bluuebunny/crossref_metadata_2025_split huggingface dataset:
A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer
Authors: Masutani Bansho , Morishita Shinichi 
Published: July 2018

Abstract

Motivation
Detection of DNA at low abundance with respect to the entire sample is an important problem in areas such as epidemiology and field research, as these samples are highly contaminated with non-target DNA. To solve this problem, many methods have been developed to date, but all require additional time-consuming and costly procedures. Meanwhile, the MinION sequencer developed by Oxford Nanopore Technology (ONT) is considered a powerful tool for tackling this problem, as it allows selective sequencing of target DNA. The main technology employed involves rejection of an undesirable read from a specific pore by inverting the voltage of that pore, which is referred to as ‘Read Until’. Despite its usefulness, several issues remain to be solved in real situations. First, limited computational resources are available in field research and epidemiological applications. In addition, a high-speed online classification algorithm is required to make a prompt decision. Lastly, the lack of a theoretical approach for modeling of selective sequencing makes it difficult to analyze and justify a given algorithm.

Results
In this paper, we introduced a statistical model of selective sequencing, proposed an efficient constant-time classifier for any background DNA profile, and validated its optimal precision. To confirm the feasibility of the proposed method in practice, for a pre-recorded mock sample, we demonstrate that the method can selectively sequence a 100 kb region, consisting of 0.1% of the entire read pool, and achieve approximately 500-fold amplification. Furthermore, the algorithm is shown to process 26 queries per second with a $500 palm-sized next unit of computing box using an Intel® CoreTMi7 CPU without extended computer resources such as a GPU or high-performance computing. Next, we prepared a mixed DNA pool composed of Saccharomyces cerevisiae and lambda phage, in which any 200 kb region of S.cerevisiae consists of 0.1% of the whole sample. From this sample, a 30–230 kb region of S.cerevisiae chromosome 1 was amplified approximately 30-fold. In addition, this method allowed on-the-fly changing of the amplified region according to the uncovered characteristics of a given DNA sample.

Availability and implementation
The source code is available at: https://bitbucket.org/ban-m/dyss.
A systematic review of the use of the electronic health record for patient identification, communication, and clinical support in palliative care
Authors: Bush Ruth A , Pérez Alexa , Baum Tanja , Etland Caroline , Connelly Cynthia D 
Published: July 2018

AbstractObjectivesGlobally, healthcare systems are using the electronic health record (EHR) and elements of clinical decision support (CDS) to facilitate palliative care (PC). Examination of published results is needed to determine if the EHR is successfully supporting the multidisciplinary nature and complexity of PC by identifying applications, methodology, outcomes, and barriers of active incorporation of the EHR in PC clinical workflow.MethodsA systematic review using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The data sources PubMed, CINAL, EBSCOhost, and Academic Search Premier were used to identify literature published 1999–2017 of human subject peer-reviewed articles in English containing original research about the EHR and PC.ResultsThe search returned 433 articles, 30 of which met inclusion criteria. Most studies were feasibility studies or retrospective cohort analyses; one study incorporated prospective longitudinal mixed methods. Twenty-three of 30 (77%) were published after 2014. The review identified five major areas in which the EHR is used to support PC. Studies focused on CDS to: identify individuals who could benefit from PC; electronic advanced care planning (ACP) documentation; patient-reported outcome measures (PROMs) such as rapid, real-time pain feedback; to augment EHR PC data capture capabilities; and to enhance interdisciplinary communication and care.DiscussionBeginning in 2015, there was a proliferation of articles about PC and EHRs, suggesting increasing incorporation of and research about the EHR with PC. This review indicates the EHR is underutilized for PC CDS, facilitating PROMs, and capturing ACPs.
Sonication Improves Pathogen Detection in Ventriculoperitoneal Shunt-Associated Infections
Authors: Prinz Vincent , Bayerl Simon , Renz Nora , Trampuz Andrej , Vajkoczy Peter , Finger Tobias 
Published: July 2018

Abstract

BACKGROUND
Antimicrobial treatment of ventriculoperitoneal (VP) shunt infections is challenging when the causative pathogen is unknown.

