bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isotropic measures and maximizing ellipsoids: Between John and Loewner
Authors: Artstein-Avidan Shiri , Katzin David 
Published: April 2018

We define a one-parametric family of positions of a centrally symmetric convex body

K
K

which interpolates between the John position and the Loewner position: for

r
>
0

r>0

, we say that

K
K

is in maximal intersection position of radius

r
r

if

Vol

n

(
K
∩
r

B

2

n

)
≥

Vol

n

(
K
∩
r
T

B

2

n

)

\textrm {Vol}_{n}(K\cap rB_{2}^{n})\geq \textrm {Vol}_{n}(K\cap rTB_{2}^{n})

for all

T
∈

S
L

n

T\in \rm {SL}_{n}

. We show that under mild conditions on

K
K

, each such position induces a corresponding isotropic measure on the sphere, which is simply the normalized Lebesgue measure on

r

−
1

K
∩

S

n
−
1

r^{-1}K\cap S^{n-1}

. In particular, for

r

M

r_{M}

satisfying

r

M

n

κ

n

=

Vol

n

(
K
)

r_{M}^{n}\kappa _{n}=\textrm {Vol}_{n}(K)

, the maximal intersection position of radius

r

M

r_{M}

is an

M
M

-position, so we get an

M
M

-position with an associated isotropic measure. Lastly, we give an interpretation of John’s theorem on contact points as a limit case of the measures induced from the maximal intersection positions.
The Second Great Debate Revisited: Exploring the Impact of the Qualitative-Quantitative Divide in International Relations
Authors: Li Quan 
Published: April 2018

AbstractHalf a century after the “Second Great Debate” in international relations (IR) started, scholars still perceive the qualitative versus quantitative division as their principal divide, and yet we do not have a good grasp of the impact of this divide. My research explores how the divide shaped the incentives and behaviors of scholars and influenced the organization of our academic communities and knowledge production. The impact of the divide expressed itself in the distribution of research among methodologies in terms of relative quantity and impact. Less obviously, and yet more importantly, the divide influenced the distribution of quantitative research among different institution types, across fields and journals, and with respect to policy engagement. Using the TRIP database of 7,792 IR articles in twelve top journals from 1980 to 2014, I classify journal articles into three categories—quantitative-only, qualitative-only, and mixed-methods—and categorize author institutions into similar types—publishing quantitative research only, producing nonquantitative work only, and publishing various proportions of quantitative research. Notably, qualitative and quantitative works switched positions over time in terms of relative quantity and impact, with quantitative research more likely published but only slightly more cited in the recent decade. More importantly, the divide produced other less obvious but more serious outcomes. Among 1,111 institutions that ever published IR research in twelve top journals over thirty-five years, two-thirds published nonquantitative research only; fifty-three institutions published more than half of all quantitative articles; institutions publishing quantitative-only or nonquantitative-only research constituted two modal categories. Political science journals published more quantitative research, persistently and with growing convergence; IR journals also evolved toward publishing more quantitative research though with persistent divergence and forming two clusters. Quantitative articles and political science journals were significantly less engaged in providing policy prescriptions than qualitative articles and IR journals. To overcome this lasting and self-perpetuating divide, we must better understand its impact, learn to appreciate alternative approaches, and change the way we train future scholars.
Scandinavian Multicenter Acute Subdural Hematoma (SMASH) Study: Study Protocol for a Multinational Population-Based Consecutive Cohort
Authors: Bartek Jiri , Laugesen Christian , Mirza Sadia , Forsse Axel , Petersen Michael Anders , Corell Alba , Dyhrfort Philip Wilhelm , Redebrandt Henrietta Nittby , Reen Linus , Zolfaghari Shaian , Tobieson Lovisa , Carlsvärd Björn , Bergholt Bo , Bashir Asma , Soerensen Preben , Bilgin Arzu , Johansson Conny , Lindvall Peter , Förander Petter , Bellander Bo-Michael , Springborg Jacob B , Jakola Asgeir S 
Published: April 2018

Abstract

BACKGROUND
Traumatic acute subdural hematomas (ASDHs) are associated with high rate of morbidity and mortality, especially in elderly individuals. However, recent reports indicate that the morbidity and mortality rates might have improved.

