bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison Between Integrated Genomic DNA/RNA Profiling and Fluorescence In Situ Hybridization in the Detection of MYC, BCL-2, and BCL-6 Gene Rearrangements in Large B-Cell Lymphomas
Authors: Cassidy Daniel P , Chapman Jennifer R , Lopez Rafael , White Kyle , Fan Yao-Shan , Casas Carmen , Severson Eric A , Vega Francisco 
Published: September 2019

Abstract

Objectives
To compare fluorescence in situ hybridization (FISH) and a commercially available sequencing assay for comprehensive genomic profiling (CGP) to determine the best approach to identify gene rearrangements (GRs) in large B-cell lymphomas (LBCLs).

Methods
Comparison of standard-of-care FISH assays (including a two-probe approach for MYC; break-apart and fusion probes) and an integrated genomic DNA/RNA sequencing CGP approach on a set of 69 consecutive LBCL cases.

Results
CGP detected GRs, including those involving MYC (1), BCL-2 (3), and BCL-6 (3), not detected by FISH. FISH detected non–IgH-MYC (4) and BCL-6 (2) GRs that were not detected by CGP. In four instances, standalone CGP or FISH testing would have missed a double-hit lymphoma.

Conclusions
CGP was superior to FISH in the detection of IgH-MYC rearrangements but was inferior for the detection of non–IgH-MYC rearrangements. Our study demonstrates the rationale for development of a customized approach to identify GRs in LBCLs.
Open-label Study with Nalmefene as Needed Use in Alcohol-Dependent Patients with Evidence of Elevated Liver Stiffness and/or Hepatic Steatosis
Authors: Mueller Sebastian , Luderer Mathias , Zhang Doris , Meulien Didier , Brach Björn Steiniger , Schou Maiken Brix 
Published: September 2019

Abstract

Aims
This open-label study in patients with alcohol dependence and evidence of elevated liver stiffness and/or hepatic steatosis was designed to explore the efficacy of nalmefene (18 mg) in reducing alcohol consumption and its subsequent effects on a variety of clinically relevant liver parameters.

Methods
Adult patients with a diagnosis of alcohol dependence and evidence of elevated liver stiffness and/or hepatic steatosis (liver stiffness >6 kPa or controlled attenuation parameter (CAP) >215 dB/m as measured by transient elastography) were recruited at two study sites in Germany. During the 12-week treatment period, patients were instructed to take nalmefene each day they perceived a risk of drinking alcohol.

Results
All 45 enrolled patients took at least one dose of nalmefene and 39 completed the study. After 12 weeks of study treatment with nalmefene patients showed a reduction in alcohol consumption of −13.5 days/month heavy drinking days and −45.8 g/day total alcohol consumption. Most liver parameters showed modest changes at Week 12; there was a 13% decrease in liver stiffness and 10% reduction in CAP values. Results indicated non-significant negative associations between alcohol consumption and liver stiffness and/or CAP over this 12-week study. Nalmefene was generally well tolerated, and most adverse events were mild or moderate, the most frequent being dizziness.

Conclusions
Patients treated with nalmefene for 12 weeks had reductions in alcohol consumption by ~50% relative to baseline and showed trends to improvement in liver stiffness and CAP.
Development of an Empirical Formula for Describing Human Inhalability of Airborne Particles at Low Wind Speeds and Calm Air
Authors: Cox Alexandra L , Handy Rodney G , Thiese Matthew S , Sleeth Darrah K 
Published: September 2019

