Miracle-dz/UniFAR-FTUs huggingface dataset:
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma

Existing microarray-based approaches for screening of DNA methylation are hampered by a number of shortcomings, such as the introduction of bias by DNA copy-number imbalances in the test genome and negligence of tissue-specific methylation patterns. We developed a method designated array-based profiling of reference-independent methylation status (aPRIMES) that allows the detection of direct methylation status rather than relative methylation. Array-PRIMES is based on the differential restriction and competitive hybridization of methylated and unmethylated DNA by methylation-specific and methylation-sensitive restriction enzymes, respectively. We demonstrate the accuracy of aPRIMES in detecting the methylation status of CpG islands for different states of methylation. Application of aPRIMES to the DNA from desmoplastic medulloblastomas of monozygotic twins showed strikingly similar methylation profiles. Additional analysis of 18 sporadic medulloblastomas revealed an overall correlation between highly methylated tumors and poor clinical outcome and identified ZIC2 as a frequently methylated gene in pediatric medulloblastoma.
One-to-one teaching with pictures--flashcard health education for British Asians with diabetes.

BACKGROUND Type 2 diabetes is up to four times more common in British Asians, but they know little about its management and complications. AIM To design and evaluate a structured pictorial teaching programme for Pakistani Moslem patients in Manchester with type 2 diabetes. METHOD A randomized controlled trial of pictorial flashcard one-to-one education in 201 patients attending a hospital outpatient clinic or diabetic clinics in ten general practices in Manchester. Patients' knowledge, self-caring skills and attitudes to diabetes were measured on four topics before the structured teaching, and compared with results six months later. RESULTS All parameters of knowledge were increased in the study group; for example, percentage scores for correctly identifying different food values increased from 57% to 71% (Analysis of Variance (ANOVA) adjusted difference +11.8%) and knowledge of one diabetic complication from 18% to 78%. Self-caring behaviour improved, with 92% of patients doing regular glucose tests at six months compared with 63% at the start. Attitudinal views were more resistant to change, with patients still finding it hard to choose suitable foods at social occasions. Haemoglobin A1c control improved by 0.34% over six months (ANOVA adjusted difference, 95% CI -0.8% to +0.1%). CONCLUSION It is concluded that this health education programme can empower Asian diabetics to take control of their diets, learn to monitor and interpret glucose results, and understand the implications of poor glycaemic control for diabetic complications.
MATHEMATICAL MODELLING OF THE CARDIOVASCULAR SYSTEM AND SKELETAL MUSCLE INTERACTION DURING EXERCISE

In this work we present a mathematical model for the coupling of cardiovascular system and metabolism under sport efforts. Effects such as oxygenation, heart rates, flow rates, blood pressure and mass transfer to tissues will be considered. A special attention will be payed to the modelling of the regulatory mechanisms (baroreflex and chemoreflex effectors) affecting the heart and the peripheral circulation. We aim at extending the existing models to describe metabolism, hemodynamics and mass transport during exercise, providing a framework to understand their mutual interactions. Numerical issues are presented for different workloads, and a quantitative analysis of dynamic aerobic exercise is discussed.
Unified Theory for Recovery of Sparse Signals in a General Transform Domain

Compressed sensing is provided a data-acquisition paradigm for sparse signals. Remarkably, it has been shown that the practical algorithms provide robust recovery from noisy linear measurements acquired at a near optimal sampling rate. In many real-world applications, a signal of interest is typically sparse not in the canonical basis but in a certain transform domain, such as wavelets or the finite difference. The theory of compressed sensing was extended to the analysis sparsity model, but known extensions are limited to the specific choices of sensing matrix and sparsifying transform. In this paper, we propose a unified theory for robust recovery of sparse signals in a general transform domain by convex programming. In particular, our results apply to the general acquisition and sparsity models and show how the number of measurements for recovery depends on properties of measurement and sparsifying transforms. Moreover, we also provide extensions of our results to the scenarios where the atoms in the transform have varying incoherence parameters and the unknown signal exhibits a structured sparsity pattern. In particular, for the partial Fourier recovery of sparse signals over a circulant transform, our main results suggest a uniformly random sampling. Numerical results demonstrate that the variable density random sampling by our main results provides a superior recovery performance over the known sampling strategies.
Applied Economics Workshop Business 33610 Spring Quarter 2012 "no Margin, No Mission? a Field Experiment on Incentives for Pro-social Tasks" No Margin, No Mission? a Field Experiment on Incentives for Pro-social Tasks

