bluuebunny/crossref_metadata_2025 huggingface dataset:
A multiple perspective method for urban subway network robustness analysis
Authors: Wang Shuliang , Nie Sen , Zhao Longfeng , Stanley H. Eugene
Published: July 2018

Most network research studying the robustness of critical infrastructure networks focuses on a particular aspect and does not take the entire system into consideration. We develop a general methodological framework for studying network robustness from multiple perspectives, i.e., Robustness assessment based on percolation theory, vulnerability analysis, and controllability analysis. Meanwhile, We use this approach to examine the Shanghai subway network in China. Specifically, (1) the topological properties of the subway network are quantitatively analyzed using network theory; (2) The phase transition process of the subway network under both random and deliberate attacks are acquired (3) Critical dense areas that are most likely to be the target of terrorist attacks are identified, vulnerability values of these critical areas are obtained; (4) The minimum number of driver nodes for controlling the whole network is calculated. Results show that the subway network exhibits characteristics similar to a scale-free network with low robustness to deliberate attacks. Meanwhile, we identify the critical area within which disruptions produce large performance losses. Our proposed method can be applied to other infrastructure networks and can help decision makers develop optimal protection strategies.
Soft x-ray optical constants of sputtered chromium thin films with improved accuracy in the L and M absorption edge regions
Authors: Delmotte Franck , Meyer-Ilse Julia , Salmassi Farhad , Soufli Regina , Burcklen Catherine , Rebellato Jennifer , Jérome Arnaud , Vickridge Ian , Briand Emrick , Gullikson Eric
Published: July 2018

In this study, we determine with improved accuracy the complex index of refraction n = 1 − δ + iβ of sputtered chromium thin films for photon energies ranging from 25 eV to 813 eV. These data include the first absolute measurements of the absorption fine structure near the Cr-L edge. First, we verified by combining Rutherford Backscattering Spectrometry and grazing-incidence x-ray reflectometry that the sputtered thin films were pure Cr with a density consistent with tabulated values. Then, we demonstrated that the Cr surface oxide layer remains stable when the samples are exposed to air for up to 4 years. The Cr absorption coefficient β was determined from the transmittance of freestanding Cr thin films with various thicknesses, measured at the ALS synchrotron radiation source. A model is proposed to correct the transmittance data from the spectral contamination of the source. Finally, we used the new β values, combined with theoretical and tabulated data from the literature, in order to calculate the δ values by the Kramers-Kronig relation. The improvement in the accuracy of β values is demonstrated by the f-sum rule. An additional validation of the new Cr optical constants (δ, β) is performed by comparing the simulated and experimental reflectance of a Cr/B4C multilayer mirror near the Cr-L2,3 edge.
Jeans anisotropic instability
Authors: Tsintsadze N. L. , Rozina Ch. , Ruby R. , Tsintsadze L. N.
Published: July 2018

The effect of quantized anisotropic magnetic pressure, arising due to a strong magnetic field, is studied on the growth rate of Jeans instability of quantum electron–ion and classical dusty plasma. Two dispersion relations are formulated for the propagation of the gravitational waves that are perpendicular and parallel to the magnetic field, respectively. It is shown that for perpendicular propagation, the quantized magnetic pressure is stabilizing the Jeans instability, whereas for the parallel propagation the plasma become more unstable with the increase in the magnetic field or we can say that Jeans instabilities becomes anisotropic in this case. The corresponding Jeans wave number is calculated in the absence of tunneling effect which shows that the magnetic field anisotropy of the Galaxy is connected with Jeans effect. Further, it is shown that the Madelung term leads to the inhomogeneity of the plasma medium. Numerical results are presented to show the effect of the anisotropic magnetic pressure on the Jeans instability.
Quasiparticle energy spectra of isolated atoms from coupled-cluster singles and doubles (CCSD): Comparison with exact CI calculations
Authors: Nishi Hirofumi , Kosugi Taichi , Furukawa Yoritaka , Matsushita Yu-ichiro
Published: July 2018

In this study, we have calculated single-electron energy spectra via the Green’s function based on the coupled-cluster singles and doubles (GFCCSD) method for isolated atoms from H to Ne. In order to check the accuracy of the GFCCSD method, we compared the results with the exact ones calculated from the full-configuration interaction. Consequently, we have found that the GFCCSD method reproduces not only the correct quasiparticle peaks but also satellite ones by comparing the exact spectra with the 6-31G basis set. It is also found that open-shell atoms such as C atom exhibit Mott gaps at the Fermi level, which the exact density-functional theory fails to describe. The GFCCSD successfully reproduces the Mott highest-occupied molecular orbital and lowest-unoccupied molecular orbital gaps even quantitatively. We also discussed the origin of satellite peaks as shake-up effects by checking the components of wave function of the satellite peaks. The GFCCSD is a novel cutting edge to investigate the electronic states in detail.
Spectrally narrow exciton luminescence from monolayer MoS2 and MoSe2 exfoliated onto epitaxially grown hexagonal BN
Authors: Courtade E. , Han B. , Nakhaie S. , Robert C. , Marie X. , Renucci P. , Taniguchi T. , Watanabe K. , Geelhaar L. , Lopes J. M. J. , Urbaszek B.
Published: July 2018

