bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calculating the Human Mutation Rate by Using a NUMT from the Early Oligocene
Authors: Logan Ian 
Published: March 2015

AbstractAs the number of whole genomes available for study increases, so also does the opportunity to find unsuspected features hidden within our genetic code. One such feature allows for an estimate of the Human Mutation Rate in human chromosomes to be made. A NUMT is a small fragment of the mitochondrial DNA that enters the nucleus of a cell, gets captured by a chromosome and thereafter passed on from generation to generation. Over the millions of years of evolution, this unexpected phenomenon has happened many times. But it is usually very difficult to be able to say just when a NUMT might have been created. However, this paper presents evidence to show that for one particular NUMT the date of formation was around 29 million ago, which places the event in the Early Oligocene; when our ancestors were small monkey-like creatures. So now all of us carry this NUMT in each of our cells as do Old World Monkeys, the Great Apes and our nearest relations, the Chimpanzees. The estimate of the Human Mutation obtained by the method outlined here gives a value which is higher than has been generally found; but this new value perhaps only applies to non-coding regions of the Human genome where there is little, if any, selection pressure against new mutations.
Intersubject information mapping: revealing canonical representations of complex natural stimuli
Authors: Kriegeskorte Nikolaus 
Published: March 2015

AbstractReal-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM) allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space). Here we introduce the more general approach of intersubject information mapping (IIM). For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI) of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These regions appear to encode the same information across subjects in their fine-grained patterns, although their spatial-average activation was not significantly correlated between subjects.
Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud
Authors: Cianfrocco Michael A. , Leschziner Andres E. 
Published: March 2015

ABSTRACTThe advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. However, calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon’s elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters that can range in size from 16 to 480+ CPUs. Importantly, these computing clusters are also cost-effective, as we illustrate here by determining a near-atomic resolution structure of the 80S yeast ribosome for $28.89 USD in ~10 hours.
LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads
Authors: Warren René L. , Vandervalk Benjamin P. , Jones Steven J.M. , Birol Inanç 
Published: March 2015

ABSTRACTMotivationOwing to the complexity of the assembly problem, we do not yet have complete genome sequences. The difficulty in assembling reads into finished genomes is exacerbated by sequence repeats and the inability of short reads to capture sufficient genomic information to resolve those problematic regions. Established and emerging long read technologies show great promise in this regard, but their current associated higher error rates typically require computational base correction and/or additional bioinformatics preprocessing before they could be of value. We present LINKS, the Long Interval Nucleotide K-mer Scaffolder algorithm, a solution that makes use of the information in error-rich long reads, without the need for read alignment or base correction. We show how the contiguity of an ABySSE. coliK-12 genome assembly could be increased over five-fold by the use of beta-released Oxford Nanopore Ltd. (ONT) long reads and how LINKS leverages long-range information inS. cerevisiaeW303 ONT reads to yield an assembly with less than half the errors of competing applications. Re-scaffolding the colossal white spruce assembly draft (PG29, 20 Gbp) and how LINKS scales to larger genomes is also presented. We expect LINKS to have broad utility in harnessing the potential of long reads in connecting high-quality sequences of small and large genome assembly drafts.Availabilityhttp://www.bcgsc.ca/bioinformatics/software/linksContactrwarren@bcgsc.ca
Hydrogen Sulfide Regulates Inward-Rectifying K+ Channels in Conjunction with Stomatal Closure
Authors: Papanatsiou Maria , Scuffi Denisse , Blatt Michael R. , García-Mata Carlos 
Published: March 2015

Abstract
Hydrogen sulfide (H2S) is the third biological gasotransmitter, and in animals, it affects many physiological processes by modulating ion channels. H2S has been reported to protect plants from oxidative stress in diverse physiological responses. H2S closes stomata, but the underlying mechanism remains elusive. Here, we report the selective inactivation of current carried by inward-rectifying K+ channels of tobacco (Nicotiana tabacum) guard cells and show its close parallel with stomatal closure evoked by submicromolar concentrations of H2S. Experiments to scavenge H2S suggested an effect that is separable from that of abscisic acid, which is associated with water stress. Thus, H2S seems to define a unique and unresolved signaling pathway that selectively targets inward-rectifying K+ channels.
Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato
Authors: Alseekh Saleh , Tohge Takayuki , Wendenberg Regina , Scossa Federico , Omranian Nooshin , Li Jie , Kleessen Sabrina , Giavalisco Patrick , Pleban Tzili , Mueller-Roeber Bernd , Zamir Dani , Nikoloski Zoran , Fernie Alisdair R. 
Published: March 2015

