Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-Coding Polymorphisms in Nucleotide Binding Domain 1 in ABCC1 Gene Associate with Transcript Level and Survival of Patients with Breast Cancer

Objectives ATP-Binding Cassette (ABC) transporters may cause treatment failure by transporting of anticancer drugs outside of the tumor cells. Multidrug resistance-associated protein 1 coded by the ABCC1 gene has recently been suggested as a potential prognostic marker in breast cancer patients. This study aimed to explore tagged haplotype covering nucleotide binding domain 1 of ABCC1 in relation with corresponding transcript levels in tissues and clinical phenotype of breast cancer patients. Methods The distribution of twelve ABCC1 polymorphisms was assessed by direct sequencing in peripheral blood DNA (n = 540). Results Tumors from carriers of the wild type genotype in rs35623 or rs35628 exhibited significantly lower levels of ABCC1 transcript than those from carriers of the minor allele (p = 0.003 and p = 0.004, respectively). The ABCC1 transcript levels significantly increased in the order CT-GT>CC-GT>CC-GG for the predicted rs35626-rs4148351 diplotype. Chemotherapy-treated patients carrying the T allele in rs4148353 had longer disease-free survival than those with the GG genotype (p = 0.043). On the other hand, hormonal therapy-treated patients with the AA genotype in rs35628 had significantly longer disease-free survival than carriers of the G allele (p = 0.012). Conclusions Taken together, our study shows that genetic variability in the nucleotide binding domain 1 has a significant impact on the ABCC1 transcript level in the target tissue and may modify survival of breast cancer patients.
Learning a Loopy Model For Semantic Segmentation Exactly

Learning structured models using maximum margin techniques has become an indispensable tool for com- puter vision researchers, as many computer vision applications can be cast naturally as an image labeling problem. Pixel-based or superpixel-based conditional random fields are particularly popular examples. Typ- ically, neighborhood graphs, which contain a large number of cycles, are used. As exact inference in loopy graphs is NP-hard in general, learning these models without approximations is usually deemed infeasible. In this work we show that, despite the theoretical hardness, it is possible to learn loopy models exactly in practical applications. To this end, we analyze the use of multiple approximate inference techniques together with cutting plane training of structural SVMs. We show that our proposed method yields exact solutions with an optimality guarantees in a computer vision application, for little additional computational cost. We also propose a dynamic caching scheme to accelerate training further, yielding runtimes that are comparable with approximate methods. We hope that this insight can lead to a reconsideration of the tractability of loopy models in computer vision.
Disruption of the C. elegans Intestinal Brush Border by the Fungal Lectin CCL2 Phenocopies Dietary Lectin Toxicity in Mammals

Lectins are non-immunoglobulin carbohydrate-binding proteins without enzymatic activity towards the bound carbohydrates. Many lectins of e.g. plants or fungi have been suggested to act as toxins to defend the host against predators and parasites. We have previously shown that the Coprinopsis cinerea lectin 2 (CCL2), which binds to α1,3-fucosylated N-glycan cores, is toxic to Caenorhabditis elegans and results in developmental delay and premature death. In this study, we investigated the underlying toxicity phenotype at the cellular level by electron and confocal microscopy. We found that CCL2 directly binds to the intestinal apical surface and leads to a highly damaged brush border with loss of microvilli, actin filament depolymerization, and invaginations of the intestinal apical plasma membrane through gaps in the terminal web. We excluded several possible toxicity mechanisms such as internalization and pore-formation, suggesting that CCL2 acts directly on intestinal apical plasma membrane or glycocalyx proteins. A genetic screen for C. elegans mutants resistant to CCL2 generated over a dozen new alleles in bre 1, ger 1, and fut 1, three genes required for the synthesis of the sugar moiety recognized by CCL2. CCL2-induced intestinal brush border defects in C. elegans are similar to the damage observed previously in rats after feeding the dietary lectins wheat germ agglutinin or concanavalin A. The evolutionary conserved reaction of the brush border between mammals and nematodes might allow C. elegans to be exploited as model organism for the study of dietary lectin-induced intestinal pathology in mammals.
The Fertility of the Irish in America in 1910

In most western societies, marital fertility began to decline in the nineteenth century. But in Ireland, fertility in marriage remained stubbornly high into the twentieth century. Explanations of Ireland's late entry to the fertility transition focus on the influence of the Roman Catholic Church in Irish society. These arguments are often backed up by claims that the Irish outside of Ireland behaved the same way. This paper investigates these claims by examining the marital fertility of Irish Americans in 1910 and produces three main findings. First, the Irish in America had smaller families than both the rural and urban Irish and their fertility patterns show clear evidence of fertility control. Second, despite the evidence of control, Irish-Americans continued to have large families, much larger, in fact, than the U.S. native-born population. The fertility differential between these populations was not due to differences in other population characteristics. Rather it was due to the fact that conditional on characteristics, Irish-Americans chose to have larger families. Third, the differential fertility patterns of Irish-Americans were not just due to the effects of being immigrants. Germans and English immigrants also had higher fertility than the native-born population, but to a much larger extent than for the Irish, this higher fertility could be explained by the population characteristics of these groups.
Using a Foundational Ontology for Reengineering a Software Process Ontology

