bluuebunny/crossref_metadata_2025_split huggingface dataset:
What is harmful for male fertility: Cell phone or the wireless internet?
Authors: Yildirim Mehmet Erol , Kaynar Mehmet , Badem Huseyin , Cavis Mucahıt , Karatas Omer Faruk , Cimentepe Ersın 
Published: July 2015

AbstractIn this study, we aimed to assess the potential harmful effects of radiofrequency‐electromagnetic radiation on sperm parameters. We requested semen for analyses from the male patients coming to our infertility division and also asked them to fill out an anonymous questionnaire. We queried their mobile phone and wireless internet usage frequencies in order to determine their radiofrequency‐electromagnetic radiation exposure. A total of 1082 patients filled the questionnaire but 51 of them were excluded from the study because of azoospermia. There was no significant difference between sperm counts and sperm morphology excluding sperm motility, due to mobile phone usage period, (p = 0.074, p = 0.909, and p = 0.05, respectively). The total motile sperm count and the progressive motile sperm count decreased due to the increase of internet usage (p = 0.032 and p = 0.033, respectively). In line with the total motile sperm count, progressive motile sperm count also decreased with wireless internet usage compared with the wired internet connection usage (p = 0.009 and p = 0.018, respectively). There was a negative correlation between wireless internet usage duration and the total sperm count (r = −0.089, p = 0.039). We have also explored the negative effect of wireless internet use on sperm motility according to our preliminary results.
Is late‐onset Alzheimer's disease really a disease of midlife?
Authors: Ritchie Karen , Ritchie Craig W. , Yaffe Kristine , Skoog Ingmar , Scarmeas Nikolaos 
Published: July 2015

AbstractIntroductionIncreasing evidence suggests that Alzheimer's disease (AD) may begin decades before evidence of dementia, indicating that it may be a disorder of midlife rather than old age.MethodsIn the absence of long‐term prospective studies from early adulthood specifically designed to address this question, a group of international experts examined evidence presently available from previous clinical and population studies to provide an evidence‐based opinion as to whether such a change in conceptualization may be justified.ResultsAlthough still lacking confirmation from dedicated prospective biomarker studies, there is already considerable evidence to suggest both risk factor exposure and brain changes may be already present in midlife.DiscussionCurrent evidence suggests (1) that a change in clinical approach notably involving promotion of cardiovascular health in persons with a family history of AD may considerably reduce disease risk and (2) that the development of biomarkers at this early stage will lead to the possibility of clinical trials at a much earlier stage.
Delayed‐start analysis: Mild Alzheimer's disease patients in solanezumab trials, 3.5 years
Authors: Liu‐Seifert Hong , Siemers Eric , Holdridge Karen C. , Andersen Scott W. , Lipkovich Ilya , Carlson Christopher , Sethuraman Gopalan , Hoog Sharon , Hayduk Roza , Doody Rachelle , Aisen Paul 
Published: July 2015

AbstractIntroductionSolanezumab is an anti‐amyloid monoclonal antibody in clinical testing for treatment of Alzheimer's disease (AD). Its mechanism suggests the possibility of slowing the progression of AD.MethodsA possible disease‐modifying effect of solanezumab was assessed using a new statistical method including noninferiority testing. Performance differences were compared during the placebo‐controlled period with performance differences after the placebo patients crossed over to solanezumab in the delayed‐start period.ResultsNoninferiority of the 14‐item Alzheimer's Disease Assessment Scale‐Cognitive subscale (ADAS‐Cog14) and Alzheimer's Disease Cooperative Study Activities of Daily Living inventory instrumental items (ADCS‐iADL) differences was met through 132 weeks, indicating that treatment differences observed in the placebo‐controlled period remained, within a predefined margin, after the placebo group initiated solanezumab. Solanezumab was well tolerated, and no new safety concerns were identified.DiscussionThe results of this secondary analysis show that the mild subgroup of solanezumab‐treated patients who initiated treatment early, at the start of the placebo‐controlled period, retained an advantage at most time points in the delayed‐start period.
Stereotactic brain injection of human umbilical cord blood mesenchymal stem cells in patients with Alzheimer's disease dementia: A phase 1 clinical trial
Authors: Kim Hee Jin , Seo Sang Won , Chang Jong Wook , Lee Jung Il , Kim Chi Hun , Chin Juhee , Choi Soo Jin , Kwon Hunki , Yun Hyuk Jin , Lee Jong Min , Kim Sung Tae , Choe Yearn Seong , Lee Kyung‐Han , Na Duk L. 
Published: July 2015