A substantial body of research investigates the design of incentives in firms, yet less is known about incentives in organizations that hire individuals to perform tasks with positive social spillovers. We conduct a field experiment in which agents hired by a public health organization are randomly allocated to four groups. Agents in the control group receive a standard volunteer contract often offered for this type of task, whereas agents in the three treatment groups receive small financial rewards, large financial rewards, and non-financial rewards, respectively. The analysis yields three main findings. First, non-financial rewards are more effective at eliciting effort than either financial rewards or the volunteer contract. The effect of financial rewards, both large and small, is much smaller and not significantly different from zero. Second, non-financial rewards elicit effort both by leveraging intrinsic motivation for the cause and by facilitating social comparison among agents. Third, contrary to existing laboratory evidence, financial incentives do not crowd out intrinsic motivation in this setting. Short sections of text, not to exceed two paragraphs, may be quoted without explicit permission provided that full credit, including © notice, is given to the source.
The impact of a dense canopy on the wind profile and evolution of the boundary layer

It has long been known that the standard surface layer flux-gradient relationships fail in a roughness sublayer (RSL) close to and within tall canopies. However there are a number of important applications where such approaches are still routinely used, for instance in operational numerical weather prediction, global climate and atmospheric dispersion models. Furthermore, due to practical reasons, most measurements made at long term flux stations are made in the RSL so a consistent theory for this region is needed. Here we address this problem by reconsidering simple onedimensional, mixing length based models for the mean flow within and above a dense canopy in light of the mixing layer analogy for the flow at canopy top (Raupach et al., 1996).
Situating the Performer and the Instrument in a Rich Social Context with PESI Extended System

In this paper we present our solutions to the design challenges of facilitating awareness of actions and development of self-identities within The notion of Participatory Enacting Sonic Interaction (PESI) project. The PESI sys-tem is a modular framework for participatory music making with three performers. We present a brief technical overview, design considerations and revisions resulting from a user study conducted during the system’s development. Through the development process of the PESI project a design approach we term: Non-Behaviourally Restrictive Digital Technology became apparent. In this approach, the shifting focus that embodied agents have in relation to the environment is accounted for and the development of sound-action relationships are encouraged. This is achieved through providing mappings relating to individual sensor values and movement information from motion tracking data. Our approach to the implementation of the PESI sys-tem can shift the collaborative music activity to a more engaging and active experience.
Clinicopathologic and prognostic characteristics of alpha-fetoprotein–producing gastric cancer

Alpha-fetoprotein–producing gastric cancer (AFPGC) accounts for 1.5%–7.1% of all gastric cancer cases. Compared with other types of gastric cancer, AFPGC is more aggressive and prone to liver and lymph node (LN) metastasis, with extremely poor prognosis. To improve understanding of AFPGC we reviewed a consecutive series of 82 AFPGC patients and investigated the prognostic factors. The incidence of AFPGC among our gastric cancer patients was 1.95%, and 29.27% of AFPGCs were diagnosed with metastasis at the time of presentation, mainly liver metastasis. The serum AFP level of patients with AFPGC was significantly associated with tumor differentiation. Histologically, these AFPGC patients were composed of 34.55% hapatiod type, 58.18% fetal gastrointestinal type, 9.09% yolk sac tumor-like type, and 14.55% mixed type. Patient gender, tumor differentiation, Lauren classification, and number of metastatic lymph nodes showed significant differences among these four subtypes. The overall survival time was 42.02 months and the 3-year cumulative survival rate was 53.13%. Age, American Joint Committee on Cancer (AJCC) TNM staging classification (TNM stage), serum AFP level, and surgery were prognostic factors for overall survival; however, TNM stage was the only independent risk factor for prognosis of AFPGC. In short, AFPGC is a rare, unique, and heterogeneous entity, and its proper identification and treatment remain a challenge. More attention should be paid to AFPGC to improve patient care and the dismal prognosis.
Bond Supply and Excess Bond Returns

