bluuebunny/crossref_metadata_2025_split huggingface dataset:
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
Authors: Chang Cheng , Li Mansheng , Guo Chaoping , Ding Yuqing , Xu Kaikun , Han Mingfei , He Fuchu , Zhu Yunping 
Published: August 2018

Abstract

Summary
As the experiment techniques and strategies in quantitative proteomics are improving rapidly, the corresponding algorithms and tools for protein quantification with high accuracy and precision are continuously required to be proposed. Here, we present a comprehensive and flexible tool named PANDA for proteomics data quantification. PANDA, which supports both label-free and labeled quantifications, is compatible with existing peptide identification tools and pipelines with considerable flexibility. Compared with MaxQuant on several complex datasets, PANDA was proved to be more accurate and precise with less computation time. Additionally, PANDA is an easy-to-use desktop application tool with user-friendly interfaces.

Availability and implementation
PANDA is freely available for download at https://sourceforge.net/projects/panda-tools/.

Supplementary information
Supplementary data are available at Bioinformatics online
Benchmarking optimization methods for parameter estimation in large kinetic models
Authors: Villaverde Alejandro F , Fröhlich Fabian , Weindl Daniel , Hasenauer Jan , Banga Julio R 
Published: August 2018

Abstract

Motivation
Kinetic models contain unknown parameters that are estimated by optimizing the fit to experimental data. This task can be computationally challenging due to the presence of local optima and ill-conditioning. While a variety of optimization methods have been suggested to surmount these issues, it is difficult to choose the best one for a given problem a priori. A systematic comparison of parameter estimation methods for problems with tens to hundreds of optimization variables is currently missing, and smaller studies provided contradictory findings.

Results
We use a collection of benchmarks to evaluate the performance of two families of optimization methods: (i) multi-starts of deterministic local searches and (ii) stochastic global optimization metaheuristics; the latter may be combined with deterministic local searches, leading to hybrid methods. A fair comparison is ensured through a collaborative evaluation and a consideration of multiple performance metrics. We discuss possible evaluation criteria to assess the trade-off between computational efficiency and robustness. Our results show that, thanks to recent advances in the calculation of parametric sensitivities, a multi-start of gradient-based local methods is often a successful strategy, but a better performance can be obtained with a hybrid metaheuristic. The best performer combines a global scatter search metaheuristic with an interior point local method, provided with gradients estimated with adjoint-based sensitivities. We provide an implementation of this method to render it available to the scientific community.

Availability and implementation
The code to reproduce the results is provided as Supplementary Material and is available at Zenodo https://doi.org/10.5281/zenodo.1304034.

Supplementary information
Supplementary data are available at Bioinformatics online.
Computational Feature Analysis of Body Movements Reveals Hierarchical Brain Organization
Authors: Vaessen Maarten J , Abassi Etienne , Mancini Maurizio , Camurri Antonio , de Gelder Beatrice 
Published: August 2018

Abstract
Social species spend considerable time observing the body movements of others to understand their actions, predict their emotions, watch their games, or enjoy their dance movements. Given the important information obtained from body movements, we still know surprisingly little about the details of brain mechanisms underlying movement perception. In this fMRI study, we investigated the relations between movement features obtained from automated computational analyses of video clips and the corresponding brain activity. Our results show that low-level computational features map to specific brain areas related to early visual- and motion-sensitive regions, while mid-level computational features are related to dynamic aspects of posture encoded in occipital–temporal cortex, posterior superior temporal sulcus and superior parietal lobe. Furthermore, behavioral features obtained from subjective ratings correlated with activity in higher action observation regions. Our computational feature-based analysis suggests that the neural mechanism of movement encoding is organized in the brain not so much by semantic categories than by feature statistics of the body movements.
Comparison of mechanical disturbance in soft sediments due to tickler-chain SumWing trawl vs. electro-fitted PulseWing trawl
Authors: Depestele Jochen , Degrendele Koen , Esmaeili Moosa , Ivanović Ana , Kröger Silke , O’Neill Finbarr G , Parker Ruth , Polet Hans , Roche Marc , Teal Lorna R , Vanelslander Bart , Rijnsdorp Adriaan D 
Published: August 2018