Abstract
A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.
Determining the Subcellular Location of Synthesis and Assembly of the Cell Wall Polysaccharide (1,3; 1,4)-β-d-Glucan in Grasses
Authors: Wilson Sarah M. , Ho Yin Ying , Lampugnani Edwin R. , Van de Meene Allison M.L. , Bain Melissa P. , Bacic Antony , Doblin Monika S. 
Published: March 2015

Abstract
The current dogma for cell wall polysaccharide biosynthesis is that cellulose (and callose) is synthesized at the plasma membrane (PM), whereas matrix phase polysaccharides are assembled in the Golgi apparatus. We provide evidence that (1,3;1,4)-β-d-glucan (mixed-linkage glucan [MLG]) does not conform to this paradigm. We show in various grass (Poaceae) species that MLG-specific antibody labeling is present in the wall but absent over Golgi, suggesting it is assembled at the PM. Antibodies to the MLG synthases, cellulose synthase-like F6 (CSLF6) and CSLH1, located CSLF6 to the endoplasmic reticulum, Golgi, secretory vesicles, and the PM and CSLH1 to the same locations apart from the PM. This pattern was recreated upon expression of VENUS-tagged barley (Hordeum vulgare) CSLF6 and CSLH1 in Nicotiana benthamiana leaves and, consistent with our biochemical analyses of native grass tissues, shown to be catalytically active with CSLF6 and CSLH1 in PM-enriched and PM-depleted membrane fractions, respectively. These data support a PM location for the synthesis of MLG by CSLF6, the predominant enzymatically active isoform. A model is proposed to guide future experimental approaches to dissect the molecular mechanism(s) of MLG assembly.
Building from Scratch: New Cities, Privatized Urbanism and the Spatial Restructuring of Johannesburg after Apartheid
Authors: Herbert Claire W. , Murray Martin J. 
Published: March 2015

AbstractBy the start of the twenty‐first century, the once dominant historical downtown core of Johannesburg had lost its privileged status as the center of business and commercial activities, the metropolitan landscape having been restructured into an assemblage of sprawling, rival edge cities. Real estate developers have recently unveiled ambitious plans to build two completely new cities from scratch: Waterfall City and Lanseria Airport City (formerly called Cradle City) are master‐planned, holistically designed ‘satellite cities’ built on vacant land. While incorporating features found in earlier city‐building efforts, these two new self‐contained, privately‐managed cities operate outside the administrative reach of public authority and thus exemplify the global trend toward privatized urbanism. Waterfall City, located on land that has been owned by the same extended family for nearly 100 years, is spearheaded by a single corporate entity. Lanseria Airport City/Cradle City is a planned ‘aerotropolis’ surrounding the existing Lanseria airport at the northwest corner of the Johannesburg metropole. These two new private cities differ from earlier large‐scale urban projects because everything from basic infrastructure (including utilities, sewerage, and the installation and maintenance of roadways), landscaping, security services, the regulation of common spaces, and selling and branding the city are firmly in the hands of private profit‐making corporate entities and outside the mandate of public authorities.
fuzzySim: applying fuzzy logic to binary similarity indices in ecology
Authors: Barbosa A. Márcia 
Published: March 2015

Summary

Binary similarity indices are widely used in ecology, for example for detecting associations between species occurrence patterns, comparing regional and temporal species assemblages, and assessing beta diversity patterns, including spatial and temporal species loss and turnover. Such indices have widespread applications in biogeography, global change biology and biodiversity conservation.

Similarity indices are commonly calculated upon binary presence/absence (or sometimes modelled suitable/unsuitable) data, which are generally incomplete and more categorical than their underlying natural patterns. Probable false absences are disregarded, amplifying the effects of data deficiencies and the scale dependence of the results.

Fuzzy occurrence data, with a degree of uncertainty attributed to localities where presence or absence cannot be safely assigned, could better reflect species distributions, compensating for incomplete knowledge and methodological errors. Similarity indices would therefore also benefit from accommodating such fuzzy data directly.

This study proposes fuzzy versions of the binary similarity indices most commonly used in ecology, so that they can be directly applied to continuous (fuzzy) rather than binary occurrence values, thus producing more realistic similarity assessments. Fuzzy occurrence can be obtained with several methods, some of which are also provided. The procedure is robust to data source disparities, gaps or other errors in species occurrence records, even for restricted species for which slight inaccuracies can affect substantial parts of their range.