The strong light-matter interaction in transition metal dichalcogenide (TMD) monolayers (MLs) is governed by robust excitons. Important progress has been made to control the dielectric environment surrounding the MLs, especially through hexagonal boron nitride (hBN) encapsulation which drastically reduces the inhomogeneous contribution to the exciton linewidth. Most studies use exfoliated hBN from high quality flakes grown under high pressure. In this work, we show that hBN grown by molecular beam epitaxy (MBE) over a large surface area substrate has a similarly positive impact on the optical emission from TMD MLs. We deposit MoS2 and MoSe2 MLs on ultrathin hBN films (few MLs thick) grown on Ni/MgO(111) by MBE. Then, we cover them with exfoliated hBN to finally obtain an encapsulated sample: exfoliated hBN/TMD ML/MBE hBN. We observe improved optical quality of our samples compared to TMD MLs exfoliated directly on SiO2 substrates. Our results suggest that hBN grown by MBE could be used as a flat and charge-free substrate for fabricating TMD-based heterostructures on a larger scale.
Research Update: Electron beam-based metrology after CMOS
Authors: Liddle J. A. , Hoskins B. D. , Vladár A. E. , Villarrubia J. S.
Published: July 2018

The magnitudes of the challenges facing electron-based metrology for post-CMOS technology are reviewed. Directed self-assembly, nanophotonics/plasmonics, and resistive switches and selectors are examined as exemplars of important post-CMOS technologies. Materials, devices, and architectures emerging from these technologies pose new metrology requirements: defect detection, possibly subsurface, in soft materials, accurate measurement of size, shape, and roughness of structures for nanophotonic devices, contamination-free measurement of surface-sensitive structures, and identification of subtle structural, chemical, or electronic changes of state associated with switching in non-volatile memory elements. Electron-beam techniques are examined in the light of these emerging requirements. The strong electron-matter interaction provides measurable signals from small sample features, rendering electron-beam methods more suitable than most for nanometer-scale metrology, but as is to be expected, solutions to many of the measurement challenges are yet to be demonstrated. The seeds of possible solutions are identified when they are available.
Advanced process-synchronized computed tomography for the investigation of periodic processes
Authors: Bieberle André , Neumann Martin , Hampel Uwe
Published: July 2018

Computed tomography (CT) is known for giving cross-sectional images of a body. As tomographic scans require mechanical movement of components, data acquisition is commonly too slow to capture dynamic processes, which are faster than the acquisition time for a single image. Time-averaged angle-resolved CT imaging is a more recent method, which has demonstrated a capability to sharply image fast rotating machinery components by synchronizing data acquisition with rotation. However, in this modality, all information on static parts disappears. In this paper, a novel data acquisition approach is introduced that combines both CT imaging methods. Eventually, the developed method is exemplarily applied to the study of gas-liquid flow in an industrial centrifugal pump using high-resolution gamma-ray tomography imaging.
Influence of carrier diffusion on photo-Seebeck effect in zinc oxide
Authors: Tanabe Kenji
Published: July 2018

We measured the electrical conductivity and Seebeck coefficient under photo-illumination in single-crystalline ZnO and investigated the dependence of the correlation between the conductivity and Seebeck coefficient on the energy of applied ultraviolet light. The correlation was found to be completely independent of the light's energy, indicating that the photo-induced non-equilibrium state is unrelated to the light's energy, but is affected by the carrier diffusion. Furthermore, by assuming that the electron mobility is not changed by the photo-illumination, we estimated the ambipolar carrier diffusion length to be about 1 μm, which is roughly consistent with the minority carrier diffusion lengths in previous reports. Our work reveals that the photo-Seebeck effect is not only influenced by the majority-carrier mobility, but also by the minority-carrier mobility.
Large reduction of threading dislocations in diamond by hot-filament chemical vapor deposition accompanying W incorporations
Authors: Ohmagari Shinya , Yamada Hideaki , Tsubouchi Nobuteru , Umezawa Hitoshi , Chayahara Akiyoshi , Tanaka Shingo , Mokuno Yoshiaki
Published: July 2018

Dislocations in semiconductor crystals are desirably minimized as much as possible, since their presence typically deteriorates device performance. While diamond electronics have demonstrated superior device properties, they have not fulfilled their material limit yet. To further improve device performance, a low dislocation density and a high-quality epitaxial layer are required. In this study, diamond films are homoepitaxially grown by hot-filament chemical vapor deposition accompanying W incorporations from heated metal-wires. The films exhibited better crystalline quality than seed substrates: a large reduction of threading dislocation from 2 × 106 to 3 × 104 cm−2 was demonstrated. The dislocation propagation was partially annihilated by W impurities. The electrical properties of Schottky barrier diodes after dislocation reduction were highly uniform, improved rectifying actions.
Design principles describe new superhard metal borides
Authors: Fellet Melissae
Published: July 2018

Doping ternary metal borides to alter both the atomic arrangement and grain size in the material could give a new generation of cost-effective superhard materials.
A compact, low-cost interferometer offers quantum key distribution systems an alternative
Authors: Kim Meeri
Published: July 2018

