Miracle-dz/UniFAR-FTUs huggingface dataset:
Mathematical model of colorectal cancer initiation

Significance Cancer evolution cannot be observed directly in patients, and new methodologies are needed for obtaining a quantitative understanding of this obscure process. We develop and analyze a stochastic model of malignant transformation in the colon that precisely quantifies the process of colorectal carcinogenesis in patients through loss of tumor suppressors APC and TP53 and gain of the KRAS oncogene. Our study employs experimentally measured mutation rates in the colon and growth advantages provided by driver mutations. We calculate the probability of a colorectal malignancy, the sizes of premalignant lesions, and the order of acquisition of driver mutations during colorectal tumor evolution. Our model can be used as a starting point in evaluating early detection and treatment efforts. Quantifying evolutionary dynamics of cancer initiation and progression can provide insights into more effective strategies of early detection and treatment. Here we develop a mathematical model of colorectal cancer initiation through inactivation of two tumor suppressor genes and activation of one oncogene, accounting for the well-known path to colorectal cancer through loss of tumor suppressors APC and TP53 and gain of the KRAS oncogene. In the model, we allow mutations to occur in any order, leading to a complex network of premalignant mutational genotypes on the way to colorectal cancer. We parameterize the model using experimentally measured parameter values, many of them only recently available, and compare its predictions to epidemiological data on colorectal cancer incidence. We find that the reported lifetime risk of colorectal cancer can be recovered using a mathematical model of colorectal cancer initiation together with experimentally measured mutation rates in colorectal tissues and proliferation rates of premalignant lesions. We demonstrate that the order of driver events in colorectal cancer is determined primarily by the fitness effects that they provide, rather than their mutation rates. Our results imply that there may not be significant immune suppression of untreated benign and malignant colorectal lesions.
That Modern Malice: Exploring Representations and Understandings of Bebop and Modern Jazz in 50 Years of Jazz Historiography

Abstract:Jazz historiography is replete with a variety of contradictions and points of departure among those who write about jazz, critics and historians alike. Because jazz is a relatively new genre in musicological terms, the conversation among musicologists writing about jazz has been relatively myopic only until very recently. One of the most dynamic and significant developmental moments in this history is connected with the origins of what is commonly referred to as the modern jazz era. This moment, associated with the development of bebop as a clearly defined style, has been the subject of much discourse in terms of origins, specific figures involved and consequences within the jazz genre as a whole. Furthermore, new perspectives and approaches to understanding the origins of modern jazz are continually added to the conversation. This article seeks to summarize the prominent approaches to understanding the development of modern jazz, and address points of disagreement and outright dissention among these approaches. This study will explore the main points of the arguments for considering the development of modern jazz as evolution or revolution and seek to identify a reasonable discourse that helps define the functions and figures important in this transition.
Female Veterans Transitioning to Community College: A Case Study