Abstract
Based on experiments conducted in low wind speed and calm air environments, the current International Organization for Standardization (ISO) and European Committee for Standardization (CEN) convention modeling human aerosol inhalability (i.e. aspiration efficiency) may not be valid when wind speeds are less than 0.5 ms−1. Additionally, the convention is based primarily on mouth breathing data and aerosols with aerodynamic diameters smaller than 100 µm. Since the convention's development, experimental inhalation data at wind speeds lower than 0.5 ms−1 for nose, mouth, and oronasal breathing have been generated for aerosols in a wider range of sizes (1.5–135 µm). These data were gathered and modeled with the intention of providing a simple convention recommendation for inhalability in low wind speed (>0 to <0.5 ms−1) and calm air (~0 ms−1) conditions to the ISO Technical Committee (TC) 146, Subcommittee 2, Working Group (WG) 1 (‘Particle Size-Selective Sampling and Analysis'), as it relates to standard ISO 7708, and to CEN TC 137/WG 3, as it relates to standard EN 481. This paper presents several equations as possibilities, all relating aspiration efficiency to aerodynamic diameter. The equation AE=1+0.000019dae2−0.009788dae stands out as a possible new convention. This polynomial model balances simplicity and fit while addressing the weakness of the current convention.
A Hypothesis-Generating Study Using Electrophysiology to Examine Cognitive Function in Colon Cancer Patients
Authors: Hung Stanley Hughwa , Mutti Jaswal Sumeet , Neil-Sztramko Sarah Elizabeth , Kam Julia W Y , Niksirat Negin , C Handy Todd , Liu-Ambrose Teresa , Lim Howard J , Hayden Sherri , Gill Sharlene , Campbell Kristin L 
Published: September 2019

Abstract

Introduction
The purpose of this study was to describe the trajectory of cognitive function using neuropsychological tests and electrophysiological measures in individuals receiving 5FU/oxaliplatin chemotherapy for colon cancer.

Methods
A total of 10 participants were tested at baseline (within 3 weeks of starting chemotherapy), 6 months (coinciding with the end of chemotherapy treatment), and 12 months (approximately 6 months post-chemotherapy). Participants completed neuropsychological tests and electrophysiology recordings of P300 event-related potential (ERP) elicited by a sustained attention to response task paired with experience sampling of attentional states (subjective reports of on-task or mind wandering).

Results
No change in mean neuropsychological test performance was observed. Comparison of mean P300 ERP amplitudes as a function of attentional states (on-task vs. mind wandering) revealed no main effect of attentional state observed at baseline or 6 months, but a significant effect of attention was observed at 12 months, consistent with effects observed in healthy individuals.

Conclusions
Future studies can consider sustained attention constructs when studying cognitive function in colon cancer patients.
Optimal multisensory integration
Authors: Munoz Nicole E , Blumstein Daniel T 
Published: September 2019

Abstract
Animals are often confronted with potentially informative stimuli from a variety of sensory modalities. Although there is a large proximate literature demonstrating multisensory integration, no general framework explains why animals integrate. We developed and tested a quantitative model that explains why multisensory integration is not always adaptive and explains why unimodal decision-making might be favored over multisensory integration. We present our model in terms of a prey that must determine the presence or absence of a predator. A greater chance of encountering a predator, a greater benefit of correctly responding to a predator, a lower benefit of correctly foraging, or a greater uncertainty of the second stimulus favors integration. Uncertainty of the first stimulus may either increase or decrease the favorability of integration. In three field studies, we demonstrate how our model can be empirically tested. We evaluated the model with field studies of yellow-bellied marmots (Marmota flaviventer) by presenting marmots with an olfactory-acoustic predator stimulus at a feed station. We found some support for the model's prediction that integration is favored when the second stimulus is less noisy. We hope additional predictions of the model will guide future empirical work that seeks to understand the extent to which multimodal integration might be situation dependent. We suggest that the model is generalizable beyond antipredator contexts and can be applied within or between individuals, populations, or species.
Multisensory integration is often studied from a very proximate view that simply describes the process of integration. We developed a model, the first of its kind, to investigate the situations under which multisensory integration is adaptive. We empirically evaluated the model by investigating the conditions under which yellow-bellied marmots integrated predatory scents and sounds. We found that integration can depend on an animal's situation at a given point in time.
Microhabitat use and body size drive the evolution of colour patterns in snapping shrimps (Decapoda: Alpheidae: Alpheus)
Authors: Elias Marco A M , Anker Arthur , Gawryszewski Felipe M 
Published: September 2019

