Miracle-dz/UniFAR-FTUs huggingface dataset:
The nucleotide composition of microsatellites impacts both replication fidelity and mismatch repair in human colorectal cells

Microsatellite instability is a key mechanism of colon carcinogenesis. We have previously studied mutations within a (CA)13 microsatellite using an enhanced green fluorescent protein (EGFP)-based reporter assay that allows the distinction of replication errors and mismatch repair (MMR) activity. Here we utilize this assay to compare mutations of mono- and dinucleotide repeats in human colorectal cells. HCT116 and HCT116+chr3 cells were stably transfected with EGFP-based plasmids harboring A10, G10, G16, (CA)13 and (CA)26 repeats. EGFP-positive mutant fractions were quantitated by flow cytometry, mutation rates were calculated and the mutant spectrum was analyzed by cycle sequencing. EGFP fluorescence pattern changed with the microsatellite's nucleotide sequence and cell type and clonal variations were observed in mononucleotide repeats. Replication errors (as calculated in HCT116) at A10 repeats were 5–10-fold higher than in G10, G16 were 30-fold higher than G10 and (CA)26 were 10-fold higher than (CA)13. The mutation rates in hMLH1-proficient HCT116+chr3 were 30–230-fold lower than in HCT116. MMR was more efficient in G16 than in A10 clones leading to a higher stability of poly-G tracts. Mutation spectra revealed predominantly 1-unit deletions in A10, (CA)13 and G10 and 2-unit deletions or 1-unit insertion in (CA)26. These findings indicate that both replication fidelity and MMR are affected by the microsatellite's nucleotide composition.
Establishing the legitimacy of a school’s claim to be “International”: the provision of an international curriculum as the institutional primary task

Abstract The recent growth in the number and diversity of schools around the world classified as “International Schools” raises questions about what makes a school’s claim to be an International School legitimate. From the analysis we report here, the provision of an international curriculum emerges as what a school must do to be legitimate as an International School. It is an International School’s primary task and those in such a school ideally undertake institutional work on that task. We consequently bring the idea of the institutional primary task into institutionalisation theory where it assumes a significant but previously unacknowledged place and a key consideration in institutional legitimacy. In the article, we use the provision of the International Baccalaureate Diploma Programme in an International School to illustrate the notions of the institutional primary task and the pillars and carriers of institutionalisation in practice. The analyses reported in the article develop understandings of International Schools and institutionalisation theory.
Random majority percolation

We shall consider the discrete time synchronous random majority‐vote cellular automata on the n by n torus, in which every vertex is in one of two states and, at each time step t, every vertex goes into the state the majority of its neighbors had at time t ‐ 1 with a small chance p of error independently of all other events. We shall show that, if n is fixed and p is sufficiently small, then the process spends almost half of its time in each of two configurations. Further more, we show that the expected time for it to reach one of these configurations from the other is Θ(1/pn+1) despite the actual time spent in transit being O(1/p3). Unusually, it appears difficult to obtain any results for this regime by simulation. © 2009 Wiley Periodicals, Inc. Random Struct. Alg. , 2010
Rethinking format: An examination of requests

Abstract This study explores the formulation of requests in an American English-speaking shoe repair shop. Taking prior work on request formats as our starting point, we explore the two primary syntactic moods (declarative and interrogative) in our collection and two of the commonly noted subtypes of these moods, need/want-declaratives and can-interrogatives. While our findings in very general terms match those of previous studies, we also find significant grammatical variation within each of these formats, and note interactional uses for each variation. Our examination yields insight into facets of requesting that were previously undescribed. We offer an Emergent Grammar perspective on the complexity of lexicosyntax in the social action of requesting. (Requests, formats, Emergent Grammar, Conversation Analysis, American English, service encounters)*
A Cretaceous mammal from Tanzania

