bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic coherence spaces are fully abstract for probabilistic PCF
Authors: Ehrhard Thomas , Tasson Christine , Pagani Michele 
Published: April 2020

Probabilistic coherence spaces (PCoh) yield a semantics of higher-order probabilistic computation, interpreting types as convex sets and programs as power series. We prove that the equality of interpretations in Pcoh characterizes the operational indistinguishability of programs in PCF with a random primitive.
This is the first result of full abstraction for a semantics of probabilistic PCF. The key ingredient relies on the regularity of power series.
Along the way to the theorem, we design a weighted intersection type assignment system giving a logical presentation of PCoh.
An operational and axiomatic semantics for non-determinism and sequence points in C
Authors: Krebbers Robbert 
Published: April 2020

The C11 standard of the C programming language does not specify the execution order of expressions. Besides, to make more effective optimizations possible (eg. delaying of side-effects and interleaving), it gives compilers in certain cases the freedom to use even more behaviors than just those of all execution orders.
Widely used C compilers actually exploit this freedom given by the C standard for optimizations, so it should be taken seriously in formal verification. This paper presents an operational and axiomatic semantics (based on separation logic) for non-determinism and sequence points in C. We prove soundness of our axiomatic semantics with respect to our operational semantics. This proof has been fully formalized using the Coq proof assistant.
A nonstandard standardization theorem
Authors: Accattoli Beniamino , Bonelli Eduardo , Kesner Delia , Lombardi Carlos 
Published: April 2020

Standardization is a fundamental notion for connecting programming languages and rewriting calculi. Since both programming languages and calculi rely on substitution for defining their dynamics, explicit substitutions (ES) help further close the gap between theory and practice.
This paper focuses on standardization for the linear substitution calculus, a calculus with ES capable of mimicking reduction in lambda-calculus and linear logic proof-nets. For the latter, proof-nets can be formalized by means of a simple equational theory over the linear substitution calculus.
Contrary to other extant calculi with ES, our system can be equipped with a residual theory in the sense of Lévy, which is used to prove a left-to-right standardization theorem for the calculus with ES but without the equational theory. Such a theorem, however, does not lift from the calculus with ES to proof-nets, because the notion of left-to-right derivation is not preserved by the equational theory. We then relax the notion of left-to-right standard derivation, based on a total order on redexes, to a more liberal notion of standard derivation based on partial orders.
Our proofs rely on Gonthier, Lévy, and Melliès' axiomatic theory for standardization. However, we go beyond merely applying their framework, revisiting some of its key concepts: we obtain uniqueness (modulo) of standard derivations in an abstract way and we provide a coinductive characterization of their key abstract notion of external redex. This last point is then used to give a simple proof that linear head reduction --a nondeterministic strategy having a central role in the theory of linear logic-- is standard.
Automata and minimization
Authors: Colcombet Thomas , Petrişan Daniela 
Published: April 2020

Already in the seventies, strong results illustrating the intimate relationship between category theory and automata theory have been described and are still investigated. In this column, we provide a uniform presentation of the basic concepts that underlie minimization results in automata theory. We then use this knowledge for introducing a new model of automata that is an hybrid of deterministic finite automata and automata weighted over a field. These automata are very natural, and enjoy minimization result by design.
The presentation of this paper is indeed categorical in essence, but it assumes no prior knowledge from the reader. It is also non-conventional in that it is neither algebraic, nor co-algebraic oriented.
Subgame Perfect Equilibria of Sequential Matching Games
Authors: Kawase Yasushi , Yamaguchi Yutaro , Yokoi Yu 
Published: April 2020