AbstractBackground matching and disruptive coloration are common strategies used by animals to increase concealment, whereas motion-dazzle may prevent capture after recognition. Studies have related background matching to habitat dependency and survival success, whereas for animals with highly contrasting patterns it has been shown that they are able to explore a broader range of habitats due to disruptive coloration, and possibly via motion-dazzle. However, the effects of these strategies are likely to be influenced by body size and to work better for smaller species. We applied phylogenetic comparative methods to test the hypothesis that smaller snapping shrimps (genus Alpheus) with high-contrast stripes would be able to utilize more microhabitats than non-striped and larger species. We used a published phylogeny of the American species of Alpheus, studies that have described alpheid microhabitats and size, and high-resolution photographs of each species in the phylogeny. Our categorical analysis suggested that generalist snapping shrimps are more likely to have stripes than specialist shrimps, and this effect was stronger in smaller species. Similarly, we found an interacting effect of body size and habitat use on the degree of luminance contrast: smaller generalist species had higher contrast values than average-sized and habitat-specialist species. Therefore, predators, body size and frequency of microhabitats are likely to have influenced the evolution of colour patterns in Alpheus.
TDP-43 cytoplasmic inclusion formation is disrupted in C9orf72-associated amyotrophic lateral sclerosis/frontotemporal lobar degeneration
Authors: Lee Samuel M , Asress Seneshaw , Hales Chadwick M , Gearing Marla , Vizcarra Juan C , Fournier Christina N , Gutman David A , Chin Lih-Shen , Li Lian , Glass Jonathan D 
Published: September 2019

Abstract
The G4C2 hexanucleotide repeat expansion mutation in the C9orf72 gene is the most common genetic cause underlying both amyotrophic lateral sclerosis and frontotemporal dementia. Pathologically, these two neurodegenerative disorders are linked by the common presence of abnormal phosphorylated TDP-43 neuronal cytoplasmic inclusions. We compared the number and size of phosphorylated TDP-43 inclusions and their morphology in hippocampi from patients dying with sporadic versus C9orf72-related amyotrophic lateral sclerosis with pathologically defined frontotemporal lobar degeneration with phosphorylated TDP-43 inclusions, the pathological substrate of clinical frontotemporal dementia in patients with amyotrophic lateral sclerosis. In sporadic cases, there were numerous consolidated phosphorylated TDP-43 inclusions that were variable in size, whereas inclusions in C9orf72 amyotrophic lateral sclerosis/frontotemporal lobar degeneration were quantitatively smaller than those in sporadic cases. Also, C9orf72 amyotrophic lateral sclerosis/frontotemporal lobar degeneration homogenized brain contained soluble cytoplasmic TDP-43 that was largely absent in sporadic cases. To better understand these pathological differences, we modelled TDP-43 inclusion formation in fibroblasts derived from sporadic or C9orf72-related amyotrophic lateral sclerosis/frontotemporal dementia patients. We found that both sporadic and C9orf72 amyotrophic lateral sclerosis/frontotemporal dementia patient fibroblasts showed impairment in TDP-43 degradation by the proteasome, which may explain increased TDP-43 protein levels found in both sporadic and C9orf72 amyotrophic lateral sclerosis/frontotemporal lobar degeneration frontal cortex and hippocampus. Fibroblasts derived from sporadic patients, but not C9orf72 patients, demonstrated the ability to sequester cytoplasmic TDP-43 into aggresomes via microtubule-dependent mechanisms. TDP-43 aggresomes in vitro and TDP-43 neuronal inclusions in vivo were both tightly localized with autophagy markers and, therefore, were likely to function similarly as sites for autophagic degradation. The inability for C9orf72 fibroblasts to form TDP-43 aggresomes, together with the observations that TDP-43 protein was soluble in the cytoplasm and formed smaller inclusions in the C9orf72 brain compared with sporadic disease, suggests a loss of protein quality control response to sequester and degrade TDP-43 in C9orf72-related diseases.
Ultrastructural Evidence for a Role of Astrocytes and Glycogen-Derived Lactate in Learning-Dependent Synaptic Stabilization
Authors: Vezzoli E , Calì C , De Roo M , Ponzoni L , Sogne E , Gagnon N , Francolini M , Braida D , Sala M , Muller D , Falqui A , Magistretti P J 
Published: September 2019

