bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-Generation Sequencing Reveals A JAGN1 Mutation in a Syndromic Child With Intermittent Neutropenia
Authors: Cifaldi Cristina , Serafinelli Jessica , Petricone Davide , Brigida Immacolata , Di Cesare Silvia , Di Matteo Gigliola , Chiriaco Maria , De Vito Rita , Palumbo Giuseppe , Rossi Paolo , Palma Paolo , Cancrini Caterina , Aiuti Alessandro , Finocchi Andrea 
Published: July 2018

Background:
Jagunal homolog 1 (JAGN1) gene was identified as a novel responsible for severe congenital neutropenia. The protein encoded by this gene is required for neutrophil differentiation, survival and function in microbial activity. JAGN1-deficient human neutrophils are characterized by alterations in trafficking within the endoplasmic reticulum and golgi compartments because of ultrastructural defects in endoplasmic reticulum and susceptibility to apoptosis.

Observations:
We report a patient exhibiting an intermittent neutropenia, for which a next-generation sequencing revealed a homozygous mutation in the JAGN1 gene.

Conclusions:
The patient extends the clinical variability associated to JAGN1 mutations, and this case highlights the importance of genetic investigations in patients with suspected neutropenia.
Postpartum Hemorrhage: Management of Massive Transfusion
Authors: Jackson Daneil L. , DeLoughery Thomas G. 
Published: July 2018

In women with postpartum hemorrhage, the need to transfuse a large amount of blood products is frequent. The ABCD of massive transfusions—Assessment/Activation, Blood products, Complications, and Drugs—can help manage this complex situation. There needs to be a defined method to activate the massive transfusion protocol and a well-defined means to assess the coagulation status of the patient by either traditional laboratory tests or point of care methods such as thromboelastography. Recent data supports more aggressive use of plasma in the massively transfused patient. Obstetricians need to be vigilant in assessing compilations, especially hypothermia. Given the increased use of antithrombotic drugs in bleeding patients, one needs to consider reversal of these agents. Finally, consideration of the role of other agents such as antifibrinolytic agents in the management of the bleeding patient is important. It is important for every hospital to have a well-defined massive transfusion protocol to streamline the care of postpartum hemorrhage.

Target Audience
Obstetricians and gynecologists, family physicians.

Learning Objectives
After completing this activity, the learner should be better able to have a systematic approach to massive transfusions in postpartum hemorrhage, describe recent clinical trials on more aggressive use of plasma and tranexamic acid, and effectively monitor coagulation and for complications of massive transfusion.
Concurrent Primary Chancre and Ocular Syphilis in an Human Immunodeficiency Virus-Negative Man
Authors: Hamill Matthew M. , Seppings Louise , Kit Vivienne , Antao Sheelah 
Published: July 2018

Abstract
We believe this to be the first report of coexisting polymerase chain reaction (PCR)-confirmed primary genital and ocular syphilis in a patient with penicillin allergy treated with doxycycline. The case examines the use of nonpenicillin and corticosteroid treatment of ocular syphilis and highlights the risk of eye involvement early in the disease process.
Illness Perception Mediates the Relationship Between the Severity of Symptoms and Perceived Health Status in Patients With Behçet Disease
Authors: Yankouskaya Alla , Boughey Alexandra , McCagh Jane , Neal Alison , de Bezenac Christophe , Davies Simon J. 
Published: July 2018

Objective
The aim of this study was to investigate the relationship between psychological representations of illness, perceived health status, and self-assessment of symptom severity in patients with Behçet disease, a rare long-term incurable condition with unclear etiology.

Methods
Using cross-sectional survey design, data on self-administered questionnaires on illness perception, health status, symptoms severity, and demographic characteristics were collected from 273 patients with Behçet disease (age range, 18–65 years). The data were subjected to mediation analysis to test whether cognitive and emotional components of illness perception mediate the relationship between the severity of symptoms and heath status.