We study a decentralized matching market in which firms sequentially make offers to potential workers. For each offer, the worker can choose “accept” or “reject,” but the decision is irrevocable. The acceptance of an offer guarantees her job at the firm, but it may also eliminate chances of better offers from other firms in the future. We formulate this market as a perfect-information extensive-form game played by the workers. Each instance of this game has a unique subgame perfect equilibrium (SPE), which does not necessarily lead to a stable matching and has some perplexing properties.
We show a dichotomy result that characterizes the complexity of computing the SPE. The computation is tractable if each firm makes offers to at most two workers or each worker receives offers from at most two firms. In contrast, it is PSPACE-hard even if both firms and workers are related to at most three offers. We also study engineering aspects of this matching market. It is shown that, for any preference profile, we can design an offering schedule of firms so that the worker-optimal stable matching is realized in the SPE.
Activation of a Subset of Evolutionarily Young Transposable Elements and Innate Immunity Are Linked to Clinical Responses to 5-Azacytidine
Authors: Ohtani Hitoshi , Ørskov Andreas D. , Helbo Alexandra S. , Gillberg Linn , Liu Minmin , Zhou Wanding , Ungerstedt Johanna , Hellström-Lindberg Eva , Sun Weili , Liang Gangning , Jones Peter A. , Grønbæk Kirsten 
Published: April 2020

Abstract

The DNA methyltransferase inhibitors (DNMTi) 5-azacytidine and 5-aza-2-deoxycytidine have been approved for the treatment of different types of hematologic malignancies. However, only about 50% of patients respond to treatment. Therefore, a more comprehensive understanding of the molecular changes in patients treated with DNMTi is needed. Here, we examined gene expression profiles in a total of 150 RNA samples from two adult cohorts and one pediatric cohort with hematologic cancers taken before, during, and after treatment with 5-azacytidine (40 patients; 15 nonresponders, 25 responders). Using each patient as their own control, malignant cells showed preferential activation of a subset of evolutionarily young transposable elements (TE), including endogenous retroviral long terminal repeats (LTR), short and long interspersed nuclear elements (SINE and LINE), and the type I IFN pathway in responders, all independent of disease classification. Transfection of eight upregulated LTRs into recipient human cells in culture showed robust and heterogenous activation of six genes in the type I IFN pathway. These results, obtained in diverse hematologic disease entities, show that common targets (TE) activated by the same drug (5-azacytidine) elicit an immune response, which may be important for patient's responses to DNMTi.

Significance:
Activation of specific classes of evolutionarily young transposable elements can lead to activation of the innate immune system.
Higher Serum Vitamin D Concentrations Are Longitudinally Associated with Better Global Quality of Life and Less Fatigue in Colorectal Cancer Survivors up to 2 Years after Treatment
Authors: Koole Janna L. , Bours Martijn J.L. , van Roekel Eline H. , Breedveld-Peters José J.L. , van Duijnhoven Fränzel J.B. , van den Ouweland Jody , Breukink Stéphanie O. , Janssen-Heijnen Maryska L.G. , Keulen Eric T.P. , Weijenberg Matty P. 
Published: April 2020

Abstract

Background:
Vitamin D status may be an important determinant of health-related quality of life of colorectal cancer survivors. The current study investigated longitudinal associations between serum 25-hydroxyvitamin D3 (25OHD3) concentrations and quality of life in stage I–III colorectal cancer survivors up to 2 years after treatment.

Methods:
Patients with colorectal cancer (n = 261) were included upon diagnosis. Home visits (including blood sampling) were performed at diagnosis and at 6 weeks, 6 months, 1 year, and 2 years after treatment. Serum 25OHD3 concentrations were measured using LC/MS-MS and adjusted for season. Validated questionnaires were used to assess global quality of life and cognitive functioning (EORTC-QLQ-C30), fatigue (EORTC-QLQ-C30 and Checklist Individual Strength, CIS), and depression and anxiety (Hospital Anxiety and Depression Scale). Statistical analyses were performed using linear mixed models and adjusted for sex, age, time since diagnosis, therapy, comorbidities, physical activity, and body mass index.

Results:
At diagnosis, 45% of patients were vitamin D deficient (&lt;50 nmol/L). After treatment, 25OHD3 concentrations increased on average with 3.1 nmol/L every 6 months. In confounder-adjusted models, 20 nmol/L increments in 25OHD3 were longitudinally associated with increased global quality of life [β 2.9; 95% confidence interval (CI), 1.5–4.3] and reduced fatigue (EORTC-QLQ-C30 subscale: β −3.5; 95% CI, −5.3 to −1.8 and CIS: β −2.8; 95% CI, −4.7 to −0.9). Observed associations were present both within and between individuals over time.

