Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal changes in endometrial gene expression and protein localization of members of the IGF family in cattle : effects of progesterone and pregnancy

McCarthy SD, Roche JF, Forde N. Temporal changes in endometrial gene expression and protein localization of members of the IGF family in cattle: effects of progesterone and pregnancy. Physiol Genomics 44: 130–140, 2012. First published November 15, 2011; doi:10.1152/physiolgenomics.00106. 2011. —In the study presented, the hypothesis that ligands of the insulin-like growth factor (IGF) family, as well as their binding proteins (BPs), are temporally regulated and are altered by elevated progesterone (P4) and/or pregnancy was tested. Heifers detected in standing estrus following synchronization (n 210, day 0), were artificially inseminated (n 140) or left as noninseminated cyclic controls (n 70). On day 3, half of each group were randomly assigned to receive a P4-releasing intravaginal device resulting in four treatment groups, pregnant and cyclic heifers with high and normal P4 concentrations on either day 5, 7, 13, or 16 of the estrous cycle/early pregnancy. Quantitative real-time PCR and immunohistochemistry were performed on endometrial homogenate and uterine cross sections to measure transcript abundance and protein localization respectively (n 5 per treatment per time point). No effect of day, treatment, or their interactions was observed for IGF2, IGFBP4, and -5 (P 0.05). IGF1 and IGFBP6 expression decreased, while IGF1R and IGFBP2 expression increased (P 0.05) as the days of the cycle or pregnancy progressed. The expression of IGFBP2 was increased by elevated P4; in addition, localization of both IGF2 and IGFBP2 protein in the luminal and superficial glandular epithelium displayed a P4 day interaction. In conclusion it is proposed that decreased IGF1 and IGFBP6 expression with a coordinate increase in IGF1R and IGFBP2 as the estrous cycle/early pregnancy progresses, along with other factors, are required to establish a uterine environment that promotes the growth and development of the conceptus prior to implantation. In addition, the increased protein abundance of both IGF2 and IGFBP2 observed in heifers supplemented with P4 contributes to the enhanced conceptus elongation observed in this model.
A new in vitro method for the simultaneous evaluation of cholesteryl ester exchange and mass transfer between HDL and apoB-containing lipoprotein subspecies. Identification of preferential cholesteryl ester acceptors in human plasma.

To date, several methods have been developed to determine the activity of plasma lipid transfer proteins. These methods have largely involved the addition of the transfer protein in question to labeled substrates, followed by prolonged incubation (4 to 18 hours) and subsequent evaluation of the radioactivity transferred to precipitated low-density lipoprotein (LDL). While adequate for determining the activity of cholesteryl ester transfer protein (CETP), these methods generally do not take into account the composition or levels of lipoproteins present within a given individual plasma because pools of high-density lipoprotein (HDL) are labeled and used for the transfer experiments. Both the direction and the extent of lipid transfer are dependent on the composition and relative abundance of both donor and acceptor particles as well as the activity of the lipid transfer protein(s). Here we describe a new method for the determination of the capacity of plasma samples to facilitate cholesteryl ester transfer from HDL to LDL and very-low-density lipoprotein (VLDL), a method that has several advantages. First, the subject's HDL is labeled and used for transfer. Second, the labeled HDL, in a quantity equivalent to 1% of the plasma HDL mass, is added to the subject's plasma, and therefore the relative abundance of both donor and acceptor particles is preserved at their physiological levels. Third, both cholesteryl ester mass and radioactivity are determined, allowing the net mass transfer of cholesteryl ester and cholesteryl ester exchange to be quantified separately. (ABSTRACT TRUNCATED AT 250 WORDS)
Gastrocnemius medialis and vastus lateralis oxygenation during whole-body vibration exercise.

PURPOSE The aim of this study was to investigate the effects of different whole-body vibration (WBV) frequencies on oxygenation of vastus lateralis (VL) and gastrocnemius medialis (GM) muscles during static squatting in sedentary and physically active healthy males. METHODS Twenty volunteers (age: 24.6 +/- 2.9 yr; body mass: 80.6 +/- 11.8 kg; height: 178.1 +/- 7.6 cm) participated in this study. Ten subjects were sedentary individuals and 10 were athletes practicing different sports. All subjects completed four trials (control, and 30-, 40-, and 50-Hz WBV) in a randomized controlled crossover design. The trials consisted of static squatting on a vibrating platform for a total duration of 110 s. Muscle-oxygenation status was recorded with near-infrared spectroscopy. RESULTS The data analysis revealed no significant treatment-by-time interactions in tissue-oxygenation index (TOI) or Delta total hemoglobin volume (tHb) in VL and GM muscles. A significant main effect of time in TOI of both VL and GM muscles was identified (P<0.001). VL TOI significantly decreased by 2.8% at 90 s in the control condition and by 3.3% at 110 s in the 30-Hz condition; VL TOI significantly increased by 2.1 and 3.0% at 30 s in the 40- and 50-Hz conditions, respectively. GM TOI significantly decreased by 3.2% at 60 s, by 4.1% at 90 s, and by 4.3% at 110 s in the control condition, and by 5.5% at 110 s in the 30-Hz condition. CONCLUSION This study showed that WBV exercise with frequencies of 30, 40, and 50 Hz and small amplitudes does not affect muscle oxygenation of VL and GM muscles to a higher degree than a nonvibration condition.
Behavioral Interventions for Children and Adolescents With Fetal Alcohol Spectrum Disorders

