bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass spectrometry–based protein identification in proteomics—a review
Authors: Noor Zainab , Ahn Seong Beom , Baker Mark S , Ranganathan Shoba , Mohamedali Abidali 
Published: November 2019

Abstract
Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent years played a pivotal role in extending and developing the science of accurately identifying the biology and interactions of groups of proteins or proteomes. Proteomics has primarily used mass spectrometry (MS)-based techniques for identifying proteins, although other techniques including affinity-based identifications still play significant roles. Here, we outline the basics of MS to understand how data are generated and parameters used to inform computational tools used in protein identification. We then outline a comprehensive analysis of the bioinformatics and computational methodologies used in protein identification in proteomics including discussing the most current communally acceptable metrics to validate any identification.
Estimation of marginal causal effects in the presence of confounding by cluster
Authors: Sjölander Arvid 
Published: November 2019

SummaryA popular way to control for unmeasured confounders is to utilize clusters (e.g. sets of siblings), in which a potentially large set of confounders are constant. By estimating the exposure–outcome association within clusters, rather than between unrelated subjects, all cluster-constant confounders are implicitly controlled for. To analyze such clustered data, it is common to use fixed effects models, which absorb all cluster-constant confounders into a cluster-specific intercept. In this article, we show how linear and log-linear fixed effects models can be used to estimate marginal counterfactual means. These counterfactual means can be estimated and presented for each exposure level separately, or contrasted to form a wide range of marginal causal effects. For binary outcomes, we propose to estimate marginal causal effects with marginal logistic between-within models. These models include a constant intercept common for all clusters, and control for unmeasured cluster-constant confounders by adding the mean exposure level in each cluster to the model. We illustrate the proposed methods by re-analyzing data from a co-twin control study on birth weight and Attention-Deficit/Hyperactivity Disorder.
Fluorescent Flags: Black Power, Publicity, and Counternarratives in Go-Go Street Posters in the 1980s
Authors: Hopkinson Natalie 
Published: November 2019

Abstract
This semiotic landscape analysis probes urban patterns of racial placement and displacement through an archive of music publicity posters. The music poster archive is a site to map the so-called “Chocolate City” of Washington, D.C., in the 1980s, explore its calendars, rhythms, textures, communication technology, history and movements of segregated black life. These posters advertising go-go music, the city's indigenous black popular music, asserted a territory of black economic, cultural and political power. They resisted the narrative of a sanitized “White City” designed for white tourists. The city's cultural entrepreneurs challenged false dominant narratives and public policies that marginalized black urban culture as dangerous and deviant. A crack-down on postering in the late 1990s was an early harbinger of gentrification.
Effectiveness and safety of edoxaban in patients with atrial fibrillation: data from the Danish Nationwide Cohort
Authors: Nielsen Peter Brønnum , Larsen Torben Bjerregaard , Skjøth Flemming , Søgaard Mette , Lip Gregory Y H 
Published: November 2019

Abstract

Aims
Edoxaban treatment for stroke prevention in atrial fibrillation (AF) has mainly been investigated in randomized controlled trials, and data reflecting clinical practice are limited. We ascertained the clinical effectiveness and safety of edoxaban 30 and 60 mg once daily among Danish patients with AF.

Methods and results
This was an observational study based on Danish nationwide registries collecting information for administrative purposes. From June 2016 through November 2018, we identified 3405 patients initiating edoxaban. After exclusions, 2285 AF patients were followed for the effectiveness outcome of thromboembolism (ischaemic stroke and/or systemic embolism) and bleeding outcomes (composite of major bleeding, gastrointestinal bleeding, and intracranial haemorrhage), as well as bleeding requiring hospitalization. Population mean age was 75 years and 43% were female; 643 patients received the 30 mg edoxaban dosage regimen and 1642 initiated 60 mg edoxaban. During follow-up, we observed 41 thromboembolic events and 89 bleeding events of which 40 events required hospitalization. Among patients with 30 mg edoxaban, the rate (per 100 person-years) of thromboembolism was 2.07 vs. 1.62 for 60 mg edoxaban. Rates of bleeding were similar for the two dosages at ∼3.85. Bleeding requiring hospitalization occurred at a rate of 1.74 for 30 mg edoxaban and 1.69 with 60 mg edoxaban.

