bluuebunny/crossref_metadata_2025_split huggingface dataset:
An efficient method for significant motifs discovery from multiple DNA sequences
Authors: Al-Ssulami Abdulrakeeb M. , Azmi Aqil M. , Mathkour Hassan 
Published: May 2017

Identification of transcription factor binding sites or biological motifs is an important step in deciphering the mechanisms of gene regulation. It is a classic problem that has eluded a satisfactory and efficient solution. In this paper, we devise a three-phase algorithm to mine for biologically significant motifs. In the first phase, we generate all the possible string motifs, this phase is followed by a filtering process where we discard all motifs that do not meet the constraints. And in the final phase, motifs are scored and ranked using a combination of stochastic techniques and [Formula: see text]-value. We show that our method outperforms some very well-known motif discovery tools, e.g. MEME and Weeder on well-established benchmark data suites. We also apply the algorithm on the non-coding regions of M. tuberculosis and report significant motifs of size 10 with excellent [Formula: see text]-values in a fraction of the time MEME and MoSDi did. In fact, among the best 10 motifs ([Formula: see text]-value wise) in the non-coding regions of M. tuberculosis reported by the tools MEME, MoSDi and ours, five were discovered by our approach which included the third and the fourth best ones. All this in 1/17 and 1/6 the time which MEME and MoSDi (respectively) took.
Stream fusion, to completeness
Authors: Kiselyov Oleg , Biboudis Aggelos , Palladinos Nick , Smaragdakis Yannis 
Published: May 2017

Stream processing is mainstream (again): Widely-used stream libraries are now available for virtually all modern OO and functional languages, from Java to C# to Scala to OCaml to Haskell. Yet expressivity and performance are still lacking. For instance, the popular, well-optimized Java 8 streams do not support the zip operator and are still an order of magnitude slower than hand-written loops.
We present the first approach that represents the full generality of stream processing and eliminates overheads, via the use of staging. It is based on an unusually rich semantic model of stream interaction. We support any combination of zipping, nesting (or flat-mapping), sub-ranging, filtering, mapping—of finite or infinite streams. Our model captures idiosyncrasies that a programmer uses in optimizing stream pipelines, such as rate differences and the choice of a “for” vs. “while” loops. Our approach delivers hand-written–like code, but automatically. It explicitly avoids the reliance on black-box optimizers and sufficiently-smart compilers, offering highest, guaranteed and portable performance.
Our approach relies on high-level concepts that are then readily mapped into an implementation. Accordingly, we have two distinct implementations: an OCaml stream library, staged via MetaOCaml, and a Scala library for the JVM, staged via LMS. In both cases, we derive libraries richer and simultaneously many tens of times faster than past work. We greatly exceed in performance the standard stream libraries available in Java, Scala and OCaml, including the well-optimized Java 8 streams.
Modules, abstraction, and parametric polymorphism
Authors: Crary Karl 
Published: May 2017

Reynolds's Abstraction theorem forms the mathematical foundation for data abstraction. His setting was the polymorphic lambda calculus. Today, many modern languages, such as the ML family, employ rich module systems designed to give more expressive support for data abstraction than the polymorphic lambda calculus, but analogues of the Abstraction theorem for such module systems have lagged far behind.
We give an account of the Abstraction theorem for a modern module calculus supporting generative and applicative functors, higher-order functors, sealing, and translucent signatures. The main issues to be overcome are: (1) the fact that modules combine both types and terms, so they must be treated as both simultaneously, (2) the effect discipline that models the distinction between transparent and opaque modules, and (3) a very rich language of type constructors supporting singleton kinds. We define logical equivalence for modules and show that it coincides with contextual equivalence. This substantiates the folk theorem that modules are good for data abstraction. All our proofs are formalized in Coq.
Rust: from POPL to practice (keynote)
Authors: Turon Aaron 
Published: May 2017