A new study proposes an alternative interferometer for use in quantum key distribution systems based on a highly birefringent optical fiber.
Clinical engagement: a new concept or common sense all round?
Authors: Bolsin Stephen , Carter Jenny , Kitson Aileen , Walter Donna , Roberts Stephen
Published: July 2018

Clinical engagement has supplemented clinical governance in healthcare to strengthen the contribution of medical professionals to the assessment of clinical outcomes for patients. Assessments of clinical engagement have, until now, been qualitative; this case study introduces the concept of quantitative assessment of clinical engagement by measuring the number of patients managed according to specialist society guidelines. Such an assessment engages all staff (medical, nursing, allied health and pharmacy) involved in patients receiving treatment according to such guidelines and provides an assessment of individual and organisational compliance with those guidelines. Clinical engagement is then quantified as the percentage of patients that have been documented to receive specialist society- or college-approved guideline-compliant treatment, relative to the total number who could receive such treatment, in any healthcare organisation. What is known about the topic? Clinical engagement has emerged in recent years as a virtue to be encouraged in healthcare organisations because of its association with improved patient outcomes and employee satisfaction. Assessments have relied on repeated staff surveys in order to gauge engagement. What does this paper add? This paper proposes a novel means of measuring clinical engagement in an organisational setting. The vision put forward is that adherence to clinical guidelines in an organisation measures clinician engagement across professional disciplines. What are the implications for practitioners? The implications are that organisations will contribute to measuring the adherence of specialty groups of clinicians to guidelines that the clinicians select and use the data for individual and organisational accreditation.
Atmospheric fate of methyl pivalate: OH/Cl-initiated degradation and the roles of water and formic acid
Authors: Bai Feng-Yang , Liu Chun-Yu , Ye Jin-Ting , Pan Xiu-Mei
Published: July 2018

Environmental contextOxygenated volatile organic compounds can lead to the formation of tropospheric ozone, and thus have an impact on climate and human health. Methyl pivalate is one such compound, but the way it breaks down in the atmosphere is not well understood. We investigate the oxidative degradation of methyl pivalate, and show that harmful peroxyacyl nitrates and organic nitrates are the major products.
AbstractThe atmospheric degradation mechanism and dynamics of methyl pivalate (MP) by OH radicals and Cl atoms are explored. The rate constants, computed using variational transition-state theory over the range of 200–2000 K at the CCSD(T)/6-311++G(d,p)//B3LYP/6-311G(d,p) level, are all in agreement with the experimental data. The alkyl radicals, which are formed from the reactions of OH or Cl with MP, can react with O2 and NO to produce the peroxyacyl nitrates, organic nitrates, and alkoxy radicals. The atmospheric evolution mechanisms for the (CH3)3CCOOCH2O•, •OCH2(CH3)2CCOOCH3, and •O(CH3)2CCOOCH3 radicals are also clarified. The OH- and Cl-determined atmospheric lifetimes and the global warming potentials (GWPs) of MP are shown to be low, suggesting that its environmental impact can be ignored. The Arrhenius expressions of kOH = 3.62 × 10−23T3.80exp(522.66/T) and kCl = 1.76 × 10−15T1.79exp(−55.89/T) cm3 molecule−1 s−1 are fitted within 200–2000 K. Compared with the OH/Cl-initiated degradation of (CH3)3CCOOCH3, the auto-decomposition reaction of (CH3)3CCOOCH3 → (CH3)2C=CH2 + HCOOCH3 may be more important at the high temperature range of 1500–2000 K. Moreover, the results show that the water and formic acid molecules can promote the degradation of MP. This study is helpful for evaluating the atmospheric implications of gaseous MP.
Compositional complexity of rods and rings
Authors: Schiavon Cara R. , Griffin Maxwell E. , Pirozzi Marinella , Parashuraman Raman , Zhou Wei , Jinnah H. A. , Reines Daniel , Kahn Richard A.
Published: July 2018

Rods and rings (RRs) are large linear- or circular-shaped structures typically described as polymers of IMPDH (inosine monophosphate dehydrogenase). They have been observed across a wide variety of cell types and species and can be induced to form by inhibitors of IMPDH. RRs are thought to play a role in the regulation of de novo guanine nucleotide synthesis; however, the function and regulation of RRs is poorly understood. Here we show that the regulatory GTPase, ARL2, a subset of its binding partners, and several resident proteins at the endoplasmic reticulum (ER) also localize to RRs. We also have identified two new inducers of RR formation: AICAR and glucose deprivation. We demonstrate that RRs can be disassembled if guanine nucleotides can be generated by salvage synthesis regardless of the inducer. Finally, we show that there is an ordered addition of components as RRs mature, with IMPDH first forming aggregates, followed by ARL2, and only later calnexin, a marker of the ER. These findings suggest that RRs are considerably more complex than previously thought and that the function(s) of RRs may include involvement of a regulatory GTPase, its effectors, and potentially contacts with intracellular membranes.
A Dictionary of Space Exploration
Authors: Dasch E. Julius
Published: July 2018

Over 2,300 entries

This fascinating and expansive dictionary covers all aspects of space exploration, from A-Train to Zvezda. This jargon-free new edition has been fully revised and updated to take into account the new developments in space exploration on an international scale over the last 13 years, with new entries such as Hitomi, Space X Dragon, and Ariane 5 Rocket.

