bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highlighting the goals for Parkinson’s care: commentary on NICE Guidelines for Parkinson’s in Adults (NG71)
Authors: Brock Peter , Fisher James M , Hand Annette , Walker Richard W 
Published: September 2018

AbstractParkinson’s disease is a chronic multi-system disease that can cause motor and non-motor symptoms, cognitive changes and variably effective medications. Optimal management of the condition requires a multi-disciplinary team of healthcare professionals to work closely with the patient and their carers. The National Institute for Health and Care Excellence published updated guidelines on managing Parkinson’s disease in adults in 2017. Here we discuss the implications of this guidance to current healthcare professionals involved in the care of people with Parkinson’s disease.The guidance highlights the importance of clear communication with people with Parkinson’s disease. We discuss examples of this, including providing a point of contact with specialist services for people with Parkinson’s disease and ensuring information about the risks of impulse control disorders are given to people on dopaminergic therapy. The breadth of services required by people with Parkinson’s disease is also described, including the need for access to physiotherapy, occupational therapy and speech and language therapy as well as treatment monitoring services for Clozapine. In addition, we emphasise the continued importance of ensuring people with Parkinson’s disease receive their medications on time when in hospital or a care home.
Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing
Authors: Budis Jaroslav , Gazdarica Juraj , Radvanszky Jan , Szucs Gabor , Kucharik Marcel , Strieskova Lucia , Gazdaricova Iveta , Harsanyova Maria , Duris Frantisek , Minarik Gabriel , Sekelska Martina , Nagy Balint , Turna Jan , Szemes Tomas 
Published: September 2018

Abstract

Motivation
Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test.

Results
We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls.

Availability and implementation
The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda.

Supplementary information
Supplementary materials are available at Bioinformatics online.
Trajectories and Milestones of Cortical and Subcortical Development of the Marmoset Brain From Infancy to Adulthood
Authors: Sawiak S J , Shiba Y , Oikonomidis L , Windle C P , Santangelo A M , Grydeland H , Cockcroft G , Bullmore E T , Roberts A C 
Published: September 2018

Abstract
With increasing attention on the developmental causes of neuropsychiatric disorders, appropriate animal models are crucial to identifying causes and assessing potential interventions. The common marmoset is an ideal model as it has sophisticated social/emotional behavior, reaching adulthood within 2 years of birth. Magnetic resonance imaging was used in an accelerated longitudinal cohort (n = 41; aged 3–27 months; scanned 2–7 times over 2 years). Splines were used to model nonlinear trajectories of grey matter volume development in 53 cortical areas and 16 subcortical nuclei. Generally, volumes increased before puberty, peaked, and declined into adulthood. We identified 3 milestones of grey matter development: I) age at peak volume; II) age at onset of volume decline; and III) age at maximum rate of volume decline. These milestones differentiated growth trajectories of primary sensory/motor cortical areas from those of association cortex but also revealed distinct trajectories between association cortices. Cluster analysis of trajectories showed that prefrontal cortex was the most heterogenous of association regions, comprising areas with distinct milestones and developmental trajectories. These results highlight the potential of high-field structural MRI to define the dynamics of primate brain development and importantly to identify when specific prefrontal circuits may be most vulnerable to environmental impact.
Modeling Cornelia de Lange syndrome in vitro and in vivo reveals a role for cohesin complex in neuronal survival and differentiation
Authors: Bottai Daniele , Spreafico Marco , Pistocchi Anna , Fazio Grazia , Adami Raffaella , Grazioli Paolo , Canu Adriana , Bragato Cinzia , Rigamonti Silvia , Parodi Chiara , Cazzaniga Gianni , Biondi Andrea , Cotelli Franco , Selicorni Angelo , Massa Valentina 
Published: September 2018

AbstractCornelia de Lange syndrome (CdLS), which is reported to affect ∼1 in 10 000 to 30 000 newborns, is a multisystem organ developmental disorder with relatively mild to severe effects. Among others, intellectual disability represents an important feature of this condition. CdLS can result from mutations in at least five genes: nipped-B-like protein, structural maintenance of chromosomes 1A, structural maintenance of chromosomes 3, RAD21 cohesin complex component and histone deacetylase 8 (HDAC8). It is believed that mutations in these genes cause CdLS by impairing the function of the cohesin complex (to which all the aforementioned genes contribute to the structure or function), disrupting gene regulation during critical stages of early development. Since intellectual disorder might result from alterations in neural development, in this work, we studied the role of Hdac8 gene in mouse neural stem cells (NSCs) and in vertebrate (Danio rerio) brain development by knockdown and chemical inhibition experiments. Underlying features of Hdac8 deficiency is an increased cell death in the developing neural tissues, either in mouse NSCs or in zebrafish embryos.
Guatemala City youth: an analysis of health indicators through the lens of a clinical registry
Authors: Golub Sarah A , Maza Reyes Juan Carlos , Stamoulis Catherine , Leal Pensabene Alejandra , Tijerino Cordón Pablo Alejandro , Calgua Erwin , Hassan Areej 
Published: September 2018

