bluuebunny/crossref_metadata_2025_split huggingface dataset:
Otitis media – Definition, Pathogenese, Klinik, Diagnose und Therapie
Authors: Leichtle A. , Hoffmann T.K. , Wigand M.C. 
Published: July 2018

ZusammenfassungUnter dem Begriff Otitis media werden die akute Otitis media, die rezidivierende akute Otitis media, die Otitis media mit Erguss, die chronische Otitis media
mesotympanalis und die chronische Otitis media epitympanalis, das Cholesteatom, zusammengefasst. Es handelt sich um vielfältige Krankheitsbilder, die teils
ineinander übergehen können und eine individuell angepasste, zielgerichtete Therapie erfordern.
PICK1 inhibits the E3 ubiquitin ligase activity of Parkin and reduces its neuronal protective effect
Authors: He Jing , Xia Mengying , Yeung Patrick K. K. , Li Jiahua , Li Zhifang , Chung Kenny K. , Chung Sookja K. , Xia Jun 
Published: July 2018

Significance
Parkinson’s disease (PD) is the second most common neurodegenerative disorder. It is characterized by progressive deterioration of motor function caused by loss of dopamine-producing neurons. Currently, there is no treatment that could stop the progress of the disease. Loss-of-function mutations in Parkin account for ∼50% of early onset PD. Parkin functions as an E3 ubiquitin ligase that exhibits multiple protective roles especially in dopaminergic neurons. Here, we demonstrate that PICK1 directly binds to Parkin. PICK1 is a potent endogenous inhibitor of Parkin’s E3 ubiquitin ligase activity and blocks Parkin’s protective functions. Conversely, knockout of PICK1 enhances the neuroprotective effect of Parkin. Thus, the reduction of PICK1 may provide a therapeutic target for the treatment of PD.
A random first-order transition theory for an active glass
Authors: Nandi Saroj Kumar , Mandal Rituparno , Bhuyan Pranab Jyoti , Dasgupta Chandan , Rao Madan , Gov Nir S. 
Published: July 2018

Significance
Understanding how activity affects the physics of dense glassy suspensions is of fundamental interest in a variety of cellular and tissue contexts. However, current simulations of dense active systems make qualitatively different predictions about the influence of activity on characteristic features of glass, such as fragility. Acknowledging the need for a broad theoretical framework, we extend random first-order transition (RFOT) theory to active glasses, based on an effective independent-particle treatment. We find that the analytic model predicts that the behavior of the active glass is strongly influenced by the microscopic details of activity. This not only resolves the apparent contradictions posed by previous studies but provides a number of testable predictions, some of which we verify using numerical simulations.
Size-dependent dynamic structures of supported gold nanoparticles in CO oxidation reaction condition
Authors: He Yang , Liu Jin-Cheng , Luo Langli , Wang Yang-Gang , Zhu Junfa , Du Yingge , Li Jun , Mao Scott X. , Wang Chongmin 
Published: July 2018

Significance
Gold is the noblest metal. However, when the size decreases to nanoscale and is supported on reducible oxides, the gold nanoparticle shows exceptionally high catalytic performance even at low temperatures. Here, through state-of-the-art in situ aberration-corrected environmental transmission electron microscopy and ab initio molecular-dynamic simulations, we discovered that, upon exposing to reactant gas (carbon monoxide and oxygen), ultrasmall gold clusters on ceria show a size-dependent order-to-disorder transformation with generation of dynamic low-coordinated atoms, which presumably can effectively boost the oxidation reaction of carbon monoxide. The findings provide much-needed insights on the origin of size-dependent catalytic properties of supported gold and demonstrate a size effect in absorbent–particle interactions that may widely exist and play an essential role in heterogeneous catalysts.
Genetic analysis of social-class mobility in five longitudinal studies
Authors: Belsky Daniel W. , Domingue Benjamin W. , Wedow Robbee , Arseneault Louise , Boardman Jason D. , Caspi Avshalom , Conley Dalton , Fletcher Jason M. , Freese Jeremy , Herd Pamela , Moffitt Terrie E. , Poulton Richie , Sicinski Kamil , Wertz Jasmin , Harris Kathleen Mullan 
Published: July 2018