All entries are fully cross-referenced for ease of use. In addition, the dictionary also contains links to over 250 space-related websites, and a comprehensive chronology of space exploration. The entries are supported by over 75 photographs, illustrations, and diagrams.
MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data
Authors: He Zongxiao , Wang Lu , DeWan Andrew T , Leal Suzanne M
Published: July 2018

Motivation

For the design of genetic studies, it is necessary to perform power calculations. Although for Mendelian traits the power of detecting linkage for pedigree(s) can be determined, it is also of great interest to determine the probability of identifying multiple pedigrees or unrelated cases with variants in the same gene. For many diseases, due to extreme locus heterogeneity this probability can be small. If only one family is observed segregating a variant classified as likely pathogenic or of unknown significance, the gene cannot be implicated in disease etiology. The probability of identifying several disease families or cases is dependent on the gene-specific disease prevalence and the sample size. The observation of multiple disease families or cases with variants in the same gene as well as evidence of pathogenicity from other sources, e.g. in silico prediction, expression and functional studies, can aid in implicating a gene in disease etiology. MendelProb can determine the probability of detecting a minimum number of families or cases with variants in the same gene. It can also calculate the probability of detecting genes with variants in different data types, e.g. identifying a variant in at least one family that can establish linkage and more the two additional families regardless of their size. Additionally, for a specified probability MendelProb can determine the number of probands which need to be screened to detect a minimum number of individuals with variants within the same gene.

Results

A single Mendelian disease family is not sufficient to implicate a gene in disease etiology. It is necessary to observe multiple families or cases with potentially pathogenic variants in the same gene. MendelProb, an R library, was developed to determine the probability of observing multiple families and cases with variants within a gene and to also establish the numbers of probands to screen to detect multiple observations of variants within a gene.

Availability and implementation

https://github.com/statgenetics/mendelprob
Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations
Authors: Salazar Alex N , Abeel Thomas
Published: July 2018

Motivation

A long-standing limitation in comparative genomic studies is the dependency on a reference genome, which hinders the spectrum of genetic diversity that can be identified across a population of organisms. This is especially true in the microbial world where genome architectures can significantly vary. There is therefore a need for computational methods that can simultaneously analyze the architectures of multiple genomes without introducing bias from a reference.

Results

In this article, we present Ptolemy: a novel method for studying the diversity of genome architectures—such as structural variation and pan-genomes—across a collection of microbial assemblies without the need of a reference. Ptolemy is a ‘top-down’ approach to compare whole genome assemblies. Genomes are represented as labeled multi-directed graphs—known as quivers—which are then merged into a single, canonical quiver by identifying ‘gene anchors’ via synteny analysis. The canonical quiver represents an approximate, structural alignment of all genomes in a given collection encoding structural variation across (sub-) populations within the collection. We highlight various applications of Ptolemy by analyzing structural variation and the pan-genomes of different datasets composing of Mycobacterium, Saccharomyces, Escherichia and Shigella species. Our results show that Ptolemy is flexible and can handle both conserved and highly dynamic genome architectures. Ptolemy is user-friendly—requires only FASTA-formatted assembly along with a corresponding GFF-formatted file—and resource-friendly—can align 24 genomes in ∼10 mins with four CPUs and <2 GB of RAM.

Availability and implementation

Github: https://github.com/AbeelLab/ptolemy

Supplementary information

Supplementary data are available at Bioinformatics online.
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions
Authors: Do Kieu Trinh , Rasp David J N -P , Kastenmüller Gabi , Suhre Karsten , Krumsiek Jan
Published: July 2018

Associations of metabolomics data with phenotypic outcomes are expected to span functional modules, which are defined as sets of correlating metabolites that are coordinately regulated. Moreover, these associations occur at different scales, from entire pathways to only a few metabolites; an aspect that has not been addressed by previous methods. Here, we present MoDentify, a free R package to identify regulated modules in metabolomics networks at different layers of resolution. Importantly, MoDentify shows higher statistical power than classical association analysis. Moreover, the package offers direct interactive visualization of the results in Cytoscape. We present an application example using complex, multifluid metabolomics data. Due to its generic character, the method is widely applicable to other types of data.

Availability and implementation

https://github.com/krumsieklab/MoDentify (vignette includes detailed workflow).

Supplementary information

Supplementary data are available at Bioinformatics online.
Quality of reporting and assessment of patient-reported health-related quality of life in patients with brain metastases: a systematic review
Authors: DiRisio Aislyn C , Harary Maya , van Westrhenen Anouk , Nassr Eman , Ermakova Anastasia , Smith Timothy R , Dirven Linda , Taphoorn Martin J B , Mekary Rania A , Broekman Marike L D
Published: July 2018

