bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Real Standard Picture, and How Facts Make It Law: a Response to Mark Greenberg
Authors: Goldsworthy Jeffrey 
Published: October 2019

Abstract
Mark Greenberg has attempted to refute what he regards as a popular metaphysical thesis about how law is constituted. He calls it the “Standard Picture,” and it includes a “Communication Theory.” His own “Moral Impact Theory” of law is built partly on that attempted refutation. I defend positions that are very close to the Standard Picture and Communication Theory, albeit different in important respects. In particular, they are not primarily metaphysical theses, although they have metaphysical implications. They are actual fundamental doctrines of constitutional law in Anglo-American legal systems, which I call Legislative Supremacy and Legislative Intention. I argue that: (a) these doctrines, and their metaphysical implications, vindicate much of the Standard Picture, and explain why so many theorists have been attracted to it; (b) the doctrines are inconsistent with Greenberg’s Moral Impact Theory; and (c) the best theory of what makes them part of the law is legal positivism: in other words, facts about legal practices make them law. In arguing for (a) and (b), I examine in detail and respond to Greenberg’s account of the legal principles and practice of statutory interpretation. I distinguish between three kinds of interpretation: clarifying, supplementing and rectifying. In arguing for (c), I contend that legal positivism satisfies Greenberg’s (questionable) insistence that any metaphysical account of what constitutes law must satisfy a “rationality requirement.”
Single-sample landscape entropy reveals the imminent phase transition during disease progression
Authors: Liu Rui , Chen Pei , Chen Luonan 
Published: October 2019

Abstract

Motivation
The time evolution or dynamic change of many biological systems during disease progression is not always smooth but occasionally abrupt, that is, there is a tipping point during such a process at which the system state shifts from the normal state to a disease state. It is challenging to predict such disease state with the measured omics data, in particular when only a single sample is available.

Results
In this study, we developed a novel approach, i.e. single-sample landscape entropy (SLE) method, to identify the tipping point during disease progression with only one sample data. Specifically, by evaluating the disorder of a network projected from a single-sample data, SLE effectively characterizes the criticality of this single sample network in terms of network entropy, thereby capturing not only the signals of the impending transition but also its leading network, i.e. dynamic network biomarkers. Using this method, we can characterize sample-specific state during disease progression and thus achieve the disease prediction of each individual by only one sample. Our method was validated by successfully identifying the tipping points just before the serious disease symptoms from four real datasets of individuals or subjects, including influenza virus infection, lung cancer metastasis, prostate cancer and acute lung injury.

Availability and implementation
https://github.com/rabbitpei/SLE.

Supplementary information
Supplementary data are available at Bioinformatics online.
Deep-learning approach to identifying cancer subtypes using high-dimensional genomic data
Authors: Chen Runpu , Yang Le , Goodison Steve , Sun Yijun 
Published: October 2019

Abstract

Motivation
Cancer subtype classification has the potential to significantly improve disease prognosis and develop individualized patient management. Existing methods are limited by their ability to handle extremely high-dimensional data and by the influence of misleading, irrelevant factors, resulting in ambiguous and overlapping subtypes.

Results
To address the above issues, we proposed a novel approach to disentangling and eliminating irrelevant factors by leveraging the power of deep learning. Specifically, we designed a deep-learning framework, referred to as DeepType, that performs joint supervised classification, unsupervised clustering and dimensionality reduction to learn cancer-relevant data representation with cluster structure. We applied DeepType to the METABRIC breast cancer dataset and compared its performance to state-of-the-art methods. DeepType significantly outperformed the existing methods, identifying more robust subtypes while using fewer genes. The new approach provides a framework for the derivation of more accurate and robust molecular cancer subtypes by using increasingly complex, multi-source data.

