bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiviral-resistant cytomegalovirus infections in solid organ transplantation in the Netherlands
Authors: Van Leer Buter Coretta C , de Voogd Danielle W K , Blokzijl Hans , de Joode Anoek A E , Berger Stefan P , Verschuuren Erik A M , Niesters Hubert G M 
Published: April 2019

Abstract

Objectives
Antiviral resistance in cytomegalovirus (CMV) may result from mutations in the molecular targets of antiviral agents. The aim of this study was to investigate both the prevalence of resistance-associated mutations and the factors associated with antiviral resistance in solid organ transplant (SOT) patients with repeated high CMV loads during antiviral treatment.

Methods
SOT patients were selected retrospectively, based on CMV loads of &gt;30000 IU/mL at least twice in a period during which treatment was given. Patient samples were tested for antiviral resistance by Sanger sequencing the UL97 and UL54 genes of CMV, which code for the viral kinase and polymerase. Factors predisposing to and resulting from the development of antiviral resistance mutations were analysed.

Results
Multiple samples from 113 SOT patients were tested, showing resistance-associated mutations in 25 patients (22%). A further 20 (18%) patients showed mutations that were not known to be associated with antiviral resistance. Several factors were associated with development of resistance-associated mutations in UL97 as well as UL54, including human leucocyte antigen (HLA) mismatch, which occurred more frequently in the group of patients with resistance mutations. High-level resistance mutations were most frequently seen in UL97.

Conclusions
This study shows that by selecting patients solely on the basis of virological response to treatment, more patients with antiviral resistance mutations are identified. In this study we confirm findings by other groups that primary infections are associated with resistance development. Moreover, we show that HLA mismatch is associated with the development of antiviral resistance, which suggests a role for host immunity in the development of resistance.
Urban Frostbite: Strategies for Limb Salvage
Authors: Shenaq Deana S , Beederman Maureen , O’Connor Annemarie , Teele Megan , Robinson Marla R , Gottlieb Lawrence J 
Published: April 2019

AbstractUnder ideal circumstances, severely frostbitten extremities are rapidly rewarmed and treated with thrombolytic therapy within 6 to 24 hours. In an “inner city,” urban environment, most patients who suffer frostbite injuries present in a delayed fashion, sustain repeated injuries further complicated by psychological issues or intoxication, and are rarely ideal candidates for thrombolytic therapy within the prescribed timeframe. We describe our experience with the treatment of urban frostbite injuries. A retrospective review of patients with cold injuries sustained between November 2013 and March 2014 treated at a verified burn center in an urban setting was performed. Fifty-three patients were treated (42 males, 11 females). Average patient age was 41.8 years (range 2–84 years). No patients met criteria for thrombolytic therapy due to multiple freeze-thaw cycles or presentation greater than 24 hours after rewarming. Deep frostbite was seen in 10 patients. Of these patients, nine underwent debridement, resulting in partial limb amputations at levels guided by Tri-phasic technetium (Tc-99m) bone scans. Wound closure and limb-length salvage was then achieved by: free flap coverage (n = 2), local flaps (n = 8), split-thickness skin grafting (n = 22), and secondary intention healing (n = 6). While tissue plasminogen activator has been successful in reducing the need for digital amputation following frostbite injuries, in our experience, this treatment modality is not applicable to the urban patient population who often present late and after cycles of reinjury. Therefore, our approach focused on salvaging limb length with durable coverage, as the injuries were unable to be reversed.
Insulin Resistance and Cancer-Specific and All-Cause Mortality in Postmenopausal Women: The Women’s Health Initiative
Authors: Pan Kathy , Nelson Rebecca A , Wactawski-Wende Jean , Lee Delphine J , Manson JoAnn E , Aragaki Aaron K , Mortimer Joanne E , Phillips Lawrence S , Rohan Thomas , Ho Gloria Y F , Saquib Nazmus , Shadyab Aladdin H , Nassir Rami , Rhee Jinnie J , Hurria Arti , Chlebowski Rowan T 
Published: April 2019

Abstract

Background
Insulin resistance has been proposed as a mediator of the increased cancer incidence and mortality associated with obesity. However, prior studies included limited cancer deaths and had inconsistent findings. Therefore, we evaluated insulin resistance and cancer-specific and all-cause mortality in postmenopausal women participating in the Women’s Health Initiative (WHI).