Abstract

Background
Despite the inclusion of adolescent health in recent global frameworks, limited data exist on health indicators in low-income countries. Our objective was to identify socioeconomic measures, risk behaviors and health indicators of young people in Guatemala.

Methods
We conducted a secondary data analysis of the Pan American Health Organization’s Sistema Informático del Adolescente of 2831 participants ages 10–24 y from 2008 to 2014. We examined frequencies for a core set of items, and generalized regression models assessed correlations between age, sex and ethnicity with health outcomes of interest.

Results
Fewer than 17% of participants reported a history of chronic illness (16.6%) and severe psychological problems (16.8%). While 66.1% of participants’ mothers and 36.6% of fathers reported job instability, far fewer families had housing instability (1.9% with no electricity, 6.3% with no running water). Fewer than one-third (29.1%) were sexually active and the majority (76.0%) routinely used condoms. About one-quarter (22.6%) reported abnormal mood. Indigenous participants were significantly more likely to have experienced psychological problems (odds ratio [OR] 1.75 [confidence interval {CI} 1.65–1.86]) and violence (OR 1.34 [CI 1.27–1.42]) compared with whites.

Conclusions
The prevalence of risk behaviors and mental health concerns is low compared with other sources of national and regional data. Further work is needed to examine the benefits and limitations of this system in order to improve health surveillance.
Outcomes of Retreatment for Intracranial Aneurysms — A Meta-Analysis
Authors: Muskens Ivo S , Hertgers Omar , Lycklama à Nijeholt Geert J , Broekman Marike L D , Moojen Wouter A 
Published: September 2018

Abstract

BACKGROUND
Long-term results from the International Subarachnoid Hemorrhage Trial (ISAT) and Barrow Ruptured Aneurysm Trial (BRAT) indicate considerably higher retreatment rates for aneurysms treated with coiling compared to clipping, but do not report the outcome of retreatment.

OBJECTIVE
To evaluate retreatment related outcomes.

METHODS
A meta-analysis in accordance with PRISMA guidelines was conducted using Medline search engines PubMed and EMBASE to identify articles describing outcomes after retreatment for intracranial aneurysms. Pooled prevalence rates for complete occlusion rate and mortality were calculated. Outcomes of different treatment and retreatment combinations were not compared because of indication bias.

RESULTS
Twenty-five articles that met the inclusion criteria were included in the meta-analysis. Surgery after coiling had a pooled complete occlusion rate of 91.2% (95% confidence interval [CI]: 87.0-94.1) and a pooled mortality rate of 5.6% (95% CI: 3.7-8.3). Coiling after coiling had a pooled complete occlusion rate of 51.3% (95% CI: 22.1-78.0) and a pooled mortality rate of 0.8% (95% CI: 0.15-3.7). Surgery after surgery did not provide a pooled estimate for complete occlusion as only one study was identified but had a pooled mortality rate of 5.9% (95% CI: 3.1-11.2). Coiling after surgery had a pooled complete occlusion rate of 56.1% (95% CI: 11.4-92.7) and a pooled mortality rate of 9.3% (95% CI: 4.1-19.9). All pooled incidence rates were produced using random-effect models.

CONCLUSION
Surgical retreatment was associated with a high complete occlusion rate but considerable mortality. Conversely, endovascular retreatment was associated with low mortality but also a low complete occlusion rate.
ESTIMATION OF ORGAN DOSES AND EFFECTIVE DOSES BASED ON IN-PHANTOM DOSIMETRY FOR INFANT DIAGNOSTIC CARDIAC CATHETERISATIONS WITH NOVEL X-RAY IMAGING TECHNOLOGY
Authors: Kawasaki Toshio , Sakakubo Masami , Ito Kanako 
Published: September 2018

