warm and cool selection treatments, the magnitude of directional selection on RGR was consistently greater at lower (suboptimal) temperatures than at higher temperatures; differences in selection between the treatments did not match model predictions. The temporal order and duration of environmental conditions may affect patterns of selection on thermal performance curves and other continuous reaction norms, complicating the connections between variation in environment, phenotype, and fitness.
Predictors and Outcomes of Pneumonia in Patients With Spontaneous Intracerebral Hemorrhage

Objectives. Pneumonia is an important complication of spontaneous intracerebral hemorrhage (sICH). The purpose of this study was to determine the predictors and outcomes of the development of pneumonia in patients with sICH. Methods. In total, 290 consecutive patients with sICH admitted within 24 hours of stroke onset were investigated in a single center, retrospective study from January 2006 to July 2009. Clinical, biochemical, and imaging variables were registered. Stroke severity and functional outcomes were evaluated with the Glasgow Coma Scale (GCS) and modified Rankin Scale (mRS). Baseline variables that predicted pneumonia were investigated and outcomes were assessed. Results. The association of our primary exposure variables, such as mechanical ventilation, tube feeding, dysphagia, and tracheostomy, with pneumonia was highly significant (P < .0001, for each variable). For mechanical ventilation, we observed an odds ratio (OR; 95% confidence interval [CI]) of 9.42 (4.24-20.9); for tube feeding, OR = 22.3 (8.91-55.8); for dysphagia, OR = 13.1 (4.66-36.7); and for tracheostomy, OR = 26.8 (8.02-89.3). After adjustment of potential confounders including GCS and mRS on admission, the use of angiotensin-converting enzyme inhibitors, proton pump inhibitors, and H2 blockers, all the adjusted OR (ORa) remained significant. For mechanical ventilation, the minimum ORa was 3.72 (95% CI: 1.68-8.26) when adjusted for GCS. For both dysphagia and tracheostomy, mRS reduced OR to 7.46 (95% CI: 3.34-10.6) in the case of dysphagia with an ORa of 16.2 (95% CI: 4.98 to 52.8) for tracheostomy. For tube feeding, both GCS and mRS reduced ORa; the former to 14.7 (95% CI: 6.16-35.0) and the latter to 15.7 (95% CI: 6.63-37.0). Pneumonia shows a significant effect on the morbidity (P = .003), length of stay (P < .0001), and mortality (P = .041) rate of the patients. Conclusion. Mechanical ventilation, tube feeding, dysphagia, and tracheostomy are exposures associated with increased risk of the development of pneumonia in patients with sICH. Pneumonia is associated with an increase in morbidity, length of stay, and mortality among patients with sICH.
Pain / Analgesia evaluation using heart rate variability analysis

The optimization of analgesic drugs delivery during general anesthesia requires to evaluate the pain/analgesia balance. Heart rate variability analysis has been shown in several studies to measure the autonomic nervous system tone, which is strongly influenced by anesthetic drugs. Recording RR series during general anesthesia enabled us to observe that the respiratory sinus arrhythmia pattern changed when a surgical stimulation was painful, even though the patient was not conscious. We developed a pain/analgesia evaluation algorithm based on the magnitude analysis of the respiratory patterns on the RR series. The parameters computed from this algorithm were recorded in thirty nine patients during general anesthesia. We retrospectively compared our parameters at different levels of analgesia during surgical stimulation, and found that they were related to pain/analgesia and relatively independent from other anesthesia related events like hypnosis and haemodynamic conditions
Visual Phonics: An English Code Buster?

Visual Phonics is an instructional program to provide print awareness, alphabet knowledge, and sound-letter correspondence for children with hearing loss who experience difficulty developing a foundation of phonemic awareness skills. Its purpose is "to clarify the sound symbol relationship between spoken English and print" (Waddy-Smith & Wilson, 2003, p. 15). It is implemented in numerous school districts, particularly in California and Florida, and can be learned in a 2-day workshop. Administrators, teachers, and speech pathologists see potential benefit in using Visual Phonics to help students with hearing loss raise their achievement scores in reading and spelling. However, it is critical to note that Visual Phonics has virtually no research base. Researchers, teachers, and speech pathologists are called upon to collect their data and begin research on the effectiveness of Visual Phonics. This is a case in which the research-to-practice gap must be closed.
Songs of the Caged, Songs of the Free: Music and the Vietnamese Refugee Experience