Abstract
Tickler-chain SumWing and electrode-fitted PulseWing trawls were compared to assess seabed impacts. Multi-beam echo sounder (MBES) bathymetry confirmed that the SumWing trawl tracks were consistently and uniformly deepened to 1.5 cm depth in contrast to 0.7 cm following PulseWing trawling. MBES backscatter strength analysis showed that SumWing trawls (3.11 dB) flattened seabed roughness significantly more than PulseWing trawls (2.37 dB). Sediment Profile Imagery (SPI) showed that SumWing trawls (mean, SD) homogenised the sediment deeper (3.4 cm, 0.9 cm) and removed more of the oxidised layer than PulseWing trawls (1 cm, 0.8 cm). The reduced PulseWing trawling impacts allowed a faster re-establishment of the oxidised layer and micro-topography. Particle size analysis suggested that SumWing trawls injected finer particles into the deeper sediment layers (∼4 cm depth), while PulseWing trawling only caused coarsening of the top layers (winnowing effect). Total penetration depth (mean, SD) of the SumWing trawls (4.1 cm, 0.9 cm) and PulseWing trawls (1.8 cm, 0.8 cm) was estimated by the depth of the disturbance layer and the layer of mobilized sediment (SumWing = 0.7 cm; PulseWing trawl = 0.8 cm). PulseWing trawls reduced most of the mechanical seabed impacts compared to SumWing trawls for this substrate and area characteristics.
Efferocytosis and autoimmune disease
Authors: Kawano Mahiru , Nagata Shigekazu 
Published: August 2018

Abstract
An enormous number of cells in the body die by apoptosis during development and under homeostasis. Apoptotic cells are swiftly engulfed by macrophages and digested into units. This removal of apoptotic cells is called ‘efferocytosis’. For efferocytosis, macrophages recognize phosphatidylserine (PtdSer) exposed on the cell surface as an ‘eat me’ signal. In healthy cells, PtdSer is exclusively localized to the inner leaflet of the plasma membrane by the action of flippases. When cells undergo apoptosis, caspase cleaves flippases to inactivate them, while it cleaves pro-scramblases to active scramblases, which quickly translocate PtdSer to the cell surface. The PtdSer is then recognized by PtdSer-binding proteins or by PtdSer receptors on macrophages, which subsequently engulf the apoptotic cells. When efferocytosis fails, apoptotic cells can rupture, releasing cellular materials that can evoke an autoimmune response. Thus, a defect in the PtdSer-exposing or PtdSer-recognizing processes triggers autoimmunity, leading to a systemic lupus erythematosus-type autoimmune disease.
Risks of Colorectal Cancer and Cancer-Related Mortality in Familial Colorectal Cancer Type X and Lynch Syndrome Families
Authors: Choi Yun-Hee , Lakhal-Chaieb Lajmi , Kröl Agnieszka , Yu Bing , Buchanan Daniel , Ahnen Dennis , Le Marchand Loic , Newcomb Polly A , Win Aung Ko , Jenkins Mark , Lindor Noralane M , Briollais Laurent 
Published: August 2018

Abstract

Background
The risk of cancers is well characterized in Lynch syndrome (LS) families but has been less studied in familial colorectal cancer type X (FCCTX) families.

Methods
In this article, we compare the risk estimates of first and second colorectal cancers (CRCs) in 168 FCTTX and 780 LS families recruited through the Colon Cancer Family Registry as well as the risk of cancer-related deaths and disease-free survival (DFS) after a first CRC. Our methodology is based on a survival analysis approach, developed specifically to model the occurrence of successive cancers (ie, first and second CRCs) in the presence of competing risk events (ie, death from any causes).

Results
We found an excess risk of first and second CRC in individuals with LS compared to FCCTX family members. However, for an average age at first CRC of 60 years in FCCTX families and 50 years in LS families, the DFS rates were comparable in men but lower in women from FCCTX vs LS families, eg , 75.1% (95% confidence interval [CI] = 69.0% to 80.9%) vs 78.9% (95% CI = 76.3% to 81.3%) for the 10-year DFS. The 10-year risk of cancer-related death was higher in FCCTX families vs LS families, eg, 15.4% in men (95% CI = 10.9% to 19.8%) and 19.3% in women (95% CI = 13.6% to 24.7%) vs 8.9% (95% CI = 7.5% to 11.4%) and 8.7% (95% CI = 7.1% to 10.8%), respectively.

Conclusions
Individuals with CRCs arising in the context of FCCTX do not experience the same improved DFS and overall survival of those with LS, and that difference may be relevant in management decisions.
SN 2014J in M82: new insights on the spectral diversity of Type Ia supernovae
Authors: Zhang Kaicheng , Wang Xiaofeng , Zhang JuJia , Zhang Tianmeng , Benetti S , Elias-Rosa N , Huang Fang , Lin Han , Li Linyi , Li Wenxiong , Ochner P , Pastorello A , Rui Liming , Tartaglia L , Tomasella L , Siviero A , Munari U , Terreran G , Song Hao , Taubenberger S , Wheeler J Craig , Xiang Danfeng , Zhao Xulin , Li Hongbin , Bai Jinming , Jiang Xiaojun , Shi Jianrong , Wu Zhenyu 
Published: August 2018

