bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality of older patients with dementia after surgery for chronic subdural hematoma: a nationwide study
Authors: Tommiska Pihla , Korja Miikka , Siironen Jari , Kaprio Jaakko , Raj Rahul 
Published: September 2020

Abstract

Background
dementia is associated with an excess risk of death but mortality after chronic subdural hematoma (CSDH) evacuation in older people with dementia is unknown. We assessed the association between dementia and 1-year case-fatality in older persons undergoing CSDH evacuation.

Methods
we conducted a nationwide Finnish cohort study including all older persons (≥60 years) undergoing CSDH evacuation during 1997–2014 (referred to as cases). We identified controls, without a diagnosis of CSDH, that were matched for age, sex and year of first hospitalisation with a new dementia diagnosis. We identified cases and controls with a pre-existing diagnosis of dementia. Outcome was 12-month mortality. Mortality was compared in case-only and case–control analyses.

Results
of 7,621 included cases, 885 (12%) had a pre-existing diagnosis of dementia. The proportion of cases increased from 9.7% in 1997–2002 to 12.2% in 2012–2014 (P = 0.038 for trend). In the case-analysis, dementia independently associated with 1-year case-fatality (dementia vs. no dementia odds ratio [OR] 1.50, 95% confidence interval [CI] 1.26–1.78). Sensitivity analysis suggested the association to be strongest for those 60–69 years old (OR 3.21, 95% CI 1.59–6.47). In the case–control matched analysis, 1-year mortality was 26% in the dementia CSDH surgery group compared to 16% in the dementia non-CSDH controls (P &lt; 0.001).

Conclusion
dementia is a significant risk factor for 1-year mortality after CSDH surgery in older people. The proportion of older CSDH patients having a pre-existing diagnosis of dementia is increasing. Thus, there is a need for improved evidence regarding the indications and benefits of CSDH evacuation among older persons.
Even when the seasons change our allometry stays the same. A Commentary on: ‘Corner’s rules pass the test of time: little effect of phenology on leaf-shoot and other scaling relationships’
Authors: Smith Duncan D 
Published: September 2020

This article comments on:
Alex Fajardo, Juan P. Mora and Etienne Robert, Corner’s rules pass the test of time: little effect of phenology on leaf–shoot and other scaling relationships, Annals of Botany, Volume 126, Issue 7, 25 November 2020, Pages 1129–1139, https://doi.org/10.1093/aob/mcaa124
Wind intensity affects fine root morphological traits with consequences for plant-soil feedback effects
Authors: Werger Luise , Bergmann Joana , Weber Ewald , Heinze Johannes 
Published: September 2020

Abstract
Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant–soil feedbacks—PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant–soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant–soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant–soil interactions under changing environmental conditions.
Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it
Authors: Nguyen Huy N , Markin Alexey , Friedberg Iddo , Eulenstein Oliver 
Published: September 2020

Abstract

Motivation
The evolution of complexity is one of the most fascinating and challenging problems in modern biology, and tracing the evolution of complex traits is an open problem. In bacteria, operons and gene blocks provide a model of tractable evolutionary complexity at the genomic level. Gene blocks are structures of co-located genes with related functions, and operons are gene blocks whose genes are co-transcribed on a single mRNA molecule. The genes in operons and gene blocks typically work together in the same system or molecular complex. Previously, we proposed a method that explains the evolution of orthologous gene blocks (orthoblocks) as a combination of a small set of events that take place in vertical evolution from common ancestors. A heuristic method was proposed to solve this problem. However, no study was done to identify the complexity of the problem.

Results
Here, we establish that finding the homologous gene block problem is NP-hard and APX-hard. We have developed a greedy algorithm that runs in polynomial time and guarantees an O(ln⁡n) approximation. In addition, we formalize our problem as an integer linear program problem and solve it using the PuLP package and the standard CPLEX algorithm. Our exploration of several candidate operons reveals that our new method provides more optimal results than the results from the heuristic approach, and is significantly faster.

Availability and implementation
The software and data accompanying this paper are available under the GPLv3 and CC0 license respectively on: https://github.com/nguyenngochuy91/Relevant-Operon.
PathFinder: Bayesian inference of clone migration histories in cancer
Authors: Kumar Sudhir , Chroni Antonia , Tamura Koichiro , Sanderford Maxwell , Oladeinde Olumide , Aly Vivian , Vu Tracy , Miura Sayaka 
Published: September 2020

Abstract

Summary
Metastases cause a vast majority of cancer morbidity and mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development. Clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells.
Here, we present a new Bayesian approach, PathFinder, for reconstructing the routes of cancer cell migrations. PathFinder uses the clone phylogeny, the number of mutational differences among clones, and the information on the presence and absence of observed clones in primary and metastatic tumors. By analyzing simulated datasets, we found that PathFinder performes well in reconstructing clone migrations from the primary tumor to new metastases as well as between metastases. It was more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor, and by increasing the number of genetic variants assayed per clone. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes.
In conclusion, we anticipate that the use of PathFinder will enable a more reliable inference of migration histories and their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and/or existing metastases.

