bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning improves antimicrobial peptide recognition
Authors: Veltri Daniel , Kamath Uday , Shehu Amarda 
Published: March 2018

Abstract

Motivation
Bacterial resistance to antibiotics is a growing concern. Antimicrobial peptides (AMPs), natural components of innate immunity, are popular targets for developing new drugs. Machine learning methods are now commonly adopted by wet-laboratory researchers to screen for promising candidates.

Results
In this work, we utilize deep learning to recognize antimicrobial activity. We propose a neural network model with convolutional and recurrent layers that leverage primary sequence composition. Results show that the proposed model outperforms state-of-the-art classification models on a comprehensive dataset. By utilizing the embedding weights, we also present a reduced-alphabet representation and show that reasonable AMP recognition can be maintained using nine amino acid types.

Availability and implementation
Models and datasets are made freely available through the Antimicrobial Peptide Scanner vr.2 web server at www.ampscanner.com.

Supplementary information
Supplementary data are available at Bioinformatics online.
A joint spatial factor analysis model to accommodate data from misaligned areal units with application to Louisiana social vulnerability
Authors: Nethery Rachel C , Sandler Dale P , Zhao Shanshan , Engel Lawrence S , Kwok Richard K 
Published: March 2018

SummaryWith the threat of climate change looming, the public health community has an interest in identifying communities at the highest risk of devastation based not only on geographic features but also on social characteristics. Indices of community social vulnerability can be created by applying a spatial factor analysis to a set of relevant social variables measured for each community; however, current spatial factor analysis methodology is ill-equipped to handle spatially misaligned data. We introduce a joint spatial factor analysis model that can accommodate spatial data from two distinct partitions of a geographic space and identify a common set of latent factors underlying them. By defining the latent factors over the intersection of the two partitions, the model minimizes loss of information. Using simulated data constructed to mimic the spatial structure of our real data, we confirm the reliability of the model and demonstrate its superiority over competing ad hoc methods for dealing with misaligned data in spatial factor analysis. Finally, we construct an index of community social vulnerability for each census tract in Louisiana, a state prone to environmental disasters, which could be exacerbated by climate change, by applying the joint spatial factor analysis model to a set of misaligned social indicator data from the state. To demonstrate the utility of this index, we integrate it with Louisiana flood insurance claims data to identify communities that may be at particularly high risk during natural disasters, based on both social and geographic features.
Seeing through†
Authors: Brander Keith M 
Published: March 2018

Abstract
The title of this paper is intended in the sense of both “seeing through things”, which requires critical, reflexive thinking and also in the sense of “seeing things through”, which requires tenacity and patience. I address some of the concerns that I have about how we think through, structure, and write about science and I introduce three major research areas that I have been involved in: (i) studies of population dynamics of fish in the Irish Sea that lead to work on plankton dynamics and marine ecosystems, but with the problems of marine policy and management in mind, (ii) the ICES/GLOBEC Cod and Climate Change programme, and (iii) global marine food production and the work of the IPCC.
Congenital Dermal Sinus and Limited Dorsal Myeloschisis: “Spectrum Disorders” of Incomplete Dysjuction Between Cutaneous and Neural Ectoderms
Authors: Lee Ji Yeoun , Park Sung-Hye , Chong Sangjoon , Phi Ji Hoon , Kim Seung-Ki , Cho Byung-Kyu , Wang Kyu-Chang 
Published: March 2018

Abstract

BACKGROUND
The existence of tethering tracts in spinal dysraphism, other than congenital dermal sinus (CDS), has been recognized and has been summated into an integrated concept of limited dorsal myeloschisis (LDM).

OBJECTIVE
To elucidate the underlying embryology of LDM in relation to CDS by focusing on the pathological features of special cases of tethering tracts.

METHODS
Out of 389 spinal dysraphism patients who were operated on from 2010 to 2016, 5 patients who had tethering tracts composed of both CDS and LDM (or “probable LDM” if only fibrous tissue was found) were identified. Their clinical presentation, radiological images, operative findings, and pathology were thoroughly reviewed.