Abstract
The present study evaluated the organ and effective doses in infant diagnostic cardiac catheterisation performed using a modern x-ray imaging unit by in-phantom dosimetry. In addition, conversion factors from dose–area product (DAP) to effective dose were determined. The organ and effective doses in 1-year old during diagnostic cardiac catheterisations were measured using radiophotoluminescence glass dosemeters implanted into an infant anthropomorphic phantom. The mean effective doses, evaluated according to the International Commission on Radiologic Protection Publication 103, were 4.0 mSv (range: 1.5–8.7 mSv). The conversion factors from DAP to effective dose were 2 and 3.5 mSv (Gy cm2)−1 for posteroanterior and lateral fluoroscopy, respectively, and 1.8 and 3.3 mSv (Gy cm2)−1 for posteroanterior and lateral cineangiography, respectively. The dose data and conversion factors evaluated in the present study may be useful for estimating radiation exposure in infants during diagnostic cardiac catheterisation.
NATURAL RADIOACTIVITY AND EVALUATION OF RADIATION HAZARDS IN SOILS FROM GRANITOIDE-GRANITE GEOLOGICAL FORMATION IN CUBA
Authors: Alonso-Hernández C M , Toledo-Sibello A L , Guillén-Arruebarrena A , Sibello-Hernández R , Morera-Gómez Y , Cartas-Águila H A 
Published: September 2018

Abstract
The natural radioactivity and the associated radiation hazards of soils from the Cumanayagua Granitoide-Granitic massif in the central south of Cuba have been studied. Mass activities of the natural radionuclides 238U, 232Th and 40K varied in the ranges 10.4–33, 4.6–21.7 and 381–1201 Bq kg−1, respectively. The radium equivalent activity (91.4 ± 22.1 Bq kg−1), absorbed dose rate (45.6 ± 11.1 nGy h−1), annual effective dose rate (56.1 ± 13.7 μSv y−1) and the external hazard index (0.25 ± 0.06) have been calculated and compared with the internationally approved values. According to these results, the area can be regarded as an area with normal natural background radiation and may not pose radiological risks to the inhabitants owing to harmful effects of ionizing radiation from the natural radionuclides in soils. This study provides background radioactivity concentrations in Cumanayagua Granitoide area and generate a baseline data for radiological mapping of Cuba in the future.
uORF-Tools – Workflow for the determination of translation-regulatory upstream open reading frames
Authors: Scholz Anica , Eggenhofer Florian , Gelhausen Rick , Grüning Björn , Zarnack Kathi , Brüne Bernhard , Backofen Rolf , Schmid Tobias 
Published: September 2018

AbstractRibosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5’ untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools identifies uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.
FirstSV: Fast and Accurate Approach of Structural Variations Detection for Short DNA fragments
Authors: Shen Jia , Zuo Qiyang , Wang Rongliang , Li Xiang , Tang Yuanhua 
Published: September 2018

ABSTRACTStructural variations caused by gene fusion represent a major class of somatically acquired variations in human malignancies, and include deletions, inversions, and translocations. Short fragmented reads are the main source of data from 2nd-generation sequencing, and detecting structural variations from this type of data is different from that of 1st-generation sequencing, where the read length is much longer. Current detection methods are low in specificity and are inefficient. We developed a hybrid algorithm, FirstSV, to meet the clinical demand for fast and accurate structural variation detection. Its main features include cluster analysis, realignment, and local assembly. FirstSV was validated with simulated data, with data from real patient samples, with data from standard testing samples, and with downloaded public data sets. FirstSV outperforms public-available methods in terms of sensitivity, precision, and operational efficiency. FirstSV is freely available at https://github.com/shenjia1/FirstSV.
Uncovering a role for the dorsal hippocampal commissure in episodic memory
Authors: Postans M , Parker GD , Lundell H , Ptito M , Hamandi K , Gray WP , Aggleton JP , Dyrby TB , Jones DK , Winter M 
Published: September 2018