We report here the discovery of a Cretaceous mammal from the “Red Sandstone Group” of southwestern Tanzania. This specimen is one of only a very few Cretaceous mammals known from Gondwana in general and Africa in particular. The specimen consists of a short, deep left dentary that bore a large, procumbent central incisor, and five single−rooted, hypsodont cheek−teeth. The specimen is very tentatively identified as a sudamericid, and thus may represent the first Afri− can record of an enigmatic clade of mammals, the Gondwanatheria, which is otherwise known from the Late Cretaceous and Paleogene of several other Gondwanan landmasses. Unfortunately, the precise age of the specimen could not be de− termined. If it is pre−Campanian and if its identity as a sudamercid is corroborated through subsequent discoveries, it rep− resents the earliest known gondwanatherian. If the specimen is from the Campanian or Maastrichtian, and again assuming its identification is correct, it has the potential to refute a recently formulated biogeographic hypothesis predicting the ab− sence of certain terrestrial and freshwater vertebrate taxa, including gondwanatherians, in Africa (i.e., those that evolved elsewhere on Gondwana after Africa became an isolated landmass).
Nitric Oxide Is Required for L-Type Ca2+ Channel-Dependent Long-Term Potentiation in the Hippocampus

Nitric oxide (NO) has long been implicated in the generation of long-term potentiation (LTP) and other types of synaptic plasticity, a role for which the intimate coupling between NMDA receptors (NMDARs) and the neuronal isoform of NO synthase (nNOS) is likely to be instrumental in many instances. While several types of synaptic plasticity depend on NMDARs, others do not, an example of which is LTP triggered by opening of L-type voltage-gated Ca2+ channels (L-VGCCs) in postsynaptic neurons. In CA3-CA1 synapses in the hippocampus, NMDAR-dependent LTP (LTPNMDAR) appears to be primarily expressed postsynaptically whereas L-VGCC-dependent LTP (LTPL−VGCC), which often coexists with LTPNMDAR, appears mainly to reflect enhanced presynaptic transmitter release. Since NO is an excellent candidate as a retrograde messenger mediating post-to-presynaptic signaling, we sought to determine if NO functions in LTPL−VGCC in mouse CA3-CA1 synapses. When elicited by a burst type of stimulation with NMDARs and the associated NO release blocked, LTPL−VGCC was curtailed by inhibition of NO synthase or of the NO-receptor guanylyl cyclase to the same extent as occurred with inhibition of L-VGCCs. Unlike LTPNMDAR at these synapses, LTPL−VGCC was unaffected in mice lacking endothelial NO synthase, implying that the major source of the NO is neuronal. Transient delivery of exogenous NO paired with tetanic synaptic stimulation under conditions of NMDAR blockade resulted in a long-lasting potentiation that was sensitive to inhibition of NO-receptor guanylyl cyclase but was unaffected by inhibition of L-VGCCs. The results indicate that NO, acting through its second messenger cGMP, plays an unexpectedly important role in L-VGCC-dependent, NMDAR-independent LTP, possibly as a retrograde messenger generated in response to opening of postsynaptic L-VGCCs and/or as a signal acting postsynaptically, perhaps to facilitate changes in gene expression.
Ensemble Theory for Stealthy Hyperuniform Disordered Ground States

It has been shown numerically that systems of particles interacting with "stealthy" bounded, long-ranged pair potentials (similar to Friedel oscillations) have classical ground states that are, counterintuitively, disordered, hyperuniform and highly degenerate. Disordered hyperuniform systems have been receiving recent attention because they are distinguishable exotic states of matter poised between a crystal and liquid with novel properties. The task of formulating an ensemble theory that yields analytical predictions for the structural characteristics and other properties of stealthy degenerate ground states in $d$-dimensional Euclidean space is highly nontrivial because the dimensionality of the configuration space depends on the number density $\rho$ and there is a multitude of ways of sampling the ground-state manifold, each with its own probability measure. The purpose of this paper is to take some initial steps in this direction. Specifically, we derive general exact relations for thermodynamic properties that apply to any ground-state ensemble as a function of $\rho$ in any $d$, and show how disordered degenerate ground states arise as part of the ground-state manifold. We then specialize our results to the canonical ensemble by exploiting an ansatz that stealthy states behave remarkably like "pseudo" equilibrium hard-sphere systems in Fourier space. Our theoretical predictions for the structure and thermodynamic properties of the stealthy disordered ground states and associated excited states are in excellent agreement with computer simulations across the first three space dimensions. The development of this theory provides provide new insights regarding our fundamental understanding of the nature and formation of low-temperature states of amorphous matter. Our work also offers challenges to experimentalists to synthesize stealthy ground states at the molecular level.
Antimicrobial Stewardship Programs