Methods
Eligible were a subsample of 22 837 WHI participants aged 50–79 years enrolled at 40 US clinical centers from 1993 to 1998 who had baseline fasting glucose and insulin levels. Baseline insulin resistance was measured by the homeostasis model assessment of insulin resistance (HOMA-IR). Cancers were verified by central medical record review and deaths verified by medical record and death certificate review enhanced by National Death Index queries. Cox proportional hazards regression models were used to calculate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for cancer-specific and all-cause mortality. All statistical tests were two-sided.

Results
During a median of 18.9 years of follow-up, 1820 cancer deaths and 7415 total deaths occurred. Higher HOMA-IR quartile was associated with higher cancer-specific mortality (Q4 vs Q1, HR = 1.26, 95% CI = 1.09 to 1.47; Ptrend = .003) and all-cause mortality (Q4 vs Q1, HR = 1.63, 95% CI = 1.51 to 1.76; Ptrend &lt; .001). A sensitivity analysis for diabetes status did not change findings. Among women with body mass index less than 25 kg/m2, higher HOMA-IR quartile was associated with higher cancer mortality (Fine and Gray, P = .004).

Conclusions
High insulin resistance, as measured by HOMA-IR, identifies postmenopausal women at higher risk for cancer-specific and all-cause mortality who could potentially benefit from early intervention.
Technical and methodological foundations of digital indexing of medieval and early modern court books
Authors: Borek Arkadiusz , Związek Tomasz , Słomski Michał , Gochna Michał , Myrda Grzegorz , Słoń Marek 
Published: April 2019

AbstractEver since the beginnings of the modern historiography, the court books have posed a challenge for editors in Poland, both due to their number and variety. They constitute one of the richest sources enabling a variety of historical research. The publication of the sources’ content can be shared owing to new approaches stemming from constant development of IT tools and their application in the humanities. The solution proposed in our article is a digital indexing based on a relational database enabling access to the sources’ scans. The characterization of the method is preceded by a description of the theoretical foundations of the presented method. The assumed principals are implemented by the use of a dedicated to this project online INDXR application which functionalities is thoroughly described. Using the INDXR application, the data acquired from the sources are collected and stored in the database which structure is also illustrated along with its theoretical foundations. The database is established in order to better reflect the typical elements comprising the court books as well as to store the acquired information. The issues stemming from the process of indexing the court books, such as categorizing of the entries, their spatial context, and the problem of how to describe the persons appearing in the manuscript are also presented.
Dating medieval texts by classification with flexible time intervals
Authors: Toner Gregory , Han Xiwu 
Published: April 2019

AbstractDetermining the date of writing is a practical problem often encountered in the study of ancient and medieval texts. The problem is compounded by differences in genre, register and style, but in particular by our frequent dependence on much later copies of lost originals. This article examines how a method of classification with flexible time intervals has been developed for a corpus of medieval Irish annals (c.700–c.1600). It is shown that the method can deal successfully with an unparsed, complex corpus containing contaminated data. A method of extending the model from good quality, uncontaminated data to more complex texts is also demonstrated by identifying temporal characteristics and typical entries in the high-quality source.
Toward a virtual research environment for the spatial humanities: heiMAP
Authors: Pfeiffer Michelle , Eller Dirk , Carré Cyril 
Published: April 2019

Abstract
This article describes the context and design of heiMAP, a virtual research environment (VRE) currently under development at Heidelberg University. heiMAP is aimed at users from a wide spectrum of disciplines within the Humanities, allowing them to collaborate and share data using space as their common frame of reference by way of a collaborative web platform. We first set out the challenges that spatial research in the Humanities poses for such a working platform, including but not limited to reflecting the often heterogeneous and imperfect nature of Humanities data in a Geographic Information System (GIS). Next, we give an overview of some existing VREs and detail where heiMAP fits into this context and show what makes it a worthwhile addition to the existing research landscape. Finally, we revisit the initially outlined challenges and showcase heiMAP’s approaches to address them.
Logics based on linear orders of contaminating values
Authors: Ciuni Roberto , Macaulay Ferguson Thomas , Szmuc Damian 
Published: April 2019