Abstract
Long-term memory formation (LTM) is a process accompanied by energy-demanding structural changes at synapses and increased spine density. Concomitant increases in both spine volume and postsynaptic density (PSD) surface area have been suggested but never quantified in vivo by clear-cut experimental evidence. Using novel object recognition in mice as a learning task followed by 3D electron microscopy analysis, we demonstrate that LTM induced all aforementioned synaptic changes, together with an increase in the size of astrocytic glycogen granules, which are a source of lactate for neurons. The selective inhibition of glycogen metabolism in astrocytes impaired learning, affecting all the related synaptic changes. Intrahippocampal administration of l-lactate rescued the behavioral phenotype, along with spine density within 24 hours. Spine dynamics in hippocampal organotypic slices undergoing theta burst-induced long-term potentiation was similarly affected by inhibition of glycogen metabolism and rescued by l-lactate. These results suggest that learning primes astrocytic energy stores and signaling to sustain synaptic plasticity via l-lactate.
Improving Human Action Recognition Using Hierarchical Features And Multiple Classifier Ensembles
Authors: Bulbul Mohammad Farhad , Islam Saiful , Zhou Yatong , Ali Hazrat 
Published: September 2019

AbstractThis paper presents a simple, fast and efficacious system to promote the human action classification outcome using the depth action sequences. Firstly, the motion history images (MHIs) and static history images (SHIs) are created from the front (XOY), side (YOZ) and top (XOZ) projected scenes of each depth sequence in a 3D Euclidean space through engaging the 3D Motion Trail Model (3DMTM). Then, the Local Binary Patterns (LBPs) algorithm is operated on the MHIs and SHIs to learn motion and static hierarchical features to represent the action sequence. The motion and static hierarchical feature vectors are then fed into a classifier ensemble to classify action classes, where the ensemble comprises of two classifiers. Thus, each ensemble includes a pair of Kernel-based Extreme Learning Machine (KELM) or ${\mathrm{l}}_{\mathrm{2}}$-regularized Collaborative Representation Classifier (${\mathrm{l}}_{\mathrm{2}}$-CRC) or Multi-class Support Vector Machine. To extensively assess the framework, we perform experiments on a couple of standard available datasets such as MSR-Action3D, UTD-MHAD and DHA. Experimental consequences demonstrate that the proposed approach gains a state-of-the-art recognition performance in comparison with other available approaches. Several statistical measurements on recognition results also indicate that the method achieves superiority when the hierarchical features are adopted with the KELM ensemble. In addition, to ensure real-time processing capability of the algorithm, the running time of major components is investigated. Based on machine dependency of the running time, the computational complexity of the system is also shown and compared with other methods. Experimental results and evaluation of the computational time and complexity reflect real-time compatibility and feasibility of the proposed system.
Benchmarking database systems for Genomic Selection implementation
Authors: Nti-Addae Yaw , Matthews Dave , Ulat Victor Jun , Syed Raza , Sempéré Guilhem , Pétel Adrien , Renner Jon , Larmande Pierre , Guignon Valentin , Jones Elizabeth , Robbins Kelly 
Published: September 2019

AbstractMotivationWith high-throughput genotyping systems now available, it has become feasible to fully integrate genotyping information into breeding programs. To make use of this information effectively requires DNA extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able to collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize it in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs, one would need an efficient genotyping data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems.ResultsWe found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix.Availabilityhttp://gobiin1.bti.cornell.edu:6083/projects/GBM/repos/benchmarking/browse
Iron deficiency in worsening heart failure is associated with reduced estimated protein intake, fluid retention, inflammation, and antiplatelet use
Authors: van der Wal Haye H , Grote Beverborg Niels , Dickstein Kenneth , Anker Stefan D , Lang Chim C , Ng Leong L , van Veldhuisen Dirk J , Voors Adriaan A , van der Meer Peter 
Published: September 2019

Abstract

Aims
Iron deficiency (ID) is common in heart failure (HF) patients and negatively impacts symptoms and prognosis. The aetiology of ID in HF is largely unknown. We studied determinants and the biomarker profile of ID in a large international HF cohort.