In 2015, a language based fundamentally on substructural typing–Rust–hit its 1.0 release, and less than a year later it has been put into production use in a number of tech companies, including some household names. The language has started a trend, with several other mainstream languages, including C++ and Swift, in the early stages of incorporating ideas about ownership. How did this come about?
Rust’s core focus is safe systems programming. It does not require a runtime system or garbage collector, but guarantees memory safety. It does not stipulate any particular style of concurrent programming, but instead provides the tools needed to guarantee data race freedom even when doing low-level shared-state concurrency. It allows you to build up high-level abstractions without paying a tax; its compilation model ensures that the abstractions boil away.
These benefits derive from two core aspects of Rust: its ownership system (based on substructural typing) and its trait system (a descendant of Haskell’s typeclasses). The talk will cover these two pillars of Rust design, with particular attention to the key innovations that make the language usable at scale. It will highlight the implications for concurrency, where Rust provides a unique perspective. It will also touch on aspects of Rust’s development that tend to get less attention within the POPL community: Rust’s governance and open development process, and design considerations around language and library evolution. Finally, it will mention a few of the myriad open research questions around Rust.
Parallel virtual machines with RPython
Authors: Meier Remigius , Rigo Armin , Gross Thomas R. 
Published: May 2017

The RPython framework takes an interpreter for a dynamic language as its input and produces a Virtual Machine (VM) for that language. RPython is being used to develop PyPy, a high-performance Python interpreter. However, the produced VM does not support parallel execution since the framework relies on a Global Interpreter Lock (GIL): PyPy serialises the execution of multi-threaded Python programs.
We describe the rationale and design of a new parallel execution model for RPython that allows the generation of parallel virtual machines while leaving the language semantics unchanged. This model then allows different implementations of concurrency control, and we discuss an implementation based on a GIL and an implementation based on Software Transactional Memory (STM).
To evaluate the benefits of either choice, we adapt PyPy to work with both implementations (GIL and STM). The evaluation shows that PyPy with STM improves the runtime of a set of multi-threaded Python programs over PyPy with a GIL by factors in the range of 1.87x up to 5.96x when executing on a processor with 8 cores.
Epstein–Barr Virus-Induced VEGF and GM-CSF Drive Nasopharyngeal Carcinoma Metastasis via Recruitment and Activation of Macrophages
Authors: Huang Di , Song Shi-Jian , Wu Zi-Zhao , Wu Wei , Cui Xiu-Ying , Chen Jia-Ning , Zeng Mu-Sheng , Su Shi-Cheng 
Published: May 2017

Abstract
Chronic inflammation induced by persistent microbial infection plays an essential role in tumor progression. Although it is well documented that Epstein–Barr virus (EBV) infection is closely associated with nasopharyngeal carcinoma (NPC), how EBV-induced inflammation promotes NPC progression remains largely unknown. Here, we report that tumor infiltration of tumor-associated macrophages (TAM) and expression of CCL18, the cytokine preferentially secreted by TAM, closely correlate with serum EBV infection titers and tumor progression in two cohorts of NPC patients. In vitro, compared with EBV− NPC cell lines, EBV+ NPC cell lines exhibited superior capacity to attract monocytes and skew them to differentiate to a TAM-like phenotype. Cytokine profiling analysis revealed that NPC cells with active EBV replications recruited monocytes by VEGF and induced TAM by GM-CSF in an NF-κB–dependent manner. Reciprocally, TAM induced epithelial–mesenchymal transition and furthered NF-κB activation of tumor cells by CCL18. In humanized mice, NPC cells with active EBV replications exhibited increased metastasis, and neutralization of CCL18, GM-CSF, and VEGF significantly reduced metastasis. Collectively, our work defines a feed-forward loop between tumor cells and macrophages in NPC, which shows how metastatic potential can evolve concurrently with virus-induced chronic inflammation. Cancer Res; 77(13); 3591–604. ©2017 AACR.
Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8+ T-cell Recognition of a Retroviral Antigen
Authors: Probst Philipp , Kopp Janine , Oxenius Annette , Colombo Mario P. , Ritz Danilo , Fugmann Tim , Neri Dario 
Published: May 2017