RESULTS
Three nonsaccular-type patients harbored stalks in which the squamous epithelial lined sinus (CDS) was found in the distal portion, and fibroneural (LDM) or fibrous (probable LDM) tissue in the proximal part. Two patients had saccular lesions, and a stalk was found inside the sac, connecting a small pit on the skin to the spinal cord. The tracts were pathologically identical to a CDS.

CONCLUSION
This study reports the coexistence of CDS and LDM (or probable LDM) components. These unique cases support the hypothesis that the CDS and LDM are among a spectrum of an anomaly that is caused by failure of complete dysjunction between cutaneous and neural ectoderms. Neurosurgeons should be aware of the possibility of coexisting “CDS” components in cases suggestive of LDM. In such cases, not only untethering but also meticulous removal of the squamous epithelium is critical.
Phage Therapy for a Multidrug-Resistant Acinetobacter baumannii Craniectomy Site Infection
Authors: LaVergne Stephanie , Hamilton Theron , Biswas Biswajit , Kumaraswamy M , Schooley R T , Wooten Darcy 
Published: March 2018

Abstract
In the era of antibiotic resistance, alternative treatment options for multidrug-resistant bacterial infections are being explored. We present a case of multidrug-resistant Acinetobacter baumannii infection treated with bacteriophages. Clinical trials are needed to further investigate bacteriophage therapy as an option to treat multidrug-resistant bacterial infections.
Semi-Automated Visualization and ANalysis of Trends: A “SAVANT” for Facilitating Antimicrobial Stewardship Using Antistaphylococcal Resistance and Consumption as a Prototype
Authors: Clifford Robert J , Chukwuma Uzo , Sparks Michael E , Richesson Douglas , Neumann Charlotte V , Waterman Paige E , Moran-Gilad Jacob , Julius Michael D , Hinkle Mary K , Lesho Emil P 
Published: March 2018

Abstract

Background
Governments and health care regulators now require hospitals and nursing homes to establish programs to monitor and report antimicrobial consumption and resistance. However, additional resources were not provided. We sought to develop an approach for monitoring antimicrobial resistance and consumption that health care systems can implement with minimal added costs or modifications to existing diagnostic and informatics infrastructure.

Methods
Using (1) the electronic laboratory information system of a nationwide managed care network, (2) the 3 most widely used commercial microbiology diagnostic platforms, and (3) Staphylococcus aureus, one of the most common causes of infections worldwide, as a prototype, we validated the approach dubbed “SAVANT” for Semi-Automated Visualization and ANalysis of Trends. SAVANT leverages 3 analytical methods (time series analysis, the autoregressive integrated moving average, and generalized linear regression) on either commercial or open source software to report trends in antistaphylococcal use and resistance.

Results
All laboratory results from January 2010 through December 2015 from an annual average of 9.2 million health care beneficiaries were queried. Inpatient and outpatient prescription rates were calculated for 8 key antistaphylococcal compounds. Trends and relationships of antistaphylococcal consumption and resistance among 81 840 unique S. aureus isolates from &gt;6.5 million cultures were revealed.

Conclusions
Using existing or freely available resources, SAVANT was successfully implemented across a complex and geographically dispersed 280-hospital network, bridging a critical gap between medical informatics, large-scale data analytics, and mandatory reporting of health care quality metrics.
Ancient Ways
Authors: Weinel Jonathan 
Published: March 2018

Abstract
This chapter discusses shamanism, explaining the ethos and mythology of several indigenous societies, and how these belief systems relate to the design of art and music. First, a general overview of shamanism is provided, which outlines the typical role and function of a shaman. An explanation of the shamanic visionary experience, a type of altered state of consciousness, is then provided. Following this, the chapter explores a variety of visual art from indigenous shamanic cultures, including examples from San, Native American, Huichol, Tukano, and Shipibo traditions. The sound and music of shamanic and trance cultures is also discussed, with reference to Vodou, Tukano, Mazatec, Kiowa, and Mayan examples, and relevant field recordings. Through the course of this discussion, the chapter establishes a view of how shamanic art and music invoke a sense of the spirit world, which informs the subsequent discourse of Inner Sound.
Stock Epithets and Cross-Cultural Cognomens
Authors: Reeves John C. , Reed Annette Yoshiko 
Published: March 2018

