bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of Proactive Self-Initiated Self-Repair as an Indicator of L2 IC Development
Authors: Kim Du Re 
Published: September 2019

AbstractThis article finds empirical evidence of second language (L2) interactional competence (IC) and its development by focusing on one of the interactional practices: self-repairing. Compared to prior repair IC studies which mainly have explored how L2 speakers deal with evident L2-related troubles in conversation, this study focuses on cases in which they deploy self-repair when there are no such linguistic problems in previous talk, taking Mauranen’s (2006) dichotomy between retroactive and proactive self-repairs. After analyzing the conversation by L2 speakers with different oral proficiency, this study discovers whereas novice and intermediate speakers self-repair for correcting what is lexically or grammatically problematic, advanced speakers deploy self-repair mostly for pre-empting possible misunderstandings. Advanced speakers replace the previous items into words that are specific in the meaning range by fine-tuning the level of ‘granularity’ (Schegloff 2000) to avoid ambiguity and further other-initiated repair. The findings suggest that the development of L2 IC involves speakers’ ability to detect potential problems in the eyes of the recipients and replace them in advance.
Psychometrics and Validity of the Survey of Memory-Related Quality of Life in HIV Disease
Authors: Sullivan Kelli L , Kulesz Paulina A , Woods Steven Paul 
Published: September 2019

Abstract

Objective
Retrospective and prospective memory deficits are associated with lower quality of life (QoL); however, there are no validated measures that comprehensively and directly assess the impact of memory problems on QoL. The Survey of Memory-Related Quality of Life (SMRQoL) was developed as a 30-item questionnaire to measure memory-related QoL.

Method
Both HIV+ (n = 195) and HIV− (n = 146) participants completed the SMRQoL, a neurocognitive research battery, and validated self-report questionnaires of memory, QoL, and mood. Participants were recruited into younger (age ≤ 40 years) and older (age ≥ 50 years) groups per the parent study design.

Results
The SMRQoL had a unidimensional factor structure and demonstrated measurement invariance across the HIV+ and HIV− participants. Analyses of 111 clinically stable participants (e.g., persons with no incident or remitting central nervous system disorders) who returned for a 14-month follow-up visit indicated that the SMRQoL had adequate test–retest stability. There was a significant interaction of age and HIV status on the SMRQoL, such that older HIV+ participants reported the lowest memory-related QoL. SMRQoL scores were associated with validated measures of mental and physical QoL, self-reported memory and cognitive symptoms, and performance-based memory and executive functions.

Conclusions
The SMRQoL shows evidence of reliability and validity as a measure of memory-related QoL that can be used to assess the impact of memory problems on everyday life, but future work is needed to demonstrate the measure’s incremental value in the context of diagnosis and treatment.
Sexual dimorphism in the biomechanical and toxicological performance in prey incapacitation of two morphologically distinct scorpion species (Chactas sp. and Centruroides sp.)
Authors: González-Gómez Julio César , Valenzuela-Rojas Juan Carlos , García Luis Fernando , Franco Pérez Lida Marcela , Guevara Giovany , Buitrago Sandra , Cubillos Allison , Van Der Meijden Arie 
Published: September 2019

Abstract
Morphological differences between the sexes are a common feature in many groups of animals and can have important ecological implications for courtship, mating, access to prey and, in some cases, intersex niche partitioning. In this study, we evaluated the role of sexual dimorphism in the performance of the two structures that mediate the ability to access prey, the pinchers or chelae and the venomous stinger, in two species of scorpions with contrasting morphologies: Chactas sp., which has marked sexual dimorphism in the chelae, and Centruroides sp., which does not have such marked dimorphism in the chelae. We evaluated aspects such as chela pinch force, toxicity to prey (LD50) and the volume of venom in males and females of each species. We found significant differences between males and females of Chactas sp. in the chela pinch force, volume of venom and LD50. In contrast, for Centruroides sp., no differences between males and females were found in any of these traits. We discuss several potential selective regimes that could account for the pattern observed.
Women with polycystic ovary syndrome present with altered endometrial expression of stanniocalcin-1†
Authors: Khatun Masuma , Arffman Riikka K , Lavogina Darja , Kangasniemi Marika , Laru Johanna , Ahtikoski Anne , Lehtonen Siri , Paulson Mariana , Hirschberg Angelica Lindén , Salumets Andres , Andersson Leif C , Piltonen Terhi T 
Published: September 2019