OBJECTIVE
To evaluate postoperative (30-d) mortality in younger vs elderly (≥70 yr) patients with ASDH. Comparing younger and elderly patients, the secondary objectives are morbidity patterns of care and 6 mo outcome according to Glasgow outcome scale (GOS). Finally, in patients with traumatic ASDH, we aim to provide prognostic variables.

METHODS
This is a large-scale population-based Scandinavian study including all neurosurgical departments in Denmark and Sweden. All adult (≥18 yr) patients surgically treated between 2010 and 2014 for a traumatic ASDH in Denmark and Sweden will be included. Identification at clinicaltrials.gov is NCT03284190.

EXPECTED OUTCOMES
We expect to provide data on potential differences between younger vs elderly patients in terms of mortality and morbidity. We hypothesize that elderly patients selected for surgery have a similar pattern of care as compared with younger patients. We will provide functional outcome in terms of GOS at 6 mo in younger vs elderly patients undergoing ASDH evacuation. Finally, clinical useful prognostic factors for favorable (GOS 4-5) vs unfavorable (GOS 1-3) will be identified.

DISCUSSION
An improved understanding of the clinical outcome, treatment and resource allocation, clinical course, and the prognostic factors of traumatic ASDH will allow neurosurgeons to make better treatment decisions.
Cortical Plasticity
Authors: Marik Sally A. , Gilbert Charles D. 
Published: April 2018

Abstract
The cerebral cortex is a learning engine. The ability to encode information about sensory experience or practiced movements is a universal property of all cortical areas. This capacity, known as cortical plasticity, is seen in experience dependent changes in the functional properties of cortical neurons and in the alteration of cortical circuits. Certain properties are mutable only during a short period in postnatal life, which is known as the critical period, while others retain the ability to change throughout life. The same changes associated with assimilating normal experiences can be implemented for functional recovery following lesions of the central nervous system.
Taxation in the Greco-Roman World
Authors: Kaye Noah 
Published: April 2018

Abstract
This article surveys taxation in the Hellenistic kingdoms of Asia Minor in the Near East, focusing on the Seleukid Empire and the Attalids of Pergamon. It argues that the study of Hellenistic systems and habits of taxation can tell us much about the distribution of sovereignty in these composite, multiscalar kingdoms. The negotiation of fiscal rights and privileges in these kingdoms drew cities, kings, courtiers, priests, and soldiers into frequent, even ritualized interactions. The article discusses taxation’s role in the competition over territory and resources, both interstate and internal, while also highlighting the role of taxation in the articulation of each state’s sovereignty claims on communities and individuals. Key sources are reviewed, both epigraphic and archaeological, including cuneiform documents from Hellenistic Babylonia and Greek inscriptions from Asia Minor (Anatolia) and Coele-Syria (Levant).
How Familiarity Warps Representation in Face Space
Authors: Chauhan Vassiki , Gobbini M. Ida 
Published: April 2018

AbstractRecognition of familiar as compared to unfamiliar faces is robust and resistant to marked image distortion or degradation. Here we tested the flexibility of familiar face recognition with a morphing paradigm where the appearance of a personally familiar face was mixed with the appearance of a stranger. The aim was to assess how categorical boundaries for recognition of identity are affected by familiarity. We found a narrower categorical boundary for the identity of personally familiar faces when they were mixed with unfamiliar identities as compared to the control condition, in which the appearance of two unfamiliar faces were mixed. Our results suggest that familiarity warps the representational geometry of face space, amplifying perceptual distances for small changes in the appearance of familiar faces that are inconsistent with the structural features that define their identities.
Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved mechanisms of social chemical signaling
Authors: Yohe Laurel R. , Davies Kalina T. J. , Rossiter Stephen J. , Dávalos Liliana M. 
Published: April 2018