Results
The results support our hypotheses that cognitive components of illness perception (perceived consequences and identity of the illness) mediate the link between symptom activity and pain, whereas emotional components of the illness (emotional representations about the illness) mediate the relationship between disease activity and perceived energy level.

Conclusions
The robustness of these mediation effects suggests potential directions for clinical psychologists and health care practitioners in developing support programs. We supplement our study with Open Access database containing information about type of medication, comorbid mood disorder, and detailed measurement of the severity of BD symptoms for sharing and accumulating multidisciplinary knowledge aiming to support the development of interventions. Addressing psychological aspects of BD will help to manage complex patients effectively.
Schmorl’s Node
Authors: Sahoo Manas Kumar , Ahlawat Kulbir , Yadav Rajiv , Gajendra Smeeta 
Published: July 2018

Abstract

68Ga–prostate-specific membrane antigen (PSMA) ligand PET/CT is commonly believed to be prostate specific as the name itself suggests. However, PSMA-expressing nonprostatic cancers as well as benign lesions are continuously being added to the list. We reported PSMA-expressing Schmorl’s node in L1 vertebra of a 74-year-old man with prostate cancer. Prostate-specific membrane antigen expression in the vertebral lesion raised a metastatic suspicion. However, on analysis of previous CT scan done 2 years before, the same lesion was observed with no significant interval change, confirming its benign nature. With more use of PSMA ligand PET/CT, more limitations and false positivities will be explored.
Primary Extragastrointestinal Stromal Tumor on FDG PET/CT
Authors: Zhang Yanyan , Zhang Annan , Song Le , Li Xinxin , Zhang Weifang 
Published: July 2018

Abstract
Primary extragastrointestinal stromal tumor is very rare. We report a case of cervical paravertebral extragastrointestinal stromal tumor involving adjacent bones revealed by FDG PET/CT in a 66-year-old man without any gastrointestinal involvement.
Molecular Pathways Underlying Adaptive Repair of the Injured Kidney
Authors: Orlando Giuseppe , Danger Richard , Okut Hayrettin , Edgar Lauren , Bussolati Benedetta , Gall Emily , Bergman Christopher R. , Tamburrini Riccardo , Gazia Carlo , Farney Alan C. , Freedman Barry I. , McPherson Gwen , Rogers Jeffrey , Stratta Robert J. , Brouard Sophie , Walker Stephen J. 
Published: July 2018

Objective:
To test the hypothesis that gene expression profiling in peripheral blood from patients who have undergone kidney transplantation (KT) will provide mechanistic insights regarding graft repair and regeneration.

Background:
Renal grafts obtained from living donors (LD) typically function immediately, whereas organs from donation after cardiac death (DCD) or acute kidney injury (AKI) donors may experience delayed function with eventual recovery. Thus, recipients of LD, DCD, and AKI kidneys were studied to provide a more complete understanding of the molecular basis for renal recovery.

Methods:
Peripheral blood was collected from LD and DCD/AKI recipients before transplant and throughout the first 30 days thereafter. Total RNA was isolated and assayed on whole genome microarrays.

Results:
Comparison of longitudinal gene expression between LD and AKI/DCD revealed 2 clusters, representing 141 differentially expressed transcripts. A subset of 11 transcripts was found to be differentially expressed in AKI/DCD versus LD. In all recipients, the most robust gene expression changes were observed in the first day after transplantation. After day 1, gene expression profiles differed depending upon the source of the graft. In patients receiving LD grafts, the expression of most genes did not remain markedly elevated beyond the first day post-KT. In the AKI/DCD groups, elevations in gene expression were maintained for at least 5 days post-KT. In all recipients, the pattern of coordinate gene overexpression subsided by 28 to 30 days.