Availability and implementation
An open-source software package for the proposed method is freely available at http://www.acsu.buffalo.edu/~yijunsun/lab/DeepType.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
Beyond the Epileptic Focus: Functional Epileptic Networks in Focal Epilepsy
Authors: Gil Francisco , Padilla Nelly , Soria-Pastor Sara , Setoain Xavier , Boget Teresa , Rumiá Jordi , Roldán Pedro , Reyes David , Bargalló Núria , Conde Estefanía , Pintor Luis , Vernet Oriol , Manzanares Isabel , Ådén Ulrika , Carreño Mar , Donaire Antonio 
Published: October 2019

Abstract
Focal epilepsy can be conceptualized as a network disorder, and the functional epileptic network can be described as a complex system of multiple brain areas that interact dynamically to generate epileptic activity. However, we still do not fully understand the functional architecture of epileptic networks. We studied a cohort of 21 patients with extratemporal focal epilepsy. We used independent component analysis of functional magnetic resonance imaging (fMRI) data. In order to identify the epilepsy-related components, we examined the general linear model-derived electroencephalography-fMRI (EEG–fMRI) time courses associated with interictal epileptic activity as intrinsic hemodynamic epileptic biomarkers. Independent component analysis revealed components related to the epileptic time courses in all 21 patients. Each epilepsy-related component described a network of spatially distributed brain areas that corresponded to the specific epileptic network in each patient. We also provided evidence for the interaction between the epileptic activity generated at the epileptic network and the physiological resting state networks. Our findings suggest that independent component analysis, guided by EEG–fMRI epileptic time courses, have the potential to define the functional architecture of the epileptic network in a noninvasive way. These data could be useful in planning invasive EEG electrode placement, guiding surgical resections, and more effective therapeutic interventions.
A Late Critical Period for Frequency Modulated Sweeps in the Mouse Auditory System
Authors: Bhumika Stitipragyan , Nakamura Mari , Valerio Patricia , Solyga Magdalena , Lindén Henrik , Barkat Tania R 
Published: October 2019

Abstract
Neuronal circuits are shaped by experience during time windows of increased plasticity in postnatal development. In the auditory system, the critical period for the simplest sounds—pure frequency tones—is well defined. Critical periods for more complex sounds remain to be elucidated. We used in vivo electrophysiological recordings in the mouse auditory cortex to demonstrate that passive exposure to frequency modulated sweeps (FMS) from postnatal day 31 to 38 leads to long-term changes in the temporal representation of sweep directions. Immunohistochemical analysis revealed a decreased percentage of layer 4 parvalbumin-positive (PV+) cells during this critical period, paralleled with a transient increase in responses to FMS, but not to pure tones. Preventing the PV+ cell decrease with continuous white noise exposure delayed the critical period onset, suggesting a reduction in inhibition as a mechanism for this plasticity. Our findings shed new light on the dependence of plastic windows on stimulus complexity that persistently sculpt the functional organization of the auditory cortex.
Development and Validation of Chromatographic Methods for Simultaneous Determination of Paracetamol, Orphenadrine Citrate and Caffeine in Presence of P-aminophenol; Quantification of P-aminophenol Nephrotoxic Impurity Using LC–MS/MS
Authors: Boltia Shereen A , Soudi Aya T , Elzanfaly Eman S , Zaazaa Hala E 
Published: October 2019

Abstract
Three chromatographic methods were developed, optimized and validated for Paracetamol (PAR), Orphenadrine citrate (Or.cit) and Caffeine (CAF) determination in their mixture and in presence of PAR toxic impurity; P-aminophenol (PAP) in tablets. The first method is based on a thin layer chromatography combined with densitometry. Separation was achieved using silica gel 60 F254 TLC plates and dichloromethane:methanol:acetone:glacial acetic acid (9:1:0.5:0.3, v/v/v) as a developing system at 230 nm. The second method is based on high-performance liquid chromatography with diode array detection. The proposed compounds are separated on a reversed phase C18 analytical column using phosphate buffer (pH 9; 0.05 M) and methanol (80:20, v/v) at 1.2 mL/min. Linear regressions are obtained in the range of 1–500 μg/mL, 25–1000 μg/mL and 1–400 μg/mL for PAR, Or.cit and CAF, respectively. Quantification of the toxic PAP is carried out using LC–MS-MS by electrospray ionization in the positive mode using triple quadrupole mass spectrometry. The limit of quantification for PAP is 1 ng/mL. All methods are validated according to the ICH guidelines and successfully applied to determine PAR, Or.cit, CAF and PAP in pure powder and in combined tablets dosage form without interference from excipients.
The Overton Window and a Less Dogmatic Approach to Antibiotics
Authors: Morgan Daniel J 
Published: October 2019