Conclusions:
Higher concentrations of 25OHD3 were longitudinally associated with better global quality of life and less fatigue in colorectal cancer survivors.

Impact:
This study suggests that higher 25OHD3 concentrations may be beneficial for colorectal cancer survivors. Future intervention studies are needed to corroborate these findings.
Reticent Digital Diasporas in Times of Crisis
Authors: Turner Simon , Berckmoes Lidewyde 
Published: April 2020

Abstract
Based on fieldwork amongst Burundians in Rwanda, the Netherlands and Belgium, this article explores how information circulates transnationally in times of political and violent crisis and how ordinary members of the diaspora seek to manage these flows of information. Our main argument is that conflict in the homeland creates a massive flow of information across various digital platforms and that while members of the diaspora eagerly take part in consuming and sharing this information, they do so reticently. Rather than simply explore the information flows, their intensity, their ‘spread’ or their content, we explore how individuals in the diaspora engage in emotion work, as they struggle between being ‘hailed’ by the images and messages flowing with ever-increasing intensity, speed and urgency and their reticence towards getting too involved.
A Method of Using WRF-Simulated Surface Temperature to Estimate Daily Evapotranspiration
Authors: Wang Dakang , Liu Yan , Yu Tao , Zhang Yin , Liu Qixin , Chen Xinran , Zhan Yulin 
Published: April 2020

AbstractSurface temperature is one of the key parameters for estimating regional evapotranspiration (ET) based on the Surface Energy Balance System (SEBS) model using remote sensing data. However, continuous daily remote sensing surface temperature data are often not available due to the weather and environmental conditions. This paper proposed a scheme to obtain reliable ET that estimating ET using WRF-simulated surface skin temperature (TSK) and then modifying the deviation using the normalized difference vegetation index (NDVI). This study aims to explore whether the model data can be a viable option when the continuous-time-series remote sensing surface temperature is missing for estimating ET. Comparison results show that the correlation between WRF TSK and the measured temperature of the 2-cm soil (Ts) is better than MODIS land surface temperature (LST) in the study area, while the correlation between MODIS LST and the measured surface radiation temperature (IRT) is better than WRF TSK. The MODIS LST is significantly higher than Ts, and the WRF TSK is closer to Ts than MODIS LST. However, the ET calculated using WRF TSK was not good, exhibiting relatively high ET in the whole area and a poor correlation with the measurements, whereby R2, RMSE, and the percent bias (PBIAS) were equal to 0.1256, 5.2783 mm, and −202.17%, respectively. According to the principle of land surface process simulation in WRF, this paper proposes using NDVI to modify ET calculated using TSK. The comparison between the modified ET and the measurements exhibited a relatively good correlation, with R2 = 0.7532, RMSE = 1.0993 mm, and PBIAS = −17.9%. Therefore, the model surface temperature data can be used to estimate continuous-time-series regional ET when NDVI is used to modify the deviation, which indicates the surface temperature data simulated by the WRF Model can become the optional data for estimating ET and compensate for the shortcoming of poor time continuity of remote sensing data, further expanding the application prospects of meteorological model data in the remote sensing field.
Impact of bedside lung ultrasound on physician clinical decision-making in an emergency department in Nepal
Authors: House Darlene R. , Amatya Yogendra , Nti Benjamin , Russell Frances M. 
Published: April 2020

Abstract
Background
Lung ultrasound is an effective tool for the evaluation of undifferentiated dyspnea in the emergency department. Impact of lung ultrasound on clinical decisions for the evaluation of patients with dyspnea in resource-limited settings is not well-known. The objective of this study was to evaluate the impact of lung ultrasound on clinical decision-making for patients presenting with dyspnea to an emergency department in the resource-limited setting of Nepal.