Abstract
Antibody–cytokine complexes may offer new tools to treat cancer. Here, we show how TNF-linked antibodies, which recognize tumor-selective splice isoforms of fibronectin (F8-TNF), can be exploited to eradicate sarcomas in immunocompetent mice. We treated mice bearing WEHI-164 fibrosarcoma with a combination of F8-TNF and doxorubicin, curing the majority of treated animals (29/37). Notably, cured mice were resistant to rechallenge not only by WEHI-164 cells but also heterologous C51 or CT26 colorectal tumor cells in a CD8+ T-cell–dependent process. Mechanistic analyses revealed that each tumor cell line presented AH1, a common endogenous retroviral peptide. Numbers of AH1-specific CD8+ T cells exhibiting cytotoxic capacity were increased by F8-TNF plus doxorubicin treatment, arguing that cognate CD8+ T cells contributed to tumor eradication. Sequence analysis of T-cell receptors of CD8+ T cells revealed the presence of H-2Ld/AH1-specific T cells and an expansion of sequence diversity in treated mice. Overall, our findings provide evidence that retroviral genes contribute to tumoral immunosurveillance in a process that can be generally boosted by F8-TNF and doxorubicin treatment. Cancer Res; 77(13); 3644–54. ©2017 AACR.
Total and Free Circulating Vitamin D and Vitamin D–Binding Protein in Relation to Colorectal Cancer Risk in a Prospective Study of African Americans
Authors: Andersen Shaneda Warren , Shu Xiao-Ou , Cai Qiuyin , Khankari Nikhil K. , Steinwandel Mark D. , Jurutka Peter W. , Blot William J. , Zheng Wei 
Published: May 2017

Abstract
Background: Previous studies rarely evaluated the associations between vitamin D–binding protein and free vitamin D with colorectal cancer risk. We assessed these biomarkers and total 25-hydroxyvitamin D in relation to colorectal cancer risk in a sample of African Americans.
Methods: Cases comprised 224 African American participants of the Southern Community Cohort Study diagnosed with incident colorectal cancer. Controls (N = 440) were selected through incidence density sampling and matched to cases on age, sex, and race. Conditional logistic regression was used to calculate odds ratios (OR) and 95% confidence intervals (CI) for associations between biomarker levels and colorectal cancer risk.
Results: Vitamin D was inversely associated with colorectal cancer risk where the OR per-SD increase in total and free 25-hydroxyvitamin D were 0.82 (95% CI, 0.66–1.02) and 0.82 (95% CI, 0.66–1.01), respectively. Associations were most apparent among cases diagnosed &gt;3 years after blood draw: ORs for the highest tertile versus the lowest were 0.69 (95% CI, 0.21–0.93) for total 25-hydroxyvitamin D and 0.71 (95% CI, 0.53–0.97) for free 25-hydroxyvitamin D. Inverse associations were seen in strata defined by sex, BMI, and anatomic site, although not all findings were statistically significant. Vitamin D–binding protein was not associated with colorectal cancer risk.
Conclusions: Our findings suggest that total and free 25-hydroxyvitamin D may be inversely associated with colorectal cancer risk among African Americans.
Impact: These findings highlight a potential role for vitamin D in colorectal cancer prevention in African Americans. Cancer Epidemiol Biomarkers Prev; 26(8); 1242–7. ©2017 AACR.
Cupid’s Arrows
Authors: Wickkiser Bronwen L. 
Published: May 2017

Abstract
Ovid’s narrative of Apollo and Daphne introduces elements not apparent in earlier extant versions of the myth, such as the involvement of Cupid and his deployment of two distinct arrows, one golden that sets Apollo’s passions aflame, and the other lead that makes Daphne averse to all male advances. The passion-averting arrow in particular is a curious addition to Cupid’s arsenal. This paper will argue that the lead arrow can be better understood when viewed alongside the practices and discourses of ancient magic and medicine, especially the widespread use of lead for erotic defixiones, antaphrodisiacs, and even contraceptives.
Do Preterm Infants Perceive Temporal Synchrony? An Analysis with the Eye-Tracking System
Authors: Provasi Joëlle , Lemoine-Lardennois Christelle , Orriols Eric , Morange-Majoux Françoise 
Published: May 2017