AbstractIn mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and also its link to fitness-related behaviors are not well understood. From vomeronasal transcriptomes, we discovered the first evidence of intact vomeronasal type-1 receptor (V1r) genes in bats, and we tested whether putatively functional bat receptors were orthologous to those of related taxa, or whether bats have evolved novel receptors. We found that V1rs in bats and show high levels of orthology to those of their relatives, as opposed to lineage-specific duplications, and receptors are under purifying selection. Despite widespread vomeronasal organ loss in bats, V1r copies have been retained for >65 million years. The highly conserved nature of bat V1rs challenges our current understanding of mammalian V1r function and suggest roles other than conspecific recognition or mating initiation in social behavior.
Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach
Authors: Kueffner Robert , Zach Neta , Bronfeld Maya , Norel Raquel , Atassi Nazem , Balagurusamy Venkat , di Camillo Barbara , Chio Adriano , Cudkowicz Merit , Dillenberger Donna , Garcia-Garcia Javier , Hardiman Orla , Hoff Bruce , Knight Joshua , Leitner Melanie L. , Li Guang , Mangravite Lara , Norman Thea , Wang Liuxia ,   the ALS Stratification Consortium, Xiao Jinfeng , Fang Wen-Chieh , Peng Jian , Stolovitzky Gustavo 
Published: April 2018

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with substantial heterogeneity in clinical presentation with an urgent need for better stratification tools for clinical development and care. In this study we used a crowdsourcing approach to address the problem of ALS patient stratification. The DREAM Prize4Life ALS Stratification Challenge was a crowdsourcing initiative using data from >10,000 patients from completed ALS clinical trials and 1479 patients from community-based patient registers. Challenge participants used machine learning and clustering techniques to predict ALS progression and survival. By developing new approaches, the best performing teams were able to predict disease outcomes better than currently available methods. At the same time, the integration of clustering components across methods led to the emergence of distinct consensus clusters, separating patients into four consistent groups, each with its unique predictors for classification. This analysis reveals for the first time the potential of a crowdsourcing approach to uncover covert patient sub-populations, and to accelerate disease understanding and therapeutic development.
Personalized Regression Enables Sample-Specific Pan-Cancer Analysis
Authors: Lengerich Benjamin J. , Aragam Bryon , Xing Eric P. 
Published: April 2018

AbstractIn many applications, inter-sample heterogeneity is crucial to understanding the complex biological processes under study. For example, in genomic analysis of cancers, each patient in a cohort may have a different driver mutation, making it difficult or impossible to identify causal mutations from an averaged view of the entire cohort. Unfortunately, many traditional methods for genomic analysis seek to estimate a single model which is shared by all samples in a population, ignoring this inter-sample heterogeneity entirely. In order to better understand patient heterogeneity, it is necessary to develop practical, personalized statistical models. To uncover this inter-sample heterogeneity, we propose a novel regularizer for achieving patient-specific personalized estimation. This regularizer operates by learning two latent distance metrics – one between personalized parameters and one between clinical covariates – and attempting to match the induced distances as closely as possible. Crucially, we do not assume these distance metrics are already known. Instead, we allow the data to dictate the structure of these latent distance metrics. Finally, we apply our method to learn patient-specific, interpretable models for a pan-cancer gene expression dataset containing samples from more than 30 distinct cancer types and find strong evidence of personalization effects between cancer types as well as between individuals. Our analysis uncovers sample-specific aberrations that are overlooked by population level methods, suggesting a promising new path for precision analysis of complex diseases such as cancer.
Molecular architecture of the mouse nervous system
Authors: Zeisel Amit , Hochgerner Hannah , Lönnerberg Peter , Johnsson Anna , Memic Fatima , van der Zwan Job , Häring Martin , Braun Emelie , Borm Lars , La Manno Gioele , Codeluppi Simone , Furlan Alessandro , Skene Nathan , Harris Kenneth D. , Hjerling Leffler Jens , Arenas Ernest , Ernfors Patrik , Marklund Ulrika , Linnarsson Sten 
Published: April 2018