Abstract
Stanniocalcin-1 (STC-1) is a pro-survival factor that protects tissues against stressors, such as hypoxia and inflammation. STC-1 is co-expressed with the endometrial receptivity markers, and recently endometrial STC-1 was reported to be dysregulated in endometriosis, a condition linked with endometrial progesterone resistance and inflammation. These features are also common in the endometrium in women with polycystic ovary syndrome (PCOS), the most common endocrine disorder in women. Given that women with PCOS present with subfertility, pregnancy complications, and increased risk for endometrial cancer, we investigated endometrial STC-1 expression in affected women. Endometrial biopsy samples were obtained from women with PCOS and controls, including samples from overweight/obese women with PCOS before and after a 3-month lifestyle intervention. A total of 98 PCOS and 85 control samples were used in immunohistochemistry, reverse-transcription polymerase chain reaction, or in vitro cell culture. STC-1 expression was analyzed at different cycle phases and in endometrial stromal cells (eSCs) after steroid hormone exposure. The eSCs were also challenged with 8-bromo-cAMP and hypoxia for STC-1 expression. The findings indicate that STC-1 expression is not steroid hormone mediated although secretory-phase STC-1 expression was blunted in PCOS. Lower expression seems to be related to attenuated STC-1 response to stressors in PCOS eSCs, shown as downregulation of protein kinase A activity. The 3-month lifestyle intervention did not restore STC-1 expression in PCOS endometrium. More studies are warranted to further elucidate the mechanisms behind the altered endometrial STC-1 expression and rescue mechanism in the PCOS endometrium.
The interplay between thyroid hormones and the placenta: a comprehensive review†
Authors: Adu-Gyamfi Enoch Appiah , Wang Ying-Xiong , Ding Yu-Bin 
Published: September 2019

AbstractThyroid hormones (THs) regulate a number of metabolic processes during pregnancy. After implantation, the placenta forms and enhances embryonic growth and development. Dysregulated maternal THs signaling has been observed in malplacentation-mediated pregnancy complications such as preeclampsia, miscarriage, and intrauterine growth restriction (IUGR), but the molecular mechanisms involved in this association have not been fully characterized. In this review, we have discussed THs signaling and its roles in trophoblast proliferation, trophoblast differentiation, trophoblast invasion of the decidua, and decidual angiogenesis. We have also explored the relationship between specific pregnancy complications and placental THs transporters, deiodinases, and THs receptors. In addition, we have examined the effects of specific endocrine disruptors on placental THs signaling. The available evidence indicates that THs signaling is involved in the formation and functioning of the placenta and serves as the basis for understanding the pathogenesis and pathophysiology of dysthyroidism-associated pregnancy complications such as preeclampsia, miscarriage, and IUGR.
The Legal Framework for UK Aid After Brexit
Authors: Manji Ambreena 
Published: September 2019

Abstract
Since 2015, when the UK legislated a target for aid spending, the nature of its spending on official development assistance has changed significantly. Government departments not traditionally associated with spending aid have found themselves in charge of disbursing aid funds as a result of that year’s spending review. The vote to exit the European Union has subsequently introduced a number of uncertainties. What considerations will be at play in UK aid spending after Brexit? What will become of official development assistance currently spent through European mechanisms? In what sort of configuration might the Department for International Development and other government departments find themselves? The focus of this paper is on how the vote to leave the European Union might affect the way the UK spends aid. It asks whether the legal framework for this spending is robust enough to withstand the demands that a new post-Brexit political and economic context will make.
rCASC: reproducible classification analysis of single-cell sequencing data
Authors: Alessandrì Luca , Cordero Francesca , Beccuti Marco , Arigoni Maddalena , Olivero Martina , Romano Greta , Rabellino Sergio , Licheri Nicola , De Libero Gennaro , Pace Luigia , Calogero Raffaele A 
Published: September 2019

Abstract

Background
Single-cell RNA sequencing is essential for investigating cellular heterogeneity and highlighting cell subpopulation-specific signatures. Single-cell sequencing applications have spread from conventional RNA sequencing to epigenomics, e.g., ATAC-seq. Many related algorithms and tools have been developed, but few computational workflows provide analysis flexibility while also achieving functional (i.e., information about the data and the tools used are saved as metadata) and computational reproducibility (i.e., a real image of the computational environment used to generate the data is stored) through a user-friendly environment.