Exposure to alcohol in utero is considered to be a leading cause of developmental disabilities of known causation. The most severe consequence of such exposure, fetal alcohol syndrome (FAS), is characterized by a distinct constellation of facial anomalies, growth retardation, and central nervous system dysfunction. Both animal and human studies, however, suggest that there may be considerable variability in the manifestations of in utero alcohol exposure across individuals, and, consequently, the term fetal alcohol spectrum disorders (FASD) has come into usage to reflect the entire continuum of effects associated with such exposure. In addition to FAS, this term encompasses the conditions of partial FAS, alcohol-related neurodevelopmental disorder, and alcohol-related birth defects. Despite extensive evidence of significant cognitive, behavioral, and social deficits in people with FASD, research on behavioral interventions for FASD has lagged behind. However, in recent years there has been a marked increase in efforts to design and test interventions for this population. This article will review current empirically tested interventions, methodological challenges, and suggestions for future directions in research on the treatment of FASD.
Sexually different growth histories of the American eel in four rivers in Maine

Abstract Growth histories of yellow-phase American eels Anguilla rostrata collected in four rivers in Maine, were back-calculated from sagittal otolith increments. Our objectives were to first determine whether sexually dimorphic growth rates exist and then compare the growth histories of American eels from four rivers within a geographic region. For female eels, the maximum growth rate was 31.9 ± 1.7 mm/year at age 8, decreasing to 25.1 ± 2.9 mm/year at age 14. Males attained a maximum of 29.8 ± 1.6 mm/year at age 3, decreasing to a minimum of 17.9 ± 1.3 mm/year at age 11. Females grew faster than males after age 4 and had a slower reduction in growth rate with age. These faster growth rates among females were similar in all four rivers. The observed growth rates are not consistent with current life history hypotheses and may indicate an alternative life history strategy. Because female eels benefit from a larger size (i.e., size refuge, increased fecundity, and greater niche breadth), they would benefit.
Leader–Member Exchange

Leader-member exchange (LMX) represents the dyadic relationship between leaders and followers. It posits that leaders form differential relationships with their followers based on the exchange of resources and support between both parties (Graen and Uhl-Bien, 1995). Those employees with high quality relationships experience more challenging work, better training and promotion opportunities, and better access to resources. Those who experience low quality relationships fulfil the basic requirements of their role, but are less likely to experience such opportunities and resources. This quality of the exchange relationship has been linked to outcomes such as commitment, job satisfaction, and organizational citizenship behavior. Much less research attention has been devoted to exploring the antecedents of LMX compared to its outcomes. However, some evidence suggests that antecedents include relationship tenure, leaders' time, span of leadership, follower competence and dependability, and perceived similarity. Other research suggests that the link between LMX and outcomes is mediated by factors such as perceptions of justice, personality differences, and both individual and group performance. Future research should focus on exploring a wider range of possible intervening variables that influence the outcomes of LMX. In addition, a better understanding of the concept of team-member exchange (TMX) is needed. Keywords: leader-member exchange; supervisor support; social exchange
An aspect-oriented approach to large-scale urban simulations

Within the Modeling and Simulation (M&S) field, a major challenge that lies ahead is integrating massively complex urban simulations. The urban environment is a multifaceted model with many components, such as transportation, land use, and water and power distribution. To produce a high fidelity simulation of a city, all components should interact as they do in the real world. Furthermore, an urban simulation should be within an ecosystem of cities, states, and nations. This study presents an aspect-oriented approach for designing distributed simulations that achieves 2 goals: 1) enables M&S experts to focus on the simulation, not on the platform or on interoperability; and 2) is scalable in terms of simulated entities and models. A middleware called Urban Simulation Platform is proposed, using an aspect-oriented approach to interface between the well known High Level Architecture interoperability standard and the traditional simulation design.
Collaborative Embodied Learning in Mixed Reality Motion-Capture Environments: Two Science Studies