Abstract
This analysis summarizes a set of recent, innovative trials in infectious diseases that redefine previous, non–evidence based “rules” for antibiotics. Recent trials in infectious diseases have led to reconsidering the traditional treatment of infectious diseases by changing the duration or type of traditional antibiotics or evaluating new antibiotics for approval. These trials have used the noninferiority trial approach. The noninferiority trial design and recent infectious disease trials of relevance are discussed in this viewpoint. My objective was to analyze recent trials in infectious disease and consider needs for future trials.
Spinal Cord Stimulator Infection: Approach to Diagnosis, Management, and Prevention
Authors: Esquer Garrigos Zerelda , Farid Saira , Bendel Markus A , Sohail M Rizwan 
Published: October 2019

AbstractSpinal cord stimulation (SCS) is the most utilized invasive electrical neuromodulation treatment for the management of refractory chronic pain syndromes. Infection is one of the most dreaded complications related to SCS implantation and may prevent patients from receiving adequate pain treatment, adding to the initial cost and disability. Most SCS infections present as generator pocket infection. However, delay in diagnosis may lead to complications such as meningitis, epidural abscess, and/or vertebral osteomyelitis. Early recognition of SCS-related infections and associated complications is based on clinical suspicion, laboratory testing, and appropriate diagnostic imaging. While superficial surgical site infection following SCS implant may be treated with antibiotic therapy alone, deep infection involving implant warrants device removal to achieve cure. Duration of antimicrobial therapy depends on severity of clinical presentation and presence or absence of associated complications. Several preventive strategies can be incorporated in surgical practice to reduce the risk of SCS infection.
Resistance of IID Noise in Differentially Private Schemes for Trajectory Publishing
Authors: Wang Hao , Li Kaiju 
Published: October 2019

AbstractAlthough analyzing and mining user’s trajectory data can provide outstanding benefit, data owners may not be willing to upload their trajectory data because of privacy concerns. Recently, differential privacy technology has achieved a good trade-off between data utility and privacy preserving by publishing noisy outputs, and relevant schemes have been proposed for trajectory release. However, we experimentally find that a relatively accurate estimate of the true data value can still be obtained from the noisy outputs by means of a posterior estimation. But there are no practical mechanisms against current schemes to verify their effectiveness and resistance. To fill this gap, we propose a solution to evaluate the resistance performance of differential privacy on trajectory data release, including a notion of correlation-distinguishability filtering (CDF) and a privacy quantification measurement. Specifically, taking advantage of the principle of filtering that independent noise can be filtered out from correlated sequence, CDF is proposed to sanitize the noise added into the trajectory. To conduct this notion in practice, we attempt to apply a Kalman/particle filter to filter out the corresponding Gaussian/Laplace noise added by differential privacy schemes. Furthermore, to quantify the distortion of privacy strength before and after filtering, an entropy-based privacy quantification metric is proposed, which is used to measure the lost uncertainty of the true locations for an adversary. Experimental results show that the resistance performance of current approaches has a degradation to varying degrees under the filtering attack model in our solution. Moreover, the privacy quantification metric can be regarded as a unified criterion to measure the privacy strength introduced by the noise that does not conform to the form required by differential privacy.
Computing Grounded Extensions Of Abstract Argumentation Frameworks
Authors: Nofal Samer , Atkinson Katie , Dunne Paul E 
Published: October 2019

Abstract
An abstract argumentation framework is a directed graph $(V,E)$ such that the vertices of $V$ denote abstract arguments and $E \subseteq V \times V$ represents the attack relation between them. We present a new ad hoc algorithm for computing the grounded extension of an abstract argumentation framework. We show that the new algorithm runs in $\mathcal{O}(|V|+|E|)$ time. In contrast, the existing state-of-the-art algorithm runs in $\mathcal{O}(|V|+|S||E|)$ time where $S$ is the grounded extension of the input graph.
Sender and receiver experience alters the response of fish to disturbance cues
Authors: Goldman Jack A , Feyten Laurence E A , Ramnarine Indar W , Brown Grant E 
Published: October 2019