ABSTRACT The development of antimicrobial agents represents one of the most significant achievements in medicine during the past century. However, the emergence of antimicrobial resistance combined with the downturn in the development of new antimicrobial agents in the pharmaceutical industry poses unanticipated challenges in the effective management of infection. The issue of how we can most effectively utilize these invaluable resources, antimicrobials, in the face of infections that are ever more difficult to treat arises. This issue serves as the fundamental basis for the concept of antimicrobial stewardship, the topic of this minireview.
Cigarette smoke induced genotoxicity and respiratory tract pathology: evidence to support reduced exposure time and animal numbers in tobacco product testing

Abstract Many laboratories are working to develop in vitro models that will replace in vivo tests, but occasionally there remains a regulatory expectation of some in vivo testing. Historically, cigarettes have been tested in vivo for 90 days. Recently, methods to reduce and refine animal use have been explored. This study investigated the potential of reducing animal cigarette smoke (CS) exposure to 3 or 6 weeks, and the feasibility of separate lung lobes for histopathology or the Comet assay. Rats were exposed to sham air or CS (1 or 2 h) for 3 or 6 weeks. Respiratory tissues were processed for histopathological evaluation, and Alveolar type II cells (AEC II) isolated for the Comet assay. Blood was collected for Pig-a and micronucleus quantification. Histopathological analyses demonstrated exposure effects, which were generally dependent on CS dose (1 or 2 h, 5 days/week). Comet analysis identified that DNA damage increased in AEC II following 3 or 6 weeks CS exposure, and the level at 6 weeks was higher than 3 weeks. Pig-a mutation or micronucleus levels were not increased. In conclusion, this study showed that 3 weeks of CS exposure was sufficient to observe respiratory tract pathology and DNA damage in isolated AEC II. Differences between the 3 and 6 week data imply that DNA damage in the lung is cumulative. Reducing exposure time, plus analyzing separate lung lobes for DNA damage or histopathology, supports a strategy to reduce and refine animal use in tobacco product testing and is aligned to the 3Rs (replacement, reduction and refinement).
Assessment and feedback in higher education: considerable room for improvement?

Assessment exerts a major influence on students’ approaches to study in higher education, so it is important to ensure that it enables students to develop and thrive as learners. Generally speaking, however, the student experience of assessment remains far from positive and assessment has been accused of having damaging effects on student engagement. Mann (2001), for instance, sees assessment as an important mediating factor in determining a student’s relationship to the university. All-too-often, she asserts, it results in alienation rather than engagement, provoking general feelings of compliance, powerlessness and subservience rather than a sense of belonging, enthusiasm, enjoyment and ownership of the learning process. For the last two decades researchers have been vigorously advocating a shift in assessment culture, such that assessment actively promotes learning rather than simply measuring it (see, for example, Brown & Knight, 1994; Birenbaum, 1996; Sambell, McDowell, & Brown, 1997; Black & Wiliam, 1998; Stiggins, 2002). In response to sustained efforts to improve the state of play there is now widespread recognition of the need for approaches to assessment which are focused specifically on stimulating and improving student learning. These are commonly referred to as assessment for learning approaches (Boud & Falchicov, 2006; Price, Carroll, O’Donovan, & Rust, 2011; Sambell, McDowell, & Montgomery, 2013) and many higher education providers have begun to acknowledge them in their learning and teaching strategies.
Questioning the HIV-AIDS Hypothesis: 30 Years of Dissent