AbstractA wide family of many-valued logics—for instance, those based on the weak Kleene algebra—includes a non-classical truth-value that is ‘contaminating’ in the sense that whenever the value is assigned to a formula $\varphi $, any complex formula in which $\varphi $ appears is assigned that value as well. In such systems, the contaminating value enjoys a wide range of interpretations, suggesting scenarios in which more than one of these interpretations are called for. This calls for an evaluation of systems with multiple contaminating values. In this paper, we consider the countably infinite family of multiple-conclusion consequence relations in which classical logic is enriched with one or more contaminating values whose behaviour is determined by a linear ordering between them. We consider some motivations and applications for such systems and provide general characterizations for all consequence relations in this family. Finally, we provide sequent calculi for a pair of four-valued logics including two linearly ordered contaminating values before defining two-sided sequent calculi corresponding to each of the infinite family of many-valued logics studied in this paper.
‘Invisible existence’: Perspectives of forced migrants’ living within Zimbabwe
Authors: Benhura Abigail R , Naidu Maheshvari 
Published: April 2019

Abstract
Involuntary human mobility within and outside national borders continue to raise connotations of these migrants being dispossessed of more than their physical shelter. In 2005, the Zimbabwean government demolished hundreds of buildings, which it had condemned as illegal through a program code named Operation Murambatsvina. Likewise, for the people dislodged by this program, the article contends that internal displacement did not only lead to loss of shelter but also denied them their inherent dignity and rendered them ‘invisible’. In turn, this heightened their susceptibility to deprivations that are synonymous with forced migration. Therefore, this article aims to explore the forced migrants’ perspectives of the effects of displacement on their lives vis-à-vis the above contentions. It mainly seeks to address the displaced people’s perceptions and socially constructed meanings of internal displacement. This qualitative article is based on empirical data gathered from Hopley and Caledonia settlements in Zimbabwe. The essay uses purposive sampling and snowballing to capture the people living in displacement. The article’s findings indicate that displacement births adaptive preferences which are used to counter the negative effects experienced due to the conditions in their settlements. Despite the conspicuousness of Hopley and Caledonia residents’ type of shelter, the article also establishes that internal displacement has ironically increased their invisibility both within and outside Zimbabwe. The article determines that their ‘invisibility’ is manifested through waning interest by institutions mandated to safeguard their assistance and protection, which exposes them to heightened vulnerabilities.
The first 62 AGN observed with SDSS-IV MaNGA – IV. Gas excitation and star formation rate distributions
Authors: Nascimento Janaína C do , Storchi-Bergmann Thaisa , Mallmann Nícolas D , Riffel Rogério , Ilha Gabriele S , Riffel Rogemar A , Rembold Sandro B , Schimoia Jáderson , da Costa Luiz Nicolaci , Maia Marcio A G , Machado Alice D 
Published: April 2019

Abstract
We present maps of the ionized gas flux distributions, excitation, star formation rate (SFR), surface mass density ΣH+, and obtain total values of SFR and ionized gas masses M for 62 active galactic nuclei (AGN) observed with SDSS-IV MaNGA and compare them with those of a control sample of 112 non-active galaxies. The most luminous AGN – with $L(\rm {[O\,{\small III}]}\lambda 5007) \ge 3.8\times 10^{40}\, \mbox{erg}\, \mbox{s}^{-1}$, and those hosted by earlier type galaxies are dominated by Seyfert excitation within 0.2 effective radius Re from the nucleus, surrounded by LINER excitation or transition regions, while the less luminous and hosted by later-type galaxies show equally frequent LINER and Seyfert excitation within $0.2\, R_\mathrm{ e}$. The extent R of the region ionized by the AGN follows the relation $R\propto \, L(\rm {[O\,{\small III}]})^{0.5}$ – as in the case of the broad-line region. The SFR distribution over the region ionized by hot stars is similar for AGN and controls, while the integrated SFR – in the range 10−3–10 M⊙ yr−1 is also similar for the late-type subsample, but higher in the AGN for 75 per cent of the early-type subsample. We thus conclude that there is no signature of AGN quenching star formation in the body of the galaxy in our sample. We also find that 66 per cent of the AGN have higher ionized gas masses M than the controls – in the range 105–3 × 107 M⊙ – while 75 per cent of the AGN have higher ΣH+ within $0.2\, R_\mathrm{ e}$ than the control galaxies.
DeepStreaks: identifying fast-moving objects in the Zwicky Transient Facility data with deep learning
Authors: Duev Dmitry A , Mahabal Ashish , Ye Quanzhi , Tirumala Kushal , Belicki Justin , Dekany Richard , Frederick Sara , Graham Matthew J , Laher Russ R , Masci Frank J , Prince Thomas A , Riddle Reed , Rosnet Philippe , Soumagnac Maayane T 
Published: April 2019