Findings
rCASC is a modular workflow providing an integrated analysis environment (from count generation to cell subpopulation identification) exploiting Docker containerization to achieve both functional and computational reproducibility in data analysis. Hence, rCASC provides preprocessing tools to remove low-quality cells and/or specific bias, e.g., cell cycle. Subpopulation discovery can instead be achieved using different clustering techniques based on different distance metrics. Cluster quality is then estimated through the new metric "cell stability score" (CSS), which describes the stability of a cell in a cluster as a consequence of a perturbation induced by removing a random set of cells from the cell population. CSS provides better cluster robustness information than the silhouette metric. Moreover, rCASC's tools can identify cluster-specific gene signatures.

Conclusions
rCASC is a modular workflow with new features that could help researchers define cell subpopulations and detect subpopulation-specific markers. It uses Docker for ease of installation and to achieve a computation-reproducible analysis. A Java GUI is provided to welcome users without computational skills in R.
Evaluation of computational genotyping of structural variation for clinical diagnoses
Authors: Chander Varuna , Gibbs Richard A , Sedlazeck Fritz J 
Published: September 2019

Abstract

Background
Structural variation (SV) plays a pivotal role in genetic disease. The discovery of SVs based on short DNA sequence reads from next-generation DNA sequence methods is error-prone, with low sensitivity and high false discovery rates. These shortcomings can be partially overcome with extensive orthogonal validation methods or use of long reads, but the current cost precludes their application for routine clinical diagnostics. In contrast, SV genotyping of known sites of SV occurrence is relatively robust and therefore offers a cost-effective clinical diagnostic tool with potentially few false-positive and false-negative results, even when applied to short-read DNA sequence data.

Results
We assess 5 state-of-the-art SV genotyping software methods, applied to short-read sequence data. The methods are characterized on the basis of their ability to genotype different SV types, spanning different size ranges. Furthermore, we analyze their ability to parse different VCF file subformats and assess their reliance on specific metadata. We compare the SV genotyping methods across a range of simulated and real data including SVs that were not found with Illumina data alone. We assess sensitivity and the ability to filter initial false discovery calls. We determined the impact of SV type and size on the performance for each SV genotyper. Overall, STIX performed the best on both simulated and GiaB based SV calls, demonstrating a good balance between sensitivity and specificty.

Conclusion
Our results indicate that, although SV genotyping software methods have superior performance to SV callers, there are limitations that suggest the need for further innovation.
Informal caregivers in Chile: the equity dimension of an invisible burden
Authors: Villalobos Dintrans Pablo 
Published: September 2019

Abstract
Population aging is driving a process of increase in long-term care needs in Chile and many countries around the world. In this context, this article asks about the consequences of this increase in informal caregivers, emphasizing the inequity issues arising from these changes. Using the CASEN 2017 survey, caregivers are identified and matched to people with long-term care needs. Results show that most caregivers are women, and a large fraction of them are also elderly; this is similar to what has been found previously in developed countries. Caregivers have fewer opportunities than non-caregivers, which translates into lower income-generating ability and higher poverty. The nature of these tasks creates a vicious cycle in which people get trapped with increasing needs and fewer resources to meet them. Important differences arise between caregivers and the rest of the population. Even more concerning is that these disparities are avoidable to some extent, adding an equity dimension to the problem. This emphasizes the need for the generation of policies that will support caregivers and meet their needs.
Developing a microscopic image dataset in support of intelligent phytoplankton detection using deep learning
Authors: Li Qiong , Sun Xin , Dong Junyu , Song Shuqun , Zhang Tongtong , Liu Dan , Zhang Han , Han Shuai 
Published: September 2019