The method is implemented in a free and open‐source software package, fuzzySim, which is available for the r statistical software and under implementation for the QGIS geographic information system. It is provided with sample data and an illustrated tutorial suitable for non‐experienced users.
Effects of Case Studies and Simulated Patients on Students' Nursing Care Plan
Authors: Karadag Mevlude , Calıskan Nurcan , Iseri Ozge 
Published: March 2015

PurposeThe aim of this study is to determine the effects of using case studies and simulated patients in teaching students to plan their nursing care.MethodsThe study sample consisted of 70 second‐year nursing students. Study data were collected using a questionnaire and by evaluating students' nursing care plans.ResultsThe highest percentages of diagnoses identified were altered oral mucous membrane, ineffective breathing pattern, disturbed sleep pattern: less than body requirement, impaired tissue integrity, pain, and risk for infection.ConclusionsThe use of simulated patients in nursing education appears to help students evaluate realistic medical cases and clinical problems, and plan their nursing care.AmaçÇalışma, vaka çalışması ve simüle hasta kullanımının öğrencilerin hemşirelik bakımını planlamaları üzerine etkisini belirlemek amacıyla yapılmıştır.MetodÇalışmanın örneklemini, hemşirelik ikinci sınıfında okuyan 70 öğrenci oluşturmuştur. Çalışmanın verileri, araştırmacılar tarafından hazırlanan soru formu ve öğrencilerin hazırladıkları bakım planları ile toplanmıştır.BulgularÖğrencilerin en fazla belirledikleri hemşirelik tanıları Oral Mukoz Membranda Değişim, Etkisiz Solunum Örüntüsü, Uyku Biçiminde bozulma, Beslenmede Değişim: Gereksinimden Az, Doku bütünlüğünde Bozulma, Ağrı ve Enfeksiyon Riski'dir.SonuçHemşirelik eğitiminde simüle hastaların kullanımının, öğrencilerin gerçeğe en yakın tıbbi durumları, klinik problemleri değerlendirebilmelerine ve hemşirelik bakımını planlamalarına katkı sağladığı düşünülmektedir.
Self‐disinfecting sink drains reduce the Pseudomonas aeruginosa bioburden in a neonatal intensive care unit
Authors: Fusch Christoph , Pogorzelski David , Main Cheryl , Meyer Carrie‐Lynn , el Helou Salhab , Mertz Dominik 
Published: March 2015

AbstractAimWater in sink drains is a known source of gram‐negative bacteria. We aimed to evaluate the impact of self‐disinfecting sink drains on the emission of aerosolised bacteria and on Pseudomonas aeruginosa acquisition among neonates.MethodsAerosol bacterial growth and patient Pseudomonas aeruginosa acquisition rates were measured at baseline (Phase One), for 13 months after sinks were relocated or redesigned during refurbishment (Phase Two) and for 13 months after introducing self‐disinfecting sink drains (Phase Three).ResultsCultures were positive for bacterial growth in 56%, 24% and 13% of the tested aerosols in Phases One, Two and Three, respectively. Comparing Phases Two and Three produced an odds ratio (OR) of 0.47, with a 95% confidence interval (CI) of 0.22–0.99 (p = 0.047), for all bacteria and an OR of 0.31 and CI of 0.12–0.79 (p = 0.013) for Pseudomonas aeruginosa. Rates of Pseudomonas aeruginosa positive clinical cultures were 0.34, 0.27 and 0.13 per 1000 patient days during the respective phases, with a significant increase of time to the next positive clinical culture in Phase Three.ConclusionSelf‐disinfecting sink drains were superior to sink replacements in preventing emissions from aerosols pathogens and may reduce hospital‐acquired infections. The bioburden reduction should be confirmed in a larger multicentre trial.
Increased incidence of malignant melanoma and other rare cutaneous cancers in the setting of chronic lymphocytic leukemia
Authors: Brewer Jerry D. , Shanafelt Tait D. , Call Timothy G. , Cerhan James R. , Roenigk Randall K. , Weaver Amy L. , Otley Clark C. 
Published: March 2015

AbstractBackgroundPatients with chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), or non‐Hodgkin lymphoma (NHL) are at increased risk for the development of skin malignancies.ObjectivesThis study was conducted to estimate the incidences of rare skin malignancies in patients with CLL/SLL or NHL.MethodsPatients with a diagnosis of CLL/SLL or NHL recorded in the Surveillance, Epidemiology and End Results (SEER) database during 1992–2007 were identified. Diagnoses of specific skin malignancies were identified from SEER files.ResultsDuring 1992–2007, a total of 128,674 patients with first diagnoses of CLL/SLL or NHL were recorded in SEER; 4743 were excluded because follow‐up data were unavailable. Among the remaining 123,931 patients, 28,964 had CLL/SLL and 94,967 had NHL. Standardized incidence ratios (SIRs) for invasive malignant melanoma, Merkel cell carcinoma, malignant fibrous histiocytoma, dermatofibrosarcoma protuberans, Kaposi's sarcoma, and sebaceous carcinoma were 2.3, 8.2, 3.6, 2.5, 2.9, and 1.4, respectively, in CLL/SLL patients and 1.6, 3.2, 1.5, 1.3, 17.6, and 0.8, respectively, in NHL patients. When invasive melanoma was stratified by patient age and sex, the highest SIR (17.8) was found in men aged 0–49 years with CLL (P < 0.001).ConclusionsPatients with CLL/SLL or NHL have a higher risk for the subsequent development of rare skin cancers. Given the more aggressive nature of these malignancies in this setting, regular monitoring for the development and prompt treatment of cutaneous malignancy is prudent in patients with NHL and particularly in patients with CLL. Regular use of sun protection may decrease the morbidity associated with skin cancer in this immunosuppressed population.
Onychomadesis after hand‐foot‐and‐mouth disease outbreak in northern Greece: case series and brief review of the literature
Authors: Apalla Zoe , Sotiriou Eleni , Pikou Olga , Lefaki Ioanna , Lallas Aimilios , Lazaridou Elizabeth , Ioannides Demetris 
Published: March 2015