ABSTRACT
We present extensive spectroscopic observations for one of the closest Type Ia supernovae (SNe Ia), SN 2014J discovered in M82, ranging from 10.4 d before to 473.2 d after B-band maximum light. The diffuse interstellar band features detected in a high-resolution spectrum allow an estimate of line-of-sight extinction as Av ∼ 1.9 ± 0.6 mag. Spectroscopically, SN 2014J can be put into the high-velocity (HV) subgroup in Wang’s classification with a velocity of Si ii λ 6355 at maximum light of $v$0 = 1.22 ± 0.01 × 104 km s−1 but has a low velocity gradient (LVG, following Benetti’s classification) of $\dot{v}=41\pm 2$ km s−1 d−1, which is inconsistent with the trend that HV SNe Ia generally have larger velocity gradients. We find that the HV SNe Ia with LVGs tend to have relatively stronger Si iii (at ∼4400 Å) absorptions in early spectra, larger ratios of S ii λ 5468 to S ii λ 5640, and weaker Si ii 5972 absorptions compared to their counterparts with similar velocities but high velocity gradients. This shows that the HV+LVG subgroup of SNe Ia may have intrinsically higher photospheric temperature, which indicates that their progenitors may experience more complete burning in the explosions relative to the typical HV SNe Ia.
Key Concepts, Measures, and Data
Authors: Beckfield Jason 
Published: August 2018

Abstract
In this chapter, the author discusses several concepts, measures, and datasets that open new avenues for social epidemiologists to use political sociology to explain the distribution of population health. He also describes how social epidemiological concepts can feed back into political sociology to advance its agenda of understanding the social organization of power. Three themes integrate the concerns of these still-disconnected fields: (1) conceptualization of etiologic period, (2) definition of population, and (3) distinction between population averages and population variances. Mutual appreciation of the key concepts for each field is essential for the development of synthetic engagement between political sociology and social epidemiology.
Scientific Challenges to Engaging Political Sociology and Social Epidemiology
Authors: Beckfield Jason 
Published: August 2018

Abstract
Social epidemiology demonstrates clearly that social structure has profound consequences for the distribution of health, illness, and death, but it remains the case that political-sociological variables tend to be imprecisely incorporated into social epidemiological models. If the preceding chapters suggest how researchers could make a start on such incorporation, this chapter highlights the challenges to doing so in a convincing manner. Given the push from ecosocial, fundamental-cause, and social-determinants theories of disease distribution for concepts and measures for investigating politics and policies, the macroscope of political sociology holds great promise for generating new questions, new answers, and even new accountability for the generation of health inequity.
Semantic Possibility
Authors: Schwarz Wolfgang 
Published: August 2018