OBJECTIVE
To evaluate the value of sonication of explanted shunt-devices to improve the microbiological detection rate.

METHODS
All consecutive patients undergoing revision surgery due to suspected VP-shunt infection from January 2015 to February 2017 were evaluated. Intraoperative tissue samples, wound swabs, and cerebrospinal fluid (CSF) were collected for microbiological examination. In a subgroup of patients, the removed implants were additionally sent for sonication.

RESULTS
A total of 35 patients were included with a mean age of 57.5 ± 18 yr, 21 were female (60%). In 13 patient's tissue samples, CSF and wound swabs were analyzed. In 22 patients, the explanted device was additionally sent for sonication. All 22 sonication cultures showed a positive microbiological result (100%), whereas with conventional microbiological methods, the causative microorganism was identified in 8 of 13 (61%; P = .018). Analyzed by method, all 22 sonication cultures (100%) were positive and 21 of 35 conventional microbiological analysis results (60%) detected the causative agent (P < .001.) In 18 patients (51%), antimicrobial treatment was started preoperatively. In those patients, the pathogen was detected in all 12 sonication cultures (100%), whereas conventional methods grew a pathogen in 3 of 6 patients (P = .005).

CONCLUSION
Sonication significantly increases the microbiological yield in VP-shunt infections, especially in patients receiving antibiotics prior to diagnostics and in infections caused by low-virulent organisms. The implementation of sonication into the clinical routine can substantially increase the rate of pathogen detection allowing targeted treatment.
Biomarkers of Tobacco Exposure Decrease After Smokers Switch to an E-Cigarette or Nicotine Gum
Authors: Round Elaine K , Chen Peter , Taylor Anthony K , Schmidt Eckhardt 
Published: July 2018

AbstractIntroductionThe aerosol composition of electronic cigarettes (ECs) suggests that exposure to toxicants during use is greatly reduced compared to exposure from combustible cigarettes (CCs).MethodsThis randomized, parallel-group, clinical study enrolled smokers to switch to Vuse Solo (VS) Digital Vapor Cigarettes (Original or Menthol) or Nicorette 4 mg nicotine gum (NG) in a controlled setting. Subjects who smoked CCs ad libitum for 2 days during a baseline period were then randomized to ad libitum use of either VS or NG for 5 days. Biomarkers of 23 toxicants were measured in 24-hour urine samples and blood collected at baseline and following product switch.ResultsA total of 153 subjects completed the study. Total nicotine equivalents decreased in all groups, but higher levels were observed in the VS groups compared to the NG groups, with decreases of 38% and 60%–67%, respectively. All other biomarkers were significantly decreased in subjects switched to VS, and the magnitude of biomarker decreases was similar to subjects switched to NG. Decreases ranged from 30% to greater than 85% for constituents such as benzene and acrylonitrile.ConclusionsThese results indicate that exposure to toxicants when using VS is significantly reduced compared to CC smoking, and these reductions are similar to those observed with use of NG. Although statistically significantly decreased, nicotine exposure is maintained closer to CC smoking with VS use compared to NG use. This research suggests that use of VS exposes consumers to fewer and lower levels of smoke toxicants than CCs while still providing nicotine to the consumer.ImplicationsThis is the first study to report changes in nicotine delivery and biomarkers of tobacco exposure following a short-term product switch from CCs to either an EC or NG in a controlled environment. The study shows that nicotine exposure decreased in both groups but was maintained closer to CC smoking with the EC groups. Biomarkers of tobacco combustion decreased to similar levels in both EC and gum groups.
Menstrual fluid factors facilitate tissue repair: identification and functional action in endometrial and skin repair
Authors: Evans Jemma , Infusini Giuseppe , Mcgovern Jacqui , Cuttle Leila , Webb Andrew , Nebl Thomas , Milla Liz , Kimble Roy , Kempf Margit , Andrews Christine J. , Leavesley David , Salamonsen Lois A. 
Published: July 2018