Student veterans cope with a myriad of issue as they transition back into civilian life. Using Schlossberg’s “4S” transition model, this roundtable presents findings from a qualitative study involving recent military veterans transitioning into community college. Much has been published about military veterans returning to college from active duty but surprisingly, very little empirical research exists about the experience of veterans in college and specifically, their experiences in community college. While community college students exhibit high instances of risk factors, student veterans may be coping with a series of issues that compound the risk factors including adjusting from the hierarchal structure of the military to the self-directed, autonomous environment of college, navigating the bureaucracy of the VA and the GI Bill, and in some cases, dealing with physical or mental disabilities as a direct result of their service (Wurster, Rinaldi, Woods, & Ming Lui, 2013; Wheeler, 2012; Rumann, 2011; Ackerman & DiRamio, 2009). Wheeler (2012) found that student veterans experienced emotional highs and lows concerning personal relationships, feelings of separation because they were older than the other students, and stress in dealing with the campus veterans office and obtaining their GI Bill benefits through the VA. The case presented in this paper supplements the findings in Wheeler’s study and contributes to a more in-depth understanding of the experience of student veterans. Schlossberg’s (1966, 2011) 4S transition model assumes that individuals become reflective when unexpected, significant life events occur or when expected events do not occur. In their reflection on the nature of the phenomena, individuals assess the situation, self, supports, and strategies associated with the event or non-event (Sargent & Schlossberg, 1988). Through a qualitative case study methodology and a series of interviews during the first year of community college, this roundtable presents the experiences of two female student veterans through the lens of the 4S model. As is the goal with qualitative inquiry and case study in particular, this investigation sought to develop a holistic description and explanation of the transition for women from the military into college. Results The situation can encompass a series of factors including a trigger event, timing of the transition, and feelings of control (DiRamio & Jarvis, 2011). For Amy and Jessica, the situation, or in this case, the trigger event, was the desire for a “piece of paper” or the physical representation of completing an educational endeavor. They believed the “piece of paper” was the most pressing mission at this point their lives. Feeling hurried to complete her degree quickly, Amy enrolled in 6 classes (18 hours) during her first semester, arguably an excessive number for a new college student. The concept of self, or the personal traits and internalization of feelings of self-efficacy, motivation, and strengths and weaknesses, was similar for both women (Schlossberg, 1988;
Peucedanum japonicum Thunb and its Antiobesity Effects: Evidence and Related Mechanisms

Lifestyle modification is the main treatment for obesity. An understanding of the mechanisms of appetite control, nutrient metabolism, and energy expenditure has greatly enhanced drug development for disorders, such as diabetes, cancer, obesity, and inflammation. Peucedanum japonicum Thunb (PJT), also known as “Chomeiso” (長命草), is a traditional herb that has been used to provide nutrition; the herb has a broad spectrum of physiological and biological properties. In our previous studies, we found that PJT has antiobesity effects, more specifically, the ethanol extract of PJT reduces obesity and diabetes symptoms in high-fat diet–fed mice. Furthermore, in one of our recent studies, we isolated the active component of PJT with antiobesity properties called pteryxin, a previously known coumarin. However, its biological properties against obesity were unknown. We determined that pteryxin played a role in adipogenesis suppression mechanisms, both in vitro and in vivo. This study details the current understanding of antiobesity effects of PJT extracts, its active compound pteryxin, and the distinctive properties of pteryxin compared with those of other natural compounds against obesity. This review will
Hindsight vs. Real time measurement of the output gap: Implications for the Phillips curve in the Chilean Case

We examine sources of output gap revisions in Chile and document how the informational content of these measures affects forecasts of inflation using estimated Phillips curves. Data and forecasts come from Monetary Policy Reports. Output gap revisions are found well behaved because cannot be predicted. We consider backward and forward-looking specifications and also real time, quasi-real time and final output gap estimates. Median and common-factor inflation present lower forecast errors. Results suggest that the passage of time is informative to measure output gap. Inflation forecasts more accurate are found using forward-looking specifications and CB of Chile Staff’s gap estimates.
Inference in Approximately Sparse Correlated Random Effects Probit Models With Panel Data

Abstract We propose a simple procedure based on an existing “debiased” l1-regularized method for inference of the average partial effects (APEs) in approximately sparse probit and fractional probit models with panel data, where the number of time periods is fixed and small relative to the number of cross-sectional observations. Our method is computationally simple and does not suffer from the incidental parameters problems that come from attempting to estimate as a parameter the unobserved heterogeneity for each cross-sectional unit. Furthermore, it is robust to arbitrary serial dependence in underlying idiosyncratic errors. Our theoretical results illustrate that inference concerning APEs is more challenging than inference about fixed and low-dimensional parameters, as the former concerns deriving the asymptotic normality for sample averages of linear functions of a potentially large set of components in our estimator when a series approximation for the conditional mean of the unobserved heterogeneity is considered. Insights on the applicability and implications of other existing Lasso-based inference procedures for our problem are provided. We apply the debiasing method to estimate the effects of spending on test pass rates. Our results show that spending has a positive and statistically significant average partial effect; moreover, the effect is comparable to found using standard parametric methods.
The utility of immunohistochemical expression of glypican-3 (GPC3) and enhancer of zeste homologue-2 (EZH2) protein in the diagnosis of liver nodules