Significance
Genome-wide association study (GWAS) discoveries about educational attainment have raised questions about the meaning of the genetics of success. These discoveries could offer clues about biological mechanisms or, because children inherit genetics and social class from parents, education-linked genetics could be spurious correlates of socially transmitted advantages. To distinguish between these hypotheses, we studied social mobility in five cohorts from three countries. We found that people with more education-linked genetics were more successful compared with parents and siblings. We also found mothers’ education-linked genetics predicted their children’s attainment over and above the children’s own genetics, indicating an environmentally mediated genetic effect. Findings reject pure social-transmission explanations of education GWAS discoveries. Instead, genetics influences attainment directly through social mobility and indirectly through family environments.
Enhanced brain activity associated with memory access in highly superior autobiographical memory
Authors: Santangelo Valerio , Cavallina Clarissa , Colucci Paola , Santori Alessia , Macrì Simone , McGaugh James L. , Campolongo Patrizia 
Published: July 2018

Significance
Recent research has identified human subjects who have highly superior autobiographical memory (HSAM). Here, we investigated, using fMRI, the neural activation induced by retrieval of autobiographical memories (AMs) and semantic memories (SMs) in subjects with HSAM and control subjects. While their brains were being scanned, subjects had to retrieve AMs as well as SMs (e.g., examples of animals). The subjects with HSAM displayed a superior ability to retrieve details of AMs, supported by enhanced activation of several brain regions, including the medial prefrontal cortex and temporoparietal junction, as well as increased connectivity of the prefrontal cortex with the hippocampus, a region well known to be involved in memory representation. These findings suggest that activation of these systems may play a critical role in enabling HSAM.
Role of elemental carbon in the photochemical aging of soot
Authors: Li Meng , Bao Fengxia , Zhang Yue , Song Wenjing , Chen Chuncheng , Zhao Jincai 
Published: July 2018

Significance
Photochemical oxidation is an important aging pathway for soot. The organic carbon (OC) component in soot is believed to be photoactive, while the elemental carbon (EC) part with strong light absorption is photochemically inert. By considering the distinct light absorption properties of OC and EC, we have provided direct experimental evidence that EC also plays an important role in the photochemical aging of soot by absorbing the solar light. Our work reveals that the photochemical aging of soot occurs in an extended active spectrum (up to red light) by the light absorption of EC and has major environmental effects, such as enhancing the hydrophilicity of soot, that would enhance its ability to act as cloud condensation nuclei.
Picture perception reveals mental geometry of 3D scene inferences
Authors: Koch Erin , Baig Famya , Zaidi Qasim 
Published: July 2018

Significance
We show that, in both 3D scene understanding and picture perception, observers mentally apply projective geometry to retinal images. Reliance on the same geometrical function is revealed by the surprisingly close agreement between observers in making judgments of 3D object poses. These judgments are in accordance with that predicted by a back-projection from retinal orientations to 3D poses, but are distorted by a bias to see poses as closer to fronto-parallel. Reliance on retinal images explains distortions in perceptions of real scenes, and invariance in pictures, including the classical conundrum of why certain image features always point at the observer regardless of viewpoint. These results have implications for investigating 3D scene inferences in biological systems, and designing machine vision systems.
The development of referential hierarchy effects in
Sahaptian
Authors: Gildea Spike , Jansen Joana 
Published: July 2018

Abstract
Sahaptin and Nez Perce, the two languages of the Sahaptian family,
have both been cited as case studies in the typological literature
on hierarchical patterns in main clause grammar. Nez Perce has
ergative case marking on only third person singular transitive
subjects, plus a minor pattern of indexation of SAP participants via
(rarely occurring) second position enclitics. Sahaptin has one of
the more complex hierarchical systems ever described, with SAP
indexation via enclitics, third person indexation on verbs,
differential object marking, an inverse verbal direction prefix, and
two distinct ergative suffixes, each restricted to a subset of third
person singular transitive subjects (one when objects are SAP, the
other when objects are third person). This paper begins by
reviewing, evaluating, and occasionally expanding on existing
knowledge: we summarize the hierarchical patterns in Sahaptian and characterize each distinct construction. Then we compare relevant Sahaptin
morphemes with cognates in Nez Perce, and review their
reconstruction to Proto-Sahaptian. The primary contribution of this
paper is organizing the morphemes (and their accompanying
hierarchical patterns) in both languages into cognate
constructions, then reconstructing each to its
Proto-Sahaptian origins. We conclude by reviewing and evaluating
proposals for Pre-Proto-Sahaptian developments claimed to explain
the origins of hierarchical patterns that reconstruct to
Proto-Sahaptian. The mechanisms we identify as having created the
Sahaptian hierarchical effects are diverse, some motivated and
others not, some arising from internal sources, others arguably from
contact.
Diachrony and the referential hierarchy in Old Irish
Authors: Griffith Aaron 
Published: July 2018