List of Illustrations Preface Acknowledgments Introduction Part I 1. The Journey 2. Prologue 3. First Asylum: The Camp in Palawan, Philippines 4. Springboard to Resettlement: The Refugee Processing Center Part II 5. Prologue 6. Vietnamese in New Jersey: The Birth of Community 7. Orange County, California, and the Vietnamese 8. Vietnamese Americans in Orange County: The Musical Life 9. Codetta: After Normalization. Epilogue Appendix Notes References Index
Multi-view Clustering with Adaptively Learned Graph

Multi-view clustering, which aims to improve the clustering performance by exploring the data’s multiple representations, has become an important research direction. Graph based methods have been widely studied and achieve promising performance for multi-view clustering. However, most existing multi-view graph based methods perform clustering on the fixed input graphs, and the results are dependent on the quality of input graphs. In this paper, instead of fixing the input graphs, we propose Multi-view clustering with Adaptively Learned Graph (MALG), learning a new common similarity matrix. In our model, we not only consider the importance of multiple graphs from view level, but also focus on the performance of similarities within a view from sample-pair level. Sample-pair-specific weights are introduced to exploit the connection across views in more depth. In addition, the obtained optimal graph can be partitioned into specific clusters directly, according to its connected components. Experimental results on toy and real-world datasets demonstrate the efficacy of the proposed algorithm.
Distinct patterns of hepcidin and iron regulation during HIV-1, HBV, and HCV infections

Significance Altered iron levels correlate with disease progression in HIV type-1 (HIV-1) infection, and cellular iron promotes HIV-1 replication. In chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, increased liver iron levels contribute to disease. The peptide hormone hepcidin controls iron distribution. We find that hepcidin increases during the acute phase of HIV-1 infection, early hepcidin predicts later plasma viral set-point, and hepcidin remains high even in chronically infected individuals receiving antiretroviral therapy. Conversely hepcidin is not induced, and blood iron is not decreased, during the acute response to HBV and HCV. Therefore, the nature of iron redistribution during the response to infections is a pathogen-specific phenomenon; furthermore, the deleterious effects of chronic infection on hepcidin and iron appear to be established early in infection. During HIV type-1 (HIV-1), hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, altered iron balance correlates with morbidity. The liver-produced hormone hepcidin dictates systemic iron homeostasis. We measured hepcidin, iron parameters, cytokines, and inflammatory markers in three cohorts: plasma donors who developed acute HIV-1, HBV, or HCV viremia during the course of donations; HIV-1–positive individuals progressing from early to chronic infection; and chronically HIV-1–infected individuals (receiving antiretroviral therapy or untreated). Hepcidin increased and plasma iron decreased during acute HIV-1 infection, as viremia was initially detected. In patients transitioning from early to chronic HIV-1 infection, hepcidin in the first 60 d of infection positively correlated with the later plasma viral load set-point. Hepcidin remained elevated in individuals with untreated chronic HIV-1 infection and in subjects on ART. In contrast to HIV-1, there was no evidence of hepcidin up-regulation or hypoferremia during the primary viremic phases of HCV or HBV infection; serum iron marginally increased during acute HBV infection. In conclusion, hepcidin induction is part of the pathogenically important systemic inflammatory cascade triggered during HIV-1 infection and may contribute to the establishment and maintenance of viral set-point, which is a strong predictor of progression to AIDS and death. However, distinct patterns of hepcidin and iron regulation occur during different viral infections that have particular tissue tropisms and elicit different systemic inflammatory responses. The hypoferremia of acute infection is therefore a pathogen-specific, not universal, phenomenon.
Discectomy strategies for lumbar disc herniation: results of the LAPDOG trial

Since its introduction in the 1970s percutaneous treatment of lumbar disc herniation has been an attractive concept that has been the object of technical development and clinical application throughout the world. Little scientific evaluation of the efficacy and effectiveness of the procedure has been done. To estimate the success rates of automated percutaneous and conventional discectomy in comparable patients and to document the resource consumption of patients treated in these ways, a multicenter randomized clinical trial designed to compare both treatment efficacy and cost-effectiveness of automated percutaneous discectomy and conventional discectomy in adult patients with no prior lumbar spinal surgery, no coexistent lumbar spinal disease, unilateral single level lumbar radiculopathy with images confirming disc herniation at the appropriate level. In the course of the trial important technical advances allowing epidural extraction of free-fragment disc herniation was incorporated into the trial. It was not possible to enroll the required number of patients to complete the trial. Of 5735 screened patients, 95 were eligible and 36 were enrolled. Two elected watchful waiting and did not have any surgical procedure. Eight patients were lost to follow-up. Among the 27 evaluable patients, 41% of the percutaneous discectomy patients and 40% of the conventional discectomy patients were assessed as achieving "success" on the primary outcome measure. No clinical trial of any percutaneous discectomy technique provides definitive evidence supporting the efficacy or effectiveness of the procedure. Such evidence should be required by patients to whom such procedures are proposed and those who are asked to pay for them.
The role of activation functions 1 and 2 of estrogen receptor‐α for the effects of estradiol and selective estrogen receptor modulators in male mice