Brain metastases (BMs) have become increasingly prevalent and present unique considerations for patients, including neurocognitive sequelae and advanced disease burden. Therefore, assessing health-related quality of life (HRQoL) via patient-reported outcome measures (PROMs) is an important element of managing these patients. A systematic review of the literature was conducted with the aims of (1) assessing how PROMS used in BM patients were validated, (2) assessing PROM content, and (3) evaluating quality of PROM-results reporting. PROM validation and quality of reporting were assessed using the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) grading criteria and International Society of Quality of Life (ISOQOL)-recommended PROM-reporting standards, respectively. Forty-seven studies reporting on 5178 patients with a range of primacy cancer types were included. Eight different PROMs were applied, ranging from general to brain-specific questionnaires. Weaknesses in the validation of these PROMs were assessed by the COSMIN criteria. Many of these PROMs were not developed for BM patients and contained little information on cognitive symptoms. The overall quality of PROM reporting was insufficient based on the ISOQOL scale. Given the unique clinical considerations in BM patients, our results indicate the need for a standardized, validated questionnaire to assess HRQoL in this population. Additionally, there is room for quality improvement with regard to reporting of PROM-related results.
Treatment and survival differences across tumor sites in malignant peripheral nerve sheath tumors: a SEER database analysis and review of the literature
Authors: Martin Enrico , Muskens Ivo S , Coert J H , Smith Timothy R , Broekman Marike L D
Published: July 2018

Background

Currently, literature is scarce on differences across all possible tumor sites in malignant peripheral nerve sheath tumors (MPNSTs). To determine differences in treatment and survival across tumor sites and assess possible predictors for survival, we used the Surveillance, Epidemiology, and End Results (SEER) database.

Methods

MPNST cases were obtained from the SEER database. Tumor sites were recoded into: intracranial, spinal, head and neck (H&N), limbs, core (thorax/abdomen/pelvis), and unknown site of origin. Patient and tumor characteristics, treatment modalities, and survival were extracted. Overall survival (OS) was assessed using univariable and multivariable Cox regression hazard models. Kaplan-Meier survival curves were constructed per tumor site for OS and disease-specific survival (DSS).

Results

A total of 3267 MPNST patients were registered from 1973 to 2013; 167 intracranial (5.1%), 119 spinal (3.6%), 449 H&N (13.7%), 1022 limb (31.3%), 1307 core (40.0%), and 203 unknown (6.2%). The largest tumors were found in core sites (80.0 mm, interquartile range [IQR]: 60.0-115.0 mm) and the smallest were intracranial (37.4 mm, IQR: 17.3-43.5 mm). Intracranial tumors were least frequently resected (58.1%), whereas spinal tumors were most often resected (83.0%). Radiation was administered in 35.5% to 41.8%. Independent factors associated with decreased survival were: older age, male sex, black race, no surgery, partial resection, large tumor size, high tumor grade, H&N site, and core site (all P < .05). Intracranial and pediatric tumors show superior survival (both P < .05). Intracranial tumors show superior OS and DSS curves, whereas core tumors have the worst (P < .001).

Conclusion

Superior survival is seen in intracranial and pediatric MPNSTs. Core and H&N tumors have a worse prognosis.
Increasing Age Has Limited Impact on Risk of Clostridium difficile Infection in an Elderly Population
Authors: Olsen Margaret A , Stwalley Dustin , Demont Clarisse , Dubberke Erik R
Published: July 2018

Background

Numerous studies have found increased risk of Clostridium difficile infection (CDI) with increasing age. We hypothesized that increased CDI risk in an elderly population is due to poorer overall health status with older age.

Methods

A total of 174 903 persons aged 66 years and older coded for CDI in 2011 were identified using Medicare claims data. The comparison population consisted of 1 453 867 uninfected persons. Potential risk factors for CDI were identified in the prior 12 months and organized into categories, including infections, acute noninfectious conditions, chronic comorbidities, frailty indicators, and health care utilization. Multivariable logistic regression models with CDI as the dependent variable were used to determine the categories with the biggest impact on model performance.

Results

Increasing age was associated with progressively increasing risk of CDI in univariate analysis, with 5-fold increased risk of CDI in 94–95-year-old persons compared with those aged 66–67 years. Independent risk factors for CDI with the highest effect sizes included septicemia (odds ratio [OR], 4.1), emergency hospitalization(s) (OR, 3.9), short-term skilled nursing facility stay(s) (OR, 2.7), diverticulitis (OR, 2.2), and pneumonia (OR, 2.1). Exclusion of age from the full model had no impact on model performance. Exclusion of acute noninfectious conditions followed by frailty indicators resulted in lower c-statistics and poor model fit. Further exclusion of health care utilization variables resulted in a large drop in the c-statistic.

Conclusions

Age did not improve CDI risk prediction after controlling for a wide variety of infections, other acute conditions, frailty indicators, and prior health care utilization.
Missed Opportunities for HIV Testing of Patients Tested for Sexually Transmitted Infections at a Large Urban Health Care System From 2010 to 2015
Authors: Kapadia Shashi N , Singh Harjot K , Jones Sian , Merrick Samuel , Vaamonde Carlos M
Published: July 2018

Background

Appropriate testing of people at risk for HIV is an important piece of the HIV care continuum. We analyzed HIV testing patterns of patients tested for gonorrhea and chlamydia (GC/CT) at a large urban health care system in New York City.