AimThe aim of this study was to examine the immunohistochemical expression of glypican-3 (GPC3) and enhancer of zeste homologue-2 (EZH2) in various histological types of hepatic nodules to investigate their discriminatory diagnostic value between primary malignant, metastatic and non malignant nodules. Materials and methodsWe correlated markers’ expression with the clinicopathological variables of primary liver malignancy. Markers’ expression was analyzed in 82 liver true-cut needle biopsies; 59.76% were primary liver malignancies, 15.85% were metastatic carcinomas, and 24.39% were nonmalignant nodules. ResultsGPC3 expression was detected in 84.37 and 17.64% of hepatocellular carcinomas (HCC) and cholangiocarcinomas (CC), respectively, but was not expressed in any of the metastatic nodules. In HCC, GPC3 was expressed more with cirrhosis, with large masses of tumor and with high HCC grades with statistically significant differences (P=0.036, 0.024, and 0.030, respectively). EZH2 expression was detected in 90.62% of HCCs, in all cases of CC and metastatic nodules, and in 5% of nonmalignant nodules. The sensitivity, specificity, and diagnostic accuracy of differentiating HCCs from nonmalignant nodules were 84.38, 100, and 90.38%, respectively, for GPC3, and 90.63, 95, and 92.31%, respectively, for EZH2. The sensitivity, specificity, and diagnostic accuracy for differentiating HCCs from CCs were 84.38, 82.35, and 83.67%, respectively, for GPC3, and 90.63, 0.0, and 59.18%, respectively, for EZH2. The sensitivity, specificity, and diagnostic accuracy for differentiating HCCs from metastatic nodules were 84.38, 100, and 88.89%, respectively, for GPC3, and 90.63, 0.0, and 64.44%, respectively, for EZH2. ConclusionGPC3 can be used as a first-line marker for differential diagnoses of HCCs from nonmalignant nodules, CCs, and metastases (accuracy rate: 90.38, 83.67, and 88.89%, respectively). In HCC, overexpression of GPC3 is associated with poor prognostic factors such as large tumor size and high tumor grade. EZH2 is a reliable marker for HCCs compared with nonmalignant nodules (accuracy rate: 92.31%). However, EZH2 is not specific for HCC as all other examined hepatic malignancies were positive as well.
Food Habits, Obesity andNutritional Knowledge among theUniversity Students in NoakhaliRegion of Bangladesh: A CrossSectional Study

Food Habits, Obesity and Nutritional Knowledge among the University Students in Noakhali Region of Bangladesh: A Cross Sectional Study Objective: Obesity is emerging as a foremost health problem. In this regard, the study was undertaken to evaluate the prevalence of overweight and obesity rates in association with food habits and nutritional knowledge among the university students of Noakhali region, a southern coastal area of Bangladesh. Methods: This cross-sectional study was conducted during the period of October to December in 2013. A total of 200 students (50% male and 50% female) aged 18-24 years participated in the present study. Statistical analysis was done by using the SPSS software (version 16) to determine overweight and obesity among students and to sort out eating habits. Results: The study results found that the majority (70%) of the students were of normal weight; 77% male in contrast to 66% female students (P 0.05). Intake of alcohol containing beverages and smoking was not common among female students but it’s familiar with male students. Conclusion: Our findings recommend that the propensity of overweight and obesity among the university students can be reduced by providing proper knowledge at all levels (family, institution, community and government) on the healthy diet, improved lifestyle and harmful effect of obesity.
Comparison of age estimates from scales, fin rays, and otoliths of the introduced Peipsi whitefish, Coregonus maraenoides (Actinopterygii: Salmoniformes: Salmonidae), collected from the Iskar Reservoir (Danube River Basin)