AbstractThe mammalian nervous system executes complex behaviors controlled by specialised, precisely positioned and interacting cell types. Here, we used RNA sequencing of half a million single cells to create a detailed census of cell types in the mouse nervous system. We mapped cell types spatially and derived a hierarchical, data-driven taxonomy. Neurons were the most diverse, and were grouped by developmental anatomical units, and by the expression of neurotransmitters and neuropeptides. Neuronal diversity was driven by genes encoding cell identity, synaptic connectivity, neurotransmission and membrane conductance. We discovered several distinct, regionally restricted, astrocytes types, which obeyed developmental boundaries and correlated with the spatial distribution of key glutamate and glycine neurotransmitters. In contrast, oligodendrocytes showed a loss of regional identity, followed by a secondary diversification. The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system, and enables genetic manipulation of specific cell types.
xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments
Authors: Farek Jesse , Hughes Daniel , Mansfield Adam , Krasheninina Olga , Nasser Waleed , Sedlazeck Fritz J , Khan Ziad , Venner Eric , Metcalf Ginger , Boerwinkle Eric , Muzny Donna M , Gibbs Richard A , Salerno William 
Published: April 2018

AbstractMotivationThe rapid development of next-generation sequencing (NGS) technologies has lowered the barriers to genomic data generation, resulting in millions of samples sequenced across diverse experimental designs. The growing volume and heterogeneity of these sequencing data complicate the further optimization of methods for identifying DNA variation, especially considering that curated highconfidence variant call sets commonly used to evaluate these methods are generally developed by reference to results from the analysis of comparatively small and homogeneous sample sets.ResultsWe have developed xAtlas, an application for the identification of single nucleotide variants (SNV) and small insertions and deletions (indels) in NGS data. xAtlas is easily scalable and enables execution and retraining with rapid development cycles. Generation of variant calls in VCF or gVCF format from BAM or CRAM alignments is accomplished in less than one CPU-hour per 30× short-read human whole-genome. The retraining capabilities of xAtlas allow its core variant evaluation models to be optimized on new sample data and user-defined truth sets. Obtaining SNV and indels calls from xAtlas can be achieved more than 40 times faster than established methods while retaining the same accuracy.AvailabilityFreely available under a BSD 3-clause license at https://github.com/jfarek/xatlas.Contactfarek@bcm.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium
Authors: Kannan N. , Lai Y.-P. , Haug M. , Lilleness M. K. , Bakke S. S. , Marstad A. , Hov H. , Naustdal T. , Afset J. E. , Ioerger T. R. , Flo T. H. , Steigedal M. 
Published: April 2018

ABSTRACTMycobacterium avium(Mav) complex (MAC) are characterized as non-tuberculosis mycobacteria and are pathogenic mainly in immunocompromised individuals. MAC strains show a wide genetic variability, and there is growing evidence suggesting that genetic differences may contribute to a varied immune response that may impact on the infection outcome. The current study aimed to characterize the genomic changes within Mav isolates collected from single patients over time and test the host immune responses to these clinical isolates. Pulsed field gel electrophoresis and whole genome sequencing was performed on 40 MAC isolates isolated from 15 patients at the Department of Medical Microbiology at St. Olavs Hospital in Trondheim, Norway. Patients (4, 9 and 13) who contributed more than two isolates were selected for further analysis. These isolates exhibited extensive sequence variation in the form of single nucleotide polymorphisms (SNPs), suggesting that Mav accumulates mutations at high rates during persistent infections. Infection of murine macrophages and mice with sequential isolates from patients showed a tendency towards increased persistence and down-regulation of inflammatory cytokines by host-adapted Mav strains. The study revealed rapid genetic evolution of Mav in chronically infected patients accompanied with change in virulence properties of the sequential mycobacterial isolates.IMPORTANCEMAC are a group of opportunistic pathogens, consisting of Mav andM. intracellularespecies. Mav is found ubiquitously in the environment. In Mav infected individuals, Mav has been known to persist for long periods of time, and anti-mycobacterial drugs are unable to effectively clear the infection. The continued presence of the bacteria, could be attributed to either a single persistent strain or reinfection with the same or different strain. We examined sequential isolates collected over time from Mav infected individuals and observed that most patients carried the same strain overtime and were not re infected. We observed high rates of mutation within the serial isolates, accompanied with changes in virulence properties. In the light of increase in incidence of MAC related infections, this study highlights the possibility that host adapted Mav undergo genetic modifications to cope with the host environment and thereby persisting longer.
TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting
Authors: Teder Hindrek , Koel Mariann , Paluoja Priit , Jatsenko Tatjana , Rekker Kadri , Laisk-Podar Triin , Kukuškina Viktorija , Velthut-Meikas Agne , Žilina Olga , Peters Maire , Kere Juha , Salumets Andres , Palta Priit , Krjutškov Kaarel 
Published: April 2018