Methods

We retrospectively studied HIV and GC/CT testing from 2010 to 2015. Data were collected from a clinical laboratory database and linked to electronic health records. Patients were older than age 13 years, not known to be HIV positive, and had had a GC/CT test. The main outcome was the proportion of patients who had both HIV and GC/CT testing performed at the same encounter.

Results

We analyzed 85 768 patients with 139 404 GC/CT testing encounters. Most of the testing encounters (88% for men and 94% for women) were in the outpatient setting. Same-day HIV testing improved from 59% in 2010 to 70% in 2015 for male patients, and from 41% to 51% for female patients. In multivariate regression, male sex was associated with receipt of an HIV test (odds ratio [OR], 2.49; P < .001). Emergency department (OR, 0.22; P < .0001) and inpatient (OR, 0.10; P < .0001) locations were negatively associated with receipt of HIV testing. Among patients with HIV and GC/CT testing at the same encounter, 37 were HIV positive.

Conclusions

Concurrent HIV testing of patients being evaluated for GC/CT increased from 2010 to 2015. However, many patients failed to receive HIV testing, especially in emergency and inpatient settings. There continue to be missed opportunities for diagnosis of HIV among individuals with ongoing high-risk behavior.
Predictors of Mortality Among a National Cohort of Veterans With Recurrent Clostridium difficile Infection
Authors: Appaneal Haley J , Caffrey Aisling R , Beganovic Maya , Avramovic Sanja , LaPlante Kerry L
Published: July 2018

Background

Though recurrent Clostridium difficile infection (CDI) is common and poses a major clinical concern, data are lacking regarding mortality among patients who survive their initial CDI and have subsequent recurrences. Risk factors for mortality in patients with recurrent CDI are largely unknown.

Methods

Veterans Affairs patients with a first CDI (stool sample with positive C. difficile toxin(s) and ≥2 days CDI treatment) were included (2010–2014). Subsequent recurrences were defined as additional CDI episodes ≥14 days after the stool test date and within 30 days of the end of treatment. A matched (1:4) case–control analysis was conducted using multivariable conditional logistic regression to identify predictors of all-cause mortality within 30 days of the first recurrence.

Results

Crude 30-day all-cause mortality rates were 10.6% for the initial CDI episode, 8.3% for the first recurrence, 4.2% for the second recurrence, and 5.9% for the third recurrence. Among 110 cases and 440 controls, 6 predictors of mortality were identified: use of proton pump inhibitors (PPIs; odds ratio [OR], 3.86; 95% confidence interval [CI], 2.14–6.96), any antibiotic (OR, 3.33; 95% CI, 1.79–6.17), respiratory failure (OR, 8.26; 95% CI, 1.71–39.92), congitive dysfunction (OR, 2.41; 95% CI, 1.02–5.72), nutrition deficiency (OR, 2.91; 95% CI, 1.37–6.21), and age (OR, 1.04; 95% CI, 1.01–1.07).

Conclusions

In our national cohort of Veterans, crude mortality decreased by 44% from the initial episode to the third recurrence. Treatment with antibiotics, use of PPIs, and underlying comorbidities were important predictors of mortality in recurrent CDI. Our study assists health care providers in identifying patients at high risk of death after CDI recurrence.
Acute Treatment of Ruptured Fusiform Posterior Circulation Posterior Cerebral, Superior Cerebellar, and Posterior Inferior Cerebellar Artery Aneurysms With FRED Flow Diverter: Report of 5 Cases
Authors: Laukka Dan , Rautio Riitta , Rahi Melissa , Rinne Jaakko
Published: July 2018

BACKGROUND

Flow diverter (FD) treatment of ruptured fusiform posterior cerebral artery (PCA), posterior inferior cerebellar artery (PICA), and superior cerebellar artery (SCA) aneurysms are limited to single reports.

OBJECTIVE

To study the safety and efficacy of FD treatment for ruptured fusiform aneurysms of the PCA, SCA, and PICA.

METHODS

Five patients with ruptured posterior circulation fusiform aneurysms and treated with a Flow-Redirection Endoluminal Device (FRED/FRED Jr; Microvention, Tustin, California) stent in the acute phase of subarachnoid hemorrhage between 2013 and 2016 were included and reviewed retrospectively.

RESULTS

Two aneurysms located on the PICA, 2 on PCA, and 1 on the SCA. Mean treatment time with FD was 5.8 d (range, 0-11 d) from ictus. The technical success rate was 100%. On admission 2 patients were Hunt and Hess grade 1, 2 patients grade 3, and 1 patient grade 4. At discharge, 4 patients (80%) were independent (modified Ranking Scale (mRS) ≤2) and 1 patient had severe disability (mRS 4). None of the patients had aneurysmal rebleeding. All 5 aneurysms were completely occluded on angiographic follow-up (range, 3-22 mo). One patient had permanent intraprocedural in stent thrombosis and brain infarction. One patient had spontaneous nonaneurysmal intracerebral hemorrhage 1 mo after FD treatment. External ventricular drainage was inserted in 3 patients and ventriculoperitoneal shunt in 2 patients without hemorrhagic complications despite dual antiplatelet therapy.