Normal 0 21 During project planning , knowledge about software processes is useful in several situations: software processes are defined, activities are scheduled, and people are allocated to these activities. In this context, standard software processes are used as basis for defining project processes, and tools are used to support scheduling, people allocation, and so on. Ideally, people and tools should share a common conceptualization regarding this domain for allowing interoperability, and correct use of the tools. A domain ontology can be used to define an explicit representation of this shared conceptualization . Moreover, for a domain ontology to adequately serve as a reference model, it should be built explicitly taking foundational concepts into account . This paper discusses the reengineering of part of a Software Process Ontology based on the Unified Foundational Ontology (UFO). The part reengineered concerns standard processes, project processes, and activities, which are analyzed at the light of UFO concepts.
Capital Injection, Monetary Policy, and Financial Accelerators

We evaluate the implications of spread-adjusted Taylor rules and capital injection policies in response to adverse shocks to the economy, using a variant of the financial accelerator model. Our model comprises the two credit-constrained sectors that raise external finance under credit market imperfection: financial intermediaries (FIs) and entrepreneurs. With the model estimated using the U.S. data, we find that a spread-adjusted Taylor rule mitigates (amplifies) the impact of adverse shocks when the shock is accompanied by a widening (shrinking) of the corresponding spread. We formalize a capital injection policy as a positive (negative) amount of injection to either of the two sectors in response to an adverse shock (a favorable shock). In contrast to a spread-adjusted Taylor rule, a positive injection boosts the economy regardless of the type of shock. The capital injection to the FIs has a greater impact on the economy compared with that to the entrepreneurs. Our result shows support for adopting the spread-adjusted Taylor rules and capital injections, although welfare implication varies depending on the source of economic downturn and excessive responses aggravate welfare.
Moduli of Higgs Bundles

2 Local symplectic, complex and Kähler geometry: a quick review 10 2.1 Quotients . 11 2.2 Symplectic manifolds . 12 2.3 Symplectic quotients . 12 2.4 Complex manifolds . 15 2.5 Type decompositions . 16 2.6 Holomorphic vector bundles . 17 2.7 Hermitian and Kähler metrics . 18 2.8 Hodge theory . 20 2.9 Kähler quotients . 23 2.10 Holomorphic symplectic manifolds . 25
Inequalities in women's awareness of changes to the State Pension Age in England and the role of cognitive ability

Abstract As a response to the ageing population, the United Kingdom (UK) government, like many others, has increased the State Pension Age. This has involved equalising women's State Pension Age with men's, raising it from 60 to 65, with further increases already underway. It has been argued that a key issue with how this change has been implemented is the lack of notice the government gave to the women affected, impacting on their ability to plan for retirement. So far, there has been very little research exploring inequalities in awareness of these developments and, in particular, considering whether women of particular socio-economic backgrounds are less likely to know about the changes. This has implications for potentially further widening inequalities in old age. In this paper we analyse data from the English Longitudinal Study of Ageing. We consider the role of cognitive ability in mediating the relationship between socio-economic background and awareness, given recent debates on deficiencies in financial literacy. We find that socio-economic inequalities exist, especially with respect to labour force status, occupation and education. We also find that cognitive ability, especially numeracy, mediates a sizeable proportion of the relationship. These findings have important implications in terms of implementing future policy changes and awareness campaigns to help mitigate the possibility that they will further entrench inequalities in older age.
Slum-Upgrading in Tanzania: Public Infrastructure and Private Property Rights

This paper seeks to understand the relationship between the provision of public infrastructure and the demand for formal property rights in the unplanned urban settlements of Dar es Salaam, Tanzania. We analyze take-up patterns in two adjacent settlements where residents were offered the opportunity to purchase formal land titles at subsidized prices. Detailed plans for proposed infrastructure investments were drawn up for both settlements, but these infrastructure investments were only implemented in one of the two locations. We exploit this quasi-experiment to show that proximity to actual, but not hypothetical, infrastructure investment significantly increases demand for property rights, and this effect appears to be driven by both increased property values and a dramatically-higher perceived risk of expropriation. ∗University of Oxford †Center for Global Development ‡Georgetown University §We gratefully acknowledge funding from the Department for International Development, UK government, through the International Growth Centre (IGC), specifically via the IGC Research Award ”Economic Impact of Urban Property Rights and Tanzania: The Role of Infrastructure” led by the Department of International Development (DFID), University of Oxford. Further support from the DFID-funded research programme ”Improving Institutions for Pro-Poor Growth” (iiG) is also acknowledged. We are grateful to Kate Prudden for editorial comments and suggestions. All errors are our own.
Probiotic Supplementation in the First 6 Months of Life in at Risk Asian Infants: Effects on Eczema and Atopic Sensitization at the Age of 1 Year