ABSTRACTRepair after damage is essential for tissue homeostasis. Postmenstrual endometrial repair is a cyclical manifestation of rapid, scar‐free, tissue repair taking ∼3–5 d. Skin repair after wounding is slower (∼2 wk). In the case of chronic wounds, it takes months to years to restore integrity. Herein, the unique “rapid‐repair” endometrial environment is translated to the “slower repair” skin environment. Menstrual fluid (MF), the milieu of post‐menstrual endometrial repair, facilitates healing of endometrial and keratinocyte “wounds” in vitro, promoting cellular adhesion and migration, stimulates keratinocyte migration in an ex vivo human skin reconstruct model, and promotes re‐epithelialization in an in vivo porcine wound model. Proteomic analysis of MF identified a large number of proteins: migration inhibitory factor, neutrophil gelatinase–associated lipocalin, follistatin like‐1, chemokine ligand‐20, and secretory leukocyte protease inhibitor were selected for further investigation. Functionally, they promote repair of endometrial and keratinocyte wounds by promoting migration. Translation of these and other MF factors into a migration‐inducing treatment paradigm could provide novel treatments for tissue repair.—Evans, J., Infusini, G., McGovern, J., Cuttle, L., Webb, A., Nebl, T., Milla, L., Kimble, R., Kempf, M., Andrews, C. J., Leavesley, D., Salamonsen, L. A. Menstrual fluid factors facilitate tissue repair: identification and functional action in endometrial and skin repair. FASEB J. 33, 584–605 (2019). www.fasebj.org
Brief Report: Reduced Use of Illicit Substances, Even Without Abstinence, Is Associated With Improved Depressive Symptoms Among People Living With HIV
Authors: Delaney Joseph A. , Nance Robin M. , Whitney Bridget M. , Altice Frederick L. , Dong Xinyuan , Trejo Maria Esther Perez , Matsuzaki Mika , Taxman Faye S. , Chander Geetanjali , Kuo Irene , Fredericksen Rob , Strand Lauren N. , Eron Joseph J. , Geng Elvin , Kitahata Mari M. , Mathews William C. , Mayer Kenneth , Moore Richard D. , Saag Michael S. , Springer Sandra , Chandler Redonna , Kahana Shoshana , Crane Heidi M. 
Published: July 2018

Purpose:
Substance use is linked with poor outcomes among people living with HIV (PLWH) and is associated with mental health disorders. This analysis examines the impact of decreasing substance use, even without abstinence, on depressive symptoms among PLWH.

Methods:
Data are from PLWH enrolled in the Centers for AIDS Research Network of Integrated Clinical Sites cohort. Participants completed longitudinal assessments of substance use (modified ASSIST) and depressive symptoms (PHQ-9). Changes in substance use frequency were categorized as abstinence, reduced use, and nondecreasing use. Adjusted linear mixed models with time-updated change in substance use frequency and depressive symptom scores were used to examine associations between changes in the use of individual substances and depressive symptoms. Analyses were repeated using joint longitudinal survival models to examine associations with a high (PHQ-9 ≥10) score.

Results:
Among 9905 PLWH, 728 used cocaine/crack, 1016 used amphetamine-type substances (ATS), 290 used illicit opiates, and 3277 used marijuana at baseline. Changes in ATS use were associated with the greatest improvements in depressive symptoms: stopping ATS led to a mean decrease of PHQ-9 by 2.2 points (95% CI: 1.8 to 2.7) and a 61% lower odds of PHQ-9 score ≥10 (95% CI: 0.30 to 0.52), and decreasing ATS use led to a mean decrease of 1.7 points (95% CI: 1.2 to 2.3) and a 62% lower odds of PHQ-9 score ≥10 (95% CI: 0.25 to 0.56). Stopping and reducing marijuana and stopping cocaine/crack use were also associated with improvement in depressive symptoms.