Abstract
A set of Old Irish clitic person markers may co-index subject or
object markers on the verb. Only one clitic of this set may appear
at a time, however. The clitic, if present, indexes the verbal
argument highest on the scale 1st person > 2nd person > 3rd
person animate > inanimate. The restriction of one clitic per
verb, a prerequisite for the hierarchy, is explained here as a
result of the deictic origin of the clitic set. The deictic origin
further favors the marking of local persons over non-local persons.
For the upper and lower end of the hierarchy, however, the ranking
appears to be determined rather by considerations of function. Since
the clitics can mark topics, they favor 1st persons over 2nd and
animates over inanimates.
Are the Tupi-Guarani hierarchical indexing systems really
motivated by the person hierarchy?
Authors: Rose Françoise 
Published: July 2018

Abstract
Tupi-Guarani languages are supposedly perfect examples of
hierarchical indexing systems, where the relative ranking of A and P
on the 1 > 2 > 3 person hierarchy determines the selection of
the person markers. This chapter questions the relevance of the
person hierarchy as a synchronic and diachronic explanation for such
systems, with data from 28 languages. First, only SAP > 3 can
really be posited in the actual languages, and second, it explains
only part of the facts that it is supposed to account for in
Proto-Tupi-Guarani. The chapter ends by suggesting that these
systems do not result from the person hierarchy as a functional
motivation. Instead, they may result from grammaticalization of
pronominal paradigms lacking third-person forms.
An unexpected world population variation of MCT1 polymorphism 1470T > A involved in lactate transport
Authors: Onali Federico , Calò Carla M. , Massidda Myosotis , Álvarez‐Álvarez Miguel M. , Esteban Maria Esther 
Published: July 2018

ABSTRACTA common missense mutation (1470T > A) in gene SLC16A1 responsible for an amino acid substitution in protein MCT1 has been associated with differential lactate transport and hence, differences in physical performance and muscle injuries in relation to physical exercise. This study describes, for the first time, the worldwide variation of MCT1 variant 1470T > A at an intra‐ and inter‐continental level. Two thousand five hundred and four individual genotypes of 26 populations clustered in 5 population groups have been analysed with data downloaded from the public database 1000 Genomes Phase 3 Browser. Several parameters of population differentiation and structure have been explored as well as selection signatures in the whole gene. Allele T, the common variant, shows extremely high values in Sub‐Saharan African groups (frequencies 86–91%) as compared with the remaining world regions (69–49%). TT genotype also predominates in African groups, showing significant differences with the rest of world populations. In view of the evidence that the TT genotype is associated with clinical implications and a better predisposition to sprint/power performances, we suggest that the high presence of the TT genotype in African populations should be taken into account in future association studies at both medical and sports fields.
Smoking and Accelerated Lung Function Decline in HIV-Positive Individuals: A Secondary Analysis of the START Pulmonary Substudy
Authors: MacDonald David M. , Melzer Anne C. , Collins Gary , Avihingsanon Anchalee , Crothers Kristina , Ingraham Nicholas E. , Mugerwa Henry , Ristola Matti , Shuter Jonathan , Kunisaki Ken M. ,   for the INSIGHT START Pulmonary Substudy Group
Published: July 2018

Background:
Chronic obstructive pulmonary disease (COPD) is a leading cause of death and disability globally. Both cigarette smoking and HIV have been identified as independent risk factors for COPD. We used data from the strategic timing of antiretroviral treatment (START) Pulmonary Substudy to quantify the impact of smoking on rate of lung function decline in HIV.