CONCLUSION

FD could be considered as a treatment option for ruptured fusiform aneurysms located on PCA, PICA, or SCA when other treatment options are challenging.
Paris and the Cliché of History
Authors: Clark Catherine E.
Published: July 2018

Focusing on one of photography’s birthplaces, Paris and the Cliché of History tells the story of how photographs came to be imagined and deployed as documents of the past. It uncovers the changing conventions that drove the formation of public photo archives, the inclusion of photos on the pages of illustrated books, their place in historical exhibitions and public festivals, and the organization of amateur photo contests to document Paris. It explores how contemporaries looked at photos, new and old, through the lenses of war, occupation, urban renovation, and other traumas. From this point of view, Paris and the Cliché of History offers new versions of familiar stories about Haussmannization, the professionalization of history, the cultural effects of World War I, and the 1944 Liberation of Paris as well as the first in-depth accounts of the 1951 celebration of Paris’s birthday (the Bimillénaire de Paris) and the 100,000 photographs submitted to an ambitious effort to document the city for the future: the amateur photo contest “This was Paris in 1970.” It calls for historians to pull the curtain on using photographs as transparent windows onto the past and proposes a historical methodology that registers photographic production, circulation, and preservation as part and parcel of history itself. Ultimately the book presents a compelling argument for the importance of this history of photographs to the story of Paris since 1860 and to arguments about its reduction to a museum city, or merely an image, since the 1960s.
Introduction
Authors: Clark Catherine E.
Published: July 2018

What is the history of preserving, writing, exhibiting, theorizing, and imagining the history of Paris photographically? How, when, and to what end did photographs become interesting as historical evidence—and more specifically, evidence of the history of Paris—and to whom? These questions can be best answered by an institutional history of photo collecting in the city’s historical museum and library alongside an effort to traces the uses of photographs by amateur and popular historians, publishers, and photographers beyond their walls. This investigation builds on literatures about the city of Paris, its visual regimes, the relationship between history and memory, the role of the historical imagination, the reduction of Paris to an image, and histories of the “Visual Turn.” It deploys the cliché as a methodological approach to tell a new history about the relationship between Paris and its insistently photographic past.
Confirmation and Induction
Authors: Cozic Mikaël
Published: July 2018

How are scientific hypotheses and theories assessed against empirical data? Philosophers of science have tried to find out whether there are general principles underlying this activity. This chapter goes through the major types of philosophical theories of confirmation. It starts with two proposals that elaborate criteria of qualitative confirmation on the basis of (deductive) logic: instantialism and hypothetico-deductivism. The main part of the chapter is devoted to Bayesian confirmation theory (BCT), which relies on a probabilistic framework and is able to provide both qualitative and quantitative criteria of confirmation. We discuss in details the strengths and limits of BCT. In the closing section, we address the issue of how BCT (and Bayesianism in general) relate to the problem of induction.
Causality
Authors: Kistler Max
Published: July 2018

Does science need a concept of causality, and if it does, how may this concept be analyzed? The chapter introduces to the main debates regarding causality in contemporary philosophy of science. Eliminativism, as defended by Russell, is the first target: it is argued that even if the concept of causality were eliminable in fundamental physics, it would still be needed in many other contexts, including those covered by other branches of science such as biology or neuroscience. Various possible explications for the concept of causation are then successively considered, in terms of counterfactual conditionals, of probability raising, in terms of manipulability and in terms of processes.
Speaking for Ourselves
Authors: Bakan Michael B.
Published: July 2018

Since the advent of autism as a diagnosed condition in the 1940s, the importance of music in the lives of autistic people has been widely observed and researched. Articles on musical savants, extraordinary feats of musical memory and pitch recognition, and music-based therapies and interventions abound in the autism literature. Meanwhile, music historians have posited autism-centered explanatory models to account for the unique musical artistry of everyone from Glenn Gould to “Blind Tom” Wiggins. Given all of this attention, it is surprising how infrequently autistic people have been asked to account for how they themselves make and experience music, or for why it matters to them that they do. In Speaking for Ourselves, renowned ethnomusicologist Michael Bakan does just that, engaging in deep conversations—some spanning the course of years—with ten fascinating and very different individuals who share two basic things in common: an autism spectrum diagnosis and a life in which music plays a central part. These conversations offer profound insights into the intricacies and intersections of music, autism, neurodiversity, and life in general, not from an autistic point of view but rather from several different autistic points of view. They invite readers to partake of a rich tapestry of words, ideas, images, and musical sounds (on the companion website) that speak to both the diversity of autistic experience and the common humanity we all share.
The Mightie Frame
Authors: Onuf Nicholas Greenwood
Published: July 2018

Inspired by Michel Foucault’s The Order of Things, this book tells a story about epochal change in the modern world. While both books are concerned with how we moderns think about ourselves and our world, this book emphasizes the conceptual links in the ways we think, talk, get things done, conduct ourselves, and run societies. Both tell the story as a succession of epochs or ages separated by great ruptures. First is the Renaissance as the age of similitudes, ending around 1650. In its wake is the classical epoch as the age of tables, succeeded around 1800 by the modern epoch as a time of exponential growth and changing scales. Then follows the modernist age, beginning around 1900, which Foucault failed to identify as such but this book treats as the modern epoch turned inside-out. Last comes Foucault’s “end of man,” c. 1970, a time of rupture and renewal—or not. Despite Foucault’s rhetoric of rupture, modernity has changed within the confines of a “mightie frame” (a turn of phrase borrowed from John Milton). From epoch to epoch, the mighty frame has gained features that continue to function even as they recede from view, all the while fixing the limits of possible knowledge for modern minds and the conditions of rule in the modern world. These two sets of conditions constitute modernity as we know it now, give us clues about what comes next, and point to a plausible ethics for a time of uncertainty, stasis, and, quite possibly, decline.
Dissenting Print Culture
Authors: Whitehouse Tessa
Published: July 2018