Conclusions:
We demonstrated that both substance use reduction and abstinence are associated with improvements in depressive symptoms over time.
Bone Scintigraphy in Poststreptococcal Periostitis With Dysproteinemia
Authors: Bourgeois Sophie , Peetermans Willy , Noppe Nathalie , Goffin Karolien , Gheysens Olivier 
Published: July 2018

Abstract
A 39-year-old man presented with severe bone pain in the tibiae and forearms in the wake of a poststreptococcal sepsis complicated with pneumonia and erysipelas 4 months earlier. Bone scintigraphy was indicative of periostitis of the tibia, ulna, and radius bilaterally, and in combination with the increased inflammatory parameters and dysproteinemia, the diagnosis of Goldbloom syndrome was made. Goldbloom syndrome is an idiopathic periosteal hyperostosis associated with dysproteinemia and elevated inflammatory parameters. Although it has only been described in children/adolescents, this case illustrates that, in the specific clinical and biochemical setting, it should also be considered in adults.
Long-term Survival and Excellent Response to Repeated 177Lu–Prostate-Specific Membrane Antigen 617 Radioligand Therapy in a Patient With Advanced Metastatic Castration-Resistant Prostate Cancer
Authors: Roll Wolfgang , Bräuer Axel , Weckesser Matthias , Bögemann Martin , Rahbar Kambiz 
Published: July 2018

Abstract
Radiolabeled ligands targeting prostate-specific membrane antigen (PSMA) are currently being established. Prostate-specific membrane antigen radioligand therapy with 177Lu-PSMA-617 is a promising treatment in metastasized castration-resistant prostate cancer with high efficacy and safety and seems to prolong progression-free survival and overall survival. We present 68Ga-PSMA PET/CT images during and after 2 therapy courses, including each 4 cycles of 177Lu-PSMA-617, and prostate-specific antigen–level history of a 77-year-old heavily pretreated patient with metastasized castration-resistant prostate cancer.
FDG PET/CT of Cardiac Angiosarcoma With Pulmonary Metastases
Authors: Hod Nir , Shalev Aryeh , Levin Daniel , Anconina Reut , Ezroh Kazap Dina , Lantsberg Sophie 
Published: July 2018

Abstract
We present a case of an adolescent girl with a cardiac mass which was characterized as malignant on FDG PET/CT. In addition, FDG PET/CT revealed multiple hypermetabolic pulmonary lesions. The final diagnosis was primary cardiac angiosarcoma with pulmonary metastases, a rare malignancy especially in female patients at this age group. We emphasize the potential role of FDG PET/CT in patients with a cardiac neoplasm and present a literature review of FDG uptake in benign versus malignant cardiac tumors.
Waves in strongly nonlinear discrete systems
Authors: Nesterenko Vitali F. 
Published: July 2018

The paper presents the main steps in the development of the strongly nonlinear wave dynamics of discrete systems. The initial motivation was prompted by the challenges in the design of barriers to mitigate high-amplitude compression pulses caused by impact or explosion. But this area poses a fundamental mathematical and physical problem and should be considered as a natural step in developing strongly nonlinear wave dynamics. Strong nonlinearity results in a highly tunable behaviour and allows design of systems with properties ranging from a weakly nonlinear regime, similar to the classical case of the Fermi–Pasta–Ulam lattice, or to a non-classical case of sonic vacuum. Strongly nonlinear systems support periodic waves and one of the fascinating results was a discovery of a strongly nonlinear solitary wave in sonic vacuum (a limiting case of a periodic wave) with properties very different from the Korteweg de Vries solitary wave. Shock-like oscillating and monotonous stationary stress waves can also be supported if the system is dissipative. The paper discusses the main theoretical and experimental results, focusing on travelling waves and possible future developments in the area of strongly nonlinear metamaterials.This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Emergence of non-stationary regimes in one- and two-dimensional models with internal rotators
Authors: Vorotnikov K. , Kovaleva M. , Starosvetsky Y. 
Published: July 2018

In the present paper, we give a selective review of some very recent works concerning the non-stationary regimes emerging in various one- and two-dimensional models incorporating internal rotators. In one-dimensional models, these regimes are characterized by the intense energy transfer from the outer element, subjected to initial or harmonic excitation, to the internal rotator. As for the two-dimensional models (incorporating internal rotators), we will mainly focus on the two special dynamical states, namely a state of the near-complete energy transfer from longitudinal to lateral vibrations of the outer element as well as the state of a permanent, unidirectional energy locking with mild, spatial energy exchanges. In this review, we will discuss the recent theoretical and experimental advancements in the study of essentially nonlinear mechanisms governing the formation and bifurcations of the regimes of intense energy transfer. The present review is composed of two parts. The first part will be mainly devoted to the emergence of resonant energy transfer states in one-dimensional models incorporating internal rotators, while the second part will be mainly concerned with the manifestation of various energy transfer states in two-dimensional ones.
This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Forced oscillations of the string under conditions of ‘sonic vacuum’
Authors: Sminrov V. V. , Manevitch L. I. 
Published: July 2018