Methods:
We included START Pulmonary Substudy participants who contributed at least 2 good quality spirometry measures during the study. Slope of forced expiratory volume in 1 second (FEV1) was estimated using a repeated-measures model adjusted for the treatment group (immediate vs deferred treatment arm of START), age, sex, race, baseline COPD, and region.

Results:
Of 1026 START Pulmonary Substudy participants, 915 (89%) were included in this analysis. Median follow-up time was 3.9 years. Smokers and nonsmokers were similar in baseline age (median 36 years), but smokers were more likely to be white, male, and from Europe/Israel/Australia. Smokers had faster average FEV1 decline compared with nonsmokers [−38.3 mL/yr vs −25.1 mL/yr; difference of −13.2 mL/yr (95% confidence interval: −23.6 to −2.7); P = 0.013], were more likely to meet criteria for rapid FEV1 decline [7.2%–11.7% more likely (P = 0.09–P = 0.002), depending on the definition of rapid decline], and had borderline, but not statistically significant, higher incident COPD during follow-up (9.7% vs 5.8%, P = 0.06).

Conclusions:
Compared to nonsmokers, HIV-positive smokers experience faster decline in lung function. These results underscore the need for a better understanding of how to best support smoking cessation among HIV-positive populations.
Wavelet analysis techniques in cavitating flows
Authors: Brandner Paul A. , Venning James A. , Pearce Bryce W. 
Published: July 2018

Cavitating and bubbly flows involve a host of physical phenomena and processes ranging from nucleation, surface and interfacial effects, mass transfer via diffusion and phase change to macroscopic flow physics involving bubble dynamics, turbulent flow interactions and two-phase compressible effects. The complex physics that result from these phenomena and their interactions make for flows that are difficult to investigate and analyse. From an experimental perspective, evolving sensing technology and data processing provide opportunities for gaining new insight and understanding of these complex flows, and the continuous wavelet transform (CWT) is a powerful tool to aid in their elucidation. Five case studies are presented involving many of these phenomena in which the CWT was key to data analysis and interpretation. A diverse set of experiments are presented involving a range of physical and temporal scales and experimental techniques. Bubble turbulent break-up is investigated using hydroacoustics, bubble dynamics and high-speed imaging; microbubbles are sized using light scattering and ultrasonic sensing, and large-scale coherent shedding driven by various mechanisms are analysed using simultaneous high-speed imaging and physical measurement techniques. The experimental set-up, aspect of cavitation being addressed, how the wavelets were applied, their advantages over other techniques and key findings are presented for each case study.This paper is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Continuous wavelet transform and higher-order spectrum: combinatory potentialities in breath sound analysis and electroencephalogram-based pain characterization
Authors: Hadjileontiadis Leontios J. 
Published: July 2018

The combination of the continuous wavelet transform (CWT) with a higher-order spectrum (HOS) merges two worlds into one that conveys information regarding the non-stationarity, non-Gaussianity and nonlinearity of the systems and/or signals under examination. In the current work, the third-order spectrum (TOS), which is used to detect the nonlinearity and deviation from Gaussianity of two types of biomedical signals, that is, wheezes and electroencephalogram (EEG), is combined with the CWT to offer a time–scale representation of the examined signals. As a result, a CWT/TOS field is formed and a time axis is introduced, creating a time–bifrequency domain, which provides a new means for wheeze nonlinear analysis and dynamic EEG-based pain characterization. A detailed description and examples are provided and discussed to showcase the combinatory potential of CWT/TOS in the field of advanced signal processing.
This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Quantitative feature analysis of continuous analytic wavelet transforms of electrocardiography and electromyography
Authors: Wachowiak Mark P. , Wachowiak-Smolíková Renata , Johnson Michel J. , Hay Dean C. , Power Kevin E. , Williams-Bell F. Michael 
Published: July 2018