AbstractTargeted next-generation sequencing based biomarker detection methods have become essential for biomedical diagnostics. In addition to their sensitivity and high-throughput capacity, absolute molecule counting based on unique molecular identifier (UMI) has high potential to increase biomarker detection accuracy even further through the reduction of systematic technical biases. Here, we present TAC-seq, a simple and cost-effective targetedallelecounting bysequencing method that uses UMIs to estimate the original molecule counts of different biomarker types like mRNAs, microRNAs and cell-free DNA. We applied TAC-seq in three different applications and compared the results with standard sequencing technologies. RNA samples extracted from human endometrial biopsies were analyzed using previously described 57 mRNA-based receptivity biomarkers and 49 selected microRNAs at different expression levels. Cell-free DNA aneuploidy testing was based on cell line (47,XX,+21) genomic DNA. TAC-seq mRNA biomarker profiling showed identical clustering results to full transcriptome RNA sequencing, and microRNA detection demonstrated significant reduction in amplification bias, allowing to determine minor expression changes between different samples that remained undetermined by standard sequencing. The mimicking experiment for cell-free DNA fetal aneuploidy analysis showed that TAC-seq can be applied to count highly fragmented DNA, detecting significant (p=4.8×10−11) excess of molecules in case of trisomy 21. Based on three proof-of-principle applications we show that TAC-seq is a highly accurate and universal method for targeted nucleic acid biomarker profiling.
Evolution of the latitudinal diversity gradient in the hyperdiverse ant genus Pheidole
Authors: Economo Evan P. , Huang Jen-Pan , Fischer Georg , Sarnat Eli M. , Narula Nitish , Janda Milan , Guénard Benoit , Longino John T. , Knowles L. Lacey 
Published: April 2018

ABSTRACTAimThe latitudinal diversity gradient is the dominant pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyper-rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (>1100 species) ant radiation, Pheidole, and evaluate the roles of three general explanations for the latitudinal gradient: variation in diversification rate, tropical conservatism, and ecological regulation.LocationGlobal.Time PeriodThe past 35 million years.Major taxa studiedThe hyperdiverse ant genus Pheidole Westwood.MethodsWe assembled geographic data for 1499 species and morphospecies, and inferred a dated phylogeny of Pheidole of 449 species, including 150 species newly sequenced for this study. We tested correlations between diversification rate and latitude with BAMM, HiSSE, GeoSSE, and FiSSE, and examined patterns of diversification as Pheidole spread around the globe.ResultsWe found that Pheidole diversification occurred in series of bursts when new continents were colonized, followed by a slowdown in each region. There was no evidence of systematic variation of net diversification rates with latitude across any of the methods. Additionally, we found latitudinal affinity is moderately conserved with a Neotropical ancestor and phylogenetic inertia alone is sufficient to produce the gradient pattern.Main ConclusionsOverall our results are consistent with tropical conservatism explaining the diversity gradient, while providing no evidence that diversification rate varies systematically with latitude. There is evidence of ecological regulation on continental scales through the pattern of diversification after colonization. These results shed light on the mechanisms underlying the diversity gradient, while contributing toward a much-needed invertebrate perspective on global biodiversity dynamics.