AbstractIntroductionWe conducted a phase 1 clinical trial in nine patients with mild‐to‐moderate Alzheimer's disease to evaluate the safety and dose‐limiting toxicity of stereotactic brain injection of human umbilical cord blood–derived mesenchymal stem cells (hUCB‐MSCs).MethodsThe low‐ (n = 3) and high‐dose (n = 6) groups received a total of 3.0 × 106 cells/60 μL and 6.0 × 106 cells/60 μL, respectively, into the bilateral hippocampi and right precuneus.ResultsNo patient showed serious adverse events including fever during the 24‐month follow‐up period. During the 12‐week follow‐up period, the most common acute adverse event was wound pain from the surgical procedure (n = 9), followed by headache (n = 4), dizziness (n = 3), and postoperative delirium (n = 3). There was no dose‐limiting toxicity.DiscussionAdministration of hUCB‐MSCs into the hippocampus and precuneus by stereotactic injection was feasible, safe, and well tolerated. Further trials are warranted to test the efficacy.Clinical Trial RegistrationClinicalTrial.gov identifier NCT01297218 and NCT01696591.
Conserving and managing mosaics in Libya (CaMMiL): the final project review
Authors: Wootton William T. , El-Habashi Alaa , Stewart John D. , Walda Hafed 
Published: July 2015

AbstractThis is a review of a project aimed at assisting the Libyan Department of Archaeology with the conservation and management of their mosaic heritage. Over the course of a year we undertook an evaluation trip along the coast of Libya and then put on two workshops for the Department's staff to help build capacity. The workshops disseminated complementary content on the protection of mosaics and their management to two different contingents: managers and technicians. The teaching was intended to empower Libyans by giving them the confidence to make simple and sound decisions, and to encourage them to join more formal training courses run by major international organisations. The project was a collaboration with the Department and was supported by the Getty Foundation, King's College London and the Society for Libyan Studies.
UNIQUENESS FOR SINGULAR SEMILINEAR ELLIPTIC BOUNDARY VALUE PROBLEMS II
Authors: HAI D. D. , SMITH R. C. 
Published: July 2015

AbstractWe prove uniqueness of positive solutions for the boundary value problem

\begin{equation*}
\left\{
\begin{array}{l}
-\Delta u=\lambda f(u)\text{ in }\Omega , \\
\ \ \ \ \ \ \ u=0\text{ on }\partial \Omega ,
\end{array}
\right.
\end{equation*}

where Ω is a bounded domain in $\mathbb{R}$n with smooth boundary ∂ Ω, λ is a large positive parameter, f:(0,∞) → [0,∞) is nonincreasing for large t and is allowed to be singular at 0.
Quality of preimplantation embryos recovered in vivo from dairy cows in relation to their body condition
Authors: Makarevich A.V. , Stádník L. , Kubovičová E. , Hegedüšová Z. , Holásek R. , Louda F. , Beran J. , Nejdlová M. 
Published: July 2015

SummaryThis study examined the impact of cow body condition on the quality of bovine preimplantation embryos. The embryos (n = 107) were flushed from dairy cows and classified according to a five-point scale body condition score (BCS2 n = 17; BCS3 n = 31; BCS4 n = 11) on the 7th day after insemination and then analyzed for development, dead cell index (DCI), cell number and actin cytoskeleton quality. The highest embryo recovery rate (P < 0.05) was recorded in the BCS3 group and the lowest in the BCS4 group. More transferable (morula, blastocyst) embryos were obtained from the BCS4 cows (79%), compared with the BCS2 (64%) or BCS3 (63%) animals. However, cell numbers were higher in the BCS2 and BCS3 groups (P < 0.05) compared with the BCS4 embryos. Conversely, the DCI was lowest in the BCS2 (3.88%; P < 0.05) and highest in the BCS4 (6.56%) embryos. The proportion of embryos with the best actin quality (grade I) was higher in the BCS2 and BCS3 cows compared with the BCS4 group. Almost 25% of all embryos showed fragmented morphology and a higher DCI (5.65%) than normal morulas (1.76%). More fragmented embryos were revealed in the BCS2 (28.6%) and BCS4 (31.25%) groups, and less (19.15%) in the BCS3 group. The cell numbers in such embryos were lower in the BCS4 (22.57) than in the BCS2 (46.25) or BCS3 (42.4) groups. In conclusion, the body condition of dairy cows affects the quality of preimplantation embryos. A BCS over 3.0 resulted in a higher incidence of poor (fragmented) embryos.
Surgically treated pulmonary stenosis: over 50 years of follow-up
Authors: Nielsen Eva A. , Hjortdal Vibeke E. 
Published: July 2015