AbstractThis chapter assembles sources which utilize several popular epithets that accompany the figure of Enoch and serve to identify him even in those literary contexts which do not explicitly use the name “Enoch.” These include distinctive phraseology like “seventh from Adam,” “righteous,” “scribe of righteousness,” and even certain messianic correlations. Included also in this chapter are a series of literary portraits found primarily in Arabic language texts which provide a description of the physical appearance of this antediluvian forefather. Attention is also drawn to certain popular aliases borne by Enoch in later literary settings, such as the angel Metatron, the Graeco-Egyptian teacher Hermes Trismegistus, and the qur’ānic prophet Idrīs.
The future of eDNA metabarcoding
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
Environmental DNA-based research is undergoing rapid developments, but its democratization in basic and applied research remains hampered by the biases introduced by molecular approaches, the difficulties in estimating absolute organisms’ abundances, and a lack of general consensus in molecular protocols. Chapter 19 “The future of eDNA metabarcoding” provides an overview of these current challenges and discusses how shotgun sequencing, capture-based methods, inclusion of internal standards, and development of new data repositories could alleviate these limits and facilitate cross-experiments comparisons. This chapter finally turns to open questions on the potentiality of new sequencing methods and proposes directions to improve biodiversity estimates and ecological inferences and predictions from eDNA data, and ultimately stimulate further developments and integration of eDNA metabarcoding into academic and operational ecological research and monitoring.
Republican Satire in the Dock
Authors: Goh Ian 
Published: March 2018

AbstractThis chapter treats the account of the courtroom activities—Q. Mucius Scaevola Augur defending himself when brought to trial for extortion in 119 bc by T. Albucius—in book 2 of Gaius Lucilius’ satires as an example of forensic oratory in post-Gracchan Republican Rome. The fragments of Lucilius’ verse record of the trial are considered in their historical and literary context, with a view to their influence on later satirical tradition. The fragments reveal intimations of force standing in for physical injury, problems resulting from the impact of philosophy on speaking styles, and ironies of mixed identity put to service in courtroom repartee. Lucilius is something of a stenographer, whose take on the trial is slanted towards its relevance for equestrians and its sensational elements redolent of Pacuvian tragedy; finally, the identification of poet and defendant encapsulates the trial’s interest and uniqueness.
Introduction
Authors: Eland John H.
                            D. , Feifel Raimund 
Published: March 2018

Abstract
After very brief historical notes, the basis of the TOF-PEPECO technique is explained and other techniques for spectra of doubly charged positive ions are described and compared with this modern method. The meaning of ionisation energies in the context of molecular double ionisation is discussed, with their relationship to electron orbital configurations. With the advent of photoelectron spectroscopy in the 1960s, new techniques allowed complete spectra of valence electron ionisations for each molecule to be revealed in a single measurement. The effects on the spectra of the different major pathways from starting molecules to final doubly ionised states are explained. Details of the experiments are given, including pulsed lamps, synchrotron radiation as light sources, and the magnetic bottle time-of-flight electron spectrometer.
Atomic xenon, Xe
Authors: Eland John H.
                            D. , Feifel Raimund 
Published: March 2018

Abstract
This chapter shows, using atomic xenon as a prototype, how coincidence maps and double photionisation spectra are created from the raw electron timing data, and how direct and indirect photoionisation pathways can be distinguished in the maps. A minor feature in the maps is recognised as coming from electron-impact single ionisation, which can be studied by the same technique. The chapter also explains how a simple formula can be used, with constants calibrated by measuring electrons of known energy, to convert the times of flight into kinetic energies. This introductory chapter concludes with a summary of some basic features of double photoionisation and of the spectra presented in this book, exemplified by Xe, including times of flight, energy resolution, ionisation, and Auger decay.
Diatomic molecules
Authors: Eland John H.
                            D. , Feifel Raimund 
Published: March 2018