AbstractThis chapter starts out from the idea that semantics is a “special science” whose aim, like that of chemistry or ecology, is to identify systematic, high-level patterns in a fundamentally physical world. I defend an approach to this task on which sentences are associated with sets of possible worlds (of some kind). These sets of worlds, however, are not postulated for the compositional treatment of intensional contexts; they are not meant to capture what is intuitively asserted or communicated by an utterance; nor are they supposed to shed light on the cognitive processes that underlie our linguistic competence. Instead, their job description is to capture certain regularities in the interactions between subjects using the relevant language. I also raise some questions about how the relevant worlds might be construed.
Work and energy
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
Definition of work, and distinction between work done ‘on’ a system and work done ‘by’ a system. Definitions of path function, and quasistatic path. Introduction to P,V diagrams, and how changes in state, and the path followed during a change in state, may be represented graphically. Definition and illustration of thermodynamic cycles. Introduction of the concept of energy.
The First Law of Thermodynamics
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
The First Law of Thermodynamics, and how the First Law relates a change in a state function, internal energy, to changes in the path functions work and heat. Thermodynamic cycles. Heat capacities at constant volume, and the definition CV = (∂U/∂T)V. Mathematics of internal energy. Examples of the application of the First Law to isothermal, isobaric, isochoric and adiabatic changes. Reversible and irreversible paths. Mixing and friction as irreversible processes. Proof that that any path involving friction (or any other dissipative process) must be irreversible, implying that all real paths are irreversible.
Clausius, Kelvin, Planck, Carathéodory and Carnot
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
A chapter that draws together, and compares and contrasts, the principal alternative formulations of the Second Law – The Clausius statement, the Kelvin-Planck statement, the Carathéodory statement, and the Carnot cycle. This includes a discussion of heat engines and heat pumps, and of the efficiency of devices that transform heat into work.
Free energy
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
A critical chapter, explaining how the principles of thermodynamics can be applied to real systems. The central concept is the Gibbs free energy, which is explored in depth, with many examples. Specific topics addressed are: Spontaneous changes in closed systems. Definitions and mathematical properties of Gibbs free energy and Helmholtz free energy. Enthalpy- and entropy-driven reactions. Maximum available work. Coupled reactions, and how to make non-spontaneous changes happen, with examples such as tidying a room, life, and global warming. Standard Gibbs free energies. Mixtures, partial molar quantities and the chemical potential.
Phase equilibria
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
This chapter extends the discussion of gas phase equilibria to phase equilibria. The central concept is the vapour pressure, and the key proof is that the criterion for phase equilibrium is the equality of the molar Gibbs free energies, or chemical potentials, of each phase. This then leads to the Clapeyron and Clausius-Clapeyron equations. A notable feature of this chapter is the discussion of non-ideal gases, answering the question “Given that, by definition, an ideal gas can never liquefy, what is it about a real gas that enables the gas to change phase into a liquid?”. A unique feature of this discussion is the rigorous analysis of the Gibbs free energy of a van der Waals gas under compression, and the proof of the ‘Maxwell construction’.
Acids, bases and buffer solutions
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
Many reactions in solution involve acids and bases, and so this chapter examines these important reactions in detail. Topics covered include the ionisation of water, pH, pOH, acids and bases, conjugate acids and conjugate bases, acid and base dissociation constants, the Henderson-Hasselbalch equation, the Henderson-Hasselbalch approximation, buffer solutions and buffer capacity. A unique feature of this chapter is a ‘first principles’ analysis of how a reaction buffered at a particular pH achieves an equilibrium composition different from that of the same reaction taking place in an unbuffered solution. This introduces some concepts which are important in understanding the biochemical standard state, as required for Chapter 23.
Macromolecular conformations and interactions
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
As a polymer of many amino acids, any given protein can, in principle, adopt a huge number of configurations. In reality, however, the biologically stable protein adopts a single configuration that is stable over time. Thermodynamically, this configuration must represent a Gibbs free energy minimum. This chapter therefore explores how the thermodynamics and kinetics of protein folding and unfolding can be investigated experimentally (using, for example, chaotropes, heating or ligand interactions), and how these measurements can be used to enrich our understanding of protein configurations and stability.
Elements, biochemicals, and structures of microbes
Authors: Kirchman David L. 
Published: August 2018

Abstract
Microbiologists focus on the basic biochemical make-up of microbes, such as relative amounts of protein, RNA, and DNA in cells, while ecologists and biogeochemists use elemental ratios, most notably, the ratio of carbon to nitrogen (C:N), to explore biogeochemical processes and to connect up the carbon cycle with the cycle of other elements. Microbial ecologists make use of both types of data and approaches. This chapter combines both and reviews all things, from elements to macromolecular structures, that make up bacteria and other microbes. The most commonly used elemental ratio was discovered by Alfred Redfield who concluded that microbes have a huge impact on the chemistry of the oceans because of the similarity in nitrogen-to-phosphorus ratios for organisms and nitrate-to-phosphate ratios in the deep oceans. Although statistically different, the C:N ratios in soil microbes are remarkably similar to the ratios of aquatic microbes. The chapter moves on to discussing the macromolecular composition of bacteria and other microbes. This composition gives insights into the growth state of microbes in nature. Geochemists use specific compounds, “biomarkers”, to trace sources of organic material in ecosystems. The last section of the chapter is a review of extracellular polymers, pili, and flagella, which serve a variety of functions, from propelling microbes around to keeping them stuck in one place.
Community structure of microbes in natural environments
Authors: Kirchman David L. 
Published: August 2018

Abstract
Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.
Asymmetries in Vowel Harmony
Authors: van der Hulst Harry 
Published: August 2018

AbstractThis book deals with the phenomenon of vowel harmony, a phonological process whereby all the vowels in a word are required to share a specific phonological property, such as front or back articulation. Vowel harmony occurs in the majority of languages of the world, though only in very few European languages, and has been a central concern in phonological theory for many years. In this volume, Harry van der Hulst puts forward a new theory of vowel harmony, which accounts for the patterns of and exceptions to this phenomenon in the widest range of languages ever considered. The book begins with an overview of the general causes of asymmetries in vowel harmony systems. The two following chapters provide a detailed account of a new theory of vowel harmony based on unary elements and licensing, which is embedded in a general dependency-based theory of phonological structure. In the remaining chapters, this theory is applied to a variety of vowel harmony phenomena from typologically diverse languages, including palatal harmony in languages such as Finnish and Hungarian, labial harmony in Turkic languages, and tongue root systems in Niger-Congo, Nilo-Saharan, and Tungusic languages.