Estradiol (E2) is important for male skeletal health and the effect of E2 is mediated via estrogen receptor (ER)‐α. This was demonstrated by the findings that men with an inactivating mutation in aromatase or a nonfunctional ERα had osteopenia and continued longitudinal growth after sexual maturation. The aim of the present study was to evaluate the role of different domains of ERα for the effects of E2 and selective estrogen receptor modulators (SERMs) on bone mass in males. Three mouse models lacking either ERαAF‐1 (ERαAF‐10), ERαAF‐2 (ERαAF‐20), or the total ERα (ERα−/−) were orchidectomized (orx) and treated with E2 or placebo. E2 treatment increased the trabecular and cortical bone mass and bone strength, whereas it reduced the thymus weight and bone marrow cellularity in orx wild type (WT) mice. These parameters did not respond to E2 treatment in orx ERα−/− or ERαAF‐20 mirx ERαAF‐10 mice were tissue‐dependent, with a clear response in cortical bone parameters and bone marrow cellularity, but no response in trabecular bone. To determine the role of ERαAF‐1 for the effects of SERMs, we treated orx WT and ERαAF‐10 mice with raloxifene (Ral), lasofoxifene (Las), bazedoxifene (Bza), or vehicle. These SERMs increased total body areal bone mineral density (BMD) and trabecular volumetric BMD to a similar extent in orx WT mice. Furthermore, only Las increased cortical thickness significantly and only Bza increased bone strength significantly. However, all SERMs showed a tendency toward increased cortical bone parameters. Importantly, all SERM effects were absent in the orx ERαAF‐10 mice. In conclusion, ERαAF‐2 is required for the estrogenic effects on all evaluated parameters, whereas the role of ERαAF‐1 is tissue‐specific. All evaluated effects of Ral, Las and Bza are dependent on a functional ERαAF‐1. Our findings might contribute to the development of bone‐specific SERMs in males. © 2013 American Society for Bone and Mineral Research.
Rapid Construction of Co-Simulations of Cyber-Physical Systems in HLA Using a DSL

The development of cyber-physical systems (CPSs) is a multi-disciplinary process. A model-based approach during the design of a system is important for making design decisions during the exploration of alternatives. However, all disciplines use different modelling tools and techniques, which makes the integration of these models difficult and time-consuming. The use of the High Level Architecture (HLA) simplifies this problem, but still requires quite an effort to implement. Our work focuses on minimising the effort required to construct co-simulations. We have created a Domain Specific Language (DSL) to define a system design consisting of different types of models. We demonstrate how this DSL can be used to experiment with alternative designs of the system quickly. The DSL allows us to build virtual prototypes of CPSs without the large overhead of constructing the co-simulation.
Scenario-Based Observation Approach for Eliciting User Requirements for Haptic User Interfaces

As tactual information processing of visually impaired users has not been investigated sufficiently and there are few guidelines on the development of haptic user interfaces, development of haptic assistive system can pose many challenges. Despite the breadth and variety of tools available for elicitation of user requirements, no single tool adequately provides the needed information to develop such a specialized system for a unique user population where the understanding of user behaviors is limited. This article explores the state-of-art of requirements engineering, discusses the challenges in developing a haptic assistive system, and proposes a methodology of combining a controlled observation in a naturalistic setting with scenario-based design for effective and efficient user requirements elicitation. A case study of developing a haptically enhanced, collaborative learning-by-feeling science education system for visually impaired students was conducted to show validity and effectiveness of the proposed methodology. The case study showed that the methodology has a variety of benefits including the reduced uncertainty and a better fit to the natural behaviors of the user population.
Validity of conventional endoscopy using “non-extension sign” for optical diagnosis of colorectal deep submucosal invasive cancer

