bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity of Pneumocystis jirovecii from a cluster of cases of pneumonia in renal transplant patients: Cross‐sectional study
Authors: Ricci Giannina , Santos Daniel Wagner , Kovacs Joseph A. , Nishikaku Angela Satie , de Sandes‐Freitas Taina Veras , Rodrigues Anderson Messias , Kutty Geetha , Affonso Regina , Silva Hélio Tedesco , Medina‐Pestana José Osmar , de Franco Marcello Fabiano , Colombo Arnaldo Lopes 
Published: July 2018

SummaryPneumocystis jirovecii can cause severe potentially life‐threatening pneumonia (PCP) in kidney transplant patients. Prophylaxis of patients against PCP in this setting is usually performed during 6 months after transplantation. The aim of this study is to describe the molecular epidemiology of a cluster of PCP in renal transplant recipients in Brazil. Renal transplant patients who developed PCP between May and December 2011 had their formalin‐fixed paraffin‐embedded (FFPE) lung biopsy samples analysed. Pneumocystis jirovecii 23S mitochondrial large subunit of ribosomal RNA (23S mtLSU‐rRNA), 26S rRNA, and dihydropteroate synthase (DHPS) genes were amplified by polymerase chain reaction (PCR), sequenced, and analysed for genetic variation. During the study period, 17 patients developed PCP (only four infections were documented within the first year after transplantation) and six (35.3%) died. Thirty FFPE samples from 11 patients, including one external control HIV‐infected patient, had fungal DNA successfully extracted for further amplification and sequencing for all three genes. A total of five genotypes were identified among the 10 infected patients. Of note, four patients were infected by more than one genotype and seven patients were infected by the same genotype. DNA extracted from FFPE samples can be used for genotyping; this approach allowed us to demonstrate that multiple P. jirovecii strains were responsible for this cluster, and one genotype was found infecting seven patients. The knowledge of the causative agents of PCP may help to develop new initiatives for control and prevention of PCP among patients undergoing renal transplant and improve routine PCP prophylaxis.
Exploring the putative role of kallikrein‐6, calpain‐1 and cathepsin‐D in the proteolytic degradation of α‐synuclein in multiple system atrophy
Authors: Kiely A. P. , Miners J. S. , Courtney R. , Strand C. , Love S. , Holton J. L. 
Published: July 2018

AimsThere is evidence that accumulation of α‐synuclein (α‐syn) in Parkinson's disease (PD) and dementia with Lewy bodies (DLB) results from impaired removal of α‐syn rather than its overproduction. Kallikrein‐6 (KLK6), calpain‐1 (CAPN1) and cathepsin‐D (CTSD) are among a small number of proteases that cleave α‐syn and are dysregulated in PD and DLB. Our aim in this study was to determine whether protease activity is altered in another α‐synucleinopathy, multiple system atrophy (MSA), and might thereby modulate the regional distribution of α‐syn accumulation.MethodsmRNA and protein level and/or activity of KLK6, CAPN1 and CTSD were measured and assessed in relation to α‐syn load in multiple brain regions (posterior frontal cortex, caudate nucleus, putamen, occipital cortex, pontine base and cerebellar white matter), in MSA (n = 20) and age‐matched postmortem control tissue (n = 20).ResultsCTSD activity was elevated in MSA in the pontine base and cerebellar white matter. KLK6 and CAPN1 levels were elevated in MSA in the putamen and cerebellar white matter. However, the activity or level of these proteolytic enzymes did not correlate with the regional distribution of α‐syn.ConclusionsAccumulation of α‐syn in MSA is not due to reduced activity of the proteases we have studied. We suggest that their upregulation is likely to be a compensatory response to increased α‐syn in MSA.
Fatalism and the Logic of Unconditionals
Authors: Bledin Justin 
Published: July 2018