Since 1984, when the hypothesis that HIV-causes-AIDS was announced, many scholars have questioned the premise and offered alternative explanations. Thirty years later, competing propositions as well as questioning of the mainstream hypothesis persist, often supported by prominent scientists. This article synthesizes the most salient questions raised, alongside theories proposing non-viral causes for AIDS. The synthesis is organized according to four categories of data believed to support the HIV-AIDS hypothesis: retroviral molecular markers; transmission electron microscopy (EM) images of retroviral particles; efficacy of antiretroviral drugs; and epidemiological data. Despite three decades of concerted investments in the mainstream hypothesis, the lingering questions and challenges synthesized herein offer public health professionals an opportunity to reflect on their assumptions and practices regarding HIV/AIDS.
Methods for Observed-Cluster Inference When Cluster Size Is Informative: A Review and Clarifications

Clustered data commonly arise in epidemiology. We assume each cluster member has an outcome Y and covariates X . When there are missing data in Y, the distribution of Y given X in all cluster members (“complete clusters”) may be different from the distribution just in members with observed Y (“observed clusters”). Often the former is of interest, but when data are missing because in a fundamental sense Y does not exist (e.g., quality of life for a person who has died), the latter may be more meaningful (quality of life conditional on being alive). Weighted and doubly weighted generalized estimating equations and shared random‐effects models have been proposed for observed‐cluster inference when cluster size is informative, that is, the distribution of Y given X in observed clusters depends on observed cluster size. We show these methods can be seen as actually giving inference for complete clusters and may not also give observed‐cluster inference. This is true even if observed clusters are complete in themselves rather than being the observed part of larger complete clusters: here methods may describe imaginary complete clusters rather than the observed clusters. We show under which conditions shared random‐effects models proposed for observed‐cluster inference do actually describe members with observed Y. A psoriatic arthritis dataset is used to illustrate the danger of misinterpreting estimates from shared random‐effects models.
Exploring Machine Learning Methods to Automatically Identify Students in Need of Assistance

Methods for automatically identifying students in need of assistance have been studied for decades. Initially, the work was based on somewhat static factors such as students' educational background and results from various questionnaires, while more recently, constantly accumulating data such as progress with course assignments and behavior in lectures has gained attention. We contribute to this work with results on early detection of students in need of assistance, and provide a starting point for using machine learning techniques on naturally accumulating programming process data. When combining source code snapshot data that is recorded from students' programming process with machine learning methods, we are able to detect high- and low-performing students with high accuracy already after the very first week of an introductory programming course. Comparison of our results to the prominent methods for predicting students' performance using source code snapshot data is also provided. This early information on students' performance is beneficial from multiple viewpoints. Instructors can target their guidance to struggling students early on, and provide more challenging assignments for high-performing students. Moreover, students that perform poorly in the introductory programming course, but who nevertheless pass, can be monitored more closely in their future studies.
Family Systems Variables as Predictors of Eating Styles and Body Mass Index

ii DEDICATION. iv ACKNOWLEDGMENTS . v TABLE OF CONTENTS. vi LIST OF TABLES . viii CHAPTER I -Introduction . 1 CHAPTER II -Literature Review. 8 Introduction . 8 Genetic Research.8 Behavioral Research.9 Psychological Research . 11 Family Research and Theory . 16 Research beginnings. 16 Psychosomatic families. 19 Family of origin research. 22 Parenting styles related to food/eating. 26 Marital research. 28 Consideration of eating patterns. 37 Summary of previous research. 38 Conceptual Framework of Current Study.40 Differentiation.40 Intimacy. 41 Triangulation. 42 Sexuality.43 Feeding and Mealtime Behaviors. 44 External Eating. 45 Binge Eating. 46 Restrained Eating and Emotional Eating. 47 Purpose of Current Study and Research Questions . 48 CHAPTER III -Methodology. 50 Sample.50 Procedures . 50 Survey.53 Instruments . 54 PAFS-Q.54 DEBQ. 56 Binge Scale Questionnaire.58 Childhood feeding questions. 59 Sexual attitude questions.60
Mesoscopic analysis of online social networks - The role of negative ties