We examine empirically how the maturity structure of government debt affects bond yields and excess returns. Our analysis is based on a theoretical model of preferred habitat in which clienteles with strong preferences for specific maturities trade with arbitrageurs. Consistent with the model, we find that (i) the supply of long- relative to short-term bonds is positively related to the term spread, (ii) supply predicts positively long-term bonds' excess returns even after controlling for the term spread and the Cochrane-Piazzesi factor, (iii) the effects of supply are stronger for longer maturities, and (iv) following periods when arbitrageurs have lost money, both supply and the term spread are stronger predictors of excess returns.
Combined liver vein and spleen pulp pressure measurements in patients with portal or splenic vein thrombosis

Background: Patients with thrombosis of the portal or splenic vein may develop portal hypertension with bleeding from oesophageal or gastric varices. The relevant portal pressure cannot be measured by liver vein catheterization or transhepatic puncture of the portal vein because the obstruction is peripheral to the accessible part of the portal system. Methods: Liver vein catheterization was combined with percutaneous splenic pressure measurement in 10 patients with portal or splenic vein thrombosis and no cirrhosis, and 10 cirrhotic patients without thrombosis. The splenic pressure was measured by percutaneous puncture below the curvature of the ribs with an angle of the needle to skin of 30° in order to minimize the risk of cutting the spleen if the patient took a deep breath. Results: None of the patients in whom the described procedure was followed had complications. Pressure measurements in the spleen pulp and splenic vein were concordant. The pressure gradient across the portal venous system (splenic‐to‐wedged hepatic vein pressure) was −1.3 to 8.5 mmHg (median, 2.8 mmHg) in cirrhosis patients and 0–44 mmHg (median, 18 mmHg) in thrombosis patients, the variation reflecting various degrees of obstruction to flow in the portal venous system. Peripheral portal pressure (splenic‐to‐free liver vein pressure gradient) was 1.1–28 mmHg (median, 17 mmHg) in cirrhotic patients and 11–52 mmHg (median, 23 mmHg) in thrombosis patients. Conclusions: Liver vein catheterization combined with percutaneous splenic pressure measurement is feasible in quantifying pressure gradient across a thrombosis of the portal/splenic vein and in quantifying portal pressure peripheral to this kind of thrombosis.
NATICID CONFAMILIAL DRILLING PREDATION THROUGH TIME

Abstract: Gastropod drilling predation in the fossil record is prevalent and has been documented by many workers; however, vivid documentation of confamilial naticid predation is poor. Here, data compiled from previously published sources, supplemented by unpublished museum collections, document different aspects of naticid confamilial predation (NCP) in a temporal-latitudinal context. Confamilial drilling frequency (DF) showed a Cretaceous low, a small rise to a stable plateau in the Eocene, followed by a peak in the Oligocene, and finally a drop to a stable level from the Miocene to the Holocene. The stepwise rise in DF is comparable with the overall history of drilling predation. However, the temporal increase in DF was visible only in the mid-latitudes, while in other latitudes, no temporal trend was observed. The frequency of failed attack has always been very low. In comparison, a decrease in prey effectiveness (PE) was observed in the Neogene relative to the Cretaceous and Paleocene–Eocene intervals. In case of site selectivity, either apertural or abapertural sites were targeted until the Oligocene, and subsequently became more random. Some of these trends may be biased based on insufficient site selectivity data as well as uneven sampling from different latitudes representing different time intervals. More data on quantification of predation intensities along with the behavioral aspects of NCP are required to properly document other aspects of this interaction.
High-dimensional analysis of semidefinite relaxations for sparse principal components