Comparison of age estimates from scales, fin rays, and otoliths of the introduced Peipsi whitefish, Coregonus maraenoides (Actinopterygii: Salmoniformes: Salmonidae), collected from the Iskar Reservoir (Danube River Basin). Acta Ichthyol. Piscat. 50 (1): 13– 21. Background. Peipsi whitefish, Coregonus maraenoides Polyakov, 1874, is an endemic species of Lake Peipsi (Chudskoe) in Estonia and Russia. In the mid-1970s, it was introduced into the biggest Bulgarian artificial body of water—the Iskar Reservoir (Danube River basin). A recent survey confirmed the existence of a self-sustaining population of the Peipsi whitefish in the dam lake. Establishing a suitable method for determining Peipsi whitefish age would allow fishery managers and biologists to extract valuable information on various population parameters. Therefore, the aim of the presently reported study was to test the suitability of scales, pectoral fin rays, and otoliths for the most reliable age determining of Peipsi whitefish. Material and methods. Age estimates were obtained from transverse sections of sagittal otoliths and pectoral fins, and scales from 54 Peipsi whitefish, collected between October and March 2016–2017. Two readers estimated ages from all three structures independently. The precision and bias of age estimates between readers and among structures were compared using age bias plots, coefficient of variation (CV), percent agreement (PA), and level of readability. Mean consensus ages from two readers for each structure were compared. Results. Mean consensus age estimates obtained by analysing the scales (2.0 years) were significantly lower than those obtained by analysing the fin rays (2.6) and otoliths (2.7). Between-reader percent agreement was lower and the coefficient of variation was higher for otoliths (PA = 22.2%; CV = 27.6) compared with scales (PA = 46.6%; CV = 10.02) and pectoral fin rays (PA = 67.4%; CV = 10.12). Comparison of age estimates from the different structures revealed the highest PA and the lowest CV values between otoliths and pectoral fin rays (PA = 62.6%; CV = 10.03%), while the lowest PA and highest CV (PA = 35%, CV = 25.03) were observed between age estimates from fin rays and scales (CV, P > 0. 005). The otolith and scale ages agreed for 46.7% and CV was 21.5. The scales were considered by both readers with the highest level of readability (88.9%) than the pectoral fin rays (70.4%) and otoliths (50%). Conclusion. The use of fin rays is recommended for the age estimation of C. maraenoides from the Iskar Reservoir but further work is needed to validate the accuracy of ageing methodology for small, under one-year old Peipsi whitefish.
The Mediating Role of Sleep Quality on Well-Being Among Japanese Working Family Caregivers

The purpose of this study was to investigate whether the well-being of caregivers is mediated by the association between behavioral and psychological symptoms in elderly relatives and the quality of sleep experienced by caregivers using a mediational model. The participants were 105 working family caregivers in Japan. We assessed well-being based on the Kessler Scale 10, self-rated health, and satisfaction in daily life. Our results showed that the well-being in working family caregivers was impacted by the severity of behavioral and psychological symptoms in elderly relatives. Well-being in working family caregivers was also affected by quality of sleep. Maintaining good quality of sleep in working family caregivers is important for reducing caregiver burden and psychological distress, and for improving the balance between work and family life.
Conceptions of critical thinking for nursing judgement held by nurse educators : thesis submitted to Massey University, in accordance with the regulations, in partial fulfilment for the degree of Master of Education at College of Education, Massey University