AbstractPhytoplankton plays an important role in marine ecological environment and aquaculture. However, the recognition and detection of phytoplankton rely on manual operations. As the foundation of achieving intelligence and releasing human labour, a phytoplankton microscopic image dataset PMID2019 for phytoplankton automated detection is presented. The PMID2019 dataset contains 10 819 phytoplankton microscopic images of 24 different categories. We leverage microscopes to collect images of phytoplankton in the laboratory environment. Each object in the images is manually labelled with a bounding box and category of ground-truth. In addition, living cells move quickly making it difficult to capture images of them. In order to generalize the dataset for in situ applications, we further utilize Cycle-GAN to achieve the domain migration between dead and living cell samples. We built a synthetic dataset to generate the corresponding living cell samples from the original dead ones. The PMID2019 dataset will not only benefit the development of phytoplankton microscopic vision technology in the future, but also can be widely used to assess the performance of the state-of-the-art object detection algorithms for phytoplankton recognition. Finally, we illustrate the performances of some state-of-the-art object detection algorithms, which may provide new ideas for monitoring marine ecosystems.
Optimal Estimates for Steklov Eigenvalue Gaps and Ratios on Warped Product Manifolds
Authors: Xiong Changwei 
Published: September 2019

Abstract
We consider an $n$-dimensional smooth Riemannian manifold $M^n=[0,R)\times \mathbb{S}^{n-1}$ endowed with a warped product metric $g=dr^2+h^2(r)g_{\mathbb{S}^{n-1}}$ and diffeomorphic to a Euclidean ball. Suppose that $M$ has strictly convex boundary. First, for the classical Steklov eigenvalue problem, we derive an optimal lower (upper, respectively) bound for its eigenvalue gaps in terms of $h^{\prime}(R)/h(R)$ when $n\geq 2$ and $Ric_g\geq 0$ ($\leq 0$, respectively). Second, in the same spirit, for two 4th-order Steklov eigenvalue problems studied by Kuttler and Sigillito in 1968, we deduce an optimal lower bound for their eigenvalue gaps in terms of either $h^{\prime}(R)/h^3(R)$ or $h^{\prime}(R)/h(R)$ when $n=2$ and the Gaussian curvature is nonnegative. We also consider optimal estimates on the eigenvalue ratios for these eigenvalue problems.
K3 surfaces from configurations of six lines in ℙ2 and mirror symmetry II—λK3-functions
Authors: Hosono Shinobu , Lian Bong H , Yau Shing-Tung 
Published: September 2019

AbstractWe continue our study on the hypergeometric system $E(3,6)$ that describes period integrals of the double cover family of K3 surfaces. Near certain special boundary points in the moduli space of the K3 surfaces, we construct the local solutions and determine the so-called mirror maps expressing them in terms of genus 2 theta functions. These mirror maps are the K3 analogues of the elliptic $\lambda $-function. We find that there are two nonisomorphic definitions of the lambda functions corresponding to a flip in the moduli space. We also discuss mirror symmetry for the double cover K3 surfaces and their higher dimensional generalizations. A follow-up paper will describe more details of the latter.
Prognostic impact of local radiotherapy on metastatic urothelial carcinoma patients receiving systemic chemotherapy
Authors: Abe Takashige , Minami Keita , Harabayashi Toru , Sazawa Ataru , Chiba Hiroki , Kikuchi Hiroshi , Miyata Haruka , Frumido Jun , Matsumoto Ryuji , Osawa Takahiro , Junji Ishizaki , Tango Mochizuki , Satoshi Chiba , Tomoshige Akino , Masashi Murakumo , Naoto Miyajima , Kunihiko Tsuchiya , Satoru Maruyama , Murai Sachiyo , Shinohara Nobuo 
Published: September 2019

Abstract

Objective
To clarify the prognostic impact of local radiotherapy on metastatic urothelial carcinoma patients treated by systemic chemotherapy.