Methods and results
We studied 2357 worsening HF patients from the BIOSTAT-CHF cohort. ID was defined as transferrin saturation &lt;20%. Univariable and multivariable logistic regression models were constructed to identify determinants for ID. We measured 92 cardiovascular markers (Olink Cardiovascular III) to establish a biomarker profile of ID. The primary endpoint was the composite of all-cause mortality and first HF rehospitalization. Mean age (±standard deviation) of all patients was 69 ± 12.0 years, 26.1% were female and median N-terminal pro B-type natriuretic peptide levels (+interquartile range) were 4305 (2360–8329) ng/L. Iron deficiency was present in 1453 patients (61.6%), with highest prevalence in females (71.1% vs. 58.3%; P &lt; 0.001). Independent determinants of ID were female sex, lower estimated protein intake, higher heart rate, presence of peripheral oedema and orthopnoea, chronic kidney disease, lower haemoglobin, higher C-reactive protein levels, lower serum albumin levels, and P2Y12 inhibitor use (all P &lt; 0.05). None of these determinants were sex-specific. The biomarker profile of ID largely consisted of pro-inflammatory markers, including paraoxonase 3 (PON3) and tartrate-resistant acid phosphatase type 5. In multivariable Cox proportional hazard regression analyses, ID was associated to worse outcome, independently of predictors of ID (hazard ratio 1.25, 95% confidence interval 1.06–1.46; P = 0.007).

Conclusion
Our data suggest that the aetiology of ID in worsening HF is complex, multifactorial and seems to consist of a combination of reduced iron uptake (malnutrition, fluid overload), impaired iron storage (inflammation, chronic kidney disease), and iron loss (antiplatelets).
General practitioners' provision of end-of-life care and associations with dying at home: a registry-based longitudinal study
Authors: Kjellstadli Camilla , Allore Heather , Husebo Bettina S , Flo Elisabeth , Sandvik Hogne , Hunskaar Steinar 
Published: September 2019

Abstract

Background
General practitioners (GPs) may play an important role in providing end-of-life care to community-dwelling people.

Objective
To investigate patients' contacts with GPs, GPs' interdisciplinary collaboration, out-of-hours services and hospitalizations in the last 13 weeks of life and associations with dying at home. Second, investigate whether GP contacts were associated with fewer out-of-hours contacts or days hospitalized.

Methods
Individually linked data from the Norwegian Cause of Death Registry, Norwegian Patient Registry, Statistics Norway and Control and Payment of Reimbursement to Health Service Providers database for all 80 813 deceased people in Norway within 2012–13. Outcomes were analyzed with logistic regression and negative binomial multilevel mixed-effect models.

Results
Overall, 1% of people received GP home visits in Week 13 and 4.6% in the last week before death. During the last 4 weeks of life, 9.2% received one or more GP home visits. Altogether, 6.6% received one or more home visits when the GP had one or more interdisciplinary collaborations during the last 4 weeks, of which &lt;3% died at home. GP office consultations decreased towards the end of life. The likelihood of home death versus another location increased in relation to GP home visits [one home visit odds ratio (OR) 1.92, confidence interval (CI) 1.71–2.15; two or more OR 3.49, CI 3.08–3.96] and GP interdisciplinary collaboration (one contact OR 1.76, CI 1.59–1.96; two or more OR 2.52, CI 2.32–2.74).

Conclusions
GPs play a role in enabling people to die at home by performing home visits and collaborating with other health care personnel. Only a minority received such services in Norway.
Precarity and Aging: A Scoping Review
Authors: Grenier Amanda , Hatzifilalithis Stephanie , Laliberte-Rudman Debbie , Kobayashi Karen , Marier Patrik , Phillipson Chris 
Published: September 2019

Abstract

Background and Objective
The concept of precarity holds the potential to understand insecurities and risks experienced by older people in the contemporary social, economic, political and cultural context. This study maps existing conceptualizations of precarity in relation to aging and later life, identifies key themes, and considers the use of precarity in two subfields.

Research Design and Methods
This article presents the findings of a two-phase scoping study of the international literature on precarity in later life. Phase I involved a review of definitions and understandings of precarity and aging. Phase II explored two emerging subthemes of disability and im/migration as related to aging and late life.

Results
A total of 121 published studies were reviewed across Phase I and Phase II. Findings reveal that the definition of precarity is connected with insecurity, vulnerability, and labor and that particular social locations, trajectories, or conditions may heighten the risk of precarity in late life.

Implications and Discussion
The article concludes by outlining the need for conceptual clarity, research on the unique multidimensional features of aging and precarity, the delineation of allied concepts and emerging applications, and the importance of linking research results with processes of theory building and the development of policy directives for change.