bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invasional meltdown hypothesis.
Authors: Braga R. R. , Gómez Aparicio L. , Heger T. , Vitule J. R. S. , Jeschke J. M. 
Published: May 2018

Abstract

Positive interactions among species can be central for community structure and ecosystem functioning. Given the current scenario of species invasions worldwide, the question arises how non-native species will interact in the new environment. Such reasoning has led to the invasional meltdown hypothesis (IM) which states that non-native species facilitate one another's invasion, increasing their likelihood of survival, ecological impact and possibly the magnitude of their impact. However, given the importance of antagonistic interactions in natural communities, it is not yet known to what extent these facilitative effects of non-native species occur. We used the hierarchy-of-hypotheses (HoH) approach to differentiate key aspects of IM and link empirical studies to specific sub-hypotheses of the overall hypothesis. Evidence related to IM was gathered by assessing citations of Simberloff and Von Holle (1999) who first defined it. Our HoH was categorized by the type of interaction among non-native species (e.g. facilitation, mutualism and multi-species interactions), ecological level of evidence and the outcome of the interaction for each non-native species (i.e. response variable measured in the study). We additionally looked for taxonomic and geographic variability. On the basis of the 208 relevant studies we found, the broad hypothesis and the majority of sub-hypotheses indicate that positive interactions among non-natives are happening more frequently than negative ones. Thus, IM is broadly supported by currently available studies. Evidence against IM relates to sub-hypotheses involving reciprocal interactions (e.g. competition between non-native species). We suggest that future research focuses on controlled experimental setups aiming at elucidating the community- or ecosystem-level effects of non-native species interactions, especially for reciprocal interactions.
Enemy release hypothesis.
Authors: Heger T. , Jeschke J. M. 
Published: May 2018

Abstract

The enemy release hypothesis is a prominent explanation for invasion success. It is, however, a complex multi-faceted hypothesis and has multiple sub-hypotheses. Empirical tests of the enemy release hypothesis therefore often address very different questions. For this reason, we previously applied the hierarchy-of-hypotheses (HoH) approach to analyse the level of evidence for the enemy release hypothesis and its sub-hypotheses, taking into account this variety of formulations and research questions. This chapter provides an update and extension of that analysis by including recently published evidence and implementing some of the suggestions made in Chapters 3 to 6, this volume, concerning the HoH approach. In detail, we: (i) re-organized the HoH, now separating research approaches from working hypotheses; (ii) displayed results including bar charts in order to avoid a classification of the level of evidence for the different hypotheses; and (iii) tested the robustness of our results based on the precision of the tests (estimated as number of replicates), their generality (using number of focal species as a proxy), realism (i.e. whether they were conducted in the lab, an enclosure or in the field) and their general approach (observation or experiment). We found relatively strong support for the enemy release hypothesis in studies looking at release in the sense of reduced enemy pressure. However, this is not paralleled by strong evidence for enhanced performance. Support for the enemy release hypothesis differs according to which question is asked. It is highest if species in their native vs introduced range are compared and lowest if invasive aliens are compared to non-invasive aliens. There is a comparatively high level of supporting evidence if specialist enemies are considered. From these findings, we conclude that future studies should focus on testing whether invaders show enhanced performance if released from specialist enemies - an underexplored research question so far. Our robustness analysis indicates that empirical results are influenced by the generality (estimated by the number of focal species) and realism (estimated by the number of replicates) of studies addressing the enemy release hypothesis. We suggest that future studies in the context of enemy release should preferentially be done in the field rather than in the lab and use more than ten focal alien species.
Tens rule.
Authors: Jeschke J. M. , Pyšek P. 
Published: May 2018

Abstract

The tens rule became a popular invasion hypothesis in the 1990s and is still widely used today, even though empirical support has been mixed from the beginning and the number of studies questioning it has been increasing in the past decade. Also, the rule is not based on a model or other defensible concept or argument. Here we divide the tens rule into two more specific sub-hypotheses: the invasion tens rule and the impact tens rule, where the former predicts that about 10% of species successfully take consecutive steps of the invasion process, and the latter that about 10% of established non-native species and about 1% of all introduced non-native species cause significant detrimental impacts. A quantitative metaanalysis of 102 empirical tests of the tens rule from 65 publications shows no support for this hypothesis. Looking at the invasion tens rule and comparing different taxonomic groups, about 25% of non-native plants and invertebrates, and about 50% of non-native vertebrates are on average successful in taking consecutive steps of the invasion process. We thus suggest replacing the invasion tens rule by two taxon-dependent hypotheses: the 50% invasion rule for vertebrates and the 25% invasion rule for other organisms, particularly plants and invertebrates. The impact tens rule is not supported by currently available evidence, either, and more data are needed before a reasonable alternative hypothesis can be formulated. In a nutshell, we suggest abandoning the tens rule and using the 50% invasion rule for vertebrates and the 25% invasion rule for other organisms. These hypotheses provide new standards that are supported by currently available data and against which future data can be tested.
Darwin's naturalization and limiting similarity hypotheses.
Authors: Jeschke J. M. , Erhard F. 
Published: May 2018