AbstractBackgroundNail abnormalities in childhood are generally uncommon. Recently, onychomadesis was described as a late complication of hand‐foot‐and‐mouth disease (HFMD). Onychomadesis outbreaks following HFMD have been reported in many countries worldwide.AimTo present a case series of onychomadesis in children, following HFMD outbreak in Northern Greece, and review literature data.MethodsChildren with evident onychomadesis attending the outpatient clinic between November 2012 and January 2013 were included in the study. A questionnaire including demographic personal and family history information of the children was completed by the parents. Patients were clinically examined, and their pediatric and dermatological records were studied to confirm precedent HFMD. Direct microscopic examination and cultures for fungi were performed. Exposure of participants to coxsackievirus, based on serology testing during infection, was also recorded.ResultsSixty‐eight children with onychomadesis were included. The mean number of affected nails was 8.82. Fingernails were more often involved. Previous clinical diagnosis of HFMD was confirmed in 67/68 cases. The mean time from HFMD diagnosis to onychomadesis development was 39.6 days (range: 28–56 days, STD: 7.33). Direct microscopic examination, as well as cultures for fungal species, was negative for the whole sample size. All the nail changes were transient with spontaneous regrowth after 1–4 months.ConclusionOur data indicate that onychomadesis outbreak in the region of Thessaloniki during fall–winter 2012–13 was highly related to the outbreak of HFMD. Our study reinforces existing evidence for the association between onychomadesis and HFMD.
Effect of Vitamin D Replacement on Atrial Electromechanical Delay in Subjects with Vitamin D Deficiency
Authors: CANPOLAT UĞUR , YAYLA ÇAĞRI , AKBOĞA MEHMET KADRI , ÖZCAN ELIF HANDE , TURAK OSMAN , ÖZCAN FIRAT , TOPALOĞLU SERKAN , ARAS DURSUN 
Published: March 2015

AEMD and Vitamin D DeficiencyObjectivesLimited data are available regarding cardiac arrhythmias in vitamin D (VitD) deficiency. Therefore, we aimed to assess whether atrial electromechanical delay (AEMD) measured by tissue Doppler imaging (TDI), which is an indicator for atrial fibrillation (AF) development, is prolonged in patients with VitD deficiency as compared to the control group. The effect of vitD replacement on AEMD was also evaluated.MethodsIn this prospective study a total of 28 VitD‐deficient and 56 age‐, gender‐, and BMI‐matched VitD‐sufficient healthy participants were enrolled. P‐wave dispersion (PWd) was calculated on the 12‐lead electrocardiogram. Both intra‐ and inter‐AEMD were calculated by TDI. Measurements were performed at baseline in both groups and were repeated after 6‐month replacement therapy in subjects with vitD deficiency.ResultsPWd and inter‐ and left intra‐AEMD were significantly prolonged in patients with VitD deficiency compared to the control group (P < 0.001). While serum 25(OH)D levels were significantly and negatively correlated with left intra‐AEMD (r = −0.657, P < 0.001), there was a positive correlation between serum 25(OH)D level and PWd (r = 0.523, P < 0.001). The serum 25(OH)D level was found as the independent predictor of the both left intra‐ and inter‐AEMD in the multivariate linear regression analysis (β:−0.552, P < 0.001 and β:−0.555, P < 0.001, respectively). The serum 25(OH)D level was significantly increased after replacement therapy. While inter‐AEMD was significantly decreased (P = 0.013), there was no change in PWD and left and right intra‐AEMD (P > 0.05) following replacement therapy.ConclusionPWd and left intra‐ and inter‐AEMD are increased in patients with VitD deficiency. The serum 25(OH)D level was found as an independent predictor for AEMD in patients with VitD deficiency. Also a significant decrement was observed in inter‐AEMD following vitD replacement therapy. Studies with longer follow‐up are needed to investigate whether vitD‐deficient patients with prolonged AEMD develop clinical arrhythmia and vitD replacement reduces the risk of atrial arrhythmias.