Over the last decade there has been a major shift in nursing education with an emphasis on facilitating students to think critically. Nurses engaged in professional practice encounter, in their every day work, situations requiring multidimensional decision-making. In order to be safe in their practice nurses need to be critical thinkers. The Nursing Council of New Zealand (1999) requires nurses to make sound professional judgement based on research, and reflection, in decision-making and problem solving . In the literature there is no clear definition of critical thinking as it relates to nursing judgement. In recent years there has been a move to broaden the conception of critical thinking from a linear problem solving process to include aspects of the affective domain. If nurse educators are to facilitate the development of critical thinking in students it seems essential that they have a clear understanding of the concept. The purpose of this study was to explore the conceptions of critical thinking for nursing judgement held by a group of nurse educators working in the Health Studies Department of a large city Institute of technology. Methods they used to facilitate the development of critical thinking and measure its achievement in students was also investigate A semi-structured interview was used to explore the nurse educator's conceptions. In addition the nurse educators where asked to discuss students work and critical incidents in clinical performance, which, in their opinion, demonstrated critical thinking. The study revealed that the nurse educators considered that critical thinking included both a rational/analytical component and an intuitive/reflective aspect. They considered critical thinking to be essential for caring nursing practice. The most common means of facilitating critical thinking was dialogue and encouraging reflection on practice through journal writing
On the near-field interfaces of homogeneous and immiscible round turbulent jets

Quantifying accidental opaque discharges is a challenging task, since probing beyond their visible interfaces may be difficult or impossible. In this case, we show that the visible interface features near the jet exit can be used to gauge the flow. This work examines the interface in the near-field features of submerged homogeneous and immiscible turbulent jets. Experiments were carried out with water jets and immiscible silicone oil jets of two viscosities in a water tank. The jet Reynolds numbers are in the range of $Re\sim 4500{-}50\,000$ for homogeneous water jets and $Re\sim 3500{-}27\,000$ for silicone oil jets in water. The jet fluids are made visible by doping with fluorescent dye and excitation with directional illumination. The jet interfaces are continuous and convoluted for water jets, while convoluted and discontinuous with droplets and ligaments for oil jets. Direct flow visualization, schlieren photography, shadowgraph photography and particle image velocimetry are employed as appropriate. Interface length scales are characterized using various image processing techniques. Droplet sizes are quantified using Hough transformation. Interface length scales decrease with Reynolds number and increase gradually with distance from the exit plane for a given Reynolds number. These scales are isotropic for the homogeneous water jets and exhibit a streamwise-to-cross-stream ratio of approximately 1.3 for the oil jets. Interfacial tension, hence the Weber number, determines the average droplet size in the immiscible jets.
Missing the forest because of the trees: slower alternations during binocular rivalry are associated with lower levels of visual detail during ongoing thought

Conscious awareness of the world fluctuates, either through variation in the quality with which we perceive the environment, or, when attention switches to information generated using imagination rather than the external environment. Our study combined individual differences in experience sampling, psychophysical reports of perception, and neuroimaging descriptions of structural connectivity, to better understand these changes in conscious awareness. In particular, we (a) examined if aspects of ongoing thought, as measured by multi-dimensional experience sampling during a sustained attention task, are associated with the white matter fibre organization of the cortex as reflected by their relative degree of anisotropic diffusion, and (b) whether these neuro-cognitive descriptions of ongoing experience are related to a more constrained measure of visual consciousness provided by the analysis of bistable perception during binocular rivalry. Individuals with greater fractional anisotropy (FA) in right hemisphere white matter regions involving the inferior fronto-occipital fasciculus, the superior longitudinal fasciculus and the cortico-spinal tract, described their ongoing thoughts as lacking external details. Subsequent analysis indicated that the combination of low FA in these right hemisphere regions, with reports of high level external details, was associated with the shortest periods of dominance during binocular rivalry. Since variation in binocular rivalry reflects differences between bottom-up and top-down influences on vision, our study suggests that reports of ongoing thoughts with vivid external details may occur when conscious precedence is given to bottom-up representation of perceptual information and that this may partly be rooted in the white matter fibre organization of the cortex.