Print culture was expanding rapidly in the eighteenth century. Yet religious literature remained the largest category of printed book and Dissenters were significant contributors to this genre. From 1695 pre-publication censorship disappeared within England so print was an important mechanism through which Dissenting identity was created and sustained. Religious works could be doctrinal, controversial, or practical and it was the latter category that had the largest lay readership. Material related to Scripture, either translated or paraphrased, accounted for much of the printed religious output but life writing and poetry were also influential. Many of the authors were ministerial and male, although the audiences for which they were writing were more varied. While it is easier to trace the uses to which material designed to educate ministers was put, there were also significant examples of Dissenters using print to fashion a wider sense of community, often through the use of non-commercial publishing models.
Sizing up Consciousness
Authors: Massimini Marcello , Tononi Giulio
Published: July 2018

Sizing up Consciousness explores, at an introductory level, the potential practical, clinical, and ethical implications of a general principle about the nature of consciousness. Using information integration theory (IIT) as a guiding principle, the book takes the reader along a scientific trajectory to face fundamental questions about the relationships between matter and experience. What is so special about a piece of flesh that can host a subject who sees light or experiences darkness? Why is the brain associated with a capacity for consciousness, but not the liver or the heart, as previous cultures believed? Why the thalamocortical system, but not other complicated neural structures? Why does consciousness fade during deep sleep, while cortical neurons remain active? Why does it recover, vivid, and intense, when the brain is disconnected from the external world during a dream? Can unresponsive patients with a functional island of cortex surrounded by widespread damage be conscious? Is a parrot that talks, or an octopus that learns and plays conscious? Can computers be conscious? Could a system behave like us and yet be devoid of consciousness—a zombie? The authors take on these basic questions by translating theoretical principles into anatomical observations, novel empirical measurements—such as an index of brain complexity that can be applied at the bedside of brain-injured patients—and thought experiments. The aim of the book is to describe, in an accessible way, a preliminary attempt to identify a general rule to size up the capacity for consciousness within the human skull and beyond.
John Stuart Mill
Authors: Larsen Timothy
Published: July 2018

John Stuart Mill observed in his Autobiography that he was a rare case in nineteenth-century Britain because he had not lost his religion but never had any. He was a freethinker from beginning to end. What is not often realized, however, is that Mill’s life was nevertheless impinged upon by religion at every turn. This is true both of the close relationships that shaped him and of his own thoughts. Mill was a religious sceptic, but not the kind of person which that term usually conjures up. The unexpected prominence of spirituality is not only there in Mill’s late, startling essay, ‘Theism’, in which he makes the case for hope in God and in Christ. It is everywhere—in his immediate family, his best friends, and his vision for the future. It is even there in such a seemingly unlikely place as his Logic, which repeatedly addresses religious themes. John Stuart Mill: A Secular Life is a full biography which follows one of Britain’s most well-respected intellectuals through all of the key moments in his life from falling in love to sitting in Parliament and beyond. It also explores his classic works including, On Liberty, Principles of Political Economy, Utilitarianism, and The Subjection of Women. In this well-researched study which offers original findings and insights, you will encounter the Mill you never knew; the Mill that even some of his closest disciples never knew. This is John Stuart Mill, the Saint of Rationalism—a secular life and a spiritual life.
Vanity and Vexation of Spirit
Authors: Larsen Timothy
Published: July 2018

This chapter explores Mill’s famous mental crisis and period of despondency as a young man. He wrote of it in language that strongly and explicitly paralleled loss-of-faith narratives (in this case, the faith that was in crisis was not a conventionally religious one, but rather Benthamism) and the evangelical conversion narrative (again, in this case, what he was being converted to was not a conventional religious faith, but rather Romanticism). This chapter also traces Mill’s strong connections with Unitarian Christianity, not least through his relationship with the Reverend William Johnson Fox. His substitute mother, Sarah Austin, was also a Unitarian, as was the great love of his life, Harriet Taylor.
Love Thy Neighbour as Thyself
Authors: Larsen Timothy
Published: July 2018

The focus of this chapter is on the mature Mill and Utilitarianism, not least his 1861 treatise of that name which attempted to offer a broader, more defensible version of the Benthamite legacy. It uncovers the Christian Utilitarianism of William Paley and explores Mill’s own claim that Utilitarianism was the teaching of Jesus of Nazareth. This chapter then goes on to discuss the Catholic faith and commitment to the Mass of Mill’s stepdaughter and closest companion and collaborator during the last fifteen years of his life, Helen Taylor, as well as the devout Christianity of his stepson, Algernon, whom Mill even had write about a church father for the Westminster Review.