Conclusions:
Gene expression in peripheral blood of AKI/DCD recipients offers a novel platform to understand the potential mechanisms and timing of kidney repair and regeneration after transplantation.
Efficacy and Safety of Atypical Antipsychotics in Bipolar Disorder With Comorbid Substance Dependence: A Systematic Review
Authors: Sepede Gianna , Lorusso Marco , Spano Maria Chiara , Di Nanno Piero , Di Iorio Giuseppe , Di Giannantonio Massimo 
Published: July 2018

Objectives
Bipolar disorder (BD) patients with a comorbid substance use disorder (SUD) are notoriously difficult to treat. Atypical antipsychotics (AAPs) are widely prescribed in BD, but their efficacy in patients with comorbid SUD is still debated. The aim of the present article is to systematically review the literature findings on the efficacy and safety of AAPs in BD patients with comorbid SUD.

Methods
We searched PubMed to identify original studies focused on the treatment of dual diagnosed BD with AAPs.

Results
Ten articles met our inclusion/exclusion criteria, involving a total of 969 subjects, 906 affected by BD and 793 with comorbid SUD: 4 were randomized controlled trials, 4 were open label trials and 2 were observational studies, published between 2002 and 2017. The most commonly abused substances were alcohol and cocaine. The AAPs used to treat patients were quetiapine (n = 337), asenapine (n = 119), olanzapine (n = 80), risperidone (n = 62), and aripiprazole (n = 48). In terms of safety, AAPs were usually well tolerated. Atypical antipsychotics were usually efficacious on acute mood symptoms, whereas their impact on substance-related issues was reported only in those studies without a placebo comparison.

Conclusions
According to our results, even though AAPs are widely used and efficacious in treating the clinical symptoms of BD, there are not enough data to suggest their adjunctive benefit on craving and substance consumption.
Transient dynamics in strongly nonlinear systems: optimization of initial conditions on the resonant manifold
Authors: Perchikov Nathan , Gendelman O. V. 
Published: July 2018

We consider a system of two linear and linearly coupled oscillators with ideal impact constraints. Primary resonant energy exchange is investigated by analysis of the slow flow using the action–angle (AA) formalism. Exact inversion of the action-energy dependence for the linear oscillator with impact constraints is not possible. This difficulty, typical for many models of nonlinear oscillators, is circumvented by matching the asymptotic expansions for the linear and impact limits. The obtained energy–action relation enables the complete analysis of the slow flow and the accurate description of the critical delocalization transition. The transition from the localization regime to the energy-exchange regime is captured by prediction of the critical coupling value. Accurate prediction of the delocalization transition requires a detailed account of the coupling energy with appropriate redefinition and optimization of the limiting phase trajectory on the resonant manifold.
This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Passive nonlinear targeted energy transfer
Authors: Vakakis Alexander F. 
Published: July 2018

Nonlinearity in dynamics and acoustics may be viewed as scattering of energy across frequencies/wavenumbers. This is in contrast with linear systems when no such scattering exists. Motivated by irreversible large-to-small-scale energy transfers in turbulent flows, passive targeted energy transfers (TET) in mechanical and structural systems incorporating intentional strong nonlinearities are considered. Transient or permanent resonance captures are basic mechanisms for inducing TET in such systems, as well as nonlinear energy scattering across scales caused by strongly nonlinear resonance interactions. Certain theoretical concepts are reviewed, and some TET applications are discussed. Specifically, it is shown that the addition of strongly nonlinear local attachments in an otherwise linear dynamical system may induce energy scattering across scales and ‘redistribution' of input energy from large to small scales in the linear modal space, in similarity to energy cascades that occur in turbulent flows. Such effects may be intentionally induced in the design stage and may lead to improved performance, e.g. it terms of vibration and shock isolation or energy harvesting. In addition, a simple mechanical analogue in the form of a nonlinear planar chain of particles composed of linear stiffness elements but exhibiting strong nonlinearity due to kinematic and geometric effects is discussed, exhibiting similar energy scattering across scales in its acoustics. These results demonstrate the efficacy of intentional utilization of strong nonlinearity in design to induce predictable and controlled intense multi-scale energy transfers in the dynamics and acoustics of a broad class of systems and structures, thus achieving performance objectives that would be not possible in classical linear settings.
This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Demonstration of accelerating and decelerating nonlinear impulse waves in functionally graded granular chains
Authors: Chaunsali Rajesh , Kim Eunho , Yang Jinkyu 
Published: July 2018