The aim of this study was to investigate auditory–visual temporal asynchrony in preterm infants using a habituation procedure coupled with an eye-tracking system in order to examine visual behavior accurately and determine specific visual areas of interest. Sixteen term infants, twelve low-risk near-term (LBW) preterm infants and eight Very Low Birth Weight (VLBW) preterm infants were tested at four months post term. Infants were habituated with an auditory–visual synchronic situation: a visual ball bounced back in synchrony with an auditory sound. In the test phase, an asynchronized situation and a synchronized situation were presented alternately three times. The results showed that VLBW infants spent more time looking at the target before being habituated compared to LBW preterm infants and full-term infants.
Specific areas of interest showed that VLBW infants spent less time on the target than LBW and full-term infants and had a more heterogeneous visual exploration. Nevertheless, VLBW infants had the same novelty reaction as the other infant groups. Moreover, the study of areas of interest revealed that whatever the age group, infants looked more at the area where the sound was produced during the asynchronized trial. This result suggests that infants perceive asynchrony. We suggest that VLBW preterm infants show the same ability to habituate and novelty recovery through an early learning experience due to earlier additional extra-uterine exposure.
Sound Properties Associated With Equiluminant Colours
Authors: Hamilton-Fletcher Giles , Witzel Christoph , Reby David , Ward Jamie 
Published: May 2017

There is a widespread tendency to associate certain properties of sound with those of colour (e.g., higher pitches with lighter colours). Yet it is an open question how sound influences chroma or hue when properly controlling for lightness. To examine this, we asked participants to adjust physically equiluminant colours until they ‘went best’ with certain sounds. For pure tones, complex sine waves and vocal timbres, increases in frequency were associated with increases in chroma. Increasing the loudness of pure tones also increased chroma. Hue associations varied depending on the type of stimuli. In stimuli that involved only limited bands of frequencies (pure tones, vocal timbres), frequency correlated with hue, such that low frequencies gave blue hues and progressed to yellow hues at 800 Hz. Increasing the loudness of a pure tone was also associated with a shift from blue to yellow. However, for complex sounds that share the same bandwidth of frequencies (100–3200 Hz) but that vary in terms of which frequencies have the most power, all stimuli were associated with yellow hues. This suggests that the presence of high frequencies (above 800 Hz) consistently yields yellow hues. Overall we conclude that while pitch–chroma associations appear to flexibly re-apply themselves across a variety of contexts, frequencies above 800 Hz appear to produce yellow hues irrespective of context. These findings reveal new sound–colour correspondences previously obscured through not controlling for lightness. Findings are discussed in relation to understanding the underlying rules of cross-modal correspondences, synaesthesia, and optimising the sensory substitution of visual information through sound.
An Integrated Damage, Visual, and Radar Analysis of the 2015 Foshan, Guangdong, EF3 Tornado in China Produced by the Landfalling Typhoon Mujigae (2015)
Authors: Bai Lanqiang , Meng Zhiyong , Huang Ling , Yan Lijun , Li Zhaohui , Mai Xuehu , Huang Yipeng , Yao Dan , Wang Xi 
Published: May 2017

AbstractThis work presents an integrated damage, visual, and radar analysis of a tropical cyclone (TC) tornado that has not been documented as detailed as midlatitude tornadoes. On 4 October 2015, an enhanced Fujita 3 (EF3) tornado spawned into Typhoon Mujigae and hit Foshan, Guangdong Province, China. This tornado was generated in a minisupercell ∼350 km northeast of the TC center and lasted about 32 minutes, leaving a southeast-to-northwest damage swath 30.85 km long and 20–570 m wide. Near-surface wind patterns and the size of the tornado, juxtaposition of the condensation funnel with the damage swath and radar signatures, and consistency between near-surface wind speed estimated from visual observations and that estimated using EF scale were revealed based on ground and aerial surveys, radar and surface observations, photographs, and tornado videos. Tornado videos showed two occurrences of vertical subvortices followed by the formation of a horizontal vortex. Some features of the tornado, the parent supercell and mesocyclone, and the convective environment were compared to their U.S. counterparts. This work provides a case review of a tornado with the most comprehensive information ever in China. Damage indicators used to estimate the tornado intensity in this Chinese case were compared with those in the United States, demonstrating the potential applicability of the EF scale in tornado damage surveys outside the United States.
Nonlinear Wave Kinematics near the Ocean Surface
Authors: Smit P. B. , Janssen T. T. , Herbers T. H. C. 
Published: May 2017