ABSTRACT
We present DeepStreaks, a convolutional-neural-network, deep-learning system designed to efficiently identify streaking fast-moving near-Earth objects that are detected in the data of the Zwicky Transient Facility (ZTF), a wide-field, time-domain survey using a dedicated 47 deg2 camera attached to the Samuel Oschin 48-inch Telescope at the Palomar Observatory in California, United States. The system demonstrates a 96–98 per cent true positive rate, depending on the night, while keeping the false positive rate below 1 per cent. The sensitivity of DeepStreaks is quantified by the performance on the test data sets as well as using known near-Earth objects observed by ZTF. The system is deployed and adapted for usage within the ZTF Solar system framework and has significantly reduced human involvement in the streak identification process, from several hours to typically under 10 min per day.
The 3XMM/SDSS Stripe 82 Galaxy Cluster Survey – II. X-ray and optical properties of the cluster sample
Authors: Takey Ali , Durret Florence , Márquez Isabel , Ellien Amael , Molham Mona , Plat Adèle 
Published: April 2019

ABSTRACT
We present X-ray and optical properties of the optically confirmed galaxy cluster sample from the 3XMM/SDSS Stripe 82 cluster survey. The sample includes 54 galaxy clusters in the redshift range of 0.05–1.2, with a median redshift of 0.36. We first present the X-ray temperature and luminosity measurements that are used to investigate the X-ray luminosity–temperature relation. The slope and intercept of the relation are consistent with those published in the literature. Then, we investigate the optical properties of the cluster galaxies including their morphological analysis and the galaxy luminosity functions (GLFs). The morphological content of cluster galaxies is investigated as a function of cluster mass and distance from the cluster centre. No strong variation of the fraction of early- and late-type galaxies with cluster mass is observed. The fraction of early-type galaxies as a function of cluster radius varies as expected. The individual GLFs of red sequence galaxies were studied in the five ugriz bands for 48 clusters. The GLFs were then stacked in three mass bins and two redshift bins. Twenty clusters of the present sample are studied for the first time in X-rays, and all are studied for the first time in the optical range. Altogether, our sample appears to have X-ray and optical properties typical of ‘average’ cluster properties.
Additive Traits Lead to Feeding Advantage and Reproductive Isolation, Promoting Homoploid Hybrid Speciation
Authors: Masello Juan F , Quillfeldt Petra , Sandoval-Castellanos Edson , Alderman Rachael , Calderón Luciano , Cherel Yves , Cole Theresa L , Cuthbert Richard J , Marin Manuel , Massaro Melanie , Navarro Joan , Phillips Richard A , Ryan Peter G , Shepherd Lara D , Suazo Cristián G , Weimerskirch Henri , Moodley Yoshan 
Published: April 2019