Soh SE, Aw M, Gerez I, et al. Clin Exp Allergy. 2009;39(4):571–578 PURPOSE OF THE STUDY. To determine the effect of probiotic supplementation from birth to 6 months of age on eczema and allergic sensitization at 1 year of age in Asian infants at risk of allergic disease. STUDY POPULATION. A total of 253 infants with a family history of allergic disease, defined as having a first-degree relative with doctor-diagnosed asthma, allergic rhinitis, or eczema, and positive skin-prick test result to dust mite, were voluntarily recruited prenatally at the clinics at the …
Load Responsiveness of Protein Synthesis in Adult Mammalian Myocardium: Role of Cardiac Deformation Linked to Sodium Influx

Exposure of adult mammalian myocardium to increased hemodynamic loads augments cardiac protein synthesis, ultimately leading to hypertrophy of the affected chamber. This established relationship between loading conditions and protein synthesis was examined in terms of two questions. First, is there a basic difference between the anabolic effect of a passive load imposed on diastolic myocardium and that of an active load generated by systolic myocardium? This issue was addressed by measuring [3H]phenylalanine incorporation into muscle protein in either quiescent or contracting ferret papillary muscles, set at known isometric lengths. Myocardial protein synthesis increased in proportion to total muscle tension in each case, with an equivalent relation describing both quiescent and contracting muscles. Synthesis of two contractile proteins, actin and myosin heavy chain, were enhanced by muscle loading. Thus, a quantitative rather than qualitative difference between the anabolic effects of diastolic and systolic loading was demonstrated. Second, since increased sodium influx is an initial cellular response requisite to the growth-inducing activity of many substances, and since sodium entry through stretch-activated ion channels is stimulated by deformation of the sarcolemma, does cardiac deformation during increased loading promote sodium influx as a signal to increase anabolic activity? In either quiescent or contracting papillary muscles, the rate of 24Na+ uptake was found to increase with load. Streptomycin, a cationic blocker of the mechanotransducer ion channels, was without effect on protein synthesis in stimulated but slack muscles; however, it inhibited, in a dose-related manner, the augmented protein synthesis otherwise observed in contracting muscles developing tension. At 500 μM, streptomycin did not reduce active tension, but it did reduce the synthesis of both actin and myosin heavy chain. In a second pharmacologic approach, inotropic agents were chosen which uniformly increased muscle tension development but which had contrasting effects on sodium influx. Protein synthesis increased in the presence of Na+ influx enhancers, monensin or veratridine; however, protein synthesis decreased in the presence of amiloride, a sodium influx inhibitor. Thus, myocardial protein synthesis varied directly with sodium influx despite the positive inotropic effect observed with each of these agents. In addition, inhibition of protein synthesis by ouabain demonstrated that activation of the Na+ pump is required for the anabolic effect of load. This study, therefore, identifies deformation-dependent sodium influx as an early signal in the transduction of load into growth in adult mammalian myocardium.
And now to something completely different: Spatial coupling as a proof technique

The aim of this paper is to show that spatial coupling can be viewed not only as a means to build better graphical models, but also as a tool to better understand uncoupled models. The starting point is the observation that some asymptotic properties of graphical models are easier to prove in the case of spatial coupling. In such cases, one can then use the so-called interpolation method to transfer results known for the spatially coupled case to the uncoupled one. Our main application of this framework is to LDPC codes, where we use interpolation to show that the average entropy of the codeword conditioned on the observation is asymptotically the same for spatially coupled as for uncoupled ensembles. We use this fact to prove the so-called Maxwell conjecture for a large class of ensembles. In a first paper last year, we have successfully implemented this strategy for the case of LDPC ensembles where the variable node degree distribution is Poisson. In the current paper we now show how to treat the practically more relevant case of general left degree distributions. In particular, regular ensembles fall within this framework. As we will see, a number of technical difficulties appear when compared to the simpler case of Poisson-distributed degrees. For our arguments to hold we need symmetry to be present. For coding, this symmetry follows from the channel symmetry; for general graphical models the required symmetry is called Nishimori symmetry.
A Bibliometric Analysis of Publications on Pluripotent Stem Cell Research