AbstractBackgroundSurgical correction was the treatment of choice for pulmonary stenosis until three decades ago, when balloon valvuloplasty was implemented. The natural history of surgically relieved pulmonary stenosis has been considered benign but is actually unknown, as is the need for re-intervention.The objective of this study was to investigate the morbidity and mortality of patients with surgically treated pulmonary stenosis operated at Aarhus University Hospital between 1957 and 2000.ResultsThe total study population included 80 patients. In-hospital mortality was 2/80 (2.5%), and an additional four patients died after hospital discharge; therefore, the long-term mortality was 5%. The maximum follow-up period was 57 years, with a median of 33 years. In all, 16 patients (20%) required at least one re-intervention. Pulmonary valve replacement due to pulmonary regurgitation was the most common re-intervention (67%). Freedom from re-intervention decreased >20 years after the initial repair. In addition, 45% of patients had moderate/severe pulmonary regurgitation, 38% had some degree of right ventricular dilatation, and 40% had some degree of tricuspid regurgitation, which did not require re-intervention at the present stage.ConclusionSurgical relief for pulmonary stenosis is efficient in relieving outflow obstruction; however, this efficiency is achieved at the cost of pulmonary regurgitation, leading to right ventricular dilatation and tricuspid regurgitation. When required, pulmonary valve replacement is performed most frequently >20 years after the initial surgery. Lifelong follow-up of patients treated surgically for pulmonary stenosis is emphasised in this group of patients, who might otherwise consider themselves cured.
Sudden cardiac death associated with premature atheroma in the young: an autopsy study emphasising single-vessel lesions
Authors: Green Anna C. , Sheppard Mary N. 
Published: July 2015

AbstractAimsThis is the first autopsy study in the United Kingdom to analyse the demographic and pathological characteristics of atheroma associated with sudden cardiac death in young people.MethodsAn observational retrospective study of referred cases of sudden cardiac death in the young (⩽35 years) associated with premature atheroma was carried out.ResultsIn total, 46 cases were referred, with a median age of 30 years (27, 32); 72% of the referred cases were male, with a mean body mass index of 30 kg/m2. Circumstances of death were as follows: at rest (n=21), exertion (n=7), in bed (n=7), related to drugs/alcohol (n=4), and unknown (n=7). A previous cardiac history was provided in 10 cases. A history of class A/B drug use was found in eight cases. There was macroscopic evidence of infarction in 10 cases (acute, n=3 and chronic, n=7). Microscopically, 10 cases demonstrated contraction band necrosis, 11 acute infarction, and 11 chronic infarction. Single-vessel disease predominated (n=28). The left anterior descending coronary artery was involved in 39/46 cases. Thrombosis was seen in 16 cases, mainly due to erosion; one case showed dual pathology with arrhythmogenic right ventricular cardiomyopathy and another showed left ventricular hypertrophy.ConclusionsThis study highlights premature atheroma mainly in a single vessel in young people with or without evidence of ischaemic damage in the ventricle. Dual pathology may occur. The role of arrhythmias and channelopathies are important considerations. Premature atheroma should prompt investigation for dyslipidaemias in family members.
Export of environmental goods: India's potential and constraints
Authors: Nguyen Van Son , Kalirajan Kaliappa 
Published: July 2015

AbstractUsing data from the period 1996–2010, this paper identifies the nature of constraints that make India, which is one of the emerging environmental goods and services (EGS) exporters, unable to realize its export potential of environmental goods (EG). The empirical results show that the growth of India's exports of EG was negatively affected by ‘behind the border’ constraints such as weak infrastructure and institutions, while the effect of ‘explicit beyond the border’ constraints such as partner countries' tariffs and exchange rates on the exports of EG was relatively small. The reduction of India's trading partners' ‘implicit beyond the border’ constraints such as weak infrastructure and institutions significantly contributed toward India's exports of EG, especially during the period 2005–2010.
The motivation and actions of Australians concerning brain health and dementia risk reduction
Authors: Smith Ben J. , Ali Suha , Quach Henry 
Published: July 2015