In problem of sparse principal components analysis (SPCA), the goal is to use n i.i. d. samples to estimate the leading eigenvector(s) of a p times p covariance matrix, which are known a priori to be sparse, say with at most k non-zero entries. This paper studies SPCA in the high-dimensional regime, where the model dimension p, sparsity index k, and sample size n all tend to infinity simultaneously. We first analyze a simple and computationally inexpensive diagonal cut-off method, and establish a threshold of the order thetasdiag = n/[k2 log(p-k)] separating success from failure. We then analyze a more complex semidefinite programming (SDP) relaxation due to dpsilaAspremont et al., and prove that it succeeds once the sample size is of the order thetassdp = n/[k log(p - k)]. Our results thus highlight an interesting tradeoff between statistical and computational efficiency in high-dimensional estimation problems.
Changes in Tetracycline Susceptibility of Enteric Bacteria following Switching to Nonmedicated Milk Replacer for Dairy Calves

ABSTRACT A randomized intervention study was conducted to determine if discontinuing use of calf milk replacer medicated with oxytetracycline results in increased tetracycline susceptibility in Salmonella and Campylobacter spp. and Escherichia coli in dairy calves over a 12-month period. Dairy herds with enteric bacteria with known low tetracycline susceptibility were enrolled for the study. Fecal samples from preweaned calves and environmental samples were collected from eight dairy herds in Michigan and New York State. Samples were collected monthly for 3 months prior to and 12 months after four of the eight herds discontinued medicated milk replacer feeding. Salmonella and Campylobacter spp. and E. coli were isolated, and antimicrobial susceptibility testing was conducted using automated broth microdilution. A total of 804 intervention and 1,026 control calf fecal samples and 122 intervention and 136 control environmental samples were collected for testing. No differences in owner-reported morbidity and mortality between treatment groups were seen. The intervention was significantly associated with increasing tetracycline susceptibility in E. coli and Salmonella. Tetracycline susceptibility increased in intervention herds for the first 3 months after switching to nonmedicated milk replacer but declined in subsequent months. Discontinuing the practice of feeding medicated milk replacers to calves increased tetracycline susceptibility in E. coli and Salmonella on dairy farms, without increasing cattle disease, but declines in effectiveness after 3 months suggest that other factors contribute to decreasing susceptibility on the farm.
Survival effect of PDGF-CC rescues neurons from apoptosis in both brain and retina by regulating GSK3β phosphorylation

Platelet-derived growth factor CC (PDGF-CC) is the third member of the PDGF family discovered after more than two decades of studies on the original members of the family, PDGF-AA and PDGF-BB. The biological function of PDGF-CC remains largely to be explored. We report a novel finding that PDGF-CC is a potent neuroprotective factor that acts by modulating glycogen synthase kinase 3β (GSK3β) activity. In several different animal models of neuronal injury, such as axotomy-induced neuronal death, neurotoxin-induced neuronal injury, 6-hydroxydopamine–induced Parkinson’s dopaminergic neuronal death, and ischemia-induced stroke, PDGF-CC protein or gene delivery protected different types of neurons from apoptosis in both the retina and brain. On the other hand, loss-of-function assays using PDGF-C null mice, neutralizing antibody, or short hairpin RNA showed that PDGF-CC deficiency/inhibition exacerbated neuronal death in different neuronal tissues in vivo. Mechanistically, we revealed that the neuroprotective effect of PDGF-CC was achieved by regulating GSK3β phosphorylation and expression. Our data demonstrate that PDGF-CC is critically required for neuronal survival and may potentially be used to treat neurodegenerative diseases. Inhibition of the PDGF-CC–PDGF receptor pathway for different clinical purposes should be conducted with caution to preserve normal neuronal functions.
Salmonella Type III Effector AvrA Stabilizes Cell Tight Junctions to Inhibit Inflammation in Intestinal Epithelial Cells