These 2 studies investigate the extent to which an Embodied Mixed Reality Learning Environment (EMRELE) can enhance science learning compared to regular classroom instruction. Mixed reality means that physical tangible and digital components were present. The content for the EMRELE required that students map abstract concepts and relations onto their gestures and movements so that the concepts would become grounded in embodied action. The studies compare an immersive, highly interactive learning platform that uses a motion-capture system to track students’ gestures and locomotion as they kinesthetically learn with a quality classroom experience (teacher and content were held constant). Two science studies are presented: chemistry titration and disease transmission. In the counterbalanced design 1 group received the EMRELE intervention, while the other group received regular instruction; after 3 days and a midtest, the interventions switched. Each study lasted for 6 days total, with 3 test points: pretest, midtest, and posttest. Analyses revealed that placement in the embodied EMRELE condition consistently led to greater learning gains (effect sizes ranged from 0.53 to 1.93), compared to regular instruction (effect sizes ranged from 0.09 to 0.37). Order of intervention did not affect the final outcomes at posttest. These results are discussed in relation to a new taxonomy of embodiment in educational settings. We hypothesize that the positive results are due to the embodiment designed into the lessons and the high degree of collaboration engendered by the co-located EMRELE.
Peer Prediction with Heterogeneous Users

Peer prediction mechanisms incentivize agents to truthfully report their signals, in the absence of a verification mechanism, by comparing their reports with those of their peers. Prior work in this area is essentially restricted to the case of homogeneous agents, whose signal distributions are identical. This is limiting in many domains, where we would expect agents to differ in taste, judgment and reliability. Although the Correlated Agreement (CA) mechanism [30] can be extended to handle heterogeneous agents, the new challenge is with the efficient estimation of agent signal types. We solve this problem by clustering agents based on their reporting behavior, proposing a mechanism that works with clusters of agents and designing algorithms that learn such a clustering. In this way, we also connect peer prediction with the Dawid and Skene [5] literature on latent types. We retain the robustness against coordinated misreports of the CA mechanism, achieving an approximate incentive guarantee of ε-informed truthfulness. We show on real data that this incentive approximation is reasonable in practice, and even with a small number of clusters.
A new distance for high level RNA secondary structure comparison

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.
Tissues Use Resident Dendritic Cells and Macrophages to Maintain Homeostasis and to Regain Homeostasis upon Tissue Injury: The Immunoregulatory Role of Changing Tissue Environments

Most tissues harbor resident mononuclear phagocytes, that is, dendritic cells and macrophages. A classification that sufficiently covers their phenotypic heterogeneity and plasticity during homeostasis and disease does not yet exist because cell culture-based phenotypes often do not match those found in vivo. The plasticity of mononuclear phagocytes becomes obvious during dynamic or complex disease processes. Different data interpretation also originates from different conceptual perspectives. An immune-centric view assumes that a particular priming of phagocytes then causes a particular type of pathology in target tissues, conceptually similar to antigen-specific T-cell priming. A tissue-centric view assumes that changing tissue microenvironments shape the phenotypes of their resident and infiltrating mononuclear phagocytes to fulfill the tissue's need to maintain or regain homeostasis. Here we discuss the latter concept, for example, why different organs host different types of mononuclear phagocytes during homeostasis. We further discuss how injuries alter tissue environments and how this primes mononuclear phagocytes to enforce this particular environment, for example, to support host defense and pathogen clearance, to support the resolution of inflammation, to support epithelial and mesenchymal healing, and to support the resolution of fibrosis to the smallest possible scar. Thus, organ- and disease phase-specific microenvironments determine macrophage and dendritic cell heterogeneity in a temporal and spatial manner, which assures their support to maintain and regain homeostasis in whatever condition. Mononuclear phagocytes contributions to tissue pathologies relate to their central roles in orchestrating all stages of host defense and wound healing, which often become maladaptive processes, especially in sterile and/or diffuse tissue injuries.
Controlled randomised crossover trial of the effects of physiotherapy on mobility in chronic multiple sclerosis