AbstractIn this paper, I consider a variant of the ancient Idle Argument involving so‐called “unconditionals” with interrogative antecedents. This new Idle Argument provides an ideal setting for probing the logic of these close relatives ofif‐conditionals, which has been comparatively underexplored. In the course of refuting the argument, I argue that contrary to received wisdom, many unconditionals do not entail their main clauses, yetmodus ponensis still unrestrictedly valid for this class of expressions. I make these lessons precise in a formal system drawing on recent work in inquisitive semantics. My larger aim is to challenge standard truth preservation accounts of logic and deductive argumentation.
Plant‐made E2 glycoprotein single‐dose vaccine protects pigs against classical swine fever
Authors: Laughlin Richard C. , Madera Rachel , Peres Yair , Berquist Brian R. , Wang Lihua , Buist Sterling , Burakova Yulia , Palle Sreenath , Chung Chungwon J. , Rasmussen Max V. , Martel Erica , Brake David A. , Neilan John G. , Lawhon Sara D. , Adams L. Garry , Shi Jishu , Marcel Sylvain 
Published: July 2018

AbstractClassical Swine Fever Virus (CSFV) causes classical swine fever, a highly contagious hemorrhagic fever affecting both feral and domesticated pigs. Outbreaks of CSF in Europe, Asia, Africa and South America had significant adverse impacts on animal health, food security and the pig industry. The disease is generally contained by prevention of exposure through import restrictions (e.g. banning import of live pigs and pork products), localized vaccination programmes and culling of infected or at‐risk animals, often at very high cost. Current CSFV‐modified live virus vaccines are protective, but do not allow differentiation of infected from vaccinated animals (DIVA), a critical aspect of disease surveillance programmes. Alternatively, first‐generation subunit vaccines using the viral protein E2 allow for use of DIVA diagnostic tests, but are slow to induce a protective response, provide limited prevention of vertical transmission and may fail to block viral shedding. CSFV E2 subunit vaccines from a baculovirus/insect cell system have been developed for several vaccination campaigns in Europe and Asia. However, this expression system is considered expensive for a veterinary vaccine and is not ideal for wide‐spread deployment. To address the issues of scalability, cost of production and immunogenicity, we have employed an Agrobacterium‐mediated transient expression platform in Nicotiana benthamiana and formulated the purified antigen in novel oil‐in‐water emulsion adjuvants. We report the manufacturing of adjuvanted, plant‐made CSFV E2 subunit vaccine. The vaccine provided complete protection in challenged pigs, even after single‐dose vaccination, which was accompanied by strong virus neutralization antibody responses.
High‐throughput development of SSR marker candidates and their chromosomal assignment in rye (Secale cereale L.)
Authors: Li Jianjian , Zhou Ruonan , Endo Takashi R. , Stein Nils 
Published: July 2018

AbstractShotgun survey sequences of flow‐sorted individual rye chromosomes were data mined for the presence of simple sequence repeats (SSRs). For 787,850 putative SSR loci, a total of 358,660 PCR primer pairs could be designed and 51,138 nonredundant SSR marker candidates were evaluated by in silico PCR. Of the 51,138 SSR primer candidates, 1,277 were associated with 1,125 rye gene models. A total of 2,112 of the potential SSR markers were randomly selected to represent about equal numbers for each of the rye chromosomes, and 856 SSRs were assigned to individual rye chromosomes experimentally. Potential transferability of rye SSRs to wheat and barley was of low efficiency with 4.3% (2,189) and 0.4% (223) of rye SSRs predicted to be amplified in wheat and barley, respectively. This data set of rye chromosome‐specific SSR markers will be useful for the specific detection of rye chromatin introgressed into wheat as well as for low‐cost genetic and physical mapping in rye without the need for high‐tech equipment.
The phylogeny of the genus Indoplanorbis (Gastropoda, Planorbidae) from Africa and the French West Indies
Authors: Mouahid Gabriel , Clerissi Camille , Allienne Jean‐François , Chaparro Cristian , Al Yafae Salem , Mintsa Nguema Rodrigue , Ibikounlé Moudachirou , Moné Hélène 
Published: July 2018