Conclusion
In this nationwide cohort of Caucasian AF patients treated with edoxaban for stroke prevention, the clinical effectiveness and safety were in line with data from the ENGAGE AF-TIMI 48 trial. Studies investigating comparative effectiveness and safety for edoxaban in comparison with other choices of antithrombotic treatment options are needed.
Bioinformatic and genetic characterization of three genes localized adjacent to the major replication origin of Haloferax volcanii
Authors: Wolters Maike , Borst Andreas , Pfeiffer Friedhelm , Soppa Jörg 
Published: November 2019

ABSTRACT
In haloarchaea, a cluster of three genes is localized directly adjacent to the major replication origin, and, hence, the encoded proteins were annotated as ‘origin-associated proteins’ (Oap). However, prior to this study, no experimental data were available for these conserved hypothetical proteins. Bioinformatic analyses were performed, which unraveled, 1) that the amino acid composition of all three proteins deviate from the average, 2) that OapA is a GTP-binding protein, 3) that OapC has an N-terminal zinc-finger motif, and 4) that the sequences of OapA and OapB are highly conserved while OapC conservation is restricted to short terminal regions. Surprisingly, transcript analyses revealed a complex expression pattern of the oap genes, despite their close proximity. Based on the high degree of conservation in haloarchaea it could be expected that one or more of the oap genes might be essential. However, in frame deletion mutants of all three genes could be readily generated, were viable, and had no growth phenotype. In addition, quantification of the chromsome copy numbers revealed no significant differences between the wild-type and the three mutants. In summary, experimental evidence is inconsistent with Oap proteins being essential for or involved in key steps of DNA replication.
Detection of carotenoids of halophilic prokaryotes in solid inclusions inside laboratory-grown chloride and sulfate crystals using a portable Raman spectrometer: applications for Mars exploration
Authors: Culka Adam , Košek Filip , Oren Aharon , Mana Lily , Jehlička Jan 
Published: November 2019

ABSTRACT
Inclusions in evaporitic minerals sometimes contain remnants of microorganisms or biomarkers, which can be considered as traces of life. Raman spectroscopy with resonance enhancement is one of the best analytical methods to search for such biomarkers in places of interest for astrobiology, including the surface and near subsurface of planet Mars. Portable Raman spectrometers are used as training tools for detection of biomarkers. Investigations of the limits and challenges of detecting biomolecules in crystals using Raman spectroscopy is important because natural occurrences often involve mineral assemblages as well as their fluid and solid inclusions. A portable Raman spectrometer with 532 nm excitation was used for detection of carotenoid biomarkers: salinixanthin of Salinibacter ruber (Bacteroidetes) and α-bacterioruberin of Halorubrum sodomense (Halobacteria) in laboratory-grown artificial inclusions in compound crystals of several chlorides and sulfates, simulating entrapment of microorganisms in evaporitic minerals. Crystals of halite (NaCl), sylvite (KCl), arcanite (K2SO4) and tschermigite ((NH4)Al(SO4)2·12H2O) were grown from synthetic solutions that contained microorganisms. A second crystalline layer of NaCl or K2SO4 was grown subsequently so that primary crystals containing microorganisms are considered as solid inclusions. A portable Raman spectrometer with resonance enabling excitation detected signals of both carotenoid pigments. Correct positions of diagnostic Raman bands corresponding to the specific carotenoids were recorded.
Diet and Nutrition Risk Affect Mobility and General Health in Osteoarthritis: Data from the Canadian Longitudinal Study on Aging
Authors: Chopp-Hurley Jaclyn N , Wiebenga Emily G , Keller Heather H , Maly Monica R 
Published: November 2019