Availability and implementation
PathFinder is available on the web at https://github.com/SayakaMiura/PathFinder.
Detecting evolutionary patterns of cancers using consensus trees
Authors: Christensen Sarah , Kim Juho , Chia Nicholas , Koyejo Oluwasanmi , El-Kebir Mohammed 
Published: September 2020

Abstract

Motivation
While each cancer is the result of an isolated evolutionary process, there are repeated patterns in tumorigenesis defined by recurrent driver mutations and their temporal ordering. Such repeated evolutionary trajectories hold the potential to improve stratification of cancer patients into subtypes with distinct survival and therapy response profiles. However, current cancer phylogeny methods infer large solution spaces of plausible evolutionary histories from the same sequencing data, obfuscating repeated evolutionary patterns.

Results
To simultaneously resolve ambiguities in sequencing data and identify cancer subtypes, we propose to leverage common patterns of evolution found in patient cohorts. We first formulate the Multiple Choice Consensus Tree problem, which seeks to select a tumor tree for each patient and assign patients into clusters in such a way that maximizes consistency within each cluster of patient trees. We prove that this problem is NP-hard and develop a heuristic algorithm, Revealing Evolutionary Consensus Across Patients (RECAP), to solve this problem in practice. Finally, on simulated data, we show RECAP outperforms existing methods that do not account for patient subtypes. We then use RECAP to resolve ambiguities in patient trees and find repeated evolutionary trajectories in lung and breast cancer cohorts.

Availability and implementation
https://github.com/elkebir-group/RECAP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Long-term Infective Endocarditis Mortality Associated With Injection Opioid Use in the United States: A Modeling Study
Authors: Barocas Joshua A , Eftekhari Yazdi Golnaz , Savinkina Alexandra , Nolen Shayla , Savitzky Caroline , Samet Jeffrey H , Englander Honora , Linas Benjamin P 
Published: September 2020

Abstract

Background
The expansion of the US opioid epidemic has led to significant increases in infections, such as infective endocarditis (IE), which is tied to injection behaviors. We aimed to estimate the population-level IE mortality rate among people who inject opioids and compare the risk of IE death against the risks of death from other causes.

Methods
We developed a microsimulation model of the natural history of injection opioid use. We defined injection behavior profiles by both injection frequency and injection techniques. We accounted for competing risks of death and populated the model with primary and published data. We modeled cohorts of 1 million individuals with different injection behavior profiles until age 60 years. We combined model-generated estimates with published data to project the total expected number of IE deaths in the United States by 2030.

Results
The probabilities of death from IE by age 60 years for 20-, 30-, and 40-year-old men with high-frequency use with higher infection risk techniques compared to lower risk techniques for IE were 53.8% versus 3.7%, 51.4% versus 3.1%, and 44.5% versus 2.2%, respectively. The predicted population-level attributable fraction of 10-year mortality from IE among all risk groups was 20%. We estimated that approximately 257 800 people are expected to die from IE by 2030.

Conclusions
The expected burden of IE among people who inject opioids in the United States is large. Adopting a harm reduction approach, including through expansion of syringe service programs, to address injection behaviors could have a major impact on decreasing the mortality rate associated with the opioid epidemic.
The Presence of (1→3)-β-D-Glucan as Prognostic Marker in Patients After Major Abdominal Surgery
Authors: White P Lewis , Posso Raquel , Parr Christian , Price Jessica S , Finkelman Malcolm , Barnes Rosemary A 
Published: September 2020

Abstract

Background
While the serological detection of (1→3)-β-D-glucan (BDG) can indicate invasive fungal disease (IFD), false positivity occurs. Nevertheless, the presence of BDG can still be recognized by the host’s innate immune system and persistent BDG antigenemia, in the absence of IFD, can result in deleterious proinflammatory immune responses.

Methods
During the XXX (INTENSE) study into the preemptive use of micafungin to prevent invasive candidiasis (IC) after abdominal surgery, the serum burden of BDG was determined to aid diagnosis of IC. Data from the INTENSE study were analyzed to determine whether BDG was associated with organ failure and patient mortality, while accounting for the influences of IC and antifungal therapy.