AbstractIndoplanorbis exustus is a freshwater snail known as the intermediate host of various trematode parasites, including different species of the genus Schistosoma. Although its genetic diversity is well described in Asia, the phylogenetic diversity of strains from Africa and Guadeloupe (French West Indies) and their relationship to Asian and South‐East Asian strains remain unknown. To tackle this issue, we sampled individuals from Africa and Guadeloupe, and we computed phylogenetic reconstructions using five molecular markers: partial sequences of two mitochondrial genes, cox1 and 16S, and three nuclear markers, ITS1, ITS2 (Internal Transcribed Spacer 1 and 2) and 5.8S. Our results suggest that strains in Africa and Guadeloupe come from Asia and that they all belong to a single clade that is widespread around the globe.
Evaluation of patient-reported outcome measurements as a reliable tool to measure acceptability of the taste of paediatric medicines in an inpatient paediatric population
Authors: Mistry Punam , Stirling Heather , Callens Claire , Hodson James , Batchelor Hannah 
Published: July 2018

ObjectiveTo evaluate the age appropriateness and suitability of patient-reported outcome measures to assess the acceptability of the taste of oral liquid medicines in children.Design and settingAn observational mixed-methods study involving children aged 2–16 years taking oral liquid medicine in paediatric inpatient wards across the West Midlands (UK). Assessment tools included patient-reported scores on the taste of medicines via a five-point Facial Hedonic Scale; a Visual Analogue Scale (VAS); a question, ‘Did you think the medicine tasted OK?’ and researcher observations of facial expressions and behaviours immediately before, during and after administration.Results611 children participated. The percent unable to complete the scales was 7% (n=46) for the VAS; 2% (n=15) for the hedonic scale and 1% (n=7) for the question about taste. Significant correlations (Spearman’s r) were observed between the patient-reported outcome measures: 0.80 and 0.78 for the taste question and hedonic and VAS, respectively, and 0.84 for the hedonic and VAS. Researcher observations demonstrated the ability of the patient to take the medicine as intended but did not provide sensitive measures of taste. 5% of administrations were not taken as intended by the children. Medicines known to have poor taste (clarithromycin and prednisolone) showed mean hedonic and VAS scores of ≥3.5 and >65 mm, respectively.ConclusionsPatient-reported outcome measures correlate with each other and are a useful means to assess the taste (and acceptability) of medicines. Hedonic scales are better understood by children and should be the first choice tool in the assessment of medicines taste.
Synthesis, processing and electron paramagnetic resonance response of Y1.98Eu0.02O3 micro rods
Authors: Santos S. C. , Rodrigues O. , Campos L. L. 
Published: July 2018

Innovating dosimetric materials, which includes design and development of new dosimetric materials based on rare earth oxides, is challenging. Yttrium oxide (Y[Formula: see text]O[Formula: see text] is one of the most important sesquioxides and presents crystal characteristics that enable doping with rare earth ions, making it a promising material for radiation dosimetry. This paper reports on the development and measurement of Electron Paramagnetic Resonance (EPR) signal response for Y[Formula: see text]Eu[Formula: see text]O[Formula: see text][Formula: see text]micro rods that have undergone facile low-pressure hydrothermal synthesis and bio-prototyping. As- synthesized powders with narrow sub-micrometer particle size distribution with d[Formula: see text][Formula: see text] of 584 nm exhibited a reactive surface, which led to the formation of stable aqueous suspensions by controlling the surface charge density of particles through alkaline pH adjustment. Ceramic samples with dense microstructure were formed by sintering at 1600 [Formula: see text]C for 4h at ambient atmosphere. Y[Formula: see text]Eu[Formula: see text]O[Formula: see text][Formula: see text]micro rods were irradiated using a [Formula: see text]Co source with doses from 1 to 100 kGy, and EPR spectra were measured at room temperature in X-band microwave frequencies. Sintered samples exhibited linearity of the main EPR signal response from 10 Gy to 10 kGy. Supralinearity was observed for higher doses, which is possibly ascribed to formation of more defects. Using europium as a dopant enhanced the EPR signal of yttrium rods remarkably, due to 4f–4f transitions of the Eu[Formula: see text] ion. These innovative findings make europium-doped yttrium oxide a promising material for radiation dosimetry.
Investigating artifacts associated with β-particle interactions in charge-coupled devices
Authors: Newton Rosie , Scott Mike J. , Joyce Malcolm J. 
Published: July 2018