OBJECTIVES To determine whether physiotherapy can improve mobility in chronic multiple sclerosis and whether there is a difference between treatment at home and as a hospital outpatient? METHODS A randomised controlled crossover trial was undertaken in patients with chronic multiple sclerosis who had difficulty walking and were referred from neurology clinics: allocation was to one of six permutations of three 8 week treatment periods separated by 8 week intervals: treatments consisted of physiotherapy at home, as an outpatient, or “no therapy”. The main outcome measures were based on independent assessments at home and included mobility related disability (primary outcome: the Rivermead mobility index), gait impairments, arm function, mood, and subjective patient and carer ratings. Therapy was assessed by recording delivery, achievement of set targets, patient and carer preference, and cost. RESULTS On the Rivermead mobility index (scale 0–15) (primary outcome) there was a highly significant (p<0.001) treatment effect of 1.4–1.5 units favouring hospital or home based therapy over no therapy: this was supported by other measures of mobility, gait, balance, and the assessor's global “mobility change” score: there was no major difference between home and hospital. Carers preferred home treatment but neither they nor patients discerned greater benefit there. Estimated costs of home physiotherapy were £25/session and those at hospital were £18 (including £7 patient travel costs). CONCLUSION A course of physiotherapy is associated with improved mobility, subjective wellbeing, and improved mood in chronic multiple sclerosis compared with no treatment but benefit may only last a few weeks: there is little to choose between home and hospital based therapy but the first is more costly, mainly due to skilled staff travelling time.
Feature Learning Based Deep Supervised Hashing with Pairwise Labels

Recent years have witnessed wide application of hashing for large-scale image retrieval. However, most existing hashing methods are based on handcrafted features which might not be optimally compatible with the hashing procedure. Recently, deep hashing methods have been proposed to perform simultaneous feature learning and hash-code learning with deep neural networks, which have shown better performance than traditional hashing methods with hand-crafted features. Most of these deep hashing methods are supervised whose supervised information is given with triplet labels. For another common application scenario with pairwise labels, there have not existed methods for simultaneous feature learning and hash-code learning. In this paper, we propose a novel deep hashing method, called deep pairwise-supervised hashing (DPSH), to perform simultaneous feature learning and hashcode learning for applications with pairwise labels. Experiments on real datasets show that our DPSH method can outperform other methods to achieve the state-of-the-art performance in image retrieval applications.
Optimal Monetary Policy with Informational Frictions

We study optimal policy in a business-cycle setting in which firms hold dispersed private information about, or are rationally inattentive to, the state of the economy. The informational friction is the source of both nominal and real rigidity. Because of the latter, the optimal monetary policy does not target price stability. Instead, it targets a negative relation between the nominal price level and real economic activity. Such leaning against the wind helps maximize production efficiency. An additional contribution is the adaptation of the primal approach of the Ramsey literature to a flexible form of informational friction.
Consensus Guidelines for the Management of Women With Cervical Cytological Abnormalities

EACH YEAR APPROXIMATELY 50 million women undergo Papanicolaou testing in the United States. Of these, approximately 3.5 million (7%) are diagnosed with a cytological abnormality requiring additional follow-up or evaluation. Determining which women with cytological abnormalities are at risk for significant cervical disease, performing appropriate diagnostic workups, and treating cancer precursors present a major public health challenge. There are a number of reasons why comprehensive, evidence-based guidelines are needed for the management of women with cervical cytological abnormalities. One reason is that a National Cancer Institute workshop recently revised the criteria used by cytologists to render certain cytological interpretations, as well as the terminology used for reporting cervical cytology results (ie, the Bethesda System). Other reasons include a better understanding of the pathogenesis and natural history of human papillomavirus (HPV) and cervical cancer precursors, and the availability of data from the National Cancer Institute’s randomized Atypical Squamous Cells of Undetermined Significance/Low-grade Squamous Intraepithelial Lesion (ASCUS/LSIL) Triage Study (ALTS) (D. Solomon, MD, written communication, September 6-8, 2001). Moreover, existing guidelines were developed before sensitive molecular methods for detecting high-risk types of HPV and liquid-based cytology methods became widely available. Data are now available suggesting that these new technologies, when used together, are attractive alternatives to older approaches for managing women with cer-
Exploring New Zealand year 11 students' understanding of Nature of Science concepts

Nature of Science (NOS) is a core part of science education. Extensive effort has gone into establishing educationally appropriate NOS tenets, teaching practices and assessments tools. However, while previous research has identified the importance of prior knowledge in science education, there is limited research that investigates students’ prior knowledge and beliefs about NOS. This information is critical in identifying what teachers need to target in order develop informed NOS beliefs amongst students. In this study the NOS beliefs of year 11 secondary school students in New Zealand were explored using a mixed methods approach. Factor analysis of the students’ (N=502) NOS questionnaire responses revealed that students’ conceptions of NOS differed from the constructs identified in the NOS literature. Coding of the purposively selected sample of student interviews (n=22) revealed a naïve realist model of science was common. This model along with the alternative constructs provided insights into students’ NOS conceptions. The findings were used to develop a model that could help teachers’ better identify explicit and implicit teaching practices to help students develop more appropriate NOS models.