We propose a tunable cylinder-based granular system that is functionally graded in its stiffness distribution in space. With no initial compression given to the system, it supports highly nonlinear waves propagating under an impulse excitation. We investigate analytically, numerically and experimentally the ability to accelerate and decelerate the impulse wave without a significant scattering in the space domain. Moreover, the gradient in stiffness results in the scaling of contact forces along the chain. We envision that such tunable systems can be used for manipulating highly nonlinear impulse waves for novel sensing and impact mitigation purposes.
This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Quasiperiodic granular chains and Hofstadter butterflies
Authors: Martínez Alejandro J. , Porter Mason A. , Kevrekidis P. G. 
Published: July 2018

We study quasiperiodicity-induced localization of waves in strongly precompressed granular chains. We propose three different set-ups, inspired by the Aubry–André (AA) model, of quasiperiodic chains; and we use these models to compare the effects of on-site and off-site quasiperiodicity in nonlinear lattices. When there is purely on-site quasiperiodicity, which we implement in two different ways, we show for a chain of spherical particles that there is a localization transition (as in the original AA model). However, we observe no localization transition in a chain of cylindrical particles in which we incorporate quasiperiodicity in the distribution of contact angles between adjacent cylinders by making the angle periodicity incommensurate with that of the chain. For each of our three models, we compute the Hofstadter spectrum and the associated Minkowski–Bouligand fractal dimension, and we demonstrate that the fractal dimension decreases as one approaches the localization transition (when it exists). We also show, using the chain of cylinders as an example, how to recover the Hofstadter spectrum from the system dynamics. Finally, in a suite of numerical computations, we demonstrate localization and also that there exist regimes of ballistic, superdiffusive, diffusive and subdiffusive transport. Our models provide a flexible set of systems to study quasiperiodicity-induced analogues of Anderson phenomena in granular chains that one can tune controllably from weakly to strongly nonlinear regimes.
This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
A study of deformation localization in nonlinear elastic square lattices under compression
Authors: Pal Raj Kumar , Bonetto Federico , Dieci Luca , Ruzzene Massimo 
Published: July 2018

The paper investigates localized deformation patterns resulting from the onset of instabilities in lattice structures. The study is motivated by previous observations on discrete hexagonal lattices, where a variety of localized deformations were found depending on loading configuration, lattice parameters and boundary conditions. These studies are conducted on other lattice structures, with the objective of identifying and investigating minimal models that exhibit localization, hysteresis and path-dependent behaviour. To this end, we first consider a two-dimensional square lattice consisting of point masses connected by in-plane axial springs and vertical ground springs, which may be considered as a discrete description of an elastic membrane supported by an elastic substrate. Results illustrate that, depending on the relative values of the spring constants, the lattice exhibits in-plane or out-of-plane instabilities leading to localized deformations. This model is further simplified by considering the one-dimensional case of a spring–mass chain sitting on an elastic foundation. A bifurcation analysis of this lattice identifies the stable and unstable branches and sheds light on the mechanism of transition from affine deformation to global or diffuse deformation to localized deformation. Finally, the lattice is further reduced to a minimal four-mass model, which exhibits a deformation qualitatively similar to that in the central part of a longer chain. In contrast to the widespread assumption that localization is induced by defects or imperfections in a structure, this work illustrates that such phenomena can arise in perfect lattices as a consequence of the mode shapes at the bifurcation points.This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Pathologically distinct fibroblast subsets drive inflammation and tissue damage in arthritis
Authors: Croft Adam P , Campos Joana , Jansen Kathrin , Turner Jason D , Marshall Jennifer , Attar Moustafa , Savary Loriane , Perlman Harris , Barone Francesca , McGettrick Helen M , Fearon Douglas T , Wei Kevin , Raychaudhuri Soumya , Lorsunsky Ilya , Brenner Michael B , Coles Mark , Sansom Stephen N , Filer Andrew , Buckley Christopher D 
Published: July 2018