Charge-coupled devices (CCDs) show potential for detecting charged particles and ionizing radiation. In particular, the clusters in the pixel images produced can be distinctive for [Formula: see text] and [Formula: see text] radiation, with [Formula: see text] particles causing symmetrical clusters or vertical tracks, and [Formula: see text] particles causing long, curved tracks. This distinction may be exploited by means of a handheld, portable device for in-situ detection, and identification of radioactive contamination. [Formula: see text]-particle track interactions in CCDs have been investigated. Simulative results using CASINO (Monte Carlo Simulation of Electron Trajectory in Solids) attempt to predict the size of [Formula: see text]-particle pixel clusters, using 512 keV and 310 keV electrons to represent [Formula: see text]Cs and [Formula: see text]Co, respectively. The number of pixels that higher-energy electrons traversed peaked at two, while lower-energy electrons had a smaller peak of 2.5 pixels, with a higher proportion of large cluster sizes. This finding is consistent with the higher scattering cross-section for lower-energy [Formula: see text] particles. By contrast, experimental data show a peak at one pixel for both sources, owing to the addition of smaller [Formula: see text] clusters. The [Formula: see text]Co source shows a higher proportion of large cluster sizes than the [Formula: see text]Cs, as was also seen in the simulation; however, the difference was small, as these sources are similar in energy. Simulative and experimental data will be used to process the CCD images further, with the objective of distinguishing between [Formula: see text] and [Formula: see text] radiation. Investigations have also been carried out using a [Formula: see text]Po [Formula: see text] particle source. Horizontal streaks were seen in the images produced, with an average length of 14 pixels. Further research will be performed using an accelerator to obtain different [Formula: see text]-particle energies.
Pursuit disorder and saccade dysmetria after caudal fastigial inactivation in the monkey
Authors: Bourrelly Clara , Quinet Julie , Goffart Laurent 
Published: July 2018

The caudal fastigial nuclei (cFN) are the output nuclei by which the medio-posterior cerebellum influences the production of saccadic and pursuit eye movements. We investigated the consequences of unilateral inactivation on the pursuit eye movement made immediately after an interceptive saccade toward a centrifugal target. We describe here the effects when the target moved along the horizontal meridian with a 10 or 20°/s speed. After muscimol injection, the monkeys were unable to track the present location of the moving target. During contralesional tracking, the velocity of postsaccadic pursuit was reduced. This slowing was associated with a hypometria of interceptive saccades such that gaze direction always lagged behind the moving target. No correlation was found between the sizes of saccade undershoot and the decreases in pursuit speed. During ipsilesional tracking, the effects on postsaccadic pursuit were variable across the injection sessions, whereas the interceptive saccades were consistently hypermetric. Here also, the ipsilesional pursuit disorder was not correlated with the saccade hypermetria either. The lack of correlation between the sizes of saccade dysmetria and changes of postsaccadic pursuit speed suggests that cFN activity exerts independent influences on the neural processes generating the saccadic and slow eye movements. It also suggests that the cFN is one locus where the synergy between the two motor categories develops in the context of tracking a moving visual target. We explain how the different fastigial output channels can account for these oculomotor tracking disorders. NEW & NOTEWORTHY Inactivation of the caudal fastigial nucleus impairs the ability to track a moving target. The accuracy of interceptive saccades and the velocity of postsaccadic pursuit movements are both altered, but these changes are not correlated. This absence of correlation is not compatible with an impaired common command feeding the circuits producing saccadic and pursuit eye movements. However, it suggests an involvement of caudal fastigial nuclei in their synergy to accurately track a moving target.
Data-Driven Approach to Identify Subgroups of Heart Failure With Reduced Ejection Fraction Patients With Different Prognoses and Aldosterone Antagonist Response Patterns
Authors: Ferreira João Pedro , Duarte Kevin , McMurray John J.V. , Pitt Bertram , van Veldhuisen Dirk J. , Vincent John , Ahmad Tariq , Tromp Jasper , Rossignol Patrick , Zannad Faiez 
Published: July 2018

Background:
Patients with heart failure with reduced ejection fraction have a poor prognosis. The identification of subgroups with different outcomes and treatment response patterns may help to tailor strategies to each individual patient. We present an exploratory study of patients enrolled in the EMPHASIS-HF trial (Eplerenone in Patients With Systolic Heart Failure and Mild Symptoms) using latent class analysis with validation using the EPHESUS trial (Eplerenone, a Selective Aldosterone Blocker, in Patients With Left Ventricular Dysfunction After Myocardial Infarction) to identify subgroups of patients with different prognosis and response to eplerenone therapy.