Methods
A prospective, cross-sectional study of clinicians working in the Patan Hospital Emergency Department was performed. Clinicians performed lung ultrasounds on patients presenting with dyspnea and submitted ultrasounds with their pre-test diagnosis, lung ultrasound interpretation, post-test diagnosis, and any change in management.

Results
Twenty-two clinicians participated in the study, completing 280 lung ultrasounds. Diagnosis changed in 124 (44.3%) of patients with dyspnea. Clinicians reported a change in management based on the lung ultrasound in 150 cases (53.6%). Of the changes in management, the majority involved treatment (83.3%) followed by disposition (13.3%) and new consults (2.7%).

Conclusions
In an emergency department in Nepal, bedside lung ultrasound had a significant impact on physician clinical decision-making, especially on patient diagnosis and treatment.
Further development of the 12-item EDE-QS: identifying a cut-off for screening purposes
Authors: Prnjak Katarina , Mitchison Deborah , Griffiths Scott , Mond Jonathan , Gideon Nicole , Serpell Lucy , Hay Phillipa 
Published: April 2020

AbstractBackgroundThe Eating Disorder Examination – Questionnaire Short (EDE-QS) was developed as a 12-item version of the Eating Disorder Examination Questionnaire (EDE-Q) with a 4-point response scale that assesses eating disorder (ED) symptoms over the preceding 7 days. It has demonstrated good psychometric properties at initial testing. The purpose of this brief report is to determine a threshold score that could be used in screening for probable ED cases in community settings.MethodsData collected from Gideon et al. (2016) were re-analyzed. In their study, 559 participants (80.86% female; 9.66% self-reported ED diagnosis) completed the EDE-Q, EDE-QS, SCOFF, and Clinical Impairment Assessment (CIA). Discriminatory power was compared between ED instruments using receiver operating characteristic (ROC) curve analyses.ResultsA score of 15 emerged as the threshold that ensured the best trade-off between sensitivity (.83) and specificity (.85), and good positive predictive value (.37) for the EDE-QS, with discriminatory power comparable to other ED instruments.ConclusionThe EDE-QS appears to be an instrument with good discriminatory power that could be used for ED screening purposes.
Adaptive Fisher method detects dense and sparse signals in association analysis of SNV sets
Authors: Cai Xiaoyu , Chang Lo-Bin , Potter Jordan , Song Chi 
Published: April 2020

Abstract
Background
With the development of next generation sequencing (NGS) technology and genotype imputation methods, statistical methods have been proposed to test a set of genomic variants together to detect if any of them is associated with the phenotype or disease. In practice, within the set, there is an unknown proportion of variants truly causal or associated with the disease. There is a demand for statistical methods with high power in both dense and sparse scenarios, where the proportion of causal or associated variants is large or small respectively.

Results
We propose a new association test – weighted Adaptive Fisher (wAF) that can adapt to both dense and sparse scenarios by adding weights to the Adaptive Fisher (AF) method we developed before. Using simulation, we show that wAF enjoys comparable or better power to popular methods such as sequence kernel association tests (SKAT and SKAT-O) and adaptive SPU (aSPU) test. We apply wAF to a publicly available schizophrenia dataset, and successfully detect thirteen genes. Among them, three genes are supported by existing literature; six are plausible as they either relate to other neurological diseases or have relevant biological functions.

Conclusions
The proposed wAF method is a powerful disease-variants association test in both dense and sparse scenarios. Both simulation studies and real data analysis indicate the potential of wAF for new biological findings.
Pseudogene-gene functional networks are prognostic of patient survival in breast cancer
Authors: Smerekanych Sasha , Johnson Travis S. , Huang Kun , Zhang Yan 
Published: April 2020