AbstractBackgroundThis study examined whether aspects of diet and nutrition risk explain variance in physical capacity and general health, after controlling for covariates, in Canadian adults with osteoarthritis (OA).MethodsThis was a cross-sectional study of baseline data from the Canadian Longitudinal Study on Aging (CLSA). Data from 1,404 participants with hand, hip, and/or knee OA were included. A series of regression analyses were conducted with independent variables of food intake (fiber and high calorie snack intake) and nutrition risk; and dependent variables of physical capacity and general health. Physical capacity was characterized through grip strength and a pooled index of four mobility tests. General health was characterized through an index of self-reported general health, mental health, and healthy aging.ResultsHigher fiber intake was related to greater mobility (p = .01). Food intake was not related to any other outcome. Nutrition risk was significantly associated with mobility (p &lt; .001) and general health (p &lt; .001); those with a high nutrition risk classification had poorer general health (p &lt; .001, d = 0.65) than those at low nutrition risk. As well, those with moderate nutrition risk had poorer general health than those with low nutrition risk (p = .001, d = 0.31).ConclusionsNutrition risk screening for older adults with OA provides insight into behavioral characteristics associated with reduced mobility and poorer general health. Also, those consuming greater amounts of fiber demonstrated better mobility. Thus, this research suggests that quality of diet and nutritional behaviors can impact both physical and mental aspects of health in those with OA.
Detection of 3-D inhomogeneities of the medium at magnetotelluric sounding in the Arctic (numerical experiment)
Authors: Plotkin Valery V , Mogilatov Vladimir S , Gurev Vladimir A , Potapov Vladimir V 
Published: November 2019

SUMMARY
The magnetotelluric sounding (MTS) conducted on drifting ice floes in the Arctic is of particular interest for detection of 3-D inhomogeneities in crustal conductivity. Their manifestations in behaviour of standard magnetotelluric curves are shielded by the well conducting layers of seawater and sediment. As target objects, these inhomogeneities are shown as small changes (only hundredths of per cent) in apparent resistivity, and as very weak variations of vertical magnetic field component. Therefore, accounting for additional data on the vertical electric field component or the electric field potential of the transverse magnetic (TM) mode is of interest. For recording the TM-mode potential, we offer to use the circular electric dipole (CED) located on the ice surface as a receiver in MTS. We investigate possibilities of crustal 3-D inhomogeneity detection using the TM-mode potential received with the CED. A numerical experiment showed that the potential of electric field of the TM-mode on the ice surface reaches values suitable for detection. Examples of the inverse problem solution using synthetic data on the TM-mode field are presented. We found that the information on the depth of 3-D object could be obtained by the analytical continuation of the profile data on the TM-mode potential. Using the MTU-5 Phoenix Geophysics stations for the CED system, we carried out preliminary measurements on the ice surface on the Ob river. We checked the measurement results of the TM-mode potential using the MTS data obtained earlier near the CED system. We compared results of the TM-mode potential calculation for the found 3-D-medium model to the CED experimental data. Our results showed that the potential dependences on the period measured by the СED and those obtained for the 3-D model have similar characteristics. We believe recording the TM-mode potential in the Arctic allows to reveal the existence and characteristics of crustal conductivity 3-D heterogeneities.
Memory of Violence and Drama in Peru: The Experience of the Truth Commission and Grupo Cultural Yuyachkani – Violence and Dehumanization
Authors: Lerner Febres Salomón 
Published: November 2019

ABSTRACT∞
The theater collective Yuyachkani, a Quechua word meaning ‘I am remembering,’ were not strangers to the history the Peruvian Truth and Reconciliation Commission was rediscovering when they offered to contribute to the transitional justice process. They had been following the violence in Peru through their various performances and felt highly committed to the process of truth seeking and the search for reconciliation. The performances of Yuyachkani do not seek to reproduce the facts. They do not commit the naive error of certain realist art efforts, to portray social violence per se in a supposedly concrete way. Their tools are rather the symbols through which culture is expressed. It is not a matter so much of reproducing the facts as of producing effects, to reveal and convey the tragedies of Peruvian society. Performance heightens the senses and opens our imaginations to the deep truths that have been lost among the facts.
“Just tell me what’s going on”: The views of parents of children with genetic conditions regarding the research use of their child’s electronic health record
Authors: Andrews Sara M , Raspa Melissa , Edwards Anne , Moultrie Rebecca , Turner-Brown Lauren , Wagner Laura , Alvarez Rivas Alexandra , Frisch Mary Katherine , Wheeler Anne C 
Published: November 2019

Abstract

Objective
The purpose of this study was to understand the ethical, legal, and social issues described by parents of children with known or suspected genetic conditions that cause intellectual and developmental disabilities regarding research use of their child’s electronic health record (EHR).