Methods and Results:

Latent class analysis identifies mutually exclusive groups of individuals maximizing within-group similarities and between-group differences. In the EMPHASIS-HF trial, 2279 heart failure with reduced ejection fraction patients were randomized to eplerenone or placebo and were characterized according to 18 clinical features. Subgroup definitions were applied to 6472 patients enrolled in the EPHESUS trial to validate observations. Event-free survival and effect of eplerenone on the composite of cardiovascular death and heart failure hospitalization were determined for each subgroup. Four subgroups were identified with significant differences in event-free survival (
P
=0.002). The subgroup C had the worst event-free survival in both studies and was characterized by older age, lower body mass index, worse renal function, higher baseline potassium levels, high prevalence of anemia, diabetes mellitus, previous revascularization and higher rates of eplerenone discontinuation, and hyperkalemia during follow-up. Two subgroups (B and C) showed a poorer response to eplerenone in both studies and these groups shared common features such as lower body mass index and high prevalence of anemia. Clinical profiles, prognosis, and treatment response patterns of the 4 subgroups applied in EPHESUS trial presented similarities to those observed in EMPHASIS.

Conclusions:
Using a data-driven approach, we identified heart failure with reduced ejection fraction subgroups with significantly different prognoses and potentially different responses to eplerenone. However, these data should be regarded as hypothesis-generating and prospective validation is warranted, to assess the potential clinical implications of these subgroups.

Clinical Trial Registration:

URL:
https://www.clinicaltrials.gov
. Unique identifier: NCT00232180.
The Application of the Pilot Judgment Procedure and Other Forms of Handling Large-Scale Dysfunctions in the Case Law of the European Court of Human Rights
Authors: Czepek Jakub 
Published: July 2018

Abstract
Over the years, the Pilot Judgment Procedure has become a common element of the Strasbourg landscape. Since the first pilot judgment in the case of Broniowski v. Poland in 2004, the procedure is now a well-recognised mechanism for solving systemic and structural problems. Nevertheless, it is not the only measure of solving large-scale dysfunctions arising from the legal systems of States Parties to the European Convention on Human Rights. The European Court of Human Rights (ECrtHR) has developed several mechanisms designed to eradicate systemic and structural problems, such as: Quasi-Pilot Judgments, Third Tier Judgments, Simplified Committee Procedure, Grouped Judgments, Joined Judgments, Judgments of Principle, and other methods, concerning mostly effective “Case-Management”. This article presents and analyses these methods used by the ECrtHR in order to eliminate structural and systemic problems and dysfunctions.
Reply to “Comments on ‘Revisiting the Balanced and Unbalanced Aspects of Tropical Cyclone Intensification’”
Authors: Heng Junyao , Wang Yuqing , Zhou Weican 
Published: July 2018

Abstract
In their comment, Montgomery and Smith critique the recent study of Heng et al. that revisited the balanced and unbalanced aspects of tropical cyclone (TC) intensification based on diagnostics of a full-physics model simulation using the Sawyer–Eliassen equation. Heng et al. showed that the balanced dynamics reproduced to a large extent the secondary circulation in the full-physics model simulation and concluded that balanced dynamics can well explain TC intensification in their full-physics model simulation. Montgomery and Smith suspect the balanced solution in Heng et al. because the basic-state vortex is not exactly in thermal wind balance in the boundary layer and possibly a too-large diffusivity in the numerical model was used. In this reply, we first indicate that the boundary layer spinup mechanism proposed by Smith et al. is a fast response of the TC boundary layer to surface friction and should not be a major mechanism of TC intensification. We then evaluate the possible effect of imbalance in the basic state in the boundary layer on the balanced solution. The results show that although the removal of the imbalance in the boundary layer leads to about a one-third reduction in the maximum inflow near the surface in the inner-core region, the overall effect on the tangential wind budget is marginal because of other compensations. We also show that both the horizontal and vertical diffusivities in the model used in Heng et al. are reasonable based on previous observational studies. Therefore, we conclude that all results in Heng et al. are valid. Some related issues are also discussed.