Issue addressedAlzheimer's disease and dementia are recognised as critical public health priorities. This study investigated intentions and behaviours concerning brain health and dementia risk reduction among Australians.MethodsA cross‐sectional survey of 1000 persons aged 20–75 years measured knowledge, beliefs, intentions and behaviours concerning brain health and dementia. The demographic, experiential and cognitive factors associated with intentions and actions were examined.ResultsAround half of respondents were motivated to improve brain health. Behaviours most often reported were mental activity (19%), physical activity (9.6%) and dietary action (6.5%). Actions were most likely among women (OR 1.59, 95% CI 1.19–2.14), those aged 60 years and over (OR 3.07, 95% CI 2.01–2.58), with university education (OR 1.67, 95% CI 1.08–2.58) or with prior contact with a person with dementia (OR 1.99, 95% CI 1.12–3.56). Both intentions and actions were associated with moderate to high knowledge, and beliefs and confidence that favoured dementia risk reduction.ConclusionsA lower proportion of Australians reported taking action to improve brain health than who expressed intentions in this regard. Strategies are needed to improve knowledge about the range of behaviours that contribute to dementia risk reduction and to increase confidence that this outcome is personally achievable.
Spaced seeds improvek-mer-based metagenomic classification
Authors: Břinda Karel , Sykulski Maciej , Kucherov Gregory 
Published: July 2015

AbstractMotivation: Metagenomics is a powerful approach to study genetic content of environmental samples, which has been strongly promoted by next-generation sequencing technologies. To cope with massive data involved in modern metagenomic projects, recent tools rely on the analysis of k-mers shared between the read to be classified and sampled reference genomes.Results: Within this general framework, we show that spaced seeds provide a significant improvement of classification accuracy, as opposed to traditional contiguous k-mers. We support this thesis through a series of different computational experiments, including simulations of large-scale metagenomic projects.Availability and implementation, Supplementary information: Scripts and programs used in this study, as well as supplementary material, are available from http://github.com/gregorykucherov/spaced-seeds-for-metagenomics.Contact: gregory.kucherov@univ-mlv.fr
Mapping networks of light–dark transition in LOV photoreceptors
Authors: Kaur Grewal Rajdeep , Mitra Devrani , Roy Soumen 
Published: July 2015

Abstract
Motivation: In optogenetics, designing modules of long or short signaling state lifetime is necessary for control over precise cellular events. A critical parameter for designing artificial or synthetic photoreceptors is the signaling state lifetime of photosensor modules. Design and engineering of biologically relevant artificial photoreceptors is based on signaling mechanisms characteristic of naturally occurring photoreceptors. Therefore identifying residues important for light–dark transition is a definite first step towards rational design of synthetic photoreceptors. A thorough grasp of detailed mechanisms of photo induced signaling process would be immensely helpful in understanding the behaviour of organisms.
Results: Herein, we introduce the technique of differential networks. We identify key biological interactions, using light-oxygen-voltage domains of all organisms whose dark and light state crystal structures are simultaneously available. Even though structural differences between dark and light states are subtle (other than the covalent bond formation between flavin chromophore and active site Cysteine), our results successfully capture functionally relevant residues and are in complete agreement with experimental findings from literature. Additionally, using sequence-structure alignments, we predict functional significance of interactions found to be important from network perspective yet awaiting experimental validation. Our approach would not only help in minimizing extensive photo-cycle kinetics procedure but is also helpful in providing first-hand information on the fundamentals of photo-adaptation and rational design of synthetic photoreceptors in optogenetics.
Contact: devrani.dbs@presiuniv.ac.in or soumen@jcbose.ac.in
Supplementary information: Supplementary data are available at Bioinformatics online.
Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data
Authors: Kumar Runjun D. , Searleman Adam C. , Swamidass S. Joshua , Griffith Obi L. , Bose Ron 
Published: July 2015