Abstract

Darwin's naturalization hypothesis (DN) and the limiting similarity hypothesis (LS) are topically similar: DN posits that the invasion success of non-native species is higher in areas that are poor in closely related species than in areas that are rich in closely related species; LS says that the invasion success of non-native species is high if they strongly differ from native species and low if they are similar to native species. We performed systematic reviews for both DN and LS, and divided these into sub-hypotheses using the hierarchy-of-hypotheses (HoH) approach. For DN, we thereby considered if studies used phylogenies to assess relatedness of native and non-native species or if they did so by using taxonomic groups (e.g. the number of native species in the same genus as the non-native species). We found that studies using phylogenies usually support DN, whereas those using taxonomic groups typically question DN. We divided the limiting similarity hypothesis into subhypotheses according to how functional similarity was assessed between native and non-native species. This hypothesis was largely empirically supported. Both DN and LS, however, have basically only been addressed in terrestrial habitats, and limiting similarity hypothesis only for plants, thus studies in other habitats and for other taxonomic groups are needed to test the general validity of both hypotheses. Due to their similarity, these hypotheses can be seen as sub-hypotheses of an overarching limiting similarity hypothesis sensu lato.
Effects of Rhinoplasty on Labyrinthine Function
Authors: Tekin Ahmet Mahmut , Soylu Erkan , Dizdar Handan Turan , Yılmaz Fahrettin , Bayazit Yildirim Ahmet 
Published: May 2018

Abstract

Background
Rhinoplasty is a common surgical procedure that is requested and accepted by patients for cosmetic and functional reasons. Osteotomies are performed on nasal bone, maxillary crest, or vomer to fix the deviations of the nasal dorsum or septum. During the percussion of the osteotomes with the surgical mallet, the vibration energy diffuses to the cranium. Auditory and vestibular systems may be affected by these vibrations.

Objectives
To assess the effects of rhinoplasty, in which osteotomies were performed using a hammer, on the audiovestibular system.

Methods
Thirty adults who underwent rhinoplasty were included in the study group. Ten age and gender matched adults who had nasal surgery without surgical mallet or osteotome served as the control group. The patients in both groups were assessed using pure tone audiometry, tympanometry, distortion product otoacoustic emission testing, and vestibular-evoked myogenic potential, as well as video head impulse tests (vHIT) before the operation and 1 week after the operation.

Results
On auditory assessment, there was no significant difference between the study and control groups regarding pure tone thresholds at frequencies of 250 Hz to 8 kHz (P &gt; 0.05) as well as otoacoustic emissions. The vestibular assessment performed by using vestibular-evoked myogenic potential and vHIT did not reveal a statistically significant difference between the groups, before surgery or after surgery (P &gt; 0.05).

Conclusions
Rhinoplasty appears to be a safe operation in terms of audiovestibular functions, and osteotomy, in which a hammer is usually used, does not have an impact on hearing or balance functions of the ear.

Level of Evidence: 2
pyABC: distributed, likelihood-free inference
Authors: Klinger Emmanuel , Rickert Dennis , Hasenauer Jan 
Published: May 2018

Abstract

Summary
Likelihood-free methods are often required for inference in systems biology. While approximate Bayesian computation (ABC) provides a theoretical solution, its practical application has often been challenging due to its high computational demands. To scale likelihood-free inference to computationally demanding stochastic models, we developed pyABC: a distributed and scalable ABC-Sequential Monte Carlo (ABC-SMC) framework. It implements a scalable, runtime-minimizing parallelization strategy for multi-core and distributed environments scaling to thousands of cores. The framework is accessible to non-expert users and also enables advanced users to experiment with and to custom implement many options of ABC-SMC schemes, such as acceptance threshold schedules, transition kernels and distance functions without alteration of pyABC’s source code. pyABC includes a web interface to visualize ongoing and finished ABC-SMC runs and exposes an API for data querying and post-processing.