Abstract
Predation is a pervasive selection pressure, shaping morphological, physiological, and behavioral phenotypes of prey species. Recent studies have begun to examine how the effects of individual experience with predation risk shapes the use of publicly available risk assessment cues. Here, we investigated the effects of prior predation risk experience on disturbance cue production and use by Trinidadian guppies Poecilia reticulata under laboratory conditions. In our first experiment, we demonstrate that the response of guppies from a high predation population (Lopinot River) was dependent upon the source of disturbance cue senders (high vs. low predation populations). However, guppies collected from a low predation site (Upper Aripo River) exhibited similar responses to disturbance cues, regardless of the sender population. In our second experiment, we used laboratory strain guppies exposed to high versus low background risk conditions. Our results show an analogous response patterns as shown for our first experiment. Guppies exposed to high background risk conditions exhibited stronger responses to the disturbance cues collected from senders exposed to high (vs. low) risk conditions and guppies exposed to low risk conditions were not influenced by sender experience. Combined, our results suggest that experience with background predation risk significantly impacts both the production of and response to disturbance cues in guppies.
The haemodynamic basis of lung congestion during exercise in heart failure with preserved ejection fraction
Authors: Reddy Yogesh N V , Obokata Masaru , Wiley Brandon , Koepp Katlyn E , Jorgenson Caitlin C , Egbe Alexander , Melenovsky Vojtech , Carter Rickey E , Borlaug Barry A 
Published: October 2019

Abstract

Aims
Increases in extravascular lung water (EVLW) during exercise contribute to symptoms, morbidity, and mortality in patients with heart failure and preserved ejection fraction (HFpEF), but the mechanisms leading to pulmonary congestion during exercise are not well-understood.

Methods and results
Compensated, ambulatory patients with HFpEF (n = 61) underwent invasive haemodynamic exercise testing using high-fidelity micromanometers with simultaneous lung ultrasound, echocardiography, and expired gas analysis at rest and during submaximal exercise. The presence or absence of EVLW was determined by lung ultrasound to evaluate for sonographic B-line artefacts. An increase in EVLW during exercise was observed in 33 patients (HFpEFLW+, 54%), while 28 (46%) did not develop EVLW (HFpEFLW−). Resting left ventricular function was similar in the groups, but right ventricular (RV) dysfunction was two-fold more common in HFpEFLW+ (64 vs. 31%), with lower RV systolic velocity and RV fractional area change. As compared to HFpEFLW−, the HFpEFLW+ group displayed higher pulmonary capillary wedge pressure (PCWP), higher pulmonary artery (PA) pressures, worse RV-PA coupling, and higher right atrial (RA) pressures during exercise, with increased haemoconcentration indicating greater loss of water from the vascular space. The development of lung congestion during exercise was significantly associated with elevations in PCWP and RA pressure as well as impairments in RV-PA coupling (area under the curve values 0.76–0.84).

Conclusion
Over half of stable outpatients with HFpEF develop increases in interstitial lung water, even during submaximal exercise. The acute development of lung congestion is correlated with increases in pulmonary capillary hydrostatic pressure that favours fluid filtration, and systemic venous hypertension due to altered RV-PA coupling, which may interfere with fluid clearance.

Clinical trial registration
NCT02885636.
Emergence of Lyme disease as a social problem: analysis of discourse using the media content
Authors: Pascal Clélia , Arquembourg Jocelyne , Vorilhon Philippe , Lesens Olivier 
Published: October 2019

Abstract

Background
Chronic Lyme disease (LD) is a matter of debate worldwide and has emerged as a social problem. We aim to analyze the media content and describe the transformation process of a collective pain into a social problem in France.

Methods
Using social science methodology, a corpus of articles from 20 newspapers and videos from seven major TV stations from 1987 to 2017 were analyzed for discourse content. The speaking times and the frequency of interventions between doctors supporting the official guidelines and those against them were compared using the Mann–Whitney test and the Chi-square test, respectively.