AbstractSpeciation through homoploid hybridization (HHS) is considered extremely rare in animals. This is mainly because the establishment of reproductive isolation as a product of hybridization is uncommon. Additionally, many traits are underpinned by polygeny and/or incomplete dominance, where the hybrid phenotype is an additive blend of parental characteristics. Phenotypically intermediate hybrids are usually at a fitness disadvantage compared with parental species and tend to vanish through backcrossing with parental population(s). It is therefore unknown whether the additive nature of hybrid traits in itself could lead successfully to HHS. Using a multi-marker genetic data set and a meta-analysis of diet and morphology, we investigated a potential case of HHS in the prions (Pachyptila spp.), seabirds distinguished by their bills, prey choice, and timing of breeding. Using approximate Bayesian computation, we show that the medium-billed Salvin’s prion (Pachyptila salvini) could be a hybrid between the narrow-billed Antarctic prion (Pachyptila desolata) and broad-billed prion (Pachyptila vittata). Remarkably, P. salvini’s intermediate bill width has given it a feeding advantage with respect to the other Pachyptila species, allowing it to consume a broader range of prey, potentially increasing its fitness. Available metadata showed that P. salvini is also intermediate in breeding phenology and, with no overlap in breeding times, it is effectively reproductively isolated from either parental species through allochrony. These results provide evidence for a case of HHS in nature, and show for the first time that additivity of divergent parental traits alone can lead directly to increased hybrid fitness and reproductive isolation.
Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins
Authors: Monteuuis Geoffray , Miścicka Anna , Świrski Michał , Zenad Lounis , Niemitalo Olli , Wrobel Lidia , Alam Jahangir , Chacinska Agnieszka , Kastaniotis Alexander J , Kufel Joanna 
Published: April 2019

AbstractUtilization of non-AUG alternative translation start sites is most common in bacteria and viruses, but it has been also reported in other organisms. This phenomenon increases proteome complexity by allowing expression of multiple protein isoforms from a single gene. In Saccharomyces cerevisiae, a few described cases concern proteins that are translated from upstream near-cognate start codons as N-terminally extended variants that localize to mitochondria. Using bioinformatics tools, we provide compelling evidence that in yeast the potential for producing alternative protein isoforms by non-AUG translation initiation is much more prevalent than previously anticipated and may apply to as many as a few thousand proteins. Several hundreds of candidates are predicted to gain a mitochondrial targeting signal (MTS), generating an unrecognized pool of mitochondrial proteins. We confirmed mitochondrial localization of a subset of proteins previously not identified as mitochondrial, whose standard forms do not carry an MTS. Our data highlight the potential of non-canonical translation initiation in expanding the capacity of the mitochondrial proteome and possibly also other cellular features.
Symptoms associated with inflammatory arthritis are common in the primary care population: results from the joint symptoms survey
Authors: Hider Samantha L , Muller Sara , Helliwell Toby , Prior James A , Scott Ian , Lawton Sarah A , Zwierska Irena , van Schaardenburg Dirkjan , van der Helm-van Mil Annette , Raza Karim , Mallen Christian D 
Published: April 2019

Abstract

Objectives
To describe the prevalence of self-reported inflammatory joint symptoms, such as joint pain, stiffness and swelling, in UK primary care patients consulting for both musculoskeletal (MSK) and non-musculoskeletal (non-MSK) complaints.

Methods
A joint symptoms questionnaire survey was sent to 10 161 individuals, of whom 5050 had consulted for MSK problems. These were matched by age, gender and general practice to non-MSK consulters. Participants provided data on relevant symptoms such as joint pain, stiffness and swelling. The prevalence of these symptoms, their severity and impact were compared between MSK and non-MSK consulters.

Results
A total of 4549 adults responded to the survey (adjusted response 45.8%) of whom 52.3% consulted for a MSK problem. The mean (s.d.) age was 61.6 (14.8) years and 58.9% were female. Persistent (on at least half of the days in the last month) inflammatory symptoms were common even in non-MSK consulters, with 42% reporting joint pain, 36% reporting joint stiffness and 18% reporting joint swelling. This is in comparison with 62% reporting joint pain, 50% stiffness and 24% swelling among MSK consulters.

Conclusions
Although symptoms such as persistent joint pain, swelling and stiffness are predictive of inflammatory arthritis, large numbers of people consulting primary care for non-MSK reasons report these symptoms when asked by questionnaire. This compounds the challenges of diagnosing inflammatory arthritis in a non-specialist setting where new approaches are needed to ensure accurate, early diagnosis, facilitating a treat-to-target approach.