Theoretical and practical advances in time–frequency analysis, in general, and the continuous wavelet transform (CWT), in particular, have increased over the last two decades. Although the Morlet wavelet has been the default choice for wavelet analysis, a new family of analytic wavelets, known as generalized Morse wavelets, which subsume several other analytic wavelet families, have been increasingly employed due to their time and frequency localization benefits and their utility in isolating and extracting quantifiable features in the time–frequency domain. The current paper describes two practical applications of analysing the features obtained from the generalized Morse CWT: (i) electromyography, for isolating important features in muscle bursts during skating, and (ii) electrocardiography, for assessing heart rate variability, which is represented as the ridge of the main transform frequency band. These features are subsequently quantified to facilitate exploration of the underlying physiological processes from which the signals were generated.This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Scrublet: computational identification of cell doublets in single-cell transcriptomic data
Authors: Wolock Samuel L. , Lopez Romain , Klein Allon M. 
Published: July 2018

AbstractSingle-cell RNA-sequencing has become a widely used, powerful approach for studying cell populations. However, these methods often generate multiplet artifacts, where two or more cells receive the same barcode, resulting in a hybrid transcriptome. In most experiments, multiplets account for several percent of transcriptomes and can confound downstream data analysis. Here, we present Scrublet (Single-Cell Remover of Doublets), a framework for predicting the impact of multiplets in a given analysis and identifying problematic multiplets. Scrublet avoids the need for expert knowledge or cell clustering by simulating multiplets from the data and building a nearest neighbor classifier. To demonstrate the utility of this approach, we test Scrublet on several datasets that include independent knowledge of cell multiplets.
Identification of Transcription Factor Binding Sites using ATAC-seq
Authors: Li Zhijian , Schulz Marcel H. , Zenke Martin , Costa Ivan G. 
Published: July 2018

1AbstractTransposase-Accessible Chromatin (ATAC) followed by sequencing (ATAC-seq) is a simple and fast protocol for detection of open chromatin. However, computational footprinting in ATAC-seq, i.e. search for regions with depletion of cleavage events due to transcription factor binding sites, has been poorly explored so far. We propose HINT-ATAC, a footprinting method that addresses ATAC-seq specific protocol artifacts. HINT-ATAC uses a probabilistic framework based on Variable-order Markov models to learn the complex sequence cleavage preferences of the transposase enzyme. Moreover, we observed specific strand specific cleavage patterns around the binding sites of transcription factors, which are determined by local nucleosome architecture. HINT-ATAC explores local nucleosome architecture to significantly outperform competing footprinting methods in predicting transcription factor binding sites by ChIP-seq. HINT-ATAC is an open source software and available online at www.regulatory-genomics.org/hint
The immune cell landscape in kidneys of lupus nephritis patients
Authors: Arazi Arnon , Rao Deepak A. , Berthier Celine C. , Davidson Anne , Liu Yanyan , Hoover Paul J. , Chicoine Adam , Eisenhaure Thomas M. , Jonsson A. Helena , Li Shuqiang , Lieb David J. , Browne Edward P. , Noma Akiko , Sutherby Danielle , Steelman Scott , Smilek Dawn E. , Tosta Patti , Apruzzese William , Massarotti Elena , Dall’Era Maria , Park Meyeon , Kamen Diane L. , Furie Richard A. , Payan-Schober Fernanda , Buyon Jill P. , Petri Michelle A. , Putterman Chaim , Kalunian Kenneth C. , Woodle E. Steve , Lederer James A. , Hildeman David A. , Nusbaum Chad , Wofsy David , Kretzler Matthias , Anolik Jennifer H. , Brenner Michael B. ,   the Accelerating Medicines Partnership in RA/SLE network, Hacohen Nir , Diamond Betty 
Published: July 2018

ABSTRACTLupus nephritis is a potentially fatal autoimmune disease, whose current treatment is ineffective and often toxic. To gain insights into disease mechanisms, we analyzed kidney samples from lupus nephritis patients and healthy controls using single-cell RNA-seq. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid, T, NK and B cells, demonstrating both pro-inflammatory and resolving responses. We found evidence of local activation of B cells correlated with an age-associated B cell signature, and of progressive stages of monocyte differentiation within the kidney. A clear interferon response was observed in most cells. Two chemokine receptors, CXCR4 and CX3CR1, were broadly expressed, pointing to potential therapeutic targets. Gene expression of immune cells in urine and kidney was highly correlated, suggesting urine may be a surrogate for kidney biopsies. Our results provide a first comprehensive view of the complex network of leukocytes active in lupus nephritis kidneys.