Salmonella Typhimurium is a major cause of human gastroenteritis. The Salmonella type III secretory system secretes virulence proteins, called effectors. Effectors are responsible for the alteration of tight junction (TJ) structure and function in intestinal epithelial cells. AvrA is a newly described bacterial effector found in Salmonella. We report here that AvrA expression stabilizes cell permeability and tight junctions in intestinal epithelial cells. Cells colonized with an AvrA-deficient bacterial strain (AvrA−) displayed decreased cell permeability, disruption of TJs, and an increased inflammatory response. Western blot data showed that TJ proteins, such as ZO-1, claudin-1, decreased after AvrA- colonization for only 1 hour. In contrast, cells colonized with AvrA-sufficient bacteria maintained cell permeability with stabilized TJ structure. This difference was confirmed in vivo. Fluorescent tracer studies showed increased fluorescence in the blood of mice infected with AvrA- compared to those infected with the AvrA-sufficient strains. AvrA- disrupted TJ structure and function and increased inflammation in vivo, compared to the AvrA- sufficient strain. Additionally, AvrA overexpression increased TJ protein expression when transfected into colonic epithelial cells. An intriguing aspect of this study is that AvrA stabilized TJs, even though the other TTSS proteins, SopB, SopE, and SopE2, are known to disrupt TJs. AvrA may play a role in stabilizing TJs and balancing the opposing action of other bacterial effectors. Our findings indicate an important role for the bacterial effector AvrA in regulation of intestinal epithelial cell TJs during inflammation. The role of AvrA represents a highly refined bacterial strategy that helps the bacteria survive in the host and dampen the inflammatory response.
Dizziness and the genetic influences on subjective experiences to initial cigarette use.

AIM To examine individual differences in positive and negative subjective experiences to initial cigarette use. DESIGN Retrospective self-reports of initial subjective experiences were examined to estimate the genetic and environmental influences and the extent of their covariation across different effects. PARTICIPANTS Data was drawn from 2482 young adult same-and opposite sex twins- and siblings participating in the National Longitudinal Study of Adolescent Health. MEASUREMENT Subjective experiences were retrospectively collected using the Early Smoking Experience (ESE) questionnaire. FINDINGS Positive experiences evidenced moderate heritable contributions (40%, 95% CI: 0.22 to 0.56), as did an overall hedonic measure (34%, 95% CI: 0.22 to 0.46) and dizziness (34%, 95% CI: 0.15 to 0.52). Negative experiences evidenced small heritable contributions (13%, 95% CI: 0.00 to 0.36). Individual specific environmental influences were strong and accounted for the remaining proportion of observed variation in these experiences. Multivariate genetic modeling identified a moderately heritable underlying factor (37%, 95% CI: 0.22 to 0.52) that influenced the covariation of diverse subjective experiences and loaded most heavily on dizziness. Positive experiences also evidence residual genetic influences that were uncorrelated with other subjective experiences. CONCLUSIONS How a person experiences their initial few cigarettes is due to both heritable contributions and environmental experiences unique to the person. The covariation of diverse subjective experiences appears to be due to a heritable latent sensitivity to the chemicals contained in an average cigarette and is best indexed by dizziness.
Dartboard Arrangements

This note considers possible arrangements of the sectors of a generalised dartboard. The sum of the pth powers of the absolute differences of the numbers on adjacent sectors is introduced as a penalty cost function and a string reversal algorithm is used to determine all arrangements that maximise the penalty, for any p ≥ 1. The maximum value of the penalty function for p = 1 is well known in the literature, and has been previously stated without proof for p = 2. We determine it also for p = 3 and p = 4.
Learning and Strain Among Newcomers: A Three-Wave Study on the Effects of Job Demands and Job Control

The present 3-wave longitudinal study was an examination of job-related learning and strain as a function of job demand and job control. The participants were 311 newcomers to their jobs. On the basis of R. A. Karasek and T. Theorell's (1990) demand-control model, the authors predicted that high demand and high job control would lead to high levels of learning; low demand and low job control should lead to low levels of learning; high demand and low job control should lead to high levels of strain; and low demand and high job control should lead to low levels of strain. The relation between strain and learning was also examined. The authors tested the hypotheses using ANCOVA and structural equation modeling. The results revealed that high levels of strain have an adverse effect on learning; the reverse effect was not confirmed. It appears that Karasek and Theorell's model is very relevant when examining work socialization processes.