AbstractEstimation of second-order, near-surface wave kinematics is important for interpretation of ocean surface remote sensing and surface-following instruments, determining loading on offshore structures, and understanding of upper-ocean transport processes. Unfortunately, conventional wave theories based on Stokes-type expansions do not consider fluid motions at levels above the unperturbed fluid level. The usual practice of extrapolating the fluid kinematics from the unperturbed free surface to higher points in the fluid is generally reasonable for narrowband waves, but for broadband ocean waves this results in dramatic (and nonphysical) overestimation of surface velocities. Consequently, practical approximations for random waves are at best empirical and are often only loosely constrained by physical principles. In the present work, the authors formulate the governing equations for water waves in an incompressible and inviscid fluid, using a boundary-fitted coordinate system (i.e., sigma or s coordinates) to derive expressions for near-surface kinematics in nonlinear random waves from first principles. Comparison to a numerical model valid for highly nonlinear waves shows that the new results 1) are consistent with second-order Stokes theory, 2) are similar to extrapolation methods in narrowband waves, and 3) greatly improve estimates of surface kinematics in random seas.
Protein palmitoylation: Palmitoyltransferases and their specificity
Authors: Tabaczar Sabina , Czogalla Aleksander , Podkalicka Joanna , Biernatowska Agnieszka , Sikorski Aleksander F 
Published: May 2017

A plethora of novel information has emerged over the past decade regarding protein lipidation. The reversible attachment of palmitic acid to cysteine residues, termed S-palmitoylation, has focused a special attention. This is mainly due to the unique role of this modification in the regulation of protein trafficking and function. A large family of protein acyltransferases (PATs) containing a conserved aspartate–histidine–histidine–cysteine motif use ping-pong kinetic mechanism to catalyze S-palmitoylation of a substrate protein. Here, we discuss the topology of PAT proteins and their cellular localization. We will also give an overview of the mechanism of protein palmitoylation and how it is regulated. New information concerning the recent discovery of depalmitoylating enzymes belonging to the family of α/β-hydrolase domain-containing protein 17 (ABHD17A) is included. Considering the recent advances that have occurred in understanding the mechanisms underlying the interplay between palmitoylation and depalmitoylation, it is clear that we are beginning to understand the fundamental nature of how cellular signal-transduction mediates membrane-level organization in health and disease. Impact statement Protein palmitoylation is one of most important reversible post-translational modifications of protein function in cell-signaling systems. This review gathers the latest information on the molecular mechanism of protein palmitoyl transferase action. It also discusses the issue of substrate specificity of palmitoyl transferases. Another important question is the role of depalmitoylation enzymes. This review should help to formulate questions concerning the regulation of activity of particular PATs as well as of depalmitoylating enzymes (APT).
Assessment of early treatment response by rapid cardiothoracic ultrasound in acute heart failure: Cardiac filling pressures, pulmonary congestion and mortality
Authors: Öhman Jonas , Harjola Veli-Pekka , Karjalainen Pasi , Lassus Johan 
Published: May 2017

Background: It is unclear how to optimally monitor acute heart failure (AHF) patients. We evaluated the timely interplay of cardiac filling pressures, brain natriuretic peptides (BNPs), lung ultrasound (LUS) and symptoms during AHF treatment. Methods: We enrolled 60 patients who had been hospitalised for AHF. Patients were examined with a rapid cardiothoracic ultrasound (CaTUS) protocol, combining LUS and focused echocardiographic evaluation of cardiac filling pressures (i.e. medial E/e’ and inferior vena cava index [IVCi]). CaTUS was done at 0, 12, 24 and 48 hours (±3 hours) and on the day of discharge, alongside clinical evaluation and laboratory samples. Patients free of congestion (B lines or pleural fluid) on LUS at discharge were categorised as responders, whereas the rest were categorised as non-responders. Improvement in congestion parameters was evaluated separately in these groups. The effect of congestion parameters on prognosis was also analysed. Results: Responders experienced a significantly larger decline in E/e’ (2.58 vs. 0.38, p = 0.037) and dyspnoea visual analogue scale (1–10) score (7.68 vs. 3.57, p = 0.007) during the first 12 hours of treatment, while IVCi and BNPs declined later without no such rapid initial decline. Among patients experiencing a >3 U decline in E/e’ during the first 12 hours of treatment, 18/21 were to become responders ( p < 0.001). LUS response was the only congestion parameter independently predicting both 6-month survival regarding all-cause mortality and the composite endpoint of all-cause mortality or rehospitalisation for AHF. Conclusion: E/e’ seemed like the most useful congestion parameter for monitoring early treatment response, predicting prognostically beneficial resolution of pulmonary congestion.