Methods
Of the 228 metastatic urothelial carcinoma patients treated with systemic chemotherapy, 97 received radiotherapy mainly to metastatic sites. In patients for whom the purpose of radiotherapy was not specified, more than 50 Gy irradiation was considered to be for disease consolidation for survival analysis, while less than 50 Gy was categorized as palliation. According to the Kaplan–Meier method, we analysed overall survival from the initiation of treatment for metastatic urothelial carcinoma until death or the last follow-up, using the log-rank test to assess the significance of differences. The Cox model was applied for prognostic factor analysis.

Results
Overall, there was no significant difference in survival between patients with and those without radiotherapy (P = 0.1532). When analysing the patients undergoing consolidative radiotherapy separately, these 25 patients showed significantly longer survival than the 72 patients with palliative radiotherapy (P = 0.0047), with a 3-year overall survival of 43.3%. Of the present cohort, 22 underwent metastasectomy for disease consolidation, and there was no overlapping case between the metastasectomy cohort and cohort receiving consolidative radiotherapy. After controlling for four independent prognostic factors (sex, performance status, haemoglobin level and number of organs with metastasis) in our previous study, radiotherapy for disease consolidation showed a marginal value (hazard ratio = 0.666, P = 0.0966), while metastasectomy remained significant (hazard ratio = 0.358, P = 0.0006).

Conclusions
In the selected patients, long-term disease control could be achieved after consolidative radiotherapy for metastatic urothelial carcinoma disease. Our observations suggest that local ablative therapy (surgery or radiotherapy) could facilitate long-term disease control. However, the treatment decision should be individualized because of the lack of randomized control trials.
Price Discovery in a Continuous-Time Setting
Authors: Dias Gustavo F. , Fernandes Marcelo , Scherrer Cristina M. 
Published: September 2019

AbstractWe formulate a continuous-time price discovery model and investigate how the standard price discovery measures vary with respect to the sampling interval. We find that the component share (CS) measure is invariant to the sampling interval, and hence, discrete-sampled prices suffice to identify the continuous-time CS. In contrast, information share (IS) estimates are not comparable across different sampling intervals because the contemporaneous correlation between markets increases in magnitude as the sampling interval grows. We show how to back out the continuous-time IS from discrete-sampled prices under certain assumptions on the contemporaneous correlation. We assess our continuous-time model by comparing the estimates of the (continuous-time) CS and IS at different sampling intervals for 30 stocks in the United States. We find that both price discovery measures are typically stable across the different sampling intervals, suggesting that our continuous-time price discovery model fits the data very well.
Exposure to Tomographic Scans and Cancer Risks
Authors: Shao Yu-Hsuan , Tsai Kevin , Kim Sinae , Wu Yu-Jen , Demissie Kitaw 
Published: September 2019

Abstract

Background
Worldwide use of computed tomography (CT) scans has increased. However, the ionizing radiation from CT scans may increase the risk of cancer. This study examined the association between medical radiation from CT scans and the risk of thyroid cancer, lymphoma, and non-Hodgkin lymphoma (NHL) in adults.

Methods
We conducted a nested case-control study in a cohort constructed from a population-based universal health insurance dataset in Taiwan in 2000–2013. In total, 22 853 thyroid cancer, 13 040 leukemia, and 20 157 NHL cases with their matched controls were included. Median follow-up times were 9.29–9.90 years for the three case-control groups. Medical radiation from CT scans was identified through physician order codes in medical insurance data from the index date to 3 years before a cancer diagnosis. Conditional logistic regression modeling was used for the overall and subsets of the population defined by sex and age groups to estimate the odds ratio (OR) and 95% confidence interval (CI) of the cancer risk associated with medical radiation.

Results
Exposure to medical radiation from CT scans was associated with elevated risk of thyroid cancer (OR = 2.55, 95% CI = 2.36 to 2.75) and leukemia (OR = 1.55, 95% CI = 1.42 to 1.68). The elevated risk of thyroid cancer and leukemia in association with medical CT was stronger in women than in men. No statistically significant association between the risk of cancer and CT scans was observed in overall patients with NHL (OR = 1.05, 95% CI = 0.98 to 1.12); however, increased risks were found in patients aged 45 years or younger. A clear dose-response relationship was observed in patients 45 years or younger for all three cancers.

Conclusions
CT scans may be associated with an increased risk of thyroid cancer and leukemia in adults and in those diagnosed with NHL at a younger age.