Availability and Implementation
pyABC is written in Python 3 and is released under a 3-clause BSD license. The source code is hosted on https://github.com/icb-dcm/pyabc and the documentation on http://pyabc.readthedocs.io. It can be installed from the Python Package Index (PyPI).

Supplementary information
Supplementary data are available at Bioinformatics online.
AC-DIAMOND v1: accelerating large-scale DNA–protein alignment
Authors: Mai Huijun , Zhang Yifan , Li Dinghua , Leung Henry Chi-Ming , Luo Ruibang , Wong Chi-Kwong , Ting Hing-Fung , Lam Tak-Wah 
Published: May 2018

Abstract

Summary
AC-DIAMOND (v1) is a DNA–protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed-up the matching between query and reference sequences; second, adopting a compact form of dynamic programing to fully utilize the parallelism of the SIMD capability.

Availability and implementation
Software source codes and binaries available at https://github.com/Maihj/AC-DIAMOND/

Supplementary information
Supplementary data are available at Bioinformatics online.
Risk Factors for Treatment Failure and Mortality Among Hospitalized Patients With Complicated Urinary Tract Infection: A Multicenter Retrospective Cohort Study (RESCUING Study Group)
Authors: Eliakim-Raz Noa , Babitch Tanya , Shaw Evelyn , Addy Ibironke , Wiegand Irith , Vank Christiane , Torre-Vallejo Laura , Joan-Miquel Vigo , Steve Morris , Grier Sally , Stoddart Margaret , Nienke Cuperus , Leo van den Heuvel , Vuong Cuong , MacGowan Alasdair , Carratalà Jordi , Leibovici Leonard , Pujol Miquel ,   RESCUING Study Group, Tancheva Dora , Vatcheva-Dobrevska Rossitza , Tsiodras Sotirios , Roilides Emmanuel , Várkonyi Istvan , Bodnár Judit , Farkas Aniko , Zak-Doron Yael , Carmeli Yehuda , Mangoni Emanuele Durante , Mussini Cristina , Petrosillo Nicola , Vata Andrei , Hristea Adriana , Origüen Julia , Rodriguez-Baño Jesus , Yetkin Arzu , Saltoglu Nese 
Published: May 2018

Abstract

Background
Complicated urinary tract infections (cUTIs) are responsible for a major share of all antibiotic consumption in hospitals. We aim to describe risk factors for treatment failure and mortality among patients with cUTIs.

Methods
A multinational, multicentre retrospective cohort study, conducted in 20 countries in Europe and the Middle East. Data were collected from patients’ files on hospitalised patients with a diagnosis of cUTI during 2013-2014. Primary outcome was treatment failure, secondary outcomes included 30 days all-cause mortality,among other outcomes. Multivariable analysis using a logistic model and the hospital as a random variable was performed to identify independent predictors for these outcomes.

Results
A total of 981 patients with cUTI were included. Treatment failure was observed in 26.6% (261/981), all cause 30-day mortality rate was 8.7% (85/976), most of these in patients with catheter related UTI (CaUTI). Risk factors for treatment failure in multivariable analysis were ICU admission (OR 5.07, 95% CI 3.18-8.07), septic shock (OR 1.92, 95% CI 0.93-3.98), corticosteroid treatment (OR 1.92, 95% CI 1.12-3.54), bedridden (OR 2.11, 95%CI 1.4-3.18), older age (OR 1.02, 95% CI 1.0071.03-), metastatic cancer (OR 2.89, 95% CI 1.46-5.73) and CaUTI (OR 1.48, 95% CI 1.04-2.11). Management variables, such as inappropriate empirical antibiotic treatment or days to starting antibiotics were not associated with treatment failure or 30-day mortality. More patients with pyelonephritis were given appropriate empirical antibiotic therapy than other CaUTI [110/171; 64.3% vs. 116/270; 43%, p &lt;0.005], nevertheless, this afforded no advantage in treatment failure rates nor mortality in these patients.