Abstract
Motivation: Several tools exist to identify cancer driver genes based on somatic mutation data. However, these tools do not account for subclasses of cancer genes: oncogenes, which undergo gain-of-function events, and tumor suppressor genes (TSGs) which undergo loss-of-function. A method which accounts for these subclasses could improve performance while also suggesting a mechanism of action for new putative cancer genes.
Results: We develop a panel of five complementary statistical tests and assess their performance against a curated set of 99 HiConf cancer genes using a pan-cancer dataset of 1.7 million mutations. We identify patient bias as a novel signal for cancer gene discovery, and use it to significantly improve detection of oncogenes over existing methods (AUROC = 0.894). Additionally, our test of truncation event rate separates oncogenes and TSGs from one another (AUROC = 0.922). Finally, a random forest integrating the five tests further improves performance and identifies new cancer genes, including CACNG3, HDAC2, HIST1H1E, NXF1, GPS2 and HLA-DRB1.
Availability and implementation : All mutation data, instructions, functions for computing the statistics and integrating them, as well as the HiConf gene panel, are available at www.github.com/Bose-Lab/Improved-Detection-of-Cancer-Genes.
Contact: rbose@dom.wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The MI bundle: enabling network and structural biology in genome visualization tools
Authors: Céol Arnaud , Müller Heiko 
Published: July 2015

Abstract
Summary: Prioritization of candidate genes emanating from large-scale screens requires integrated analyses at the genomics, molecular, network and structural biology levels. We have extended the Integrated Genome Browser (IGB) to facilitate these tasks. The graphical user interface greatly simplifies building disease networks and zooming in at atomic resolution to identify variations in molecular complexes that may affect molecular interactions in the context of genomic data. All results are summarized in genome tracks and can be visualized and analyzed at the transcript level.
Availability and implementation: The MI Bundle is a plugin for the IGB. The plugin, help, video and tutorial are available at http://cru.genomics.iit.it/igbmibundle/ and https://github.com/CRUiit/igb-mi-bundle/wiki. The source code is released under the Apache License, Version 2.
Contact: arnaud.ceol@iit.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Magna Carta: Its Confirmation at Simon de Montfort’s Parliament of 1265
Authors: Ambler S.T. 
Published: July 2015

Abstract
During the course of the parliament held between January and March 1265 by the revolutionary council led by Simon de Montfort, earl of Leicester, Henry III confirmed Magna Carta. Although the significance of Montfort’s parliament has been debated throughout the intervening centuries, its role in the story of Magna Carta has generally been forgotten. This is probably because it is not generally appreciated that the text of the 1265 confirmation of Magna Carta still survives. The confirmation was not enrolled on the Charter Rolls and no engrossments have been discovered. Yet the text has been preserved in four copies, three of them giving the witness list detailing those who endorsed the confirmation. It supplies extremely valuable evidence for the nature of the Montfortian support base at this momentous parliament, as well as for the strategies that Montfort’s council pursued to entrench its authority. It is the purpose of the present article to bring attention to this little-known text, to make its contents more accessible by providing a transcription and translation and to discuss its context and significance.
Applying Phytophthora ramorum Inoculum to Hosts: A New Method That Simulates Overhead Irrigation
Authors: Rollins Lucy , Elliott Marianne , Chastagner Gary 
Published: July 2015

The inoculum threshold for Phytophthora ramorum in irrigation water required for infection of plant material was investigated using a novel pressurized device designed to deliver zoospore inoculum in a way that simulated certain aspects of overhead irrigation. The measured-inoculum spray applicator (MISA) was made from plastic plumbing parts and worked by spraying measured volumes of pressurized zoospore inoculum onto plant material through an adjustable misting nozzle attached to the bottom of the device. Pressurization and spraying of P. ramorum zoospores through the MISA did not significantly affect zoospore viability or infectivity on wounded and non-wounded detached Rhododendron x ‘Nova Zembla’ leaves under controlled laboratory conditions. An inoculum threshold of 51 zoospores/ml was found for infection of Rhododendron leaves by P. ramorum using regression analysis. The MISA can potentially be used to simulate overhead irrigation in research involving pathogenic Phytophthora spp., and the results of the current research may assist nursery managers, property owners, and regulatory agencies in assessing the risk of using P. ramorum infested water for irrigation within nurseries and private landscapes. Accepted for publication 19 June 2015. Published 26 June 2015.