Abstract Background and study aims The non-extension sign relates to a localized increase in thickness and rigidity due to deep submucosal invasive (SM-d: depth of 1000 μm or more) cancer. The present study aimed to evaluate the efficacy of the non-extension sign in assessing the optical diagnosis of colorectal SM-d cancer. Patients and methods We retrospectively analyzed 309 patients with 315 early colorectal cancers that had been endoscopically or surgically resected. The non-extension sign was judged from chromoendoscopy (CE) using conventional white-light imaging with indigo carmine, and is taken to be positive when any one of the findings of rigidity of a circular arc, trapezoid elevation, or converging mucosal folds are seen. We assessed comparing the accuracy of CE, magnifying chromoendoscopy (M-CE), and magnifying narrow-band imaging (M-NBI) for the optical diagnosis of colorectal SM-d cancer. Results Sensitivity, specificity, and accuracy for the diagnosis of SM-d cancer were 66.0 %, 95.8 %, and 86.3 % for CE; 80 %, 90.7 %, and 87.3 % for M-CE; and 65.0 %, 94.4 %, and 85.1 % for M-NBI, respectively. The specificity of CE was significantly higher than that of M-CE (P = 0.034). The sensitivity of M-CE was significantly higher than that of CE (P = 0.026). In a comparison of positive and negative groups for the non-extension sign in SM-d cancer, SM invasion was significantly deeper in the positive group than in the negative group (3012.5 μm vs 2002.4 μm, respectively; P < 0.0001) and the rate of lymphovascular invasion was significantly higher in the positive group than in the negative group (63.6 % vs 41.2 %, respectively; P = 0.032). Conclusions The non-extension sign offers high diagnostic specificity for SM-d cancer, and surgery should be considered in patients with a positive non-extension sign.
Using the Karhunen-Loe've transformation in the back-propagation training algorithm

A novel training approach based on the back-propagation algorithm is introduced. In the proposed approach, initially, a set of training vectors is obtained by applying the Karhunen-Loe've transform on the training patterns. The training is first started in the direction of the major eigenvectors of the correlation matrix of the training patterns and then continues by gradually including the remaining components, in their order of significance. With this approach, the number of computations is significantly reduced and the learning rate is improved. The performance of this method is compared with the standard back-propagation algorithm in segmenting a synthetic noisy image.
Functional Characterization and Subcellular Localization of Poplar ( Populus trichocarpa 3 Populus deltoides ) Cinnamate 4-Hydroxylase 1

Cinnamic acid 4-hydroxylase (C4H), a member of the cytochrome P450 monooxygenase superfamily, plays a central role in phenylpropanoid metabolism and lignin biosynthesis and possibly anchors a phenylpropanoid enzyme complex to the endoplasmic reticulum (ER). A full-length cDNA encoding C4H was isolated from a hybrid poplar ( Populus trichocarpa 3 P. deltoides ) young leaf cDNA library. RNA-blot analysis detected C4H transcripts in all organs tested, but the gene was most highly expressed in developing xylem. C4H expression was also strongly induced by elicitor-treatment in poplar cell cultures. To verify the catalytic activity of the putative C4H cDNA, two constructs, C4H and C4H fused to the FLAG epitope (C4H::FLAG), were expressed in yeast. Immunoblot analysis showed that C4H was present in the microsomal fraction and microsomal preparations from strains expressing both enzymes efficiently converted cinnamic acid to p -coumaric acid with high specific activities. To investigate the subcellular localization of C4H in vivo, a chimeric C4H-green fluorescent protein (GFP) gene was engineered and stably expressed in Arabidopsis. Confocal laser microscopy analysis clearly showed that in Arabidopsis the C4H::GFP chimeric enzyme was localized to the ER. When expressed in yeast, the C4H::GFP fusion enzyme was also active but displayed significantly lower specific activity than either C4H or C4H::FLAG in in vitro and in vivo enzyme assays. These data definitively show that C4H is localized to the ER in
Antithrombin III Pescara: a defective AT III variant with no alterations of plasma crossed immunoelectrophoresis, but with an abnormal crossed immunoelectrofocusing pattern

Summary. An abnormal AT III variant was found in five members from a family where a high incidence of thromboembolism occurred. In all the affected subjects AT III antigen concentration was normal, whereas antithrombin and anti‐factor Xa progressive activities as well as heparin cofactor activities were low. Crossed immunoelectrophoresis performed either in absence or in presence of heparin showed a normal plasma pattern. Further chromatographic investigations showed a normal affinity to heparin. An abnormal plasma pattern was evidentiated by crossed immunoelectrofocusing throughout all the AT III pH range. These data are consistent with the presence of an abnormal AT III variant with a defective binding to serine proteases and clearly identifiable only by crossed immunoelectrofocusing. This variant appeared different from the other qualitative AT III defects so far described and was named ‘Antithrombin III Pescara’.