A class of networks are those with both positive and negative links. In this manuscript, we studied the interplay between positive and negative ties on mesoscopic level of these networks, i.e., their community structure. A community is considered as a tightly interconnected group of actors; therefore, it does not borrow any assumption from balance theory and merely uses the well-known assumption in the community detection literature. We found that if one detects the communities based on only positive relations (by ignoring the negative ones), the majority of negative relations are already placed between the communities. In other words, negative ties do not have a major role in community formation of signed networks. Moreover, regarding the internal negative ties, we proved that most unbalanced communities are maximally balanced, and hence they cannot be partitioned into k nonempty sub-clusters with higher balancedness (k≥2). Furthermore, we showed that although the mediator triad ++- (hostile-mediator-hostile) is underrepresented, it constitutes a considerable portion of triadic relations among communities. Hence, mediator triads should not be ignored by community detection and clustering algorithms. As a result, if one uses a clustering algorithm that operates merely based on social balance, mesoscopic structure of signed networks significantly remains hidden.
Pharmacists’ attitudes and awareness towards the use and safety of herbs in Kuwait

Objectives The purpose of this study was to investigate the knowledge and attitudes among pharmacists in Kuwait towards the use of herbs. Methods Self-administered questionnaire was designed as the study instrument and distributed among 100 qualified pharmacists working in government and private pharmacies in Kuwait. Results The mean age was 34.2 (SD=7.5) years. About 51% of pharmacists reported they had used herbal therapy in their lifetime. The majority were interested in herbal information, and their herbal information came mainly from their previous classes during college. Although the pharmacists’ knowledge about uses of selected herbs was good, their awareness about side effects of those herbs was modest. About 31% of the pharmacists did not have enough information about potential interactions between herbs and conventional medicines. Conclusion Herbal information is needed for pharmacy students as part of the Pharmacy College curriculum. Continuing education programs for practising pharmacists about the safety of different herbal products should be established in Kuwait.
Phase Transitions in Neutron Stars and Maximum Masses

Using the most recent realistic effective interactions for nuclear matter with a smooth extrapolation to high densities including causality, we constrain the equation of state and calculate maximum masses of rotating neutron stars. First- and second-order phase transitions to, e.g., quark matter at high densities are included. If neutron star masses of ~2.3 M☉ from quasi-periodic oscillations in low-mass X-ray binaries are confirmed, a soft equation of state as well as strong phase transitions can be excluded in neutron star cores.
Protecting the Great Barrier Reef: analysing the impact of a conservation documentary and post-viewing strategies on long-term conservation behaviour

Abstract Nature-based tourism experiences have the potential to change the environmental knowledge, attitudes and behavior of visitors; but such experiences may be beyond the physical and/or financial reach of many people. To influence the conservation behavior of populations world-wide, a more accessible yet equally effective strategy is required. Using an experimental design, this study explored whether a conservation documentary about Australian marine environments, together with post-viewing support materials, prompted the adoption of conservation behaviours. Questionnaires revealed environmental knowledge, attitudes and behavioural intentions rose immediately after viewing the documentary. Ten weeks later, these levels were maintained or decreased slightly for those who received post-viewing support (Facebook, help sheet or both), but decreased markedly in the control group. Results are similar to those reported in wildlife tourism studies. Implications for the use of documentaries in place of nature experiences are discussed.
IMPROVED REDUNDANCY REDUCTION FOR JPEG FILES

In this paper several methods are presented that allow improved compression of JPEG image files. This is mainly achieved through segmented entropy coding in reference to the EOBs (End-of-Block) of the 8x8 DCT transformed macroblocks. All of the algorithms discussed here are implemented in the freely available JPEG compression software 'packJPG' [9]. Our approach reduces baseline JPEG image file sizes by an average of 15%, based on tests with the Kodak image set [1] and 800 randomly selected JPEG files. This is an improvement of about 5% over a recent proposal [2] for the JPEG standard.