Abstract
Double ionisation of most of the experimentally accessible diatomic molecules has been studied previously by several techniques, including Auger spectroscopy, double electron transfer, kinetic energy release, and high-level theory. New double photoionisation spectra of HBr, HI, N2, CO, NO, O2, Br2, ICl, and I2 are presented here with analysis to identify the electronic states of the doubly charged ions. A simple empirical model is introduced to estimate double ionisation energies on the basis of orbital energies. For CO, NO, and O2, an indirect double ionisation mechanism is found, involving dissociation of a singly charged molecular ion followed by atomic autoionisation of one fragment. Energies of the dication states are listed with distinction between adiabatic and vertical values.
Core–core and core–valence double ionisation
Authors: Eland John H.
                            D. , Feifel Raimund 
Published: March 2018

Abstract
Basic concepts of inner shell double ionisation phenomena are discussed and examples are presented. An empirical model to calculate single-site K-shell double ionisation energies is proposed and the enhanced chemical shifts in double L-shell ionisation are illustrated. Core–valence double ionisation spectra are shown to closely resemble photoelectron spectra from single ionisation in many cases. Core–valence double ionisation spectra of NH3, CO, CO2, OCS, CS2, CF4, Si(CH3)4, benzene, and C60 are presented with analysis. In the context of core ionisation it is customary to use the very economical ‘KLM’ notation, which is universally used in Auger spectroscopy, as well as the chemists’ familiar 1s, 2s, 2p, and so on. This chapter uses the KLM notation sparingly where its brevity is an advantage, so a short table list of equivalents is also included here.
Life and Works: A Sketch
Authors: Darrigol Olivier 
Published: March 2018

Abstract
This is a brief scientific biography of Boltzmann, including the vicissitudes of his uncommon life and the principal developments of his works about the kinetic-molecular theory. Boltzmann was a man of broad culture with many interests in literature, poetry, music, mathematics, philosophy, technology, pedagogy, and more; he was a man of action, an efficient administrator, a caring husband and father, a thoughtful colleague, an inborn teacher, and a joyous, humorous companion in informal circumstances. Of these many facets of Boltzmann’s personality, this chapter will examine reflections in the theory that made him most famous.
Lectures on Gas Theory (1896, 1898)
Authors: Darrigol Olivier 
Published: March 2018

Abstract
This chapter is devoted mostly to the two volumes of Boltzmann’s Lectures on gas theory, published in 1896 and 1898, with special attention to the novel elements in Boltzmann’s representation of his own contributions and to his silencing of earlier aspects of his theory. Although Boltzmann’s primary intention probably was to improve the diffusion of his own results and to clarify their foundation, he also wanted to give a full, partly historical account of the developments of the theory, including topics to which he had little contributed, such as van der Waals’ theory, and even approaches he had proved to be unsatisfactory, such as Maxwell’s first method for the computation of transport phenomena.
Parton Distribution Functions
Authors: Campbell John , Huston Joey , Krauss Frank 
Published: March 2018

Abstract
Parton Distribution Functions (PDFs) are a necessary ingredient in the calculation of cross sections at collider experiments with hadron beams. This chapter explores the techniques of determining the PDFs and their uncertainties, based on global analyses of data sets arising from a variety of hard-scattering processes. PDFs are determined at leading order, next-to-leading order, and next-to-next-to-leading order, with the corresponding orders of hard coefficients and evolution. Differences in the PDFs of different orders, and in their uncertainties, are described. Combinations of PDFs from different global fitting groups are discussed, and several useful tools for comparisons of PDFs are described.
Evaluations of Police Reforms: Utility or Futility?
Authors: Holmberg Lars 
Published: March 2018