AbstractThe dorsal hippocampal commissure (DHC) is a white matter tract that provides inter-hemispheric connections between temporal lobe brain regions. Despite the importance of these regions for learning and memory, there is scant evidence of a role for the DHC in successful memory performance. We used diffusion-weighted MRI (DW-MRI) and white matter tractography to reconstruct the DHC across both humans (in vivo) and nonhuman primates (ex vivo). Across species, our findings demonstrate close consistency between the known anatomy and tract reconstructions of the DHC. Anterograde tract-tracer techniques also highlighted the parahippocampal origins of DHC fibers in nonhuman primates. Finally, we derived Diffusion Tensor MRI (DT-MRI) metrics from the DHC in a large sample of human subjects to investigate whether inter-individual variation in DHC microstructure is predictive of memory performance. The mean diffusivity of the DHC was correlated with performance in a standardised episodic memory task; an effect that was not reproduced in a comparison commissure tract – the anterior commissure. These findings highlight a role for the DHC in episodic memory, and our tract reconstruction approach has the potential to generate further novel insights into the role of this previously understudied white matter tract in both health and disease.
Genome based meta-QTL analysis of grain weight in tetraploid wheat identifies rare alleles ofGRF4associated with larger grains
Authors: Avni Raz , Oren Leah , Shabtai Gai , Assili Siwar , Pozniak Curtis , Hale Iago , Ben-David Roi , Peleg Zvi , Distelfeld Assaf 
Published: September 2018

AbstractThe domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTLs) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession ‘Zavitan’ and durum wheat variety ‘Svevo’. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four SNPs between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele ofTtGRF4-Athat also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, positTtGRF4-Aas a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles ofTtGRF4-Ahave potential to increase wheat yields in breeding programs.
HSCs Contribute Actively to Native Multilineage Hematopoiesis but With Reduced Differentiation Capacity Upon Aging
Authors: Säwén Petter , Eldeeb Mohamed , Erlandsson Eva , Kristiansen Trine A , Laterza Cecilia , Kokaia Zaal , Karlsson Göran , Yuan Joan , Soneji Shamit , Mandal Pankaj K. , Rossi Derrick J , Bryder David 
Published: September 2018

ABSTRACTA hallmark of adult hematopoiesis is the continuous replacement of blood cells with limited lifespans. It is well established that adult hematopoietic stem cells (HSCs) are active contributors to these processes after transplantation, yet their role in native hematopoiesis has recently been called into question. Here, we use inducible lineage tracing from genetically marked adult HSCs to explore their roles in the steady state. We show that adult HSCs contribute robustly to all lineages via intermediate progenitor cells, but with neglible production of hematopoietic cells with a known fetal origin. We further reveal that the timing for regeneration of distinct blood lineages varies substantially. Finally, HSC contribution to multilineage hematopoiesis in aged animals declines with increasing age. Therefore, while HSCs are active contributors to native adult hematopoiesis, it appears that the numerical increase of HSCs is a physiologically relevant compensatory mechanism to account for a reduced differentiation capacity with age.
Cortical Mechanisms for Reaches Versus Saccades: Progression of Effector-Specificity Through Target Memory to Movement Planning and Execution
Authors: Cappadocia David C. , Monaco Simona , Chen Ying , Crawford J. Douglas 
Published: September 2018

AbstractEffector-specific cortical mechanisms can be difficult to establish using fMRI, in part because low time resolution might temporally conflate different signals related to target representation, motor planning, and motor execution. Here, we used an event-related fMRI protocol and a cue-separation paradigm to temporally separate these three major sensorimotor stages for saccades vs. reaches. In each trial, subjects (N=12) 1) briefly viewed a target 4-7° left or right of midline fixation on a touchscreen, followed by an 8 second delay (effector-independent target memory phase), 2) were instructed by an auditory cue to perform a reach or a saccade, followed by a second delay of 8 seconds (effector-specific planning phase), and finally 3) were prompted to move by reaching-to-touch or performing a saccade towards the remembered target (effector-specific execution phase). Our analysis of saccade and reach activation (vs. a non-spatial control task) revealed modest effector-agnostic target memory activity (left AG, bilateral mIPS) followed by independent effector parietofrontal sites and time courses during the motor components of the task, specifically: more medial (pIPS, mIPS, M1, and PMd) activity during both reach planning and execution, and more lateral (mIPS, AG, and FEF) activity only during saccade execution. These motor activations were bilateral, with a left (contralateral) preference for reach. A conjunction analysis revealed that left mIPS and right AG, PCu, SPOC, FEF/PMv and LOTC showed activation for both saccades and reaches. Overall, effector-preference contrasts (reach vs. saccade) revealed significantly more parietofrontal activation for reaches than saccades during both planning and execution, with the exception of FEF. Cross-correlation of reach, saccade, and reach-saccade activation through time revealed correlated activation both within and across effectors in each hemisphere, but with a tendency toward higher correlations in the right hemisphere, especially between the eye and hand. These results demonstrate substantially independent but temporally correlated cortical networks for human eye, hand, and eye-hand control, that follow explicit spatiotemporal rules for effector-specific timing, medial-lateral distribution, and hemispheric lateralization.