Results
In France, the media discourse is carried through testimonials from patient organizations and a professor of infectiology who acted as a whistleblower (WB). We showed that the emergence of the LD alert in the media corresponds to the process described by social sciences as ‘naming, blaming, claiming’. Since his first article in 2014, the WB has featured in 24% (22/89) of newspaper articles compared with 20% (18/89) for doctors defending the official guidelines (P = 0.52). Since his first appearance on a TV newscast in 2014, the WB has appeared in 45% (22/49) of news reports on LD with 24% of the speaking time compared with 22% (11/49) for doctors defending the official guidelines (P = 0.018).

Conclusions
Media coverage of LD has been unbalanced since 2014 and promotes associations as well as the WB, who seems to be better identified than any of the different doctors defending the official guidelines.
Social determinants of sleep disturbance in safety-net primary care: unmet needs, classist discrimination, and anxiety
Authors: Tan Joseph S , Cariello Annahir N , Pugh Mickeal , Henry Richard S , Perrin Paul B , Dautovich Natalie D , Rybarczyk Bruce 
Published: October 2019

Abstract

Background
The 3P model proposes that predisposing, precipitating, and perpetuating factors all play a role in sleep disturbance.

Objective
The purpose of the current study is to investigate social determinants of sleep disturbance by applying the 3P model to a safety-net primary care setting, specifically by evaluating the role of classism and unmet needs as precipitating factors for sleep disturbance, and anxiety as a perpetuating factor for sleep disturbance.

Methods
Participants (N = 210) were a convenience sample of racially/ethnically diverse adults over the age of 18 (age M = 44.7 years) recruited from a safety-net primary care clinic in an urban area. The study employed a cross-sectional design. Participants completed a survey assessing sleep disturbances, anxiety, unmet needs, classism, social support, and a researcher-generated demographic form.

Results and Conclusions
The unmet need for affordable long-term housing and greater experiences of classism were associated with more sleep disturbance, suggesting that both acted as precipitating factors. In a structural equation model with adequate fit indices, anxiety mediated the relationships with sleep disturbance for both the unmet need for affordable long-term housing and classism, suggesting that it serves as a perpetuating factor. Medical providers are recommended to explore these potential needs in safety-net primary care when patients present with sleep disturbance or anxiety. Assisting with connections to long-term housing and helping patients counteract and cope with classist discrimination may be effective in improving sleep in safety-net primary care.
Health literacy among Malawian HIV-positive youth: a qualitative needs assessment and conceptualization
Authors: Uwamahoro Nadege Sandrine , Ngwira Bagrey , Vinther-Jensen Kirsten , Rowlands Gill 
Published: October 2019

Abstract
Despite growing evidence of the significance of health literacy in managing and coping with acquired immune deficiency syndrome (HIV), it is not yet an integrated part of HIV/AIDS-related health promotion research and practice in Africa. This article contributes to addressing the gap in research on health literacy and HIV in Sub-Saharan Africa. We aimed to assess health literacy-related needs of young people living with HIV (YPLHIV) and adapt existing health literacy frameworks to the context of HIV/AIDS in Malawi. We used focus group discussions to collect data from a sample of the membership of the national association of YPLHIV. Twenty-four HIV-positive youth (18–29 years) participated in focus group discussions. Participants came from three regions of Malawi. Additionally, we conducted three in-depth interviews with key informants. We used a thematic framework approach to analyse data in MAXQDA. We contextualized definitions of four dimensions of health literacy: functional, interactive, critical and distributed health literacy, which we used as an a priori analytical framework. To further contextualize the framework, we revised it iteratively throughout the analysis process. We identified the need for comprehensive information about HIV and sexual reproductive health, skills to interact with healthcare providers and navigate the health system, and skills to appraise information from different sources, among others. The identified needs were translated into nine action recommendations for the national association of YPLHIV, and with relevance within the wider HIV sector in Malawi and beyond. We found that the dimensions in our analytical framework operate on the individual, system and public policy levels.