AbstractIn recent years, four Nordic countries have implemented large-scale police reforms. Reforms have been evaluated and the present article discusses the merits of such processes. Three topics are discussed: first, it is argued that such evaluations are by nature of limited methodological rigour. The common model of nationwide implementation at one point in time limits possibilities for more sophisticated models of evaluation. Second, due to the nature of such evaluations, they are of limited value as a tool for organizational reorganization. In fact, organizational response to evaluation may take the form of denial rather than change. Third, it might be assumed that countries planning major police reforms would study such evaluations in detail and revise their plans accordingly, but available evidence from Norway and Sweden suggests otherwise. The article concludes with a discussion whether it would be possible to devise evaluations in ways that would increase their worth and impact.
‘Treatment Not Trident’: Medical Activism, Health Inequality and Anti-Militarism in 1980s Britain
Authors: Laucht Christoph 
Published: March 2018

Summary
In 1985, Britain’s chief group of medical anti-nuclear weapons activists, the Medical Campaign Against Nuclear Weapons (MCANW), launched its ‘Treatment, Not Trident’ (TNT) campaign. TNT called on the Thatcher Government to cancel the acquisition of the Trident nuclear weapon system and divert those funds to the National Health Service and foreign aid instead. Using TNT, this article makes some more general observations about key aspects of the history, nature and ideologies of medical activism in relation to anti-militarism and health inequality. Alongside a conceptualisation of ‘medical activism’, it offers an examination of chief ways in which the strategic mobilisation of health and welfare priorities, and a growing interest in developing nations enabled MCANW to reach a larger audience. Moreover, higher levels of professionalisation, politicisation and inclusivity contributed to TNT’s success, making it a crucial moment in the development of both MCANW and medical activism in general.
Maternal Use of Antiepileptic Agents During Pregnancy and Major Congenital Malformations in Children
Authors: Bromley Rebecca L. , Weston Jennifer , Marson Anthony G. 
Published: March 2018

(Abstracted from JAMA 2017;318(17):1700–1701)
The majority of pregnant women with epilepsy require consistent antiepileptic therapy during the course of pregnancy. Because of the necessity of these treatment regimens, information regarding epilepsy pharmaceuticals and their possible associations with congenital defects is required to help inform clinical decisions in this vulnerable patient population.
Effects of Cytochrome P450 (CYP) 2C19 Genotypes on Steady-State Plasma Concentrations of Escitalopram and its Desmethyl Metabolite in Japanese Patients With Depression
Authors: Tsuchimine Shoko , Ochi Shinichiro , Tajiri Misuzu , Suzuki Yutaro , Sugawara Norio , Inoue Yoshimasa , Yasui-Furukori Norio 
Published: March 2018

Background:
Plasma concentrations of the S-enantiomer of citalopram were different between extensive and poor CYP2C19 metabolizers in healthy subjects and depressed patients. However, most studies applied dose-corrected concentrations. Thus, we studied the effects of polymorphisms of the CYP2C19 gene on raw plasma drug concentrations in Japanese patients with depression.

Methods:
Subjects in this study consisted of 412 depressed patients receiving 5, 10, 15, or 20 mg of escitalopram once a day. Plasma concentrations of escitalopram and desmethylescitalopram were quantified using HPLC. CYP2C19 genotypes were identified using polymerase chain reaction methods.

Results:
There were no differences in the steady-state plasma concentrations of escitalopram or desmethylescitalopram in each dose group (5, 10, 15, or 20 mg of escitalopram) among CYP2C19 genotype groups. However, 1-way analysis of variance showed significant effects of CYP2C19 genotypes on the dose-adjusted plasma concentration of escitalopram but not in the dose-adjusted plasma concentration of desmethylescitalopram. Analysis of covariance including age, sex, and body weight showed significant effects of CYP2C19 genotypes on the dose-adjusted plasma concentration of escitalopram and the ratio of desmethylescitalopram to escitalopram.

Conclusions:
These findings suggest that the CYP2C19 variants are associated with steady-state plasma concentrations of escitalopram to some extent but are not associated with desmethylescitalopram.