Objective Human pluripotent stem cells are self-renewing cells with the ability to differentiate into a variety of cells and are viewed to have great potential in the field of regenerative medicine. Research in pluripotent stem cells holds great promise for patient specific therapy in various diseases. In this study, pluripotent stem cell articles published from 1991 to 2012 were screened and retrieved from Science Citation Index Expanded (SCI-EXPANDED). Materials and Methods In this retrospective study, the publication trend, citation trends for top articles, distributions of journals and Web of Science categories were analyzed. Five bibliometric indicators including total articles, independent articles, collaborative articles, first author articles, and corresponding author articles were applied to compare publications between countries and institutions. Results The impact of top articles changed from year to year. Top cited articles in previous publication years were not the same as recent years. "Induced pluripotent stem cell (s)" and "embryonic stem cell (s)" were the most used author keywords in pluripotent stem cell research. In addition, the winner of the Nobel Prize in physiology or medicine in 2012, Prof. Shinya Yamanaka, published four of the top ten most frequently cited articles. Conclusion The comprehensive analysis of highly cited articles in the stem cell field could identify milestones and important contributors, giving a historic perspective on scientific progress.
Ghosts in the Nursery 2.0

SYNOPSIS Parental working is not unambiguously beneficial for children. On the one hand, working parents can be positive role models for their children, and income can improve children’s lives in many ways. On the other hand, work can impair parent-child interactions, especially when the parents experience high levels of working stress. In my commentary, I conclude that the paper by River, enjoys strong support for the impact of maternal state anxiety (attachment anxiety) and work-interfering-with-family (WIF)-conflict related guilt on parents behaviors. Considering the cognitive-relational stress-theory by Lazarus and Folkman, the balance of personal resources and external demands can explain parental stress, which could be associated with parental behavior. Full-time-working parents, who experience high levels of guilt and report high levels of attachment anxiety, are more prone to show low levels of stress resistance toward crying infants. However, these associations are not studied in families with high risk factors. Furthermore, future studies should include aspects of mental health status in a theoretical model. Taken together, the target article provides a solid foundation for further research. I also propose to transfer the findings into more realistic research setting, which includes high-risk groups (parents with low socioeconomic status, low-income, mental health problems) to study how infant cry can influence parents’ patterns of care and abuse. The commentary tries to enrich the study by including Fraiberg’s “ghosts in the nursery” to further integrating parental mentalizing processes in the model explaining parents’ reactions to infant cry signal in the context of WIF conflicts.
The Origin of X-shaped Radio Galaxies: Clues from the Z-symmetric Secondary Lobes

Existing radio images of a few X-shaped radio galaxies reveal Z-symmetric morphologies in their weaker secondary lobes that cannot be naturally explained by either the galactic merger or radio-lobe backflow scenarios, the two dominant models for these X-shaped radio sources. We show that the merger picture can explain these morphologies provided one takes into account that, prior to the coalescence of their supermassive black holes, the smaller galaxy releases significant amounts of gas into the interstellar medium of the dominant active galaxy. This rotating gas, whose angular momentum axis will typically not be aligned with the original jets, is likely to provide sufficient ram pressure at a distance ~10 kpc from the nucleus to bend the extant jets emerging from the central engine, thus producing a Z-symmetry in the pair of radio lobes. Once the two black holes have coalesced some 107 yr later, a rapid reorientation of the jets along a direction close to that of the orbital angular momentum of the swallowed galaxy relative to the primary galaxy would create the younger primary lobes of the X-shaped radio galaxy. This picture naturally explains why such sources typically have powers close to the FR I/II break. We suggest that purely Z-symmetric radio sources are often en route to coalescence and the concomitant emission of substantial gravitational radiation, while X-shaped ones have already merged and radiated.
Carbon Fiber Reinforced Thermoset Composite with Near 100% Recyclability

Both environmental and economic factors have driven the development of recycling routes for the increasing amount of composite waste generated. This paper presents a new paradigm to fully recycle epoxy‐based carbon fiber reinforced polymer (CFRP) composites. After immersing the composite in ethylene glycol (EG) and increasing the temperature, the epoxy matrix can be dissolved as the EG molecules participate in bond exchange reactions (BERs) within the covalent adaptable network (CAN), effectively breaking the long polymer chains into small segments. The clean carbon fibers can be then reclaimed with the same dimensions and mechanical properties as those of fresh ones. Both the dissolution rate and the minimum amount of EG required to fully dissolve the CAN are experimentally determined. Further heating the dissolved solution leads to repolymerization of the epoxy matrix, so a new generation of composite can be fabricated by using the recycled fiber and epoxy; in this way a closed‐loop near 100% recycling paradigm is realized. In addition, epoxy composites with surface damage are shown to be fully repaired. Both the recycled and the repaired composites exhibit the same level of mechanical properties as fresh materials.