We present the results of analytical study of the significant regularities which are inherent to forced nonlinear oscillations of a string with uniformly distributed discrete masses, without its preliminary stretching. It was found recently that a corresponding autonomous system admits a series of nonlinear normal modes with a lot of possible intermodal resonances and that similar synchronized solutions can exist in the presence of a periodic external field also. The paper is devoted to theoretical explanation of numerical data relating to one of possible scenarios of intermodal interaction which was numerically revealed earlier. This is unidirectional energy flow from unstable nonlinear normal mode to nonlinear normal modes with higher wavenumbers under the conditions of sonic vacuum. The mechanism of such a scenario has not yet been clarified contrary to alternative mechanisms consisting in almost simultaneous energy flow to all nonlinear normal modes with breaking the above-mentioned conditions of sonic vacuum. We begin with a description of single-mode manifolds and then show that consideration of arbitrary double mode manifolds is sufficient for solution of the problem. Because of this, the two-modal equations of motion can be reduced to a linear equation which describes a perturbation of initially excited nonlinear normal mode of the forced system in the conditions of sonic vacuum. We have found analytical representation (in the parametric space) of the thresholds for all possible energy transfers corresponding to unidirectional energy flow from unstable nonlinear normal modes. The analytical results are in a good agreement with previous numerical calculations.This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Tunable, synchronized frequency down-conversion in magnetic lattices with defects
Authors: Serra-Garcia Marc , Molerón Miguel , Daraio Chiara 
Published: July 2018

We study frequency conversion in nonlinear mechanical lattices, focusing on a chain of magnets as a model system. We show that, by inserting mass defects at suitable locations, we can introduce localized vibrational modes that nonlinearly couple to extended lattice modes. The nonlinear interaction introduces an energy transfer from the high-frequency localized modes to a low-frequency extended mode. This system is capable of autonomously converting energy between highly tunable input and output frequencies, which need not be related by integer harmonic or subharmonic ratios. It is also capable of obtaining energy from multiple sources at different frequencies with a tunable output phase, due to the defect synchronization provided by the extended mode. Our lattice is a purely mechanical analogue of an opto-mechanical system, where the localized modes play the role of the electromagnetic field and the extended mode plays the role of the mechanical degree of freedom.
This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Travelling breathers and solitary waves in strongly nonlinear lattices
Authors: James Guillaume 
Published: July 2018

We study the existence of travelling breathers and solitary waves in the discrete
p
-Schrödinger (DpS) equation. This model consists of a one-dimensional discrete nonlinear Schrödinger (NLS) equation with strongly nonlinear inter-site coupling (a discrete
p
-Laplacian). The DpS equation describes the slow modulation in time of small amplitude oscillations in different types of nonlinear lattices, where linear oscillators are coupled to nearest-neighbours by strong nonlinearities. Such systems include granular chains made of discrete elements interacting through a Hertzian potential (
p
= 5/2 for contacting spheres), with additional local potentials or resonators inducing local oscillations. We formally derive three amplitude PDEs from the DpS equation when the exponent of nonlinearity is close to (and above) unity, i.e. for
p
lying slightly above 2. Each model admits localized solutions approximating travelling breather solutions of the DpS equation. One model is the logarithmic NLS equation which admits Gaussian solutions, and the other is fully nonlinear degenerate NLS equations with compacton solutions. We compare these analytical approximations to travelling breather solutions computed numerically by an iterative method, and check the convergence of the approximations when

. An extensive numerical exploration of travelling breather profiles for
p
= 5/2 suggests that these solutions are generally superposed on small amplitude non-vanishing oscillatory tails, except for particular parameter values where they become close to strictly localized solitary waves. In a vibro-impact limit where the parameter
p
becomes large, we compute an analytical approximation of solitary wave solutions of the DpS equation.

This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.