SUMMARYThe identification of lymphocyte subsets with non-overlapping effector functions has been pivotal to the development of targeted therapies in immune mediated inflammatory diseases (IMIDs). However it remains unclear whether fibroblast subclasses with non-overlapping functions also exist and are responsible for the wide variety of tissue driven processes observed in IMIDs such as inflammation and damage. Here we identify and describe the biology of distinct subsets of fibroblasts responsible for mediating either inflammation or tissue damage in arthritis. We show that deletion of FAPα+ synovial cells suppressed both inflammation and bone erosions in murine models of resolving and persistent arthritis. Single cell transcriptional analysis identified two distinct fibroblast subsets: FAPα+ THY1+ immune effector fibroblasts located in the synovial sub-lining, and FAPα+ THY1- destructive fibroblasts restricted to the synovial lining. When adoptively transferred into the joint, FAP α+ THY1- fibroblasts selectively mediate bone and cartilage damage with little effect on inflammation whereas transfer of FAP α+ THY1+ fibroblasts resulted in a more severe and persistent inflammatory arthritis, with minimal effect on bone and cartilage. Our findings describing anatomically discrete, functionally distinct fibroblast subsets with non-overlapping functions have important implications for cell based therapies aimed at modulating inflammation and tissue damage.
Carnelian: alignment-free functional binning and abundance estimation of metagenomic reads
Authors: Nazeen Sumaiya , Berger Bonnie 
Published: July 2018

AbstractAccurate assignment of metagenomic reads to their functional roles is an important first step towards gaining insights into the relationship between the human microbiomeincluding the collective genesand disease. Existing approaches focus on binning sequencing reads into known taxonomic classes or by genes, often failing to produce results that generalize across different cohorts with the same disease. We present Carnelian, a highly precise and accurate pipeline for alignment-free functional binning and abundance estimation, which leverages the recent idea of even-coverage, low-density locality sensitive hashing. When coupled with one-against-all classifiers, reads can be binned by molecular function encoded in their gene content with higher precision and accuracy. Carnelians minutes-per-metagenome processing speed enables analysis of large-scale disease or environmental datasets to reveal disease- and environment-specific changes in microbial functionality previously poorly understood. Our pipeline newly reveals a functional dysbiosis in patient gut microbiomes, not found in earlier metagenomic studies, and identifies a distinct shift from matched healthy individuals in Type-2 Diabetes (T2D) and early-stage Parkinson’s Disease (PD). We remarkably identify a set of functional markers that can differentiate between patients and healthy individuals consistently across both the datasets with high specificity.
Lysosome exocytosis is required for mitosis
Authors: Nugues Charlotte , Helassa Nordine , Rajamanoharan Dayani , Burgoyne Robert D , Haynes Lee P 
Published: July 2018

AbstractMitosis, the accurate segregation of duplicated genetic material into what will become two new daughter cells, is accompanied by extensive membrane remodelling and membrane trafficking activities. Early in mitosis, adherent cells partially detach from the substratum, round up and their surface area decreases. This likely results from an endocytic uptake of plasma membrane material. As cells enter cytokinesis they re-adhere, flatten and exhibit an associated increase in surface area. The identity of the membrane donor for this phase of mitosis remains unclear. Here we show by biochemical and imaging approaches that lysosomes undergo exocytosis at telophase and that this requires the activity of phosphatidylinositol 4-kinase-IIIβ. Inhibition of lysosome exocytosis resulted in mitotic failure in a significant proportion of cells suggesting that this facet of lysosome physiology is essential and represents a new regulatory mechanism in mitosis.