Abstract
Background
Given the vast range of molecular mechanisms giving rise to breast cancer, it is unlikely universal cures exist. However, by providing a more precise prognosis for breast cancer patients through integrative models, treatments can become more individualized, resulting in more successful outcomes. Specifically, we combine gene expression, pseudogene expression, miRNA expression, clinical factors, and pseudogene-gene functional networks to generate these models for breast cancer prognostics. Establishing a LASSO-generated molecular gene signature revealed that the increased expression of genes STXBP5, GALP and LOC387646 indicate a poor prognosis for a breast cancer patient. We also found that increased CTSLP8 and RPS10P20 and decreased HLA-K pseudogene expression indicate poor prognosis for a patient. Perhaps most importantly we identified a pseudogene-gene interaction, GPS2-GPS2P1 (improved prognosis) that is prognostic where neither the gene nor pseudogene alone is prognostic of survival. Besides, miR-3923 was predicted to target GPS2 using miRanda, PicTar, and TargetScan, which imply modules of gene-pseudogene-miRNAs that are potentially functionally related to patient survival.

Results
In our LASSO-based model, we take into account features including pseudogenes, genes and candidate pseudogene-gene interactions. Key biomarkers were identified from the features. The identification of key biomarkers in combination with significant clinical factors (such as stage and radiation therapy status) should be considered as well, enabling a specific prognostic prediction and future treatment plan for an individual patient. Here we used our PseudoFuN web application to identify the candidate pseudogene-gene interactions as candidate features in our integrative models. We further identified potential miRNAs targeting those features in our models using PseudoFuN as well. From this study, we present an interpretable survival model based on LASSO and decision trees, we also provide a novel feature set which includes pseudogene-gene interaction terms that have been ignored by previous prognostic models. We find that some interaction terms for pseudogenes and genes are significantly prognostic of survival. These interactions are cross-over interactions, where the impact of the gene expression on survival changes with pseudogene expression and vice versa. These may imply more complicated regulation mechanisms than previously understood.

Conclusions
We recommend these novel feature sets be considered when training other types of prognostic models as well, which may provide more comprehensive insights into personalized treatment decisions.
Choroidal vascularity index as a biomarker of systemic inflammation in childhood Polyarteritis Nodosa and adenosine deaminase-2 deficiency
Authors: BAYTAROĞLU Ata , KADAYIFÇILAR Sibel , AĞIN Abdullah , DELİKTAŞ Özge , DEMİR Selcan , BİLGİNER Yelda , KARAKAYA Jale , ÖZEN Seza , ELDEM Bora 
Published: April 2020

Abstract
Background/purpose
To assess EDI-OCT (enhanced depth imaging optical coherence tomography) of choroid for inflammatory signs in children with polyarteritis nodosa (PAN) and adenosine deaminase-2 deficiency (DADA-2).

Methods
In this cross-sectional study conducted between June 2017 and September 2018, we evaluated children diagnosed with PAN (n = 11) and DADA-2 (n = 4) and an age- and sex-matched control group (n = 15). Demographic and laboratory data were retrospectively analyzed from patient charts. Disease activity was assessed using the pediatric vasculitis activity score (PVAS). Choroidal images were obtained with spectral domain-OCT to measure choroidal thickness (ChT) at 5 points (750 and 1500 μm from the foveal center in the temporal and nasal quadrants and beneath the fovea), and to calculate the total subfoveal choroidal area (TCA), luminal area (LA), stromal area (SA), and the choroidal vascularity index (CVI).

Results
The median (min-max) age was 8 (4–16) years in PAN patients, 6 (5–16) years in DADA-2 patients and 8 (8–10) years in control group at the OCT visit (p = 0.214). The ChT at 3 points and the TCA, LA, and SA were higher in children with both PAN and DADA-2 patients compared to those of the control group (p < 0.0001, p = 0.049, p = 0.007, p = 0.007, p = 0.006, p = 0.033, respectively). The CVI was similar in both groups. No association was observed between the OCT findings, PVAS, and the erythrocyte sedimentation rate, and serum leukocyte and C-reactive protein levels.

Conclusion
Similar CVI scores were obtained from PAN and DADA2 patients under treatment and from healthy controls. Increased subfoveal ChT without any other signs of ocular involvement may suggest choroidal thickening as a sign of mild subclinical inflammation.