Materials and Methods
We conducted 4 focus groups with parents of children with a known (n = 12) or suspected (n = 11) genetic condition, as well as 2 comparison groups with parents who had a child with no known genetic condition (n = 15). Focus group transcripts were coded and analyzed using directed content analysis.

Results
After weighing the risks and benefits, parents of children with known or suspected genetic conditions were willing to share their child’s EHR for research studies under certain conditions. Preferences were for studies conducted by universities or nonprofits that might benefit their child or others with the same condition. Parents also valued return of research results.

Discussion
Trust, transparency, altruism, and concerns about privacy emerged as factors that affect parents’ willingness to allow research use of their child’s EHR.

Conclusion
Researchers should consider how to build trust with parents by increasing transparency of the research process and explaining specifically how they will ensure the confidentiality of EHR data.
The three-dimensional finite element forward modelling of complex excitation source NMR
Authors: Qi Zhipeng , Li Xiu , Fan Kerui , Zhi Qingquan 
Published: November 2019

Abstract
Traditional nuclear magnetic resonance (NMR) is mainly applied to horizontal ground and one-dimensional electrical structures. However, calculations of the excitation fields rarely consider the three-dimensional electrical changes of the subsurface medium and undulating terrain, or the deformations caused by emission sources. Therefore, to analyse the influences of terrain fluctuations, emission source deformations and three-dimensional electrical changes on NMR, three-dimensional finite element forward modelling of undulating terrain NMR was conducted in this study. First, based on a scalar finite element method, the direct calculations of the excited magnetic fields of a three-dimensional electrical medium were realised, which improved calculation accuracy by avoiding the finite element calculations of magnetic vector potential and vector on the magnetic field. During the source loading process, the equivalent thin wire source of the pseudo δ function was used to load the source function directly into the equation for the purpose of achieving total field calculations. This was completed to enable the calculations to be applied to any shape of the transmitting loop and undulating terrain. Then, the components of the excitation magnetic fields perpendicular to the geomagnetic fields were calculated using the rotation matrix. Finally, the NMR sensitivity function and 3D responses were calculated. The calculations of the excitation magnetic fields were verified using a uniform half-space model. The overall algorithm was tested by the nuclear magnetic responses of the layered medium. Also, a typical undulating terrain model was adopted and the complex excitation source NMR was simulated using the algorithm proposed in this study. The algorithm provided a three-dimensional forward basis for the NMR inversion in the cases of determining the electrical medium for the subsequent undulating terrain.
Did Premodern Muslims Distinguish the Religious and Secular? The Dīn–Dunyā Binary in Medieval Islamic Thought
Authors: Abbasi Rushain 
Published: November 2019

Abstract
This article challenges the widely-held belief, within and outside academia, that premodern Muslims did not make a distinction between the religious and secular. I explore the issue by examining several usages of the dīn–dunyā binary across diverse genres of medieval Islamic writings and assessing to what extent it accords with or diverges from the categories of the religious and secular as commonly used in the modern Western world. I situate my particular counter-claim vis-à-vis the argument against the relevance of the religious–secular distinction to Islam made by Shahab Ahmed in his, What is Islam? The Importance of Being Islamic. My findings show that contrary to Ahmed and the broader consensus, premodern Muslims did in fact view the world in terms of distinct spheres of religion and non-religion and that this distinction was used to understand phenomena as diverse and significant as politics and prophethood. Nevertheless, the two categories interacted in a way distinct from the common understanding of the two in the modern world insofar as, under the medieval Islamic conception, it was religion that regulated the secular. My article will make sense of these similarities and differences in an effort to present an indigenous account of the religious–secular dialectic in medieval Islam, one that problematizes the current standard account which holds that these categories were invented within the modern West.
Ileectomy performed on a case of adult intussusception due to inversion of Meckel’s diverticulum
Authors: Abe Iku , Saito Masaaki , Ikeda Taro , Fukuda Rintaro , Tanaka Akira , Rikiyama Toshiki 
Published: November 2019