Results
A BDG concentration &gt;100 pg/mL was associated with a significantly increased Sequential Organ Failure Assessment score (≤100 pg/mL: 2 vs &gt;100 pg/mL: 5; P &lt; .0001) and increased rates of mortality (≤100 pg/mL: 13.7% vs &gt;100 pg/mL: 39.0%; P = .0002). Multiple (≥2) positive results &gt;100 pg/mL or a BDG concentration increasing &gt;100 pg/mL increased mortality (48.1%). The mortality rate in patients with IC and a BDG concentration &gt;100 pg/mL and ≤100 pg/mL was 42.3% and 25.0%, respectively. The mortality rate in patients without IC but a BDG concentration &gt;100 pg/mL was 37.3%. The use of micafungin did not affect the findings.

Conclusions
The presence of persistent or increasing BDG in the patient’s circulation is associated with significant morbidity and mortality after abdominal surgery, irrespective of IC. The potential lack of a specific therapeutic focus has consequences when trying to manage these patients, and when designing clinical trials involving patients where host-associated BDG concentrations may be elevated.

Clinical Trials Registration
NCT01122368.
Measurement of free glucocorticoids: quantifying corticosteroid binding capacity and its variation within and among mammal and bird species
Authors: Delehanty Brendan , Bossart Gregory D , Champagne Cory , Crocker Daniel E , Elliott Kyle H , Fair Patricia A , Houser Dorian , Newman Amy E M , Boonstra Rudy 
Published: September 2020

Abstract
Plasma glucocorticoid (CORT) levels are one measure of stress in wildlife and give us insight into natural processes relevant to conservation issues. Many studies use total CORT concentrations to draw conclusions about animals’ stress state and response to their environment. However, the blood of tetrapods contains corticosteroid-binding globulin (CBG), which strongly binds most circulating CORT. Only free CORT (CORT not bound by CBG) leaves the circulation and exerts biological effects on CORT-sensitive tissues. Measuring free CORT concentrations provides insight to an animal’s stress response that cannot be revealed by simply measuring total CORT. To calculate free CORT concentrations in plasma or serum samples, one needs three measurements: the binding affinity of CBG for CORT (which varies by species), the total CORT concentration in the sample and the maximum corticosteroid binding capacity (MCBC) of CBG in the sample. Here, we detail the measurement of CBG binding capacity. We compare and contrast the three main methods to measure MCBC: charcoal, cell harvester and dialysis. Each is defined by the means by which free and bound CORT are separated. We weigh the relative merits and challenges of each. We conclude that sample volume, species and taxon binding specificity, and availability of equipment are the primary considerations in selecting the appropriate separation method. For most mammals, the charcoal method is recommended. For birds, the harvester method has critical advantages over the charcoal method. The dialysis method is widely regarded as the gold standard and has lower equipment costs but is more time-intensive and costly in terms of radioactive isotope needed and is less suited to processing large numbers of samples. The binding capacity of CBG varies tremendously within and among the bird and marine mammal species studied, and we discuss the implication of this variation for understanding the role of stress in wildlife.
Prevalence and clinical implications of valvular calcification on coronary computed tomography angiography
Authors: Williams Michelle C , Massera Daniele , Moss Alastair J , Bing Rong , Bularga Anda , Adamson Philip D , Hunter Amanda , Alam Shirjel , Shah Anoop S V , Pawade Tania , Roditi Giles , van Beek Edwin J R , Nicol Edward D , Newby David E , Dweck Marc R 
Published: September 2020

Abstract

Aims
Valvular heart disease can be identified by calcification on coronary computed tomography angiography (CCTA) and has been associated with adverse clinical outcomes. We assessed aortic and mitral valve calcification in patients presenting with stable chest pain and their association with cardiovascular risk factors, coronary artery disease, and cardiovascular outcomes.

Methods and results
In 1769 patients (58 ± 9 years, 56% male) undergoing CCTA for stable chest pain, aortic and mitral valve calcification were quantified using Agatston score. Aortic valve calcification was present in 241 (14%) and mitral calcification in 64 (4%). Independent predictors of aortic valve calcification were age, male sex, hypertension, diabetes mellitus, and cerebrovascular disease, whereas the only predictor of mitral valve calcification was age. Patients with aortic and mitral valve calcification had higher coronary artery calcium scores and more obstructive coronary artery disease. The composite endpoint of cardiovascular mortality, non-fatal myocardial infarction, or non-fatal stroke was higher in those with aortic [hazard ratio (HR) 2.87; 95% confidence interval (CI) 1.60–5.17; P &lt; 0.001] or mitral (HR 3.50; 95% CI 1.47–8.07; P = 0.004) valve calcification, but this was not independent of coronary artery calcification or obstructive coronary artery disease.

Conclusion
Aortic and mitral valve calcification occurs in one in six patients with stable chest pain undergoing CCTA and is associated with concomitant coronary atherosclerosis. Whilst valvular calcification is associated with a higher risk of cardiovascular events, this was not independent of the burden of coronary artery disease.
Richafort’s Requiem: beyond Josquin
Authors: Bloxam M Jennifer 
Published: September 2020

Abstract
All polyphonic Requiem settings have a commemorative purpose, but none is more multi-layered in its memorializing aims and strategies than that by Jean Richafort (c.1480–c.1550). This piece is unique among Renaissance Requiems in drawing its materials and procedures from an earlier composer’s oeuvre: Richafort mined no fewer than three works by Josquin des Prez. Indeed, Richafort’s Requiem is so deeply indebted to Josquin that Gustave Reese suggested it was ‘written on the death of Josquin’ in 1521.
This article revisits this exquisite piece of music in order to look more deeply into its commemorative nature and purpose. First, essential musical and textual details germane to its function as tribute are identified, building on John Milsom’s essay ‘Sense and sound in Richafort’s Requiem’ in Early Music, xxx (2002). The association of this Requiem with Josquin’s death is assessed, and other possibilities for the work’s genesis suggested. Finally, ways in which this setting serves a purpose beyond the memorialization of any one individual is explored by situating it within the ritual context of the Funeral Mass, and evidence offered to suggest that certain compositional decisions made by Richafort were designed to commemorate Christ’s redeeming death and resurrection as the key to every Christian’s salvation.
SWinvert: a workflow for performing rigorous 1-D surface wave inversions
Authors: Vantassel Joseph P , Cox Brady R 
Published: September 2020

SUMMARYSWinvert is a workflow developed at The University of Texas at Austin for the inversion of surface wave dispersion data. SWinvert encourages analysts to investigate inversion uncertainty and non-uniqueness in shear wave velocity (Vs) by providing a systematic procedure and specific actionable recommendations for surface wave inversion. In particular, the workflow encourages the use of multiple layering parametrizations to address the inversion's non-uniqueness, multiple global searches for each parametrization to address the inverse problem's non-linearity and quantification of Vs uncertainty in the resulting profiles. While the workflow uses the Dinver module of the popular open-source Geopsy software as its inversion engine, the principles presented are of relevance to analysts using other inversion programs. To illustrate the effectiveness of the SWinvert workflow and to develop a set of benchmarks for use in future surface wave inversion studies, synthetic experimental dispersion data for 12 subsurface models of varying complexity are inverted. While the effects of inversion uncertainty and non-uniqueness are shown to be minimal for simple subsurface models characterized by broad-band dispersion data, these effects cannot be ignored in the Vs profiles derived for more complex models with band-limited dispersion data. To encourage adoption of the SWinvert workflow, an open-source Python package (SWprepost), for pre- and post-processing of surface wave inversion data, and an application on the DesignSafe-Cyberinfrastructure (SWbatch), for performing batch-style surface wave inversions with Dinver using high-performance computing, have been developed and released in conjunction with this work. The SWinvert workflow is shown to provide a methodical procedure and a powerful set of tools for performing rigorous surface wave inversions and quantifying the uncertainty in the resulting Vs profiles.
Iterative passive-source location estimation and velocity inversion using geometric-mean reverse-time migration and full-waveform inversion
Authors: Lyu Bin , Nakata Nori 
Published: September 2020

SUMMARYPassive-seismic provides useful information for reservoir monitoring and structural imaging; for example, the locations of microseismic events are helpful to understand the extension of the hydraulic fracturing. However, passive-seismic imaging still faces some challenges. First, it is not easy to know where the passive-seismic events happened, which is known as passive-source locating. Additionally, the accuracy of the subsurface velocity model will influence the accuracy of the estimated passive-source locations and the quality of the structural imaging obtained from the passive-seismic data. Therefore the velocity inversion using the passive-seismic data is required to provide the velocity with higher accuracy. Focusing on these challenges, we develop an iterative passive-source location estimation and velocity inversion method using geometric-mean reverse-time migration (GmRTM) and full-waveform inversion (FWI). In each iteration, the source location is estimated using a high-resolution GmRTM method, which provides a better focusing of passive-source imaging compared to conventional wavefield scanning method. The passive-source FWI is then followed to optimize the velocity model using the estimated source location provided by GmRTM. The source location estimation and velocity inversion are implemented sequentially. We evaluate this iterative method using the Marmousi model data set. The experiment result and sensitivity analysis indicate that the proposed method is effective to locate the sources and optimize velocity model in the areas with complicated subsurface structures and noisy recordings.