Conclusions
In patients with cUTI we found no benefit of early appropriate empirical treatment on survival rates or other outcomes. Physicians might consider supportive treatment and watchful waiting in stable patients until the causative pathogen is defined.
Evaluating Mobility in Advanced Dementia: A Scoping Review and Feasibility Analysis
Authors: Van Ooteghem Karen , Musselman Kristin , Gold David , Marcil Meghan N , Keren Ron , Tartaglia Maria Carmela , Flint Alastair J , Iaboni Andrea 
Published: May 2018

Abstract

Background and Objectives
Mobility decline is a symptom of advanced dementia that affects function, safety, caregiving, and quality of life. Monitoring mobility status is essential for initiating timely and targeted interventions aimed at preventing excess disability in people with dementia (PWD). The physical, cognitive, and behavioral symptoms of dementia however, present unique challenges for mobility assessment. The goals of this review were to (a) identify and describe measures of mobility used for PWD and (b) assess measures’ feasibility for use in people with advanced dementia; a group whose degree of cognitive impairment results in severe functional deficits.

Research Design and Methods
Electronic searches of Medline, Embase, CINAHL, and PsychInfo databases were conducted using keywords related to dementia, mobility, measurement, and validation. Descriptive characteristics were extracted and measures coded for mobility components. Tools were also evaluated for feasibility of use in advanced dementia and those deemed feasible, screened for psychometric strength.

Results
Thirty-eight measures were included and 68% of these tools were performance-based. Elements of mobility evaluated were walking (53% of measures), postural transitions (42%), standing (40%), mobility-related behavioral/psychological symptoms (24%), transfers (10%), bed mobility (5%), and wheeled mobility (3%). 36% of studies included people with advanced dementia. Only 18% of tools received high scores for feasibility.

Discussion and Implications
Existing measures provide only partial information regarding mobility and few target elements that become relevant as dementia progresses. Most measures are not feasible for people with advanced dementia, and the psychometric evaluation of these measures is limited. Further research is needed to develop a comprehensive, dementia-specific, mobility assessment tool.
Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries
Authors: Lu Fu-Hao , McKenzie Neil , Kettleborough George , Heavens Darren , Clark Matthew D , Bevan Michael W 
Published: May 2018

Abstract

Background
The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics.

Results
Here we use a Fosill 38-kb jumping library to assess medium and longer–range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values.

Conclusions
Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
Authors: Almeida Alexandre , Mitchell Alex L , Tarkowska Aleksandra , Finn Robert D 
Published: May 2018

Abstract

Background
Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. Quantitative Insights Into Microbial Ecology (QIIME) and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean, and soil environments. We evaluate their accuracy when paired with both different reference databases and variable sub-regions of the 16S rRNA gene.

Findings
We show that QIIME 2 provided the best recall and F-scores at genus and family levels, together with the lowest distance estimates between the observed and simulated samples. However, MAPseq showed the highest precision, with miscall rates consistently &lt;2%. Notably, QIIME 2 was the most computationally expensive tool, with CPU time and memory usage almost 2 and 30 times higher than MAPseq, respectively. Using the SILVA database generally yielded a higher recall than using Greengenes, while assignment results of different 16S rRNA variable sub-regions varied up to 40% between samples analysed with the same pipeline.

Conclusions
Our results support the use of either QIIME 2 or MAPseq for optimal 16S rRNA gene profiling, and we suggest that the choice between the two should be based on the level of recall, precision, and/or computational performance required.
A gene catalogue of the Sprague-Dawley rat gut metagenome
Authors: Pan Hudan , Guo Ruijin , Zhu Jie , Wang Qi , Ju Yanmei , Xie Ying , Zheng Yanfang , Wang Zhifeng , Li Ting , Liu Zhongqiu , Lu Linlin , Li Fei , Tong Bin , Xiao Liang , Xu Xun , Li Runze , Yuan Zhongwen , Yang Huanming , Wang Jian , Kristiansen Karsten , Jia Huijue , Liu Liang 
Published: May 2018

Abstract

Background
Laboratory rats such as the Sprague-Dawley (SD) rats are an important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report the first catalog of microbial genes in fecal samples from Sprague-Dawley rats.

Findings
The catalog was established using 98 fecal samples from 49 SD rats, divided in 7 experimental groups, and collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 bp, among which 64.6% and 26.7% were annotated to phylum and genus levels, respectively. Functionally, 53.1%, 21.8%,and 31% of the genes could be annotated to KEGG orthologous groups, modules, and pathways, respectively.

Conclusions
A comparison of rat gut metagenome catalogue with human or mouse revealed a higher pairwise overlap between rats and humans (2.47%) than between mice and humans (1.19%) at the gene level. Ninety-seven percent of the functional pathways in the human catalog were present in the rat catalogue, underscoring the potential use of rats for biomedical research.