Abstract
We report a rare case of adult intussusception caused by an inverted Meckel’s diverticulum with ectopic pancreatic tissue. A 43-year-old woman was referred to our hospital with complaints of abdominal distention, intermittent abdominal pain and nausea that she experienced 3 months ago. Abdominal computed tomography scans demonstrated ileo-ileal intussusception that contained a tumor with fat density as the lead point. Laparoscopic-assisted partial resection of the small intestine was performed. The surgical specimen showed an elongated polypoid lesion invaginated into the intestinal tract indicating an inverted Meckel’s diverticulum. Pathological findings showed a true diverticulum that ran antimesentrically, with tall columnar epithelium, a mucous gland and an islet of Langerhans. The postoperative period was uneventful, and she was discharged on the ninth postoperative day.
Suprathermal plasma distribution functions with relativistic cut-offs
Authors: Fahr H-J , Heyl M 
Published: November 2019

ABSTRACT
In typical plasma physics scenarios, when treated on kinetic levels, distribution functions with suprathermal wings are obtained. This raises the question of how the associated typical velocity moments, which are needed to arrive at magnetohydrodynamic plasma descriptions, may appear. It has become evident that the higher velocity moments in particular, for example the pressure or heat transport, which are constructed as integrations of the distribution function, contain unphysical contributions from particles with velocities greater than the velocity of light. In what follows, we discuss two possibilities to overcome this problem. One is to calculate a maximal, physically permitted, upper velocity, which can be realized in view of the underlying energization processes, and to stop the integration there. The other is to modify the distribution function relativistically so that no particles with superluminal (v ≥ c) velocities appear. On the basis of a typical collision-free plasma scenario, like the plasma in the heliosheath, we obtain the corresponding expressions for electron and proton pressures and can show that in both cases the pressures are reduced compared with their classical values; however, electrons experience a stronger reduction than protons. When calculating pressure ratios, it turns out that these are of the same order of magnitude regardless of which of the two methods is used. The electron, as the low-mass particle, undergoes the more pronounced pressure reduction. It may turn out that electrons and protons constitute about equal pressures in the heliosheath, implying that no pressure deficit need be claimed here.
On the origin of the chemical bimodality of disc stars: a tale of merger and migration
Authors: Buck Tobias 
Published: November 2019

ABSTRACT
The Milky Way’s (MW) stellar disc exhibits a bimodality in the [Fe/H] versus [α/Fe] plane, showing a distinct high- and low-α sequences whose origin is still under debate. We examine the [Fe/H]–[α/Fe] abundance plane in cosmological hydrodynamical simulations of MW-like galaxies from the NIHAO-UHD project and show that the bimodal α-sequence is a generic consequence of a gas-rich merger at some time in the Galaxy’s evolution. The high-α sequence evolves first in the early galaxies, extending to high metallicities, while it is the low-α sequence that is formed after the gas-rich merger. The merger brings in fresh metal-poor gas diluting the interstellar medium’s metallicity while keeping the [α/Fe] abundance almost unchanged. The kinematic, structural, and spatial properties of the bimodal α-sequence in our simulations reproduces that of observations. In all simulations, the high-α disc is old, radially concentrated towards the galaxy’s centre and shows large scale heights. In contrast, the low-α disc is younger, more radially extended and concentrated to the disc mid-plane. Our results show that the abundance plane is well described by these two populations that have been distributed radially across the disc by migration: at present day in the solar neighbourhood, low-α stars originate from both the inner and outer discs, while most of the high-α stars have migrated from the inner disc. We show that age dating the stars in the [Fe/H]–[α/Fe] plane can constrain the time of the low-α sequence forming merger and conclude that α